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About ChemBioFinder 13.0

1. 93 04 1004 62 0 00 Boiling_Point 1004 62 22 99 790 41 PP 22 99 MolVeight 906 81 x Molname Benzene Partition_Coe 2 142 Polar_Surfac O Figure 12 9 Filter window stacked with details and structure windows To activate a filter To remove a filter Chapter 12 BioViz Right click in the Filter window to display the context menu then click the variable to deselect it pP PerkinElmer For the Better Right click in the Filter window and select a variable from the list When you view the context menu again the var iable will appear with a check mark next to it 171 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 The following bio assay example shows two plots of the octanol water partition coefficient CLogP plotted against an activity measure called Fold_Above_Control The second is filtered on molar refractivity Note that the upper chart has been locked to prevent the filter from affecting it Figure 12 10 Locking a chart To apply the filter Press the thumb at one end of the slider and drag along the slider Inthe bottom diagram the plot is limited to Molar_Refractivity from 10 to 33 Figure 12 11 Histogram Filtering Filter slider adjustment Once the top and or bottom of the range has been set you can move the entire range For example the Boiling Point filter has been set to display a range of about 250 from 501 3 K to 753
2. A successful merge results in a new list F Note If you merge two lists and get an empty result an alert appears and the list reverts to the previous list Search examples The following are examples of searching options By specifying atom and bond properties you see how to use the query functions in ChemBioDraw to search the database more effectively All substructure search query properties recognized by ChemBioFinder 13 0 are listed and described in Structural Query Features on page 223 Multiple hit lists A detailed example of how you can use hit list management to perform specific sophisticated searches follows Chapter 8 Queries 132 of 342 ChemBioFinder 13 0 Perkin For the Better Suppose you want to search for all compounds in the CS_Demo database that contain a benzene substructure and have molecular weights between 50 and 200 After you perform this combined search you want to find which of these compounds do not contain a carbon nitrogen bond By integrating hit lists you can perform this search To create the hit list for the first part of this search 1 Open the CS_Demo database 2 Create the first query by drawing benzene in the Structure data box and entering 50 200 in the Molecular Weight Data Box 3 Search the query You get 75 hits 4 Goto Search gt Save List 5 Save the hit list as benz txt To create another hit list for the second part of the search 1 Draw the query shown below in th
3. Click Search The new list is created as a child of the previous list Ex plo rer H Queries SB Full List S Q1 1003 Molweight lt 250 Q2 110 555 query C2F Database Queries Favorites BioSAR Figure 15 1 In this example Q1 is a child list of a parent list named MW Filter Creating multiple child lists You can run similar queries each with different attributes and displayed as a child of the parent query BM Queries E Ful List E MW Filter 1187 BioSAR list 91 E Q1 807 Molweight lt 70 E Q3 178 Molweight lt 40 Y 04 848 Molweight gt 50 Database Queries Favorites BioSAR Figure 15 2 Several child lists of the parent list MW Filter To create another child list you must first select the parent list To select the parent do either of the following Double click the parent list Chapter 15 BioSAR 195 of 342 hemBioFinder 13 0 I Che oFinde PerkinElmer For the Better With a child list selected click Restore Previous List on the Search menu or toolbar You can verify that you have selected the parent list by viewing the status bar information With the parent list selected you can add another child list to your query at 1 of 1187 db 33547 Figure 15 3 The value 1187 in the status bar indicates that the parent list in figure 5 has been selected 38547 is the number of entries in the full list Merging lists with drag and drop In s
4. Goto Search gt Find Click the Find icon on the Search Toolbar Combined searching example Suppose you want to find all molecules in the CS_Demo database that contain a benzene ring and which have names related to penicillin Goto Search gt Enter Query Draw abenzene ring Enter penicillin in the Molname field Check that the Search gt Substructure option is selected Goto Search gt Find a RF OND 3 Chapter 8 Queries 110 of 342 h BioFi 13 I ChemBioFinder 13 0 PerkinElmer For the Better You get 2 hits of molecules whose names contain penicillin and whose structures have an aromatic ring of six carbon atoms f Note In a combined search progress reports are given only during the structure search part When the counters at the bottom of the screen are advancing structures are being searched You can press Esc to end a search dur ing the structure searching You cannot end a search during the SQL searching by pressing Esc SQL searches SQL Structured Query Language can be used to create powerful searches The details of the language are not dis cussed here Queries beginning with a backslash are taken as straight SQL and passed directly to the database as the WHERE clause of the SQL query These must contain column names and punctuation as dictated by SQL For example a valid query might be molname like benz and bpoint gt 200 A straight SQL query may be entered in any box of t
5. N a al E An E o 1000 1500 2000 Selecting a list by single clicking in the queries tree or choosing Color On Plot from the tree context menu causes points on the plot to be re colored The re colored points are those which are on both the selected list and the plotted one You may color more than one list at a time When a list is colored on the plot its item in the queries tree is shown with a check mark clicking it a second time removes color and also removes the check mark Synchronization of plots Multiple plots attached to a form are synchronized If you select mouse over a point in one plot the same point is highlighted in all other plots and the related structure is displayed in the Structure Window Chapter 12 BioViz 166 of 342 hemBioFi 13 ChemBioFinder 13 0 PerkinElmer For the Better This behavior is slightly modified if one of the plots is a histogram You must select not mouse over a histogram bar to highlight points in other plots Mousing over a point in a line or scatter plot will highlight the point in the center of the corresponding histogram bar 200 160 120 80 40 0 Count 0 24 0 49 0 74 0 365 0 615 0 Figure 12 3 Synchronized histogram Changing the display Once you have selected data points and produced a plot there are several options for modifying the display E Changing Colors to change the color of a plot a Open the Queries pane of
6. pP PerkinElmer For the Better 53 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 Create new forms Come ms open forms forms create forms Save changed edit forms forms change the layout of Change form lay a form out use all of the above options 3 Click the plus sign next to Automation to display the options take the appropriate action Allow CAL OLE Automation access OLE auto access mation writing and _ Note Must be programming checked to ena ble export to Excel edit scripts use all of the above Automation options 4 Click the plus sign next to Edit to display the options take the appropriate action Can use scripts use scripts menu Chapter 4 Forms 54 of 342 ChemBioFinder 13 0 clear forms Clear delete relational and structural data copy relational and structural data and multiple table rows to the clipboard paste relational and structural data from the clipboard Perform all of the Cut copy paste above functions Pyp 5 Click the plus sign next to Browse to display the options take the appropriate action Browse database browse databases records view data in forms in View form as a table table View in con tinuous forms view view data in con tinuous view edit and view struc Edit view struc tures in Chem tures in Chem BioDraw BioDraw view structures in View structures ChemBio3D in Ch
7. v Cone Figure 8 25 The Query Properties dialog box Domains If you are browsing a list other than the full database you can make it seem that the database consists only of the cur rent child list Goto Search gt Domains gt Set Domain to Current List The current list acts like a full database For example a Retrieve All command will retrieve only this list without selecting Search Over Current List searches will go over it only etc To reset searches to the full database Goto Search gt Domains gt Reset to Full Database _ Note Set Domain to Current List remains in effect until canceled If you save the form it will be saved with the form file and will still be in effect when you open the form again Saving and restoring lists You can save queries individually as cfq files or automatically when saving the form The old commands for saving and restoring lists as cfq files still appear on the Search menu and on the context menu displayed when you right click on a specific query If you close a form without having saved your queries or other changes you are prompted to save or discard changes On the General tab of the Preferences dialog box there is an option to save all queries the default or only those that have been renamed If you select this option there are two ways to save a query with the form Rename the query either with the Rename command in the context right click menu or from
8. Double click in the 3D Structure Box Click outside the box to deactivate the control To rotate the structure Drag in any direction in the box Unlike in ChemBio3D you do not have pure locked X or Y axis rotation but you can approximate them by dragging horizontally or vertically The ChemBio3D Control displays different context menus depending on whether you right click while pointing to the model or while pointing elsewhere in the Structure Box Either can be used to change the display mode To change the display method one 1 Double click in the 3D Structure Box to activate the ChemBio3D display 2 Point to an atom or bond in the model and Right click 3 Select a display mode from the Display Mode submenu Method two 1 Double click in the 3D Structure Box to activate the ChemBio3D display 2 Right click anywhere in the 3D Structure Box but not on the model itself 3 Select a display mode from the View gt Model Display gt Display Mode submenu For more information on the ChemBio3D Control see the ChemBio3D User s Manual Setting fixed and live data In the Box Properties dialog box you can designate whether the data source is fixed or from a field Fixed data is attached to the form and does not change as you browse Data from a field is stored in the database and is different for each record As you browse the record display updates according to the contents of the field To specify live data for a data bo
9. Chapter 12 BioViz 167 of 342 h BioFi 13 I ChemBioFinder 13 0 PerkinElmer For the Better b Right click The context menu displays a list of plottable fields c Select a different field to plot on that axis 7 Note You can only change fields when the chart is not locked In Data Table display you can display a substructure search as table of R group substituents Statistical analysis You can perform statistical analysis on BioViz plots When you specify two variables a third tab appears on the Bio Viz Properties dialog box BioViz Plot Properties General Display Analysis Dimension Variables One variable Logscale Base CT iable es x Molweight EJ r Style C Line chart Y Boiling_Point E Scatter plot c Bins Plot name MW vs BP a r T Locked Point limit 500 Figure 12 4 The Analysis tab appears when two variables are specified For descriptive statistics minimum maximum mean median and standard deviation can be calculated for both X and Y variables R Squared is available only when curve fitting is chosen BioViz Plot Properties General Display Analysis Descriptive Statistics Curve Fitting Show Curve Fitting Linear Minimum X C Quadratic C Cubic Standard Deviation X Minimum Y Maximum Y Mean Y Median Y Confidence Interval 0 al standard errors _ Note R
10. ChemBioFinder 13 0 supports three structure search types Normal Exact Similarity Normal and similarity searches may be in either of two modes full structure or substructure Normal and exact searches may also search for tautomerism Normal searches A Normal search finds structures that either contain Substructure or match Full Structure the query When drawing a structure query you can attach different features to a query such as atom lists and variable bond types to perform a narrower or broader search You can also modify the results of a Normal search by selecting options in the Details tab of the Preferences dialog box The query structure is highlighted in red in the hit list structures to visualize the match Exact searches The Exact search type also known as an Identity search is intended for use in compound registration when you must know if an identical copy of your query compound is already present in the database The target must be chem ically identical to the query including stereochemistry charges and isotopy It is a convenient shorthand for full Chapter 8 Queries 101 of 342 ChemBioFinder 13 0 PerkinEl For the Better structure same stereochemistry and appropriate settings of all the other options Thus generic atom and bond types such as R A and Double or Aromatic in the query will match corresponding atom and bond types in the target only if they are also of the same generic type In oth
11. For the Better Importing text You can import comma or tab delimited text files The Import Delimited Text command uses the same dialog box and has most of the same features as Import SD File Delimited text DT differs from SD files in that a DT files cannot contain structures DT files are not as well defined and require interpretation in order to determine field names and delimiter type To import text records into a new database 1 Open anew blank form 2 Go to File gt File Import gt Delimited Text 3 Inthe File Open dialog box browse to select the input file The input file is scanned to determine the field delimiter If the file extension is csv the delimiter is taken to be comma If the extension is txt the first few lines of the file are examined for the presence of commas or tabs If one or the other is found it is taken as the delimiter If not an alert is presented This alert will appear in two cases The input file contains only a single column The alert can be ignored click OK The input file has some delimiter between fields other than tab or comma In this case you must specify the delimiter using the File Export dialog box To specify the delimiter using the Role Export dialog box Click Cancel to dismiss the alert and abort the import Open a form containing data and retrieve a small hit list Go to File gt Export gt Other The File Export dialog box appears
12. MSG displays a message box with the specified text and waits for the user to click STATMSG displays information on the status line TIMEDMSG displays a message box similar to the MSG command but the message disappears automatically after a specified number of seconds For example TIMEDMSG 10 This message will disappear automatically after 10 sec onds FONT changes the current font Any boxes created subsequently adopt this font Follow the keyword with a name from your Windows font list followed optionally by Font size in points default is 8 Style from the list below default is O or plain text Color three values for red green and blue each ranging from 0 to 255 default is 0 0 0 or black Font styles are sums of bold 1 italic 2 and underline 4 Thus a style value of 1 means bold 3 means bold italic 6 means italic underline and so on SEEPTAB briefly displays the periodic table window then closes it The window will be displayed for the amount of time specified 1 decisecond 0 1 second If the duration is omitted it will be displayed for four seconds QUITECLOSE closes the active form This command is similar to FILE CLOSE but automatically discards any changes instead of prompting the user what to do HIDETABLE closes the Table View window for the current form If a subform is active it returns the subform to form view SET allows you to modify basic ChemBioFinder settings including most o
13. 10 200 206 309 of 342 ChemBioFinder 13 0 PerkinElmer For the Better fonts 44 numbers 45 text 44 toolbars 207 customizing fonts 44 D data adding 77 committing 79 83 deleting 83 displaying 36 editing 79 entering 85 exporting 93 items 12 sorting 84 data box tool 36 data boxes editing 16 read only 11 data boxes creating 36 data boxes hiding or showing 44 data source command 59 71 ODBC 71 selecting 59 71 data table displaying 65 Chapter 22 Index 310 of 342 ChemBioFinder 13 0 moving columns resizing columns resizing rows sorting subforms data tables data importing database creating database model description database size display description database tree using database connecting to a form database definition databases cells creating data items flat file logon model moving non chemical opening read only resetting selecting size vs forms Chapter 22 Index pP PerkinElme For the Better 66 66 67 84 159 65 87 62 12 34 17 13 12 70 12 70 64 12 75 71 59 62 10 85 59 10 14 311 of 342 ChemBioFinder 13 0 I PerkinElmer For the Better date fields 73 date queries see searching for dates 100 dates display preferences 100 dBASE 71 DDE to communicate with other applications 219 debugging scripts 213 delete record command 83 deleting boxes 48 contents of fields 83 data 83 fields 74 objects 48 records 83 tables
14. Search sort You get the most advantageous use of profiles in comparing compounds by using the search sort function Select one compound as your base for example an ideal compound with an overall score of zero then sort the database by increasing deviation from that score To use Search Sort to compare profiles You must be in Form View to begin this procedure 1 Browse to the compound you want to use as your base 2 Right click in the Profile data box then select Compound Profile gt Search Sort gt Sort relative to current from the context menu The database is sorted 3 For easiest comparison switch to Table View Chapter 9 Compound Profiles 142 of 342 h BioFi 13 I ChemBioFinder 13 0 PerkinElmer For the Better Profile 0 03 0 00 sa a on 0 02 0 01 Se Figure 9 4 Profiles in the table view The dist value in the profile displayed in red at the bottom of the chart changes when you sort Before sorting it matches the score value After sorting it displays the deviation of that compound from the base If you sort relative to a compound then that compound gets dist 0 since it defines the reference point The dist value for other compounds will increase as they become less similar to the base You can also sort relative to the ideal value In this case the dist value for each compound is the same as its score and the records are ordered on that basis Tip To reset the database right cli
15. Select an Object Type from the drop down menu Select the permissions you want to assign for that object type to each user or group Click Apply When you have finished assigning permissions click OK Open the database in ChemBioFinder 13 0 ON DOO FF WwW Creating a database You can create a new empty database and associate it with a form To create a database 1 Open an existing form or create a new one 2 Right click in the form and select Properties The Box Properties dialog box appears 3 Click the Database tab and then click Create Database The Save As dialog box appears 4 Type a name for your database and then click Save A data source tree appears containing the database and its tables and fields 5 Click OK Opening databases When you open a database you can access the data in any of three ways Normal access you can read and write data E Read Only access you can read but not write data Secured access the database is password protected and you are subject to the security restrictions applied to the database Chapter 5 Databases 62 of 342 hemBioFinder 13 I me Orea PerkinElmer For the Better f Note Versions of ChemBioFinder earlier than 7 0 cannot read cfw files belonging to ChemBioFinder 7 or greater Versions of ChemBioFinder earlier than 11 0 cannot read cfx files Read only access Any of the following conditions determine whether a database opens in r
16. The structure is saved to the indicated file You can read these files with any application that supports the specified file format _ Note To save most of the file types listed above you must have ChemDraw ActiveX Control Pro installed Using copy paste with structures You can copy structures and paste them into ChemBioDraw or ISIS Draw You can also use the Copy As command to copy the structure as a text string Chapter 7 Importing and Exporting Data 93 of 342 ChemBioFinder 13 0 Perkin For the Better The structure Copy As command has three options The Name command invokes the CS Struct Name utility Struct Name generates systematic chemical names with proper CIP stereochemistry descriptors The SMILES command creates a SMILES string A SMILES string is a standard way to describe a chemical struc ture in a line of text Several software packages use SMILES strings as a way to enter and store chemical structure information The InChI command invokes the CambridgeSoft implementation of the IUPAC InChI algorithm The InChI algorithm takes a chemical structure and converts it into an alphanumeric string A key aspect of the InChI algo rithm is that the generated string is independent of the way that a structure is drawn producing a consistent alpha numeric representation of different structural representations of the same structural formula canonicalization _ Note InChI is a registered trademark of t
17. sure Water solubility is measured in mg L Wiener Index Provides measure of branching defined as Where D are the off diagonal elements of the distance matrix Chapter 10 Chemical Properties 154 of 342 ChemBioFinder 13 0 ChemBio3D Chemical Properties B Balaban Index Boiling Point 0 C Cluster Count Connolly Accessible Area Connolly Molecular Area Connolly Solvent Excluded Volume Critical Pressure Critical Temperature Critical Volume D Dipole E Electron Density Electrostatic Potential Elemental Analysis Enthalpy Entropy Exact Mass F Formal Charge Frequencies ChemBioDraw Properties G Gibbs Free Energy H Harmonic Zero Point Energy Heat Capacity Heat of Formation Henry s Law Constant Hyper Polarizability Hyperfine Coupling Constants I Ideal Gas Thermal Capacity Internal Energy Ionization Potential K Kinetic Energy L LogP LogS Lowdin Charges Lowdin Populations M Mass Melting Point Mol Formula Mol Formula HTML Mol Refractivity pP PerkinElmer For the Better Mol Weight Molecular Mass Molecular Surfaces Molecular Topological Index Molecular Volume Mulliken Charges Mulliken Populations m z N Num Rotatable Bonds O Ovality P Partition Coefficient pKa Polar Surface Area Polarizability Potential Energy Principal Moment R Radius RMS Force S SCF Energy Shape Attribute Shape Coefficient The properties listed below can be
18. A to the checked unchecked ilarity state of the menu ON or OFF corresponding Search Match Stereo to the checked unchecked state of the menu Remarks Menu commands need not be spelled out in full you can enter just enough letters to identify the menu option For example to execute the Record next command you can enter rec n For File Open if the file to be launched is in ChemBioFinder s standard search path only the actual file name CS _ DATA is required Otherwise the complete file path c some long path CS_DATA CFX is necessary For File Save if the specified file does not exist it will be created otherwise it will be overwritten For File Save if the path is omitted from the file name the file will be saved in the current directory Example 1 LOOP Example This example uses the LOOP command and the Menu Command Record Next to display all of the records in the cur rent list The PAUSE command keeps each record on screen long enough for people to see it looprec nextpause 2endloop Example 2 Different Form Example This example shows how you can use a script to open a second form with some of the same fields as the original form but for example a different layout This same sort of procedure can be used to display related records if you do not want to use an explicit subform The APPEND SETVAL and GETDATA commands build a search string based on the contents of the link_field field on the original
19. As long as the Over Current List switch is on each search further refines the current list Use the Retrieve All com mand to reset You may also use the Restore Previous List command which acts like a Back button Restore Previous List goes back one in the history including any Retrieve All s you might have done Entering a structural query To begin a structural query 1 Do one of the following to clear the form a Go to Search gt Enter Query Click the Enter Query icon on the Search toolbar 2 Do one of the following to place a structure into a data box Double click in the structure box and edit with the ChemBioDraw Control z Right click and click Edit in ChemBioDraw Right click and click Read Structure to open an existing molecule file Use Edit gt Paste to insert a structure from the clipboard Goto Search gt Preferences Click the Search Type tab Select the appropriate options Optionally select options on the Details tab as well DUI fk OQ Doone of the following Go to Search gt Find Click the Find icon on the Search Toolbar The status bar counters indicate search progress When the search is complete the form displays the first hit The list you can browse is limited to the hits For Normal or Exact searches the hit portion of each molecule is highlighted in red If a search doesn t find any hits you are returned to query mode y Tip You can change the highlight color
20. Finds structures containing one or rings with a 4n 2 electron system Includes pyrrole and charged rings Antiaromatics 4n Finds structures containing one or more rings with a 4n electron system Aromatics Cyclically alternating Finds structures containing one or more rings that have 4n 2 bonds dis tributed as alternating single and double bonds This is the criterion for delocalized used since ChemFinder 10 Natural products Finds structures containing a carbon and at least nitrogen or oxygen Alkaloids Finds structures with MW gt 200 and containing carbon and basic nitrogen Heterocycles Finds structures having a ring containing a heteroatom Metals Finds structures containing a metal bond Organometallics Finds structures containing a metal carbon bond Organics Finds structures having a carbon atom Inorganics Finds structures lacking carbon Salts Finds structures that can be considered as salts Rings Finds any of the following types of ring structures selectable from a submenu Bridged Systems For example two rings share more than one bond Spiro Systems For example two rings sharing just one atom Fusion Systems For example structures with a ring fusion two rings sharing one bond Highly condensed Rings sharing at least four bonds with others in the group where the group has at least seven rings Necklace A ring bridging at least one other ring half its size or less Polyhedra A group of ri
21. K 3475298 1004 62 Figure 12 12 Filter Slider Adjustments Chapter 12 BioViz 172 of 342 ChemBioFinder 13 0 PerkinElmer For the Better By dragging the blue part of the slider you can view any 250 range of the chart that you want The range being dis played has been moved to 651 5 K 903 2 K The size of the range hasn t changed just its location Customizable styles Point shapes You can select one of the six shapes for data points square circle triangle diamond cross or star Selected or mouse over points retain the same display as in earlier versions the selected point appears as a double hollow red cir cle and points being mouse over pointed at appears as red solid with a black circle Point shape selection is from the Display tab of the BioViz Plot Properties dialog box Axes You can set both the content and the font used for each axis The default X and Y labels are the names of the fields plotted but you can now enter any text in any font to override the default You may also choose whether or not to dis play the X and or Y grids by using the check box next to each label Tip Labels are sticky that is the labels used for the previous plot are the defaults for the next plot created If you entered axis labels for Plot 1 and want to use default labels for Plot 2 you must go to the Display tab to delete the label entries when you create Plot 2 Legend You can add a legend o
22. Must not begin with leading spaces Must not include control characters ASCII values 0 through 31 Must not include a double quotation mark in table view or stored procedure names Creating a local copy of a database If you frequently use a set of data that never changes consider exporting the data as a local ChemBioFinder data base Having a local database often makes many common tasks run faster tasks such as browsing searching plot ting and analyzing Creating a local database requires two steps 1 Exporting the dataset as a CFXML file and Chapter 15 BioSAR 197 0f 342 ChemBioFinder 13 0 PerkinEl For the Better 2 Importing the file back into ChemBioFinder Once you import the file save it as a CFX file It will then be available for you to use whenever you need it Exporting the dataset To export a dataset 1 Run a query to create the dataset 2 Go to File gt Export gt CFXML The Data Export window opens 3 Select the options you want to apply to the exported dataset Inthe Data Export dialog box select a path and file name for the new database Use Fileto browse for a loca tion In the lower half of the dialog box all data fields are selected for inclusion in the exported database by default Clear the appropriate check boxes to deselect fields you want to omit Check the field names to ensure each one complies with Access database rules If necessary edit the field name by double clicking
23. Scaling structures To scale each structure so that it is as large as possible within its structure box Click the Fit to box radio button in the Structure Scaling section of the Display tab To display all structures with a constant bond length 1 Click the Uniform bond length radio button in the Structure Scaling section of the Display tab 2 Select the bond length percentage With Uniform bond length selected structures may be reduced in size if they are too large to fit within the struc ture box but they will never be enlarged Framing pictures To select whether the pictures in a form are surrounded by a border Select the Framed radio button in the Pictures section of the Display tab Grid spacing To set the grid spacing in pixels on a form Chapter 16 Customizing ChemBioFinder 13 0 201 of 342 ChemBioFinder 13 0 PerkinElmer For the Better m Type in a number or press the up and down arrows to change the current value by one unit in the Grid Spacing sec tion of the Display tab Choosing a small grid spacing allows you to place objects more precisely by snapping to a tighter matrix Color preferences To set the color preferences Click the Color tab of the Preferences dialog box The color tab allows you to specify the color of various interface elements To set a color 1 Click the button corresponding to the interface element you want to change The color dialog box appears 2 Select the ne
24. Structural Query Features 231 of 342 hemBioFi r 13 I ChemBioFinder 13 0 PerkinElmer For the Better R matches any atom including hydrogen Also used to indicate a link node See Link nodes and multivalent Rs on page 134 for details A link node may be any number of atoms including zero a X matches any halogen F Cl Br I At M matches any metal atom shaded in the periodic table below Figure 17 2 Metals in the periodic chart Atom lists As with the predefined special atom types an atom list is a list of atoms one of which must match the target atom For example CI Ag N atom must be CI or Ag or N Atom lists may contain only elements Special atom types nicknames Ph and structural fragments NH OCH CH may not be included in an atom list ChemBioFinder recognizes a maximum of five atoms in an atom list Atom not lists The opposite of an atom list is a list of atoms none of which must match the target atom For example NOT O S Se atom must not be O or S or Se but may be any of the 100 other elements Atom not lists have the same restrictions as atom lists Substituents exactly This property specifies a precise value for the number of substituents on an atom including those explicitly drawn This property is only meaningful in a substructure search With a substructure search the query X Figure 17 3 1 This atom is marked with the atom property Substituents Exactly 3
25. The Create Table dialog box appears 3 Type a name for the new table then click OK The table appears in the Data Source tree Chapter 5 Databases 70 of 342 ChemBioFinder 13 0 PerkinElmer For the Better Deleting tables To delete a table from the database Right click in the form and click Properties The Box Properties dialog box appears Click the Table tab Inthe data source tree select the table to delete Click Delete Table A Warning message appears oa A OO N Click Yes to delete the table and Cancel to keep the table The table and all data it contains are immediately deleted from the database amp Caution You cannot undo a deleted table Before you delete a table create a backup copy of the database to pre vent accidental loss of data For more information see Backing up databases on page 75 Attaching tables from other applications You can use ChemBioFinder 13 0 to add chemical structures to a database you have already developed If your data base was developed in Microsoft Access you can open it directly in ChemBioFinder 13 0 You can also work with data from other file based databases such as dBASE and xBase clones but in this case you must open or create a ChemBioFinder 13 0 database and attach the table to link to tables in the data source After you attach a table it appears and functions as if it were part of your local ChemBioFinder 13 0 database The procedure you use depends on whet
26. The EXEC command has the following arguments Chapter 20 CAL Commands 261 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 String containing arguments commandargs to be passed to that appli cation String containing the file filename name of any Windows appli cation Remarks If the file to be launched is in ChemBioFinder s standard search path only the actual file name CHEMDRAW is required Otherwise the complete file path c some long path C HEMDRAW EXE is necessary The EXEC command starts a program but does not return from it in order to return to ChemBioFinder you need to use the Task Manager or click in the ChemBioFinder frame window EXEC example This example uses the EXEC command to start Microsoft Excel The first line starts with an asterisk and so is not executed It serves only to make the example more readable for the user RUNEXCEL CFS script to start ExcelEXEC c msoffice excel excel exe CAL commands DDE syntax Sends a Dynamic Data Exchange message to a specified application DDE timeout servicename topic command The DDE command has the following arguments An optional time in seconds timeout to try establishing the con nection String containing the iden tifier of the recipient appli servicename cation often but not always the application name String identifying the nature of the message Chapter 20
27. click the X or Y variable to display the drop down menu The R Group positions are now included in the menus and may be used like any other numerical field to create a plot a Figure 5 16 Setting up an R Group plot General Display Analysis Dimension Variables C one variable Log scale Base Two variables x Mol_ID ae Bolling Point pa Gibbs_Free_Eneray _ Line chart Mol_Refractivity Scatter plot R group R1 28 Bins PlolR group RS a Synonyms SYN_ID r oy F Locked Point limit f 500 Figure 5 17 R Group 2 vs Molecular Weight The R Groups are along the X axis as shown in the preceding figure The structure on the upper right comer of the plot is the template Chapter 5 Databases 69 of 342 ChemBioFinder 13 0 PerkinElme For the Better Creating a database Instead of opening an existing database you may want to create a new empty one To create a new database using the automatic form generation technique see Tutorial 3 Creating a database on page 18 The following procedure results in a simple database with one table for storing structures To create a database 1 Right click in the form and click Properties 2 On the Database tab click the Create Database The Save As dialog box appears 3 Choose the directory to which you want to save the database 4 Specify a name for the database and click Save ChemBioFinder 13 0 creates the database cont
28. eee 246 Box manipulation commands ns 255 Program execution commands cs 259 General commands 2 2 2 0 2 occ cee rn eeeeeeeeeeeseees 263 File commando sssr 522 4 224 2224 Se0 adi youd dali la deci ebevaeehe lal ies 278 Vanable cOMMAN AS vvuotumnsessuitra iia ero letal tl sr ratas 281 Environment variables eee 288 Script only commands 22 2 cece cece cece cece cece cece cece cece cece cece E aa aaaeeeaa 289 Chapter 21 CS Oracle Cartridge 0 0 2 2 2 e cece cnn cnn cnn 296 Fast move caching Scheme 2 2 2 2 2222 ee cece eee cece ccc cece cece ce eee eee c cece LE A aaraa ranana 296 Configuring via CF_SETTINGS table 2 2 2 eee eee cece cece ce adaa eaoaai nrnna 297 SOANCMING 3222 232g 5 44 otc seater a oon tace 298 Chapter 225 UK sti ta estes sen oes ete ld o es ee eee ease 299 Table of Contents v h BioFi 13 I ChemBioFinder 13 0 PerkinElmer For the Better About ChemBioFinder 13 0 ChemBioFinder 13 0 is a database management system for anyone who works with chemical information It provides a place to store chemical structures physical properties notes tables of data and plots With ChemBioFinder 13 0 you can quickly find and organize your data About BioViz BioViz is a visualization add in for ChemBioFinder 13 0 that lets you plot numeric datafrom ChemBioFinder 13 0 data bases You can identify trends and correlations in your data without exporting to another application You can ha
29. i particular graphic file or associated with a pic ture Field in which case there could be a dif ferent graphic in each record Profile box Displays Compound Profiles Displays the chemical structure of the current Structure box record Text box Displays text Text boxes are Fixed text fields are displayed in text data boxes and may be formatted in the Box Properties dialog box Contains all the commands specific to the appli Menu bar cation for managing forms tables databases and their contents Displays details of selected or moused over point when a plot window is dis played May be displayed as tabbed with other windows Details window Chapter 2 Getting Started 6 of 342 ChemBioFinder 13 0 PerkinElmer For the Better Displays information on three tabbed over lapped windows Explorer win The Database field hierarchy dow The Queries list that is associated with the form A Favorites list of frequently used files ee ae Displays plotted data from Chem BioFinder 13 0 databases Displays the filters that modify the BioViz plot Filter window May be displayed as tabbed with other win dows Displays Python scripts output May be td rd displayed as tabbed with other windows Displays the chemical structure of the selected or moused over point when a plot window is displayed May be displayed as tabbed with other windows Structure window Displays relational inform
30. if it is not visible Goto View gt Toolbars gt Text Format The Text Format Tool appears Text Format Toolbar Arial 10 BZ 1 iit be ic x gt 4 oS ill s O N on co Figure 6 4 1 font 2 point size 3 bold 4 italics 5 underline 6 subscript 7 superscript 8 color 9 left alignment 10 center alignment 11 right alignment 12 bullets Use the toolbar to format text in Plain Text or Memo Rich Text data fields Undoing changes Before committing your text changes you can revert to the previous unmodified state To undo your changes do one of the following Go to Edit gt Undo Click the Undo icon on the Main Toolbar After you commit the changes they cannot be undone Redoing changes When you undo an action the Redo command becomes active You can reverse the effect of the Undo command by choosing the Redo command To redo the last action performed do one of the following Go to Edit gt Redo Click the Redo icon The last action undone is reinstated Deleting data You can delete the contents of individual fields by using the Delete or Backspace keys You cannot delete a structure formula molecular weight or Mol_ID To delete an entire record 1 Move to the record that you want to delete using the Record commands or toolbar Chapter 6 Working with Data 83 of 342 hemBioFi 13 I ChemBioFinder 13 0 PerkinElmer For
31. script 5 Click OK For more information about using a button to run a script see Using scripts on page 218 Adding a subform The Subform tool is used to create a subform box to display data from a related data table See Relational Data and Subforms on page 156for more information Adding a profile The Profile box tool creates a profile box on a form Compound profiles are a new feature in ChemBioFinder 13 0 See Compound Profiles on page 137 for more information Adding a control The Control box tool is used to embed an ActiveX control in a form You can use this to display a calendar spread sheet chart spectrum picture web link and so forth See Embedding ActiveX controls on page 210 for more infor mation Chapter 4 Forms 39 of 342 ChemBioFinder 13 0 PerkinEl For the Better Creating and editing tabs If you have a large number of fields in a database you can access information more easily and make the form less cluttered by using tabs to divide a long form into smaller parts contained on separate tabs To create tabs on a form Right click an empty part of a form and select Add Tab context Two tabs appear in the lower left corner of the form Clicking on the second tab will present you with a new empty form To rename a tab 1 Right click the tab and click Rename Tab The Tab Name dialog box appears 2 Type a name for the tab and click OK The new name appears on the tab To remove a tab
32. you can store four different possibilities A given absolute configuration To specify this centers must be drawn with stereo bonds and the entire structure marked Abs CHIRAL A racemic mixture of the drawn configuration and its mirror image This is drawn as above but without the Abs CHI RAL mark An unmarked structure representing unknown stereochemistry or a mixture of all possible stereo isomers A given relationship between centers That is a known orientation of the substituents with respect to each other rather than a known absolute configuration To specify this centers are drawn not with the standard hashed and wedged bonds but with thick stereo bonds If these options are checked in the Search tab of the Preferences dialog box then any stereochemistry indicated on the query must be matched by the target For more information on changing searching preferences see Setting search details preferences on page 113 3D Properties 3D queries are useful in pharmacophore searching where you are looking for a particular 3D relationship among atoms and bonds for example in a series of potential receptor ligands You can create a 3D query in ChemBioDraw Pro by adding geometries lines planes etc and constraints specified as ranges to a query structure For example you might specify that two atoms must be between 4A and 5A apart or that two planes must be separated by 80 100 ChemBioFinder 13 0 can use these propert
33. 1 From the Scripts menu select Command Line The Enter Cal Command dialog box appears 2 Inthe Enter Cal Command dialog box click Help The CAL Scripting Help window appears CAL Scripting Help Command Arguments Description TA AAMAPS ONIOFF display don t display colored 44 map ACTIVATE lt subform bo direct subsequent input to subform ADDRECORD COUNT Append one or more empty records APPEND ONIOFF set append mode on off default toggle APPENDVAL v lt text gt append text to specified variable ARROWBOX rect launches moving arrow Variable p CHIRAL 1 current mol is marked chiral 0 not chiral CLIPBOARD text from Windows Clipboard CURR_DIR current working directory CURR_TABLE current table name DATE current date DTBA_NAME_L database full path Angle bracketed lt item gt is required bracketed item optional A lt rect gt four integers left top right bottom lt box gt a point within box x y or a box name Box name a user assigned box name b field name casei y Figure 20 1 The CAL scripting window Menu commands CAL commands MENU syntax Menu commands consist of a two word command from the main menu and in some cases an optional argument Following are examples of commands file new edit paste search find Chapter 20 CAL Commands 243 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 record next You do not need to spell out menu
34. 13 0 assumes that any atoms and bonds that change in the query must be part of the reaction center of the target For example F CI a ye does not hit Figure 8 10 Query does not hit because it does not contain the reaction center when the Reaction query must hit reaction center preference is selected Even though there is a C F bond in the tar get reactant and a C Cl bond in the target product these bonds do not participate in the reaction which really affects another part of the compound If you deselect the Reaction query must hit reaction center preference this query hits the target above When creating reaction queries it is important to consider what sort of information you are really looking for Suppose you want to convert n decanal to n decanol Figure 8 11 Reduction of n decanal Chapter 8 Queries 107 of 342 ChemBioFinder 13 0 PerkinElmer For the Better Are you really interested only in these two compounds You might be interested in any reaction that converts a straight chain aldehyde to the alcohol Figure 8 12 Generic aldehyde reduction query Since the corresponding n octanal n octanol reaction would probably occur under very similar conditions it is a rea sonable thing to look at Generally you want to use substructure queries that include little beyond the reaction center in question when you are searching for reactions _ Note ChemBioFinder 13 0 supports several query properties to let you specify e
35. 2 Click the Form tab to display the Form properties Box Properties ETT Database Table Field Fom Box MolTable 00 Mol_10 Structure E Formula ME MolWeight 3 C Documents and Settings Open fom a O Move to new record O Enter query v Fom Background Query Background I Open database read only Security I Do not ask to upgrade E Ce ee m Figure 4 7 Form properties dialog box 3 Take the appropriate action Chapter 4 Forms pP PerkinElmer For the Better 46 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 the Form Back database form ground the Query Back query form ground The Color dialog box appears Figure 4 8 The Color picker dialog box 4 Select a color 5 Click OK The Form or Query Background changes to reflect the color you choose To set the default background color 1 Goto File gt Preferences The Preferences dialog Box appears 2 Click the Color tab 3 On the Color tab click Form Background 4 In the Color dialog box select a color and click OK The color you choose becomes the default form background color Editing forms You can move or resize boxes and other objects on your form with the Selection tool and the items in the Edit menu Selecting objects on a form Use the Selection tool to choose data boxes and other objects on a form that you want to move resize or delete When the selection t
36. 33 78 219 220 218 307 of 342 ChemBioFinder 13 0 commutative principle complete structure similarity see Tanimoto similarity compound profiles creating customizing display preferences dist editing score search sort concurrent access connection table file format Connolly accessible area Connolly molecular area Connolly solvent excluded Vvolume controls embedding counterions create database button create table dialog box creating and editing tabs boxes boxes with frames button data box menu data boxes databases fields forms Chapter 22 Index pP PerkinElme For the Better 241 241 137 138 144 142 143 140 137 142 63 87 147 147 147 210 81 70 70 40 36 36 39 43 15 36 62 70 72 34 308 of 342 ChemBioFinder 13 0 forms automatically forms manually forms tutorial frames multiple tables picture boxes portal databases scripts subforms tables tabs text creating a database tutorial creating a plot creating and editing forms creating and saving forms critical pressure critical temperature critical volume current list counter description size current mol as query command current record command curve fitting see BioViz customizing ChemFinder favorites tree Chapter 22 Index pP PerkinElme For the Better 32 34 15 36 85 160 38 76 212 30 156 157 70 40 37 18 26 161 32 17 147 147 147
37. 71 delimited text files 94 demo database 20 description plot points 165 details window 165 details window description 6 dimension definition 163 disabling security 57 display preferences 200 distributing objects 50 domains 129 double either bond type 224 drag and drop 91 duplicate reagents in RD or SD import 88 Chapter 22 Index 312 of 342 ChemBioFinder 13 0 I PerkinElmer For the Better duplicating records 79 E editing data 79 data boxes 16 fields 79 forms 47 labels 37 redo 49 structures 80 structures with ChemDraw 80 tabs 40 undo 49 element editor 209 element ranges in queries 99 elemental analysis 147 elements color 209 physical data 209 selecting 208 embedded controls 210 embedded controls customizing 210 empty points see BioViz 165 enter label dialog box 39 enter query command 117 enter script command dialog box 211 Chapter 22 Index 313 of 342 ChemBioFinder 13 0 I PerkinElmer For the Better entering data 85 queries 10 111 118 reaction queries 120 structural queries 119 structures T77 environment variables CAL 288 equals symbol in query 99 exact mass 148 exact searching 101 exact searching see also normal searching 101 exact searching see also similarity searching 101 Excel communicating with using CAL 210 communicating with using DDE 219 security setting when importing 54 explorer window description 7 exporting ASCII files 94 current hit list 130 data files 9
38. C5_DEMO E MolTable fae Molname 00 MOL_ID Structure E Formula Database Table Field Form a CS_DEMO Properties a Name File CS_DEMO C Documents and Setting M MolWeight Synonyms Connect det 3 x Updatable Yes v Temp Tables i e a E Conversion Errors Open Database Create Database Database Wizard Caca Figure 5 3 The CS Demo database Form properties 4 Click OK The database is now associated with the form Selecting the data to display You indicated the source of the data to display on the form but the form is still blank To see the data you need to indi cate what data to show in each box You can use the Box Properties dialog box as described in Setting box prop erties on page 40 To choose the data box to display 1 Right click in a box or frame and select Field The Field properties appears 2 From the data source tree select the field to display Chapter 5 Databases 60 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 Figure 5 4 Selecting a field in the database tree 3 Click OK The field data is displayed in the box If you use this method with a framed box the box label will remain unchanged If you want to use the field name as the box label you can do it in one step as follows 1 Right click in a framed box and select the field name from the list at the bottom of the
39. ChemBioFinder Oracle instead it presents a dialog box in which you enter a name and a line of comments for each list Restore List presents a dialog box in which you choose from the available saved lists see screen shot below Chapter 14 ChemBioFinder Oracle 184 of 342 ChemBioFinder 13 0 PerkinElmer For the Better CS Oracle Restore List Comments benzenes Replace current list Add to current ist furans i aniline by name and sss Intersect with current list nonblank molnames Subtract From current lst ful ist Restore Previous List is no longer dimmed after you have done a single search it is available and will return you to the full list This is true also in ChemBioFinder 13 0 Over Current List Omit From List and Find List work as before Setting Oracle preferences When you are working with an Oracle database the Properties dialog box contains a tab for Oracle settings Items currently in this tab are as follows Auto sort on Displays the default sort field All lists will be sorted in ascending order over this field if no other sort criterion has been specified At present the auto sort field is always the primary key and cannot be changed Primary key Names the primary key of the current table if any Saved hits Displays the name of the table in which saved hit lists are stored for the current form if one has been created Records per retrieve Sets the size of
40. ChemBioFinder mydb mdb ETVAL V1 SFORM_ NAME SHORT V1 now equals for example mydb SETVAL V1 now equals for example SSYSTI c chemfndr system Script only commands text label label GOTO label IF vl op v2 stmt Chapter 20 CAL Commands 289 of 342 ChemBioFinder 13 0 PerkinElmer For the Better IF vl op v2 lt stmt s gt ELSE lt stmt s gt ENDIF LOOP count ENDLOOP PAUSE dseconds EXIT INTERACTIVE ON OFF STEP ON OFF Script only commands are useful only in script files not interactive CAL An asterisk is used to mark a line as a comment and not a command that should be executed Labels and GOTO give a mechanism for jumping backwards or forwards in a script A label may be any text string starting or ending with a colon It may appear anywhere in the script Prior to ChemOffice 2005 it had to appear prior to any GOTO that referenced it IF is a standard conditional statement It compares two values according to an operator and then executes its final statement if the result is true In the IF ELSE format it executes the ELSE statement when the IF statement is false Valid operators are TI A V A Vv LOOP begins a section of code that will execute repeatedly until ENDLOOP is reached By default the number of times the code executes is equal to the number of records in the current list but you can provide a
41. Click the Text Options tab Choose the Other option and specify a delimiter Click Export to save the choice and carry out an export N Oo FP WD Go back to step 1 of the import procedure to begin the import again Tip Once you have specified a delimiter it will be remembered and you will not have to repeat this operation The input file scan also determines the names and types of the data fields in the input file Field names must appear in the first line of the file in the correct order separated by the same delimiter as the data items Field types are deter mined by examining all the data in each column using the same rules as for SD import if all items in one column are integers then the field type is set to integer and so on Widths of text fields are set to accommodate the largest item in the file Chapter 7 Importing and Exporting Data 92 of 342 ChemBioFinder 13 0 PerkinElme For the Better Exporting data You can create a new SDFile RDFile ASCII text or MS Word file by exporting records from an existing database Text files can be saved in text txt format or in the Comma Separated Value csv format readable by most spread sheets When you export a file all records in the current hit list are exported You can include or exclude fields to be exported from a checklist The Data Export dialog box is similar to the Data Import dialog box It gives you options for file naming and file type selection
42. If variable is omitted the text will be assigned to V1 CAL commands READVAL syntax Reads the contents of a text file into a user variable user_variable_definition READVAL v filename The READVAL command has the following arguments p User variable to which the variable y text is assigned String containing the file filename name from which to read the text Remarks The complete file path c some long path TEMP TXT is necessary when reading files If variable is omitted the text will be assigned to V1 If the file is greater than 32K in size only the first 32K is read READVAL example This example uses the READVAL command to assign the contents of a file to a variable This might be the first step for example in writing the data to a database READVAL d reports status txt CAL commands WRITEVAL syntax Copies the contents of a user variable to a text file WRITEVAL v filename The WRITEVAL command has the following arguments Chapter 20 CAL Commands 284 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 User variable from which variable the text is obtained String containing the file filename name in which to store the text Remarks The complete file path c some long path TEMP TXT is necessary when saving files If the specified file does not exist it will be created otherwise it will be overwritten WRITEVAL example This example uses the WRITEVAL command to
43. Properties Database Table Field Form Box Choices Fromtable Chemists Name 00 Mol_ID Fixed list of choices Structure E Formula ME MolWeight Murphy E MOLNAME Rubenstein Smith Dill Jones She CORP_ID Abe DATE be memo 00 Chemist_ID E E Chemists Autodink will replace the retrieved data with the matching 00 10 value from the column selected above Choose the field She Name below which is to match on MolT able Mol ID Auto ink via ID X T Hide menu Cancel In the Choices tab f the Auto link via box is unchecked the dialog box lets you define a set of choices for data input If the box is checked then you have to define both a set of input choices and an auto link connection Tip To prevent the drop down choice menu from appearing check the Hide menu box This applies only if you have set up auto link 5 Select the From table radio button In the data source tree locate the subtable and click the column of data to be displayed in the box in this case Name under Chemists 6 The label Name after the radio button From table updates to show your choice and the Auto link via check box becomes available _ Note An auto link cannot be set up if you are entering a fixed list of choices 7 Check the Auto link via box From the drop down menu choose the column of the subtable in this case Name under Chemist which is to be match
44. Remarks This command is similar to the Menu Command File Close However if the user has modified the form in any way the File Close command will present an alert asking if the user wants to save changes while the QUIETCLOSE com mand will not CAL commands HIDETABLE syntax Closes the Table View window for the active form active_form_definition HIDETABLE The HIDETABLE command takes no arguments Remarks The Table View for the active form can be displayed with the Menu Command View Data Table If the active form is a subform the HIDETABLE command will return it to form view CAL commands SET syntax Changes the values of various preferences that control the overall behavior of ChemBioFinder SET section preference setting The SET command has these arguments section String describing the general category of preference preference String naming the preference to change setting String describing new value of preference Chapter 20 CAL Commands 267 of 342 ChemBioFinder 13 0 Values The values for section preference and value are DISPLAY ATOM_LABEL_COLOR DISPLAY ATOM_NUMS DISPLAY ATOM_SPECIAL_COLOR DISPLAY BOND_NUMS DISPLAY BOND_SPACING DISPLAY FONT_ADJUSTMENT Chapter 20 CAL Commands pP PerkinElmer For the Better The color in which to display atom labels that cannot be interpreted by Chem BioFinder The default is Purple Whether or not to display atom numbers on ea
45. S are thermodynamic values found at standard temperature and pressure Chapter 10 Chemical Properties 148 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 Heat of Formation Reported in KJ mole the heat of formation is the increase in enthalpy resulting from the formation of one mole of a sub stance from its constituent elements at constant pressure Henry s Law Constant A unitless value Henry s Law Constant can be expressed as kH pc a Where p is the partial pressure of the solute in the gas above the solution c is the concentration of the solute and ky be is aconstant with the dimensions of pressure divided by concentration The constant known as the Henry s law constant depends on the solute solvent and temperature Ideal Gas Thermal Capacity The thermal capacity at constant volume of an ideal gas is Cy 22 Nk ynR V eny Y y7 Where E Cy is a constant dependent on temperature U is the internal energy Tis the absolute temperature V is the volume nis the amount of substance of the gas R is the gas constant 8 314 JK7 mor in SI units N is the number of gas particles k is the Boltzmann constant 1 381 x10723 k 1 in SI units The thermal capacity at constant pressure of an ideal gas is P T p V Where H is the enthalpy of the gas calculated as H U pV Chapter 10 Chemical Properties 149 of 342 pP PerkinElmer For the Better Che
46. Select the preferences and click OK Display preferences To set the Display preferences Click the File gt Preferences menu command The Preferences dialog box appears with the Display tab on top Structure display To display carbon atoms on methyl groups or on interior aliphatic or aromatic chains check the relevant check boxes in the Carbon labels section To display hydrogen atoms on heteroatoms or on terminal carbons Select the Fill valence option in the Hydrogen Labels section Hydrogen labels C As drawn Fill valence C No implicit C NoH atoms 6h AM NH Select No H atoms in the Hydrogen Labels section Chapter 16 Customizing ChemBioFinder 13 0 200 of 342 ChemBioFinder 13 0 PerkinElmer For the Better Hydrogen labels C As drawn C Fill valence C No implicit NoH atoms N _ Note Selecting No implicit means these types are displayed without implicit hydrogens Using keyboard shortcuts When using a form you can use keyboard shortcuts to show or hide atom to atom maps reaction centers atom numbers and bond numbers To use keyboard shortcuts Select the Enable keyboard shortcuts check box on the Display tab of the Preferences dialog box When keyboard shortcuts are enabled the following keys toggle these properties T A show hide atom numbers B show hide bond numbers M show hide atom to atom maps T R show hide reaction centers S show hide stereochemistry
47. To execute CAL commands 1 Go to Scripts gt Command Line The Enter CAL Command dialog box appears 2 Type ina single CAL command Click Help to see CAL Scripting Help 3 Click Execute to run the command You can keep entering commands one by one 4 When you have finished running commands click Done The Command drop down list contains previously entered commands To rerun a previously entered command 1 Select the command from the list 2 Click Execute For more information on the command language see CAL Commands on page 243 Getting CAL help To display information about the CAL scripting language Click Help in the Enter CAL Command dialog box The CAL Scripting Help window appears containing com mands variables and syntax notes Chapter 16 Customizing ChemBioFinder 13 0 211 of 342 ChemBioFinder 13 0 PerkinElmer For the Better W CAL Scripting Help Command Arguments Description AAMAPS ONIOFF display don t display colored AA map ACTIVATE lt subform bo direct subsequent input to subform ADDRECORD COUNT Append one or more empty records APPEND ONIOFF set append mode on off default toggle APPENDVAL v lt text gt append text to specified variable ARROWBOX rect launches moving arrow Variable Description SCHIRAL 1 current mol is marked chiral not chiral CLIPBOARD text from Windows Clipboard CURR_DIR current working directory CURR_TABLE curent table
48. Used for whole numbers such as ID s All integers in ChemBioFinder 13 0 are long so can accom modate billions of values 232 of them 88 Double field Used for real numbers such as physical constants and unit prices Real numbers in Chem BioFinder 13 0 are double precision In ChemBioFinder 13 0 double fields can serve as ID fields Picture field Allows you to store a bitmap file BMP GIF JPEG PNG or TIFF or Windows metafile WMF EMF such as a spectrum or experimental setup as a data item in a database A Picture box on a form may be used to display a static picture attached to the form such as a logo or it may be used to show pictures stored in the database which change as you move from record to record If you import a database containing pictures type Long Binary or BLOB they will be interpreted as pictures and the form generator will create a picture box for it a Memo Rich Text field Used to display text Memo fields can be of any length Because memo fields are less structured searching them can be slower than searching a text field Additionally memo fields cannot be sorted To search for text 1 Right click in a memo or plain text field and select Find Text The Find text dialog box appears 2 Enter the text and the search criteria 3 Click either Forward or Backward to search 4 Tosearch for the next occurrence do one of the following Click Find Next Use the F3 key 5 To search for the previous occur
49. about these actions please consult the Microsoft Access User s Guide Do not add or delete records to the MolTable within Access because the data component of the database will become out of synchrony with the structure component Database File Types ChemBioFinder 13 0 databases are supported by a library called MstLib This library contains a number of files for sup porting the structure column In addition ChemBioFinder 13 0 uses additional screening files for improving per formance of search operations The following table lists the various file types used by ChemBioFinder 13 0 Structure Storage Screen Traditional Screen Traditional Chapter 16 Customizing ChemBioFinder 13 0 221 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 Screen Full Exact Screen Skeletal Screen Similarity Screen 3 D Screen Hash ChemBioFinder Form ChemBioFinder Form ChemBioFinder Script MDB MS Access database Locks on database 7 Note When MSS extension is missing the MSX extension is used but the quality of the search is lower Chapter 16 Customizing ChemBioFinder 13 0 222 of 342 ChemBioFinder 13 0 PerkinElmer For the Better Structural Query Features To perform a substructure search in ChemBioFinder you must first draw the query structure itself Query structures can be drawn in many different programs but we recommend using ChemDraw and this Appendix is focused on using ChemDraw to draw q
50. also similarity searching substructure similarity sum of degrees sum of valence degrees supported file formats synchronization tables adding creating deleting tabs creating and editing Tanimoto similarity tautomers searching for temporary database tetrahedral stereo center hits text as structures creating customizing fields format toolbar sorting styled text box description Chapter 22 Index pP PerkinElme For the Better 102 22 102 102 242 153 153 87 166 85 160 70 71 40 241 103 76 117 81 37 44 72 44 83 84 83 338 of 342 ChemBioFinder 13 0 I PerkinElmer For the Better text boxes formatting 10 text files importing 92 text format toolbar description 7 themes selecting 204 toolbars customizing 207 form 8 main 8 record 9 search 9 text 83 text format 10 tools alternative group 105 attachment point 106 data box 36 frame 36 framed box 36 grid 35 layout 35 picture 38 plain text 37 record 64 topological diameter 154 topology 237 total connectivity 154 total valence connectivity 154 transferring information to other computers 75 Chapter 22 Index 339 of 342 ChemBioFinder 13 0 I PerkinElmer For the Better trigger scripts 213 Tutorial 6 Creating a BioViz chart 26 two variable plot 27 U understanding forms and databases 14 undo 49 undoing changes 83 undoing data entry 79 uniform bond length 201 union with current list 131 unsaturati
51. and Subforms on page 156 You can connect a database to the form before creating boxes or any time after If the form is already connected to a database you can change the database or the data source If the form has boxes with fields connected to them then the boxes automatically connect to fields of the same name in the newly opened database Opening an existing chemical database To open a database to associate with a form 1 Right click on the form and click Data Source The Form Properties dialog box appears 2 Click Open Database The Open dialog box appears Chapter 5 Databases 59 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 am we Look in gt samples J Oc 5 Desbr 54142 S isiccr moe Pscreen istccrsm_backup mdb MyRecert ZBacrosase os Bye md Documents ZB AGROBASE _backup mdb AJNCI_DEMO MOe q Z chem30 mdb Fnewtest endb B cs_pemo moe BNIADEMO MOB Desktop B3 cs_DemMo_backup mdbd ZB pscreensmdb 2 cs_DemoPtus mdb SOEMO mdb B reroctss mos My Documents B cenrers mdb By INFOCHEM mos 2 151_DEMO MOS My Computer Fie name MoB gt Open My Network Fies of type Molecule DB mdb x Cancel ps T Open as readonly Figure 5 2 The Open dialog box 3 Inthe Open dialog box choose a database with an MDB file extension then click Open The Form Properties dialog box displays the data source tree The CS_Demo database is shown below Form Properties
52. and click in each box o Tip To select multiple boxes you can also click drag a rectangle around the boxes To select all boxes on the form go to Edit gt Select All The frame and the box behave as one object when you select move resize or delete To separate them into two objects 1 Click on the frame of the Framed box to select it 2 Goto Edit gt Bring to Front Here are other editing options To resize a box select the box and drag a side or corner To reposition a box click drag the center of the box to a new location To move multiple boxes select them and click drag the center of the selection to a new location Many of the Windows commands you use on text can also be applied to data boxes Edit gt Cut or press DELETE Edit gt Paste Chapter 3 Tutorials 16 of 342 ChemBioFinder 13 0 PerkinElme For the Better Edit gt Undo Edit gt Redo Saving a form To save a form 1 Draw another box on the form using the Framed box tool and label it as Structure 2 Go to File gt Save As 3 Inthe Save As dialog box save the form as tut1 cfx in the directory of your choice 4 Go to File gt Close Tutorial 2 Opening a database After you create a form you can use it to connect to a database In this tutorial you will use the form you saved in the previous tutorial After you connect to the database data will appear on the form Connecting a database to a form To connect a database to your for
53. and right click The context menu is displayed 2 Click Change Color on the context menu The color picker context menu appears 3 Select a new color and click OK The color in the box changes If you have plotted data with BioViz you will see that the points that correspond to the query also change color Child lists You can add a new query either by searching the Full List or searching another query When you create a new query from another one the result is a child list For comparison purposes it is often an advantage to create multiple child lists each from a single search attribute rather than one child list based on multiple attributes You can create a child list for only the currently selected list If you are not sure that the list you want is selected dou ble click it Chapter 15 BioSAR 194 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 Before you create a child list select Over Current List on the Search menu Note that once selected Over Current List has a check mark next to it You are now ready to create a child list query The following sample procedure describes how to create a child list by searching for carboxyl structures Click the Query icon to put the form in query mode Double click in the Structure window The ChemDraw toolbar appears Using the bond tool create a carboxyl structure When you have finished creating the structure click outside the Structure window a A O N gt
54. around an atom or bond Clicking the button creates a circle that moves toward the atom bond drawing the eye toit View details about a Help warning message Fix the error auto Auto Fix matically Managing queries The Queries Tree Control in the Explorer window maintains a list of search queries from the current and previous ses sions Queries are associated with forms and the query list is saved when you save the form When you open or acti vate an existing form the tree updates to show only the queries for that form Each time you carry out a search or list operation a new query is generated in the tree A name is assigned to the query and it is displayed in the tree along with the size of the list number of hits and a brief description The gen erated name is Q lt n gt where n is a sequential number and indicates that the query has not been named or marked for saving i Caution Depending on your preference settings unnamed queries may be automatically discarded See Saving and restoring lists on page 129 for details To activate the Queries tree control 1 Go to View gt Explorer Window 2 Click the Queries tab on the Explorer window to display the Queries tree Queries are listed as children of the database displayed as Full List When you select Search Over Current List from the Search menu before performing a query it is displayed as a child of the previous list The curr
55. box appears In the left panel all of the Fields are selected by default 4 Deselect those fields in the Choose fields to be included section that you want to exclude from the form 5 Inthe Form style section select the form options you want For a detailed description of the options see Cre ating forms automatically on page 32 6 Click OK 7 Click the Properties dialog box A warning dialog box appears allowing you to create a new form or replace the existing form Click No to create a new form Yes to replace the existing form The subform is automatically changed Working with subforms You must select a subform to work with it The subform title bar is highlighted when the subform is selected After a subform is selected the toolbars affect the subform You can use the Record tools to browse the subform and add rec ords To select a subform Click anywhere in the subform To return to the main form Click the main form Chapter 11 Relational Data and Subforms 158 of 342 ChemBioFinder 13 0 PerkinElmer For the Better To select a subform box With the selection tool click in the title bar Searching a subform You search a subform the same way you search the main form You can search a subform and the main form simul taneously To search a subform 1 Go to Search gt Enter Query The subform and the main form is cleared Tip You can also click the Enter Query icon on the Search Toolbar or typ
56. by the geometry of the drawing ChemBioFinder cannot cur rently interpret other stereochemistry types allenic square planar octahedral etc and ignores them during a search When evaluating a possible match the following rules are applied Unspecified stereochemistry a plain bond may match any stereochemistry either a wedged hashed bold or a plain bond Specific bond types need not match as long as the overall stereochemistry at a given atom does match Chapter 17 Structural Query Features 227 of 342 ChemBioFinder 13 0 pP PerkinElmer For the Better Implicit hydrogens are taken into consideration in both the query and the target if doing so helps to determine the chi rality of a stereocenter With a full structure search and the Match Tetrahedral stereo option selected the query with stereochemistry HO a g OH Finds any of N N OH H OH A HO 9 HO 5 N o OH Does not find any of HO o a OH H OH HO i o H Chapter 17 Structural Query Features 228 of 342 ChemBioFinder 13 0 PerkinElmer For the Better Relative tetrahedral stereochemistry Relative Tetrahedral Stereochemistry or RTS specifies a given relationship between the centers That is a known orientation of the substituents with respect to each other rather than a known absolute configuration To specify this centers are drawn not with the standard hashed and wedged bonds but with thick bold stereo bonds Re
57. calculated in ChemBioDraw Ultra for ChemBioOffice 2012 For more information on these properties and how to calculate them see the ChemBioDraw online help B Boiling Point c Critical Pressure Critical Temperature Critical Volume CLogP CMR G Gibbs Free Energy Chapter 10 Chemical Properties H Heat of Formation Henry s Law Constant L LogP LogS M Melting Point MR pKa tPSA 155 of 342 ChemBioFinder 13 0 PerkinElmer For the Better Relational Data and Subforms Subforms lets you work with multiple data tables in a relational database You should be familiar with working with ChemBioFinder 13 0 forms and databases before proceeding to subforms Access relational data A subform is a special box within a form that behaves like a separate form file A subform is used to display infor mation stored within a database but it usually displays data from a different database or different table within the same database than the main form A subform is usually linked to the main form so that retrieval of data in the main form also retrieves related records in the subform Like other types of boxes you can move select and resize a subform on the main form However you cannot select it by clicking inside it You must click the title bar When you click inside a subform you activate the miniature form inside the box and can work within it Below are examples of subform use You have data that is associated i
58. click Either in Tetrahedral match any target stereo center hits click Any match a relative rela click Thick bonds tionship between represent relative centers stereochemistry pP PerkinElmer For the Better g Note When Thick bonds represent relative stereochemistry box is cleared default thick bonds are inter changeable with hash wedge bonds When the box is checked and Tetrahedral stereo center hits is set to Same a query marked with thick bonds will only hit a target that has the same relative relationship between centers 4 Set the Double bond hits match the target Double bond hits structure exactly click Same match any con Double bond hits click Any figuration in the tar get 5 Click OK Entering query mode To clear the form and enter Query Mode Go to Search gt Enter Query You are in Query mode Chapter 8 Queries 117 of 342 ChemBioFinder 13 0 PerkinElme For the Better In Query mode The form background color changes QRY appears in the status bar Form boxes which do not permit data entry become editable for entry of queries Form boxes are displayed according to their visibility properties For more information see Hiding data boxes on page 44 Entering and submitting a query To enter the query 1 Position the cursor over the field you want to search and click to select it 2 Enter the query in the data boxes 3 Click Search o
59. command has the following arguments Integer value representing the distance in pixels between the left edge of the box and the left edge of the active form Integer value representing the distance in pixels between the top edge of the box and the top edge of the active form Integer value representing the distance in pixels between the right edge of Chapter 20 CAL Commands 248 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 the box and the left edge of the active form Integer value representing the distance in pixels between the bottom edge of the box and the top edge of the active form Database field name def inition that will provide the data that is displayed in the data box fieldname Remarks When a new box is created it adopts the current font settings These settings can be controlled with the FONT com mand You can assign a fieldname even if there is no data source for the form If a data source is assigned at a later point and a field within that data source has the same name as assigned to the data box the data box will automatically display the contents of that field After a box is created its field name can be changed with the SETFIELD command DBOX and FRAME example This example uses the DBOX command to create a short wide data box near the top left of the form and display the Formula field within it It then uses the FRAME command to label the data box
60. context menu The frame receives the field name and the data is displayed in the box Data Source Field ChembioWiz Piot Cluster by Mol JDI Sot Mol JD Structure Mole E y MoLIDI Structural Formal MobWeighkt Cakulate Property gt q um muu_m_u Figure 5 5 Selecting a field name from the context menu Opening a secured MS Access database To open a secured Microsoft Access database in ChemBioFinder 13 0 you need to set the appropriate permissions in MS Access _ Note If your database was created in MS Access 97 as for example were some of the ChemBioFinder 13 0 sample databases and you are using a newer version of Access you must convert the database before you can edit it These instructions assume a database created in Access 2002 Other versions may differ slightly as to options and procedures To set the permissions 1 Open the desired database in MS Access 2 Goto Tools gt Security gt User and Group Permissions Chapter 5 Databases 61 of 342 hemBioFinder 13 0 I me OE PerkinElmer For the Better User and Group Permissions x Permissions Change Owner User Group Name Object Name lt New Reports gt generic_report i i List Users Groups Object Type Report y Permissions E Figure 5 6 User and Group Permissions dialog box Select the Users or Groups radio button to assign permissions to individuals or groups
61. current form except structure but including formula and molecular weight are written The second line instructs Excel to open the file Excel can automatically recognize the file format as tab delim ited The third line instructs Excel to auto size column widths 1 4 to fit their contents f Note This example requires that the text export delimiter be set to TAB otherwise Excel may not read the file cor rectly To check this go to File gt Export then open the Text Options tab of the Data Export dialog box You can include either or both of these scripts on the Scripts menu and you can activate them with buttons on the form To include a script on the Scripts menu give it a filename with extension CFS and place it in the Chem BioFinder 13 0 System directory or in the directory containing the ChemBioFinder 13 0 application To activate a script from a button label the button with a script filename or string which can be converted into a filename For exam ple if TOEXCEL CFS exists in the ChemBioFinder 13 0 System directory label a button ToExcel to start the script For more information see Adding a button on page 39 Using Visual Basic The second method of communicating between ChemBioFinder 13 0 and other applications such as Excel is using OLE Automation ChemBioFinder 13 0 is an OLE Automation server meaning that it offers a collection of data man agement capabilities to outside programs capable of communicating with OLE
62. described in Setting Oracle preferences on page 185 The features on this tab are mainly for advanced users and do not require adjustment f Note The Oracle tab appears in the Properties dialog box only when an Oracle database is open 5 Click OK The database opens in a display form if you requested one The Database Wizard can also be used to open an Oracle database A button on the Wizard labeled CS Oracle Car tridge brings up the appropriate Oracle parts of the process When you have opened an Oracle database note that some Properties dialog box tabs show entries not available in ChemBioFinder 13 0 including a Database tab CS Oracle Cartridge version if any Table tab Table owner name name of primary index if any Field tab Oracle native data type name name of associated index if any When you open an Oracle database and select a table ChemBioFinder Oracle gathers information about the col umns If you open a table you know to contain structures and ChemBioFinder Oracle does not show a structure or Chapter 14 ChemBioFinder Oracle 182 of 342 ChemBioFinder 13 0 PerkinEl For the Better formula or molweight column then it may be necessary to set up some configuration information about the table For details see Configuring via CF_SETTINGS table on page 297 Searching Searching in ChemBioFinder Oracle works basically the same way as in ChemBioFinder 13 0 you enter a query search then work with
63. distance in pixels between the left edge of the text box and the left edge of the active form Integer value representing the distance in pixels between the top edge of the text box and the top edge of the active form Integer value representing the distance in pixels between the right edge of the text box and the left edge of the active form Integer value representing the distance in pixels between the bottom edge of the text box and the top edge of the active form String displayed as the static text Remarks When a new static text box is created it adopts the current font settings These settings can be controlled with the FONT command After a static text box is created its contents can be changed with the SETTEXT command Text will wrap to fit within the dimensions specified If all text cannot be displayed within the bounds of the text box only the first part will be displayed However all text is still present and will appear if the box is resized to larger dimen sions FONT and TEXT example This example uses the FONT command to set the font to be large bold and bright 24 point Arial bold in red then uses the TEXT command to create a short wide data box near the top middle of the form FONT Arial 24 1 255 0 OTEXT 200 40 450 70 My Compound Database Chapter 20 CAL Commands 251 of 342 ChemBioFinder 13 0 PerkinElmer For the Better CAL commands PICT syntax Creates a new picture box
64. files 88 from a specified location 90 hit lists 130 log files 89 partial RD or SD files 88 RDFiles 88 SDFiles 88 security settings 56 structure data and reaction data files 88 structures 88 structures only from RD and SD files 88 text files 92 importing and exporting data 87 95 inequality symbols in query 100 integer fields 73 intermediates in queries 110 Intersect with current list command 131 Chapter 22 Index 319 of 342 ChemBioFinder 13 0 I PerkinElmer For the Better ISIS Graphic files 87 ISIS Sketch files 87 isotopes 227 L labels editing 37 fixed 36 42 fonts 44 live 42 labels formatting 10 languages other than English sorting 84 last record command 64 layout tool 35 link node 134 linking subforms to main forms 156 live labels 42 LN link node special atom type 134 232 locking plots 163 164 log files 89 logon database 64 LogP 150 LogS 150 M M metal special atom type 231 232 m z 151 main form description 5 main toolbar description 7 Chapter 22 Index 320 of 342 ChemBioFinder 13 0 I PerkinE For the Better managing queries 125 mapping atoms in reaction queries 108 Markush structures 81 mass 150 matching stereochemistry 115 mathematical operators in CAL commands 282 MDL file format 230 MDL molfiles 87 MDL rxnfiles 87 melting point 150 memo fields 73 menu bar description 6 menu commands CAL 243 menu adding to data box 43 merging a hit list 130 minus symbol in query 1
65. g Right click the tab and click Delete Tab context The tab is removed Setting box properties You can set box properties such as data source display type font and box style To set the Box properties right click a data box and select Properties _ Note The Properties option is available only in Layout mode Setting data box styles You can change the style that is applied to a data box on a form For example you can change a data box to a frame or picture Choose from these styles Data Box displays alphanumeric data Can display multiple lines of data Frame displays alphanumeric data Can display a single line of data Plain Text displays alphanumeric data Text data can be displayed in multiple lines Use CTRL ENTER to start a new line You set the field size when you create the field up to a maximum of 254 characters Picture displays Windows metafile data Pictures are scaled to fit within picture boxes with fixed height to width ratios Formula displays any kind of text but numbers are subscripted Formulas are presented in modified Hill order as follows If a substance contains both carbon and hydrogen the carbons are listed first followed by the hydrogen atoms followed by other elements alphabetically by element symbol If a substance contains carbon the carbons are listed first followed by other elements alphabetically by element symbol Otherwise all elements are listed alphabetically by eleme
66. help for menu items and other information a Database Queries Favorites r Enter search query READ ADD QRY at 11 of 3568 db 3568 4 Ww E When you first open a form the current list size equals the total database size The total database size changes when you add or delete records If you search to find a subset of the entries in the database then the current list size changes to indicate the number of hits in the search To the left of these counters are three other indicators that show the general status of the database READ indicates you are using a read only database a read only form file or if you have selected Open as read only on the open file dialog box ADD appears when you enter a new record QRY when you enter a query To hide or show the Status Bar select or deselect View gt Status Bar More UI features Style button for text and frame boxes The Box Properties dialog box makes the Style button available for frames and plain text labels This button opens the Box Style dialog box where you can set frame type printability and other display characteristics Chapter 2 Getting Started 10 of 342 ChemBioFinder 13 0 PerkinElmer For the Better Read only structure box option The Box Style dialog box has a check box Box is read only This is applied to text numeric data boxes and structure boxes If you mark a structure box read only the structure cannot be edited except in qu
67. i i the Enter Script Com the Scripts menu i mand dialog box then click Execute 4 Press any key except Escape to execute the command and go to the next command As each step is encoun tered it is displayed in the status line 5 Press the Esc key to stop debugging the script 6 Type step off in the Enter Script Command dialog box to exit the debugging mode Trigger scripts Trigger scripts run in response to certain predefined events A trigger script can for example automatically load a box with data calculated from the contents of another box whenever you move to a new record You access a trigger script from the Run script on listbox in the Form tab of the Properties dialog box The listbox shows the available trigger events and allows you to create edit enable or disable scripts for each event Chapter 16 Customizing ChemBioFinder 13 0 213 of 342 ChemBioFinder 13 0 Perkin For the Better To run a script on an event 1 Right click in the form and click the Properties context menu command 2 Click the Form tab Click the check box of the desired event in the Run script on list box If an event is not checked no script will run on that event even if one is available oO Click the event name to highlight the row of the listbox Clicking in a check box does not select the row Click Edit to write or edit the script in the CAL Editor Click OK to retum to the form The script will automatica
68. in the General tab of the Preferences dialog box The default is 0 do not warn Whether or not to display a border around forms when printing The default is 1 print a bor der The contents of the footer to be printed at the bottom of all pages containing forms Any text is valid as well as the following special codes D current date F name of the CFX file P page number ChemBioFinder 13 0 PRINT_ PRINT_HEADER OPTIONS 7 SEARCHING EXACT FIND_CHARGED_CAR BON SEARCHING pP PerkinElmer For the Better T current time The default is Chem BioFinder D T Rec ord P The contents of the header to be printed at the top of all pages containing forms Any text is valid as well as the same special codes rec ognized for the footer The default is F file name Whether or not to allow a substructure match when searching This parameter can be set manually in the Search tab of the Pref erences dialog box The default is O sub structure Whether or not to allow uncharged carbon atoms to match charged ones when searching This parameter can be set manually in the Search tab of the Pref erences dialog box The default is 1 allow the match SEARCHING FIND_CHARGED_HET Whether or not to allow Chapter 20 CAL Commands 275 0f 342 ChemBioFinder 13 0 SEARCHING MATCH_STEREO DB MATCH_STEREO_TET SEARCHING SEARCHING MAX_HITS SEARCHING SIMIL
69. in the preferences dialog box For example to show no highlighting choose black as the highlight color See Color preferences on page 202 for more information Using the current molecule as a query As you browse through a database you may submit any structure on the screen as the structural query Often you use similarity or substructure searches see above with this type of query to find related compounds To use the current molecule for a query 1 Using the Record commands go to the record containing the structure that you want to use as a query 2 Goto Search gt Current Mol As Query All boxes of the form are cleared except the structure so that the molecule on display can be used as part of the query You can then continue with the query as if you had drawn the structure from scratch Chapter 8 Queries 119 of 342 ChemBioFinder 13 0 PerkinElme For the Better Finding the current molecule The Find Current Molecule command located in the Search menu and on the Search toolbar is similar to the Current Mol as Query command discussed above As you browse through the database you may find a molecule that inter ests you and want to find other related records The Find Current Molecule feature lets you perform a quick structural search of the structure currently being displayed on the form However this feature does not let you enter other search terms The type of structure search complete structure substructure and or simi
70. it On the Text Options tab select a delimiter and other options you want to include subform data empty records and headers You also have an option to save structures in CDX or CDXML format 4 After you have made your selections click Export Importing the cfxml file Once you have saved the dataset in CFXML format you must bring it back into ChemBioFinder to save it as an MDB file f Note To avoid conflicts with field name type definitions close the master database before importing and open a blank form 1 Inablank form go to File gt Import gt CFXML and open the file The Data Import dialog box appears 2 Select deselect the fields you want to import and the options you want to apply to the file 3 After you make your selections click Import Your dataset is imported into an Access database Exporting to an Excel spreadsheet When you export a BioSAR derived form with multiple subforms into an Excel spreadsheet you must take pre cautions to get all of the subforms correctly exported This is because the exporter normally uses only the field names and the BioSAR subforms show the same set of fields from different assay tables On export they will col lide and the data will not come over correctly To prevent this ChemBioFinder 13 0 has an option on the Text Options tab of the Data Export dialog box Prefix output fieldnames When this box is checked the output names will match the input names which are prefixed fo
71. menu command to open the Database tab of the Box Properties dialog box 2 Click Oracle Database The CS Oracle Connection dialog box opens _ Note The Oracle Database button is available to any user There is no check to see whether the machine is a valid Oracle client 3 Enter values for Host name User name and Password the same values you use to log in from any Oracle client OR Choose a name from the drop down list of recently used items When you choose an item from this list it auto matically fills in the user name and the password if Save password was checked when the item was created f Note The first time you bring up the Oracle Connection dialog box there is no list of recent items so ChemBioFinder 13 0 offers to create one for you If you accept it generates a list of all available hosts as found in the file insnames ora created during Oracle client configuration The database is opened and the list of tables displayed _ Note The list of tables shown in the tree consists of all tables and views owned by the current user plus those to which the user has been granted certain privileges To see the details you can turn on SQL tracing while a database is being opened 4 Proceed as you would for any ChemBioFinder 13 0 database click to select the table you want to display set other desired options and check the box on the Form tab if you want to generate a form automatically The Oracle tab of the dialog box
72. no data until you enter structures into the database Backing up databases To back up the current ChemBioFinder 13 0 database 1 Go to File gt Copy Database A Save As dialog box appears By default your copy is named YourDatabase__ copy cfx 2 Rename your copy if you wish select a location and click OK A complete set of ChemBioFinder 13 0 database files is created in the selected location Moving databases ChemBioFinder 13 0 saves only the definition of the form and information for connecting to the database in the CFX file The actual data are stored in files with MSX and MST extensions for structure data and in files with an MDB extension for non structural data If you want to move a database to another computer you must move for a default ChemBioFinder 13 0 database at least four separate files This number might be greater if you have several forms that access the same database Chapter 5 Databases 75 of 342 ChemBioFinder 13 0 PerkinElme For the Better _ Note The MSX MST and MDB files all have the same file name but the name of the CFX files might be different depending on how you saved them After you move the database to its new location open your forms to make sure the data source links have been retained If ChemBioFinder 13 0 cannot locate the data source and displays an empty form you will need to use the File gt Database menu command to reconnect to the data source If the form is connected to a
73. objects While this collection is cur rently fairly small it is adequate for a variety of data retrieval and search tasks This feature allows you to write a custom Visual Basic procedure that directly retrieves and manipulates data from ChemBioFinder 13 0 The general procedure for accessing ChemBioFinder 13 0 data from within a Visual Basic script is as follows 1 Create a ChemBioFinder 13 0 Document object typically passing a filename so that you open a form complete with its database connection 2 Use methods of the Document object to move through the database search and access data Document meth ods include some that access Field objects used to query the data in the database and Molecule objects for accessing details of molecular structures For more information see the CambridgeSoft SDK web site Using Microsoft Access The methods described above for communicating between ChemBioFinder 13 0 and Excel apply also to Access You can start Access using the EXEC command You can send it DDE commands contained ina CAL script although Access provides fewer capabilities with DDE than does Excel Or you can write programs using Access Basic that rely on the OLE Automation methods found in ChemBioFinder 13 0 In addition you can use Access directly to oper ate on a ChemBioFinder 13 0 database Chapter 16 Customizing ChemBioFinder 13 0 220 of 342 hemBioFinder 13 I ChemBio der 13 0 PerkinElmer For the Better A ChemBioFinder
74. of the details in one place in a single operation In the new dialog box the Database Table and Field tabs reflect the data source of the subform not the parent form The database tree control in the dialog box also shows subform data source You can use the Explorer win dow to display the tree control of the parent data source if they are different Chapter 11 Relational Data and Subforms 156 of 342 ChemBioFinder 13 0 Perkin For the Better As before the Form tab shows properties of the subform while the Subform tab shows properties of the box and the linkage between the subform and its parent When creating a new subform you get the same dialog box by clicking within the subform as by clicking on the box header For convenience the dialog box comes up automatically whenever you create a new subform box After you have created a subform the subform tool is deselected This prevents the frequent mistake of drawing a subform box then trying to draw a data box within it and getting another subform Creating a subform manually To create a subform 1 Start ChemBioFinder 13 0 and open or create a form The form should have at least one data box and be linked to an existing database 2 Click Subform on the Form toolbar 3 Click somewhere in the form and drag to create a data box When you release the mouse button the Subform Properties dialog box appears By default newly created subforms are associated with t
75. only three stereo bond types are available hash wedge or either squiggly bond thick bonds are not recognized This presents a problem for the ChemBioFinder user wishing to import or export structures having relative stereocenters ChemBioFinder addresses this problem by using a proprietary tag in the file recognized only by ChemBioFinder The tag is BOND_RELS and is applied to every stereo bond of thick type For example here is an excerpt from the bond table of a molfile with relative bonds 45100002611000 lt bond 5 marked as UP4 711000 lt bond 6 marked as UPM CFW 5 BOND _RELS lt overrides type of bond 5 to be UP THICKM CFW 6 BOND_RELS lt same for bond 6 The consequences of having a ChemBioFinder only tag are When any of the MDL file formats is saved from within ChemBioFinder the tag is written Reading these files back into ChemBioFinder will retain the thick bond types If a structure is drawn in ChemDraw and saved as MDL Molfile thick bonds are lost and are converted to normal hash wedge bonds This is not true if the file is saved as CDX If a structure is saved as molfile from ChemBioFinder reading it into ChemDraw loses the thick bonds Mol or SDFiles obtained from ISIS or other programs do not know about this tag and thus cannot convey thick bonds However such files may be edited by hand to include the ChemBioFinder tag An MDL file written by ChemBioFinder containing tags should in principle be
76. query returns results based on the query structure and the previous hit list Each reaction shows the reduction of a ketone to an alcohol In the Queries Tree this search is shown as a child of the first query Chapter 3 Tutorials 25 of 342 hemBioFinder 13 l Che oFinder 13 0 PerkinElmer For the Better Queries Full List 0to 0H 23 O Ketones 13 Database Queries Favorites Figure 3 3 A child search in the queries tree O Tip If you plan to run several searches over a hit list use the Set Domain to Current List command rather than Search Over Current List Setting a domain eliminates the need to keep restoring the original hit list Tutorial 6 Creating a BioViz plot Using BioViz you can plot the data in your search results based on any numerical field in the database BioViz plots can consist of line or scatter plots with either one or two variables or Histograms with X axis data For more information on BioViz plots see BioViz on page 161 Single variable plots A single variable plot displays a Y coordinate variable vs the record number To create a single variable plot 1 Goto View gt ChemBioViz Plots gt New The ChemBioViz Plot Properties dialog box opens 2 Click One variable in the Dimension box 3 Select any numerical field from the drop down list forthe Y coordinate 4 optional Enter a name for the plot Tip Note the Point Limit field on the lower right side of the Properti
77. readable by any program which can import such a file The unrecognized tags should simply be ignored Normalization Closed rings of alternating single and double bonds are normalized This is required to make their substituents equiv alent Ortho dimethylbenzene is remains same whether there is a single or double bond between the two substituted ring atoms Chapter 17 Structural Query Features 230 of 342 hemBioFinder 13 I Che oFinder 13 0 PerkinElmer For the Better In a substructure non tautomeric query the fol lowing query N N a will get the following hits N K and will NOT hit the following O Ou O ag O Normalized query Changing the scope of a search When preparing a chemical structure to be used in a query there are two ways to broaden or narrow the scope of the search s Specify atom or bond properties E Specify atom or bond Special Types In general properties narrow a search and special types may either narrow or broaden the search Atom properties ChemBioFinder allows special atom properties to be assigned to an atom in a query These properties are usually only meaningful during a search They generally serve to broaden or narrow the scope of the search Special atom types ChemBioFinder recognizes six special atom types that can match any one of a predefined set of elements A matches any non hydrogen atom Q matches any heteroatom non hydrogen non carbon Chapter 17
78. remote data source on a network you have fewer files to move The data source can remain on the remote machine and you only move the CFX file that contains your form for accessing the data You may need to reconnect it to the data source if it is not done automatically This situation is common in large organ izations where several people access the same central data source Creating a portal database To carry out certain operations such as sorting structural data ChemBioFinder 13 0 needs to create temporary tables in a database This cannot be done in a read only source such as a data CD Instead of accessing the read only source directly you can create a portal database a local writable database with attachments to the external tables of interest The portal looks and behaves just like the target database but without the limitations ChemBioFinder 13 0 creates a portal database when needed For example if you are using a database CD perform a search and attempt to sort by formula a message appears that offers to create a local database attach the current table save the form and proceed with the sort If you create the local database you can use the new form to get the data with full functionality and performance Chapter 5 Databases 76 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 Working with Data Entering data You enter data into a database by adding a new record Adding a new record consists of thr
79. specific count in the LOOP statement Tip ENDLOOP can be used anywhere within a loop clause to mean continue to the next iteration Example LOOP RECORD NEXT IF HAS_MOL 0 ENDLOOP ENDIF CLEAN o Chapter 20 CAL Commands 290 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 ENDLOOP this example if a record has no structure the program goes to the next record and skips the CLEAN PAUSE temporarily stops the script from executing for a specified number of tenths of a second If no number is given the duration of the pause is 2 seconds EXIT ends the script immediately INTERACTIVE turns interactive mode on or off STEP toggles single step debugging mode on and off The table below shows examples of Script Only Command IF V1 MSG provide an error message if Empty the variable V1 is empty value PAUSE 100 pause 10 seconds GOTO A go to specified label begin oop to repeat ten times pause the default time 2 sec onds return to LOOP statement until done ENDLOOP _ Note Script commands are subject to change See the Readme for up to date information CAL commands syntax Marks a line as a comment and not a command to be executed text The command has the following argument String containing the com ment Chapter 20 CAL Commands 291 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 Remarks The character must be the fir
80. square is available when curve fitting is selected Figure 12 5 BioDraw Analysis In Version 12 results of descriptive statistics are displayed on the plot Version 10 plot Chapter 12 BioViz 168 of 342 hemBioFi 13 I ChemBioFinder 13 0 PerkinElmer For the Better 1000 Boiling Gean K 15182 Variance K 3556 Mean 53346 Variance 15718 D Figure 12 6 1 Descriptive statistical analysis Version 11 plot 1400 A2 0 78 BP A K Molecular Weight Figure 12 7 Displaying Statistical Analysis Results You may choose from linear quadratic or cubic curve fitting A confidence interval of one to three standard deviations may also be displayed Both descriptive statistics and the curve fit update dynamically when the recordset changes or filters are applied _ Note Curve fitting gives incorrect results if one of the axes is logarithmic For example you do a linear fit on the original data and then transform that fit to the log plot thereby creating a curve Once you have created a plot you might want to clean up the display There are two ways to do this sorting the data on a field and using filters Sorting The standard ChemBioFinder 13 0 sort feature is the first step in cleaning up a graph You may sort into ascending or descending order There are two ways to sort a dataset on a given field Right click in the field box and click the Sort context menu comman
81. started with To do this export to cfxml When exporting to SDFile you may append to or overwrite existing SD files This option is only available for SD files and delimited text exports Printing You can print out all or part of your database To print a database 1 Before printing decide if you want to print a table view or a form view Set ChemBioFinder 13 0 to the appropriate view 2 Goto File gt Print Setup 3 Inthe Print Setup dialog box set the printer paper size default US Letter and page orientation desired Click OK Tip Settings in this dialog box affect the Page Setup so it s best to start here 4 Go to File gt Page Setup 5 Inthe Page Setup dialog box set the margins and units cm inch layout and other options The Header option prints the file path at the top of the page The Footer option prints the date time and record number at the bottom of the page Click OK 6 Go to File gt Print Preview 7 Goto File gt Print The Print dialog box appears 8 Set the print range and number of copies You may also select a different printer than the default _ Note ChemBioFinder 13 0 defaults to printing a single page This is indicated by the option labeled Selection If for example you are printing in Form view and you set the layout in Page Setup to three per page you will print the Chapter 7 Importing and Exporting Data 95 of 342 ChemBioFinder 13 0 PerkinElmer For the Bet
82. than 100 different chemical topological physical and thermodynamic properties This guide describes the properties you can calculate using ChemBioFinder and lists the property cal culations that are available in other ChemBioOffice 2012 applications ChemBioFinder Chemical Properties ChemBio3D Chemical Properties ChemBioDraw properties ChemBioFinder Chemical Properties To view the properties for a given structure 1 Right click in the form and select calculate properties from the context menu 2 Select the desired property in the Property Populator window 3 Click Populate The properties listed below can be calculated in ChemBioFinder Ultra for ChemBioOffice 2012 For more information on these properties and how to calculate them see the ChemBioFinder online help B H P Balaban Index Heat of Formation pKa Boiling Point Henry s Law Constant Polar Surface Area c I Principal Moment Chemical Name Ideal Gas Thermal Capacity R Cluster Count L Radius Connolly Accessible Area LogP Partition Coefficient S Connolly Molecular Area LogS Shape Attribute Connolly Solvent Excluded Volume M Shape Coefficient Critical Pressure Mass Sum Of Degrees Critical Temperature Melting Point Sum of Valence Degrees Critical Volume Mol Formula T E Elemental Analysis Exact Mass F Formal Charge G Gibbs Free Energy Chapter 10 Chemical Properties Mol Formula HTML Mol Refractivity Mol Weight Molecular Topological Index
83. the Better Do not modify data in an existing Web Server RegDB or E Notebook database ChemBioFinder Oracle does not automatically prevent you from doing this but you are sure to foul up those systems unless you go through their nor mal registration procedures or know exactly what you re doing Most database alterations are possible as in ChemBioFinder 13 0 you can add modify and delete tables and fields assuming you have the appropriate privileges Differences include a When you create a structure field you can give it any name you like Structure columns in tables managed by the CS Oracle Cartridge can be in any of several formats but Chem BioFinder Oracle does not allow you to choose one it defaults to a character CLOB column storing text encoded CDX ChemBioFinder Oracle does not allow you to create an Oracle database in the same way ChemBioFinder 13 0 creates an Access MDB file The equivalent in ChemBioFinder Oracle is to create a table Loading You can build ChemBioFinder Oracle databases by loading from SDFiles or using Import Structures RDFiles should work also but have not been tested However because you cannot actually create a new database the procedure is somewhat different from ChemBioFinder 13 0 You must already have a database open and then you can import to an existing table or have a new one created To import data and structures into a new table 1 On an empty form right click and choos
84. the Main Toolbar icons or the Edit menu to reverse or restore recent changes to a form To reverse or restore changes a Go to Edit gt Undo to reverse a change or click the Undo icon Goto Edit gt Redo to reverse a change or click the Redo icon _ Note Undo and Redo work over multiple changes Either command can be used repeatedly to reverse multi step operations Ordering objects The Bring to Front and Send to Back commands place data boxes in a specific sequence They have two effects Select which overlapping data box is on top Set the order in which the cursor moves when you press the Tab key To put a box on top or bottom 1 Click the box to select it 2 Do one of the following Goto Edit gt Bring to Front to put it on top or Go to Edit gt Send to Back to put it on the bottom The order in which data boxes are created is the order in which the cursor moves as you press the Tab key You can set which data box the cursor moves to first or last To set the cursor to move to a data box first 1 Select the data box 2 Goto Edit gt Send to Back 3 Press the Tab key The cursor moves to the box you set To set the cursor to move to a data box last 1 Select the data box 2 Goto Edit gt Bring to Front The box you set is the last box the cursor moves to when you press Tab repeatedly Chapter 4 Forms 49 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 Aligning and distributin
85. the template similar to the query you used but with Rs attached at all positions which found substituents Figure 5 15 R Group query and template new columns are generated for all the Rs the other rows are populated with the Rs hit _ Note The data in this table is just for display It is not saved with the form The table will continue to be displayed when you toggle the Table view until you change the hit list by running another query or restoring the full list To sort an R Group Table 1 Right click the header of any R column R1 R2 etc 2 Go to Sort Column gt command The options are Ascending Descending Chapter 5 Databases 68 of 342 pP PerkinElmer j For the Better ChemBioFinder 13 0 Multiple Ascending and Descending sort by the molecular weight Multiple opens a dialog box that lets you sort by another parameter or group of parameters To set up a multiple sort 1 Select fields in the order in which you want them to apply 2 Right click selected fields to change the sort order ascending descending or to remove an unwanted parameter You can cut and paste R group cells containing either structures or text using the clipboard R Group plots Once you ve generated an R group table you can then plot the various substituent groups against any other plotable field 1 With the table view still displayed go to View gt BioVizPlots gt New 2 On the General tab
86. they may be hidden Creating a plot To begin working with BioViz select a set of data to work with You can plot an entire database or the results of data base queries You can filter the plot to limit the data range within a given dataset To create a new plot Go to View gt BioViz Plots gt New The BioViz Plot Properties dialog box appears Select a Dimension one or two variables and a Style line scatter or histogram 1 2 3 Select the variable s from the drop down list s 4 Optional select other options change the name 5 Click OK to view the plot The plot appears in a separate window In a 2D plot you may plot any numeric field on the X axis and any other on the Y Fora 1D plot you choose only the value to be plotted on the Y axis where the X axis represents record number For a histogram choose a single value to be plotted on the X axis with the frequency plotted on Y Another way to select a field to be a variable or create a 1 D plot is to right click in a property field and select BioViz Plot from the context menu When you right click in a numeric data box you may choose that value to be plotted on either axis oras a 1D plot against record number In the latter case the plot appears immediately when you release the mouse button For a 2D plot you must first select a data box for the other axis Use the Reset X Y command to clear both X and Y settings and start again Histograms Histogram plots ar
87. write the contents of a variable to a text file WRITEVAL 2 f formulas mydata txt CAL commands INPUT syntax Displays a text input dialog box accepts data from the user and stores it in a variable INPUT variable input The INPUT command has the following arguments User variable to which the variable gt a user s data is assigned String presented as the input default input Remarks If variable is omitted the text will be assigned to V1 CAL commands PASSWORD syntax Displays a text input dialog box accepts data from the user and stores it in a variable Each character entered by the user is displayed as an asterisk to conceal its identity PASSWORD v default The PASSWORD command has the following arguments Chapter 20 CAL Commands 285 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 User variable to which the variable user s data is assigned String presented as the default default password Remarks If variable is omitted the text will be assigned to V1 Password entry example This example uses the MSG command to prompt the user for a password then the PASSWORD command to retrieve it After using the IF command to test whether the password is correct it either EXITs or continues with the rest of the script msg Pleas nter the secret password password lif vl lt gt the secret password exit etc CAL commands GETDATA syntax Reads the cont
88. 00 models viewing with Chem3D 82 modifying data 79 mol formula 150 mol refractivity 151 mol weight 151 Mol_ID field 70 molecular formula queries see searching for formulas 98 molecular formula searches see searching for formulas 98 molecular topological index 151 molecular volume 151 molecular weight field 70 Chapter 22 Index 321 of 342 ChemBioFinder 13 0 moving boxes objects moving forms and databases MS Access see also Access MS Access workgroup information MSI molfile multi step reactions multi user access name searching new form creating new record indicator description next record command normal searching normal searching see also exact searching normal searching see also similarity searching number rotatable bonds numbers customizing numeric format numeric searches objects aligning deleting distributing spacing Chapter 22 Index pP PerkinEl For the Better 48 48 75 221 51 87 106 63 21 34 64 101 101 101 152 45 45 22 98 50 48 50 50 322 of 342 ChemBioFinder 13 0 I PerkinE For the Better ODBC selecting data sources 71 OLE automation communicating with other applications 220 OLE automation overview 220 open database button 59 open last form on startup 204 opening databases 59 62 existing chemical databases 59 hit lists 130 secured MS Access databases 61 opening a database tutorial 17 opening options see preferences 203 opt
89. 1 333 of 342 hemBioFi 13 I ChemBioFinder 13 0 PerkinElme For the Better selecting boxes 47 data to display 60 databases 59 objects on a form 47 selection tool 47 send to back command 49 setting alerts 203 box properties 40 color 46 data box styles 40 fixed and live data 42 numeric format 45 preferences 200 recent file list size 204 search details preferences 113 search type preferences 111 security options 51 stereochemistry search preferences 116 shape attribute 153 shape coefficient 153 showing annotations 201 data boxes 44 opening dialog 203 reaction centers 204 similarity rules 241 similarity searching 102 Chapter 22 Index 334 of 342 ChemBioFinder 13 0 I PerkinElmer For the Better similarity searching see also exact searching 102 similarity searching see also normal searching 102 single variable plot fast method 26 SMD files 87 sorting by subform aggregate Oracle 184 data 84 data tables 84 fields 84 formulas 84 from the data table 84 in reverse order 84 languages other than English 84 Oracle databases 183 structures 84 text 84 Sorting 169 special atom types list of 231 special bond types 236 special structure searches 121 SQL searches 111 statistical analysis 28 statistical analysis see BioViz 168 status bar 10 status bar description 7 stereochemistry 227 allenic 227 cis trans double bonds 227 octahedral 227 Chapter 22 Index 335 of 342 ChemBioFinder 13 0 overview queries
90. 1 2 and 3 will be displayed This is a Boolean NOT operation it shows the records in the current list that are not also in the restored list Union Displays all records in either the current list or the saved hit list This is a Boolean OR operation Subtract from Displays only those records that are in the saved hit list but are not in the current hit list This is the same as Subtract but with the order of the lists reversed The hit lists are integrated You can browse and save this new hit list just as any other hit list Drag and Drop list merge 1 Perform a search and save the hit list 2 Perform another search and save the list Two saved queries are shown in the figure below Chapter 8 Queries 131 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 Explorer H Queries Ful List Q1 1 555 query C6H6 AND Molname LIKE pencillin Y Q2 26 555 query C6H6 AND Molname LIKE benz Database Queries Favorites 3 Simply drag one query item in the tree on top of another Restore Merge dialog box comes up allowing you to choose the logic to be applied to the merge replace intersect subtract union and subtract from Restore Merge List El L1 current list El Replace useL2 gazan C Intersect L1 andL2 i L2 Subtract L1 L2 C Documents and Settings zchoo My Union 11 L2 Documents Models L C Subtract from L2 L1 Cancel
91. 13 0 molecule database consists of three components the structure storage files with file exten sions MST and MSX the data storage files which include a Microsoft Access database file extensions MDB and LDB and the forms with file extension CFX used to view the structures and the data For more information see Database File Types on page 221 If you have Access on your system double clicking an MDB file in Explorer starts up Access and opens the specified database When you open a ChemBioFinder 13 0 database in Access you will see the same tables as displayed in the Chem BioFinder 13 0 Database dialog box including the main structure table usually named MolTable but you will not see columns for structure formula or molecular weight These fields cannot be manipulated directly using Access The following are some of the operations you can perform on a ChemBioFinder 13 0 database using Access Most of these capabilities are not available through the current version of ChemBioFinder 13 0 E Compress or repair the database Change column field or names or formats Change table names Add or delete columns or tables Import or export tables Load non structural data from various file types including delimited ASCII Excel or Word Move quantities of data from one column or row to another Carry out complex queries on non structural data Permanently change the sort order of a table For more information
92. 130 93 129 33 130 39 331 of 342 ChemBioFinder 13 0 I PerkinElmer For the Better structures 93 subforms 33 vs committing 33 scaling structures 201 script only commands CAL 289 scripts communicating with other applications 218 debugging 213 executing 213 in subforms 160 writing 212 scroll bars adding 43 SDFiles exporting 93 95 SDFiles importing 56 88 search examples 132 toolbar 111 type 101 search details preferences 113 search over list command 25 search toolbar description 7 searching by reaction type 24 case insensitive 115 combined 110 for datesdate searches see searching for dates 100 for formulas 20 for formulasformula queries see searching for formulas 98 Chapter 22 Index 332 of 342 ChemBioFinder 13 0 for intermediates for names for numbers for products for reactants for substructures formula element ranges formula query rules full word fullerenes ISIS style loose delocalization more than one substructure parentheses in formulas procedures subforms tuning searching a database tutorial searching combined searching for dates searching for formulas secured Access securing forms security disabling MS Access workgroup information overriding setting options Chapter 22 Index gt PerkinElme For the Better 110 21 22 98 24 109 23 109 22 99 99 115 134 115 115 135 100 111 159 115 20 23 100 98 64 51 57 51 57 5
93. 2 or greater installed To start BioSAR 1 In Internet Explorer log into the ChemOffice Enterprise portal 2 Inthe Enterprise screen under BioSAR Enterprise open a query form using either of these links Open Form Manage your forms Performing searches in BioSAR Before exporting a BioSAR data form to ChemBioFinder you need to search on the data in the BioSAR database 1 In BioSAR open a query form of your choosing 2 Inthe form enter your search criteria and click Search Exporting the data form to ChemBioFinder After the search is complete you are ready to export the data form to ChemBioFinder To export the form 1 Click Display In BioViz If the button is not visible you may need to edit the BioSAR form properties See your administrator 2 When prompted to either save the form file or open it select Open ChemBioFinder will launch 3 At the Oracle login provide your user name and password _ Note If you don t want to view the form now simply save the file You can open the file in ChemBioFinder at any time ChemBioFinder file types Whenever you export a data form BioSAR creates a file with the extension bsbxml ChemBioFinder reads this file and opens the form linking it directly into the database The bsbxml file is read only although ChemBioFinder doesn t let you modify the bsbxml file itself you can still edit the form and save your changes When saved the form file is assigned the ChemBio
94. 2 portal database 76 precision in numerical queries 98 preferences color 202 date display 100 display 200 general 202 grid spacing 201 picture display 201 recent file list size 204 registration 203 search details 113 search type 111 setting 200 stereochemistry 116 Chapter 22 Index 325 of 342 ChemBioFinder 13 0 I PerkinElmer For the Better structure display 200 tuning 115 previous record command 64 principal moment 152 printing 95 products in queries 109 searching for 106 profile box description 6 profiles see compound profiles 137 program execution commands CAL 259 Python 214 Python interactive mode 216 Python script creation 215 Q Q heteroatom special atom type 231 QRY indicator 10 QRY indicator description 8 queries anchored substring 97 atom lists 133 232 atom not lists 232 atom properties 223 atom properties in 231 atom types 134 223 bond properties 236 bond types 134 224 booleans 97 Chapter 22 Index 326 of 342 ChemBioFinder 13 0 I PerkinElmer For the Better charges 226 context menu 126 creating from BioViz plot 29 dates 100 entering 10 111 118 exact structure 103 finding current structure 120 formulas in 98 free sites 234 full structurefull structure searching see also similarity searching 103 hydrogens in 225 ID 100 identity 101 implicit AND between fields 97 110 implicit hydrogens 235 inequalities 100 intermediates 110 isotopes 227 multiple fields 110 multiple fragmen
95. 3 delimited text files 94 security settings 56 subform fields 95 Word files 94 extraneous fragments permitting in full structure searches 114 Chapter 22 Index 314 of 342 ChemBioFinder 13 0 I PerkinElmer For the Better F fields creating 72 date 73 deleting 74 deleting contents 83 editing 79 formula 70 integer 73 memo 73 Mol_ID 70 molecular weight 70 picture 73 read only 11 real 73 sorting 84 structure 70 74 text 72 fields assigning to data boxes 17 file commands CAL 278 file formats MDL 230 file formats supported 87 files log 89 filter window description 7 filtering 170 filters 27 Chapter 22 Index 315 of 342 ChemBioFinder 13 0 find command find current molecule command find list command find text command first record command fit to box fixed labels flat file databases fonts customizing form tool toolbar form toolbar description form definition formal charge forms clearing creating automatically creating manually editing moving saving setting security vs databases forms creating and saving formula field formula input rules formula searching see searching Chapter 22 Index pP PerkinElme For the Better 118 120 100 73 64 201 36 42 70 44 35 36 13 148 117 32 34 47 75 33 51 14 17 70 239 20 316 of 342 ChemBioFinder 13 0 PerkinEl For the Better formulas input rules 239 sorting 84 FoxPro 71 fragments in full structure sear
96. 8 of 342 ChemBioFinder 13 0 PerkinElmer For the Better READMOL and WRITEMOL operate on the current molecule These commands will work only if there is at least one structure related box structure formula or molweight on the form and you are positioned to a valid entry in the data base READMOL reads a specified structure file and replaces the current molecule in the form WRITEMOL saves the current molecule to a specified structure file if the file doesn t exist it is created otherwise it is overwritten For both READMOL and WRITEMOL the format of the file is determined by its extension for example benzene cdx is a ChemDraw file READPICT and WRITEPICT transfer pictures into or out of picture boxes where boxname is the name of the picture box on the form and filename is a pathname to a graphics file with extension bmp jpg gif png emf or wmf WRITETEXT exports the current list as delimited text with whatever delimiter is specified in the Preferences dialog box The table below shows examples of File Commands READMOL read specified file to benz mol become current molecule WRITEMOL write current molecule to saved mol specified file WRITETEXT export current list to a hits txt text file OPENDB R E RE dbname CRETABLE tablename DELTABLE tablename SELTABLE tablename CREFIELD fieldname DELFIELD fieldname SORT D fieldname Oracle database commands SQL lt SQLStatement gt SOLSELECT v lt SOLSelectStat
97. ARITY Chapter 20 CAL Commands pP PerkinElmer For the Better uncharged heteroatoms to matched charged ones when searching This param eter can be set manually in the Search tab of the Pref erences dialog box The default is 1 allow the match Whether or not to match cis trans stereochemistry around double bonds This parameter can be set man ually in the General tab of the Preferences dialog box The default is 1 match stereo Whether or not to match tet rahedral stereochemistry This parameter can be set manually in the Search tab of the Preferences dialog box The default is 1 match stereo Maximum number of hits to be returned by a search The default is 2500 hits Whether or not to allow a similarity match when searching This parameter 276 of 342 ChemBioFinder 13 0 SEARCHING SRCH_TANIMOTO_PCT SRCH_USE_RXN_CTRS SEARCHING SEARCHING Chapter 20 CAL Commands STOP_AFTER_MAX_HITS pP PerkinElmer For the Better can be set manually in the Search tab of the Pref erences dialog box The default is 0 require exact match Cutoff percentage below which two compounds are not considered similar This parameter can be set man ually in the Search tab of the Preferences dialog box The default is 90 Whether or not to require that query substructures have at least one atom or bond in the reaction center of the target This parameter can be set man
98. Better OPTIONS EXPLICIT_METAL_H OPTIONS EXPORT_HEADER LOAD_LAST_FORM_ON OPTIONS STARTUP OPTIONS NON_INTERACTIVE Chapter 20 CAL Commands Whether or not to require that metals have hydrogens drawn implicitly If this parameter is off Chem BioFinder will automatically add hydrogens to fill each metal s minimum valence This parameter can be set manually in the General tab of the Preferences dialog box The default is 1 require explicit drawing ASCII value of the delimiter to use when exporting delim ited text files This param eter can be set manually in the General tab of the Pref erences dialog box The default is 9 tab Whether or not to load the last active form file the next time ChemBioFinder is launched The default is 0 do not load Whether or not to suppress non critical dialogs Prin cipally useful when Chem 273 of 342 ChemBioFinder 13 0 OPTIONS VALIDATE_VALENCE PRINT PRINT_BORDER OPTIONS 5 PRINT_FOOTER Chapter 20 CAL Commands PRINT OPTIONS pP PerkinElmer For the Better BioFinder is being used unat tended such as over the WWW It is not rec ommended to have this option on when using Chem BioFinder directly The default is 0 interactive mode Whether or not to provide a Oor 1 274 of 342 warning when attempting to enter a substance con taining an element in a non standard valence This parameter can be set man ually
99. BioFinder 11 0 In ChemBioDraw style you edit directly in the structure box using the ChemBioDraw Control The ChemBio3D style is a display only format that lets you rotate and analyze structures within a ChemBioFinder 13 0 structure window See the ChemBio3D User s Manual for information on using the ChemBio3D Control The ChemBioDraw format displays more graphically rich drawings than the ChemBioFinder 13 0 format However ChemBioFinder 13 0 does not use all of the ChemBioDraw drawing features when searching For example textual annotations are ignored and R group tables are not recognized Certain graphics such as rectangles and orbitals are not transferred nor does ChemBioFinder 13 0 consider their chemical implications To choose how to view structures 1 Right click in a structure data box and choose Properties The Box Properties dialog box appears 2 On the Box tab in the Box Style section select the structure format to view from the menu edit in the Structure Structure Chem BioDraw style box using the Chem BioDraw Control edit in Chem Structure Chem BioDraw BioFinder style insert 3D i Structure Chem inse images Bio3D style Chapter 4 Forms 41 of 342 ChemBioFinder 13 0 PerkinElme For the Better Viewing structures in ChemBio3D format Unlike the ChemBioDraw and styles ChemBio3D style is view only You cannot edit the structures in ChemBio3D style To activate the ChemBio3D Control
100. BioFinder 13 0 uses that information and does not worry about the specific fates of the other atoms For example if you don t know or don t care about the mapping of some atoms you can leave them unspec ified in the atom to atom map By default atom to atom mapping is not displayed within ChemBioFinder 13 0 To turn on this display select Atom to Atom Map on the Structure sub menu of the View menu For more information see Changing options with the view menu on page 204 7 Note For information about specifying atom to atom maps with ChemBioDraw see the ChemBioDraw User s Guide Searching for reactants If you Know what starting materials you are interested in but don t know their products you might perform a reactants query A reactants query is very similar to a reaction search except that there is nothing to the right of the arrow For example consider the query 0 is Figure 8 16 Sample reactants query If you are doing a substructure search this finds any reactions in which maleic anhydride or a compound containing a maleic anhydride substructure is consumed or transformed Searching for products If you know the desired end product but not how to get there you can do a products query A products query is similar to areaction search except that there is nothing to the left of the arrow For example consider the query Figure 8 17 Sample products query If you are doing a substructure search this finds any r
101. CAL Commands 262 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 String containing instruc tions to recipient application command indicating what you want it to do Remarks DDE commands are highly specific to each application Please consult the documentation for the desired recipient application for information on service names topic names and commands it supports The DDE command is always sent as an EXECUTE instruction Communicating with Excel example This example uses the WRITETEXT command to write the current list to a file then sends two DDE commands to open that file in Microsoft Excel and resize the columns to a nice size Finally it uses the DOS command to delete the temporary file The first line starts with an asterisk and so is not executed It serves only to make the example more readable for the user TOEXCEL CFS script to send data to ExcelWRITETEXT C DATA TMPDDE Excel System OPEN C DATA TMP DDE Excel System COLUMN WIDTH 1 C1 C4 3 1 DOS erase C DATA TMP General commands MSG message STATMSG message TIMEDMSG n lt msg gt W FONT fontname size style rg b SEEPTAB decisecs QUIETCLOSE HIDETABLE SET CLEAN cleanup tidy redraw denovo HELP GET v section number itemnumber SOUND filename wav Chapter 20 CAL Commands 263 of 342 ChemBioFinder 13 0 PerkinEl For the Better SYSMETRIC v index
102. Click OK The high and low values of each bar appears under the plot Two variable plots In two variable plots you choose both the X and the Y variables To create a two variable plot Go to View gt ChemBioViz Plots gt New Click the Two Variable option in the Dimension box Select fields for both the X and Y axes Click the Scatter plot option in the Style box Enter a name for the plot optional Click OK oa A OO N Removing a plot To remove a plot 1 Go to View gt ChemBioViz Plots gt Remove 2 Select the plot in the dialog box and click Remove 3 Click OK Filters Filters can be used in two different ways Filter a plotted variable to reduce its range Filter on other variables to add other dimensions to the plot Chapter 3 Tutorials 27 of 342 ChemBioFinder 13 0 PerkinEl For the Better To activate filters go to View gt Filter Window or use the context menu on a plot When the filter window opens right click in it to select or deselect fields There is a limit of 31 on the number of filters that can be applied to a plot 7 Note Filters act on all active plots not just the one displayed Autoscale When you filter a plot you may want to expand the scale to better display the remaining points If you select Auto scale on the BioViz context menu the scale will readjust automatically every time you adjust a filter Autoscale is a toggle that remains in effect until you cancel it Alt
103. Client We recommend version 9i or newer This is available as a free download from the Oracle Web site 1 Download and install the Oracle Client software version 9i This is available free from Oracle Note that there are different versions for 32 bit 64 bit and Itanium systems _ Note The minimum installation called Runtime is not adequate to provide support for ChemBioFinder Oracle In addition you must subsequently choose the Custom install and select Oracle Windows Interfaces If you do not have the requisite components installed an attempt to open an Oracle database will generate the error Pro vider cannot be found It may not be properly installed 2 Have the Oracle administrator install CS Oracle Cartridge 9 or 10 You can use ChemBioFinder Oracle to access any Oracle database but one without the CS Oracle Cartridge cannot be used to store or search chemical struc tures 3 Have the administrator set up a user account for you ChemBioFinder Oracle requires that you log into a tables pace for which you have write privileges For access to corporate files the administrator needs to grant you read only privileges to tables and views of interest outside your tablespace 4 On your client computer use Oracle Net Configuration Assistant to connect to each Oracle database you intend to use In principle ChemBioFinder Oracle can access any Oracle database In practice some preparations are rec ommend
104. Field tab The Field properties appear Click Create Field The Create Field dialog box appears Inthe Name box type a name Inthe Type box choose a data type from the drop down menu oa A WN For text fields only type a width number of characters in the Width box or use the thumb wheels to select a value 7 Click OK The name of the new field appears in the data source tree Deleting fields Just as you can create any field and assign it to a data box at any time you can modify the database by deleting fields from the selected table To delete a field Right click in the form and click Properties The Box Properties dialog box appears Click the Field tab The Field properties appear Inthe field list select the field to be deleted Click Delete Field Awaming message appears click OK to delete or click Cancel to leave it unmodified oa A OO N gt 2 Caution When you delete a field all data contained in the field is also deleted You are not warned explicitly about this Adding multiple structures You can include more than one structure on the same form by creating multiple structure columns in a table Each structure column you create represents four types of data The structure displayed as a diagram The Molecule ID which connects the structure to a record in a relational table The formula derived from the structure The molecular weight derived from the structur
105. Figure 13 2 Profile box form Each field in the profile box form is assigned a cost and weight Right click on the profile box CLOGP and choose Cluster By Profile the clustering engine uses all the three values of each record in the hit list together with their weight and cost and displays a normalized distance in the records Modifying Clustering To modify the cluster dialog box click the black drop down arrow that appears below the 3D structure in the CS Clus tering dialog box This drop down control panel has two tabs Dendogram and Clusters Lf Note The Dendogram and Clusters tabs may appear by default as well in the CS Clustering window Chapter 13 Clustering in BioViz 177 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 Dendogram Properties CS Clustering Linear Log scale I Invert x HB Line color l Invert Y J Il Horizontal Labels I Tepee style Background None y IV Show cutoff line FONE see Arial 6 pt Dendrogram Figure 13 3 Dendogram options Inthe Style Frame you can change the orientation of the diagram using the Invert X Invert Y and the Horizontal check boxes In Teepee style lines moves from nodes to subnodes i e it displays the dendogram in a non stand ard way Clicking the Line color Highlight or Background button opens the Colors dialog box By default the dendogram lines are in navy blue color highlighted items are in red color and background i
106. Finder extension cfx Unlike bsbxml files cfx files are not read only You can open any cfx file in ChemBioFinder edit it and save it again Mean while the bsbxml file is still available whenever you need to open the original form Chapter 15 BioSAR 190 of 342 ChemBioFinder 13 0 PerkinEl For the Better Setting save password If an Oracle connected form contains an invalid or blank or no password the program prompts you for a name and password on opening the form The same is true if the Save password box has not been checked in the form prop erties dialog box This is now the default when a form comes from BioSAR You are prompted for username and pass word every time until you check the Save password box and save the form _ Note In Ultra and Pro versions Save Password defaults to off Subforms and autolinks 7 Note Autolink boxes are available in Pro and Ultra versions but not in Standard version When you create a form in BioSAR you select from the database which fields you want to include in the form Those same fields appear in the form when you import it into ChemBioFinder After you import your form you can continue to build on it in ChemBioFinder using additional fields The fields you use can also include child tables and their fields Child tables that you add appear as subforms fields from child tables are displayed as autolink boxes To add a subform 1 Inthe Explorer Window select the BioSAR t
107. Finds any of Chapter 17 Structural Query Features 232 of 342 hemBioFinder 13 0 I mae aaa PerkinElmer For the Better P48 Does not find any of A YO Q H Substituents up to This property specifies a maximum value for the number of substituents on an atom including those explicitly drawn This property is only meaningful in a substructure search With a substructure search the query with substituent up to property u2 1 Figure 17 4 1 This atom is marked with the atom property Substituents Up to 2 Finds any of Chapter 17 Structural Query Features 233 of 342 ChemBioFinder 13 0 POS CHa Does not find any of 43 p Substituents free sites pP PerkinElmer For the Better The Substituents Free Sites property specifies the maximum number of additional substituents that may be present on an atom This property is only meaningful in a substructure search Q With a substructure search the query with free sites property 2 1 Figure 17 5 1 This atom is marked with the atom property Substituents Free Sites 2 Chapter 17 Structural Query Features Tip Specifying Free Sites 0 is a quick way to indicate that you want no further substitution at a site Target struc tures will match the query structure as drawn with no additional ligands 234 of 342 ChemBioFinder 13 0 PerkinElmer For the Better Finds any of cl o Does not find any of Implicit
108. HUMAN HEALTH ENVIRONMENTAL HEALTH ChemBioFinder 13 0 User Guide pP PerkinElmer For the Better ChemBioFinder 13 0 I PerkinElmer For the Better Table of Contents Chapter 1 About ChemBioFinder 18 0 ooooooccccccccccccccccccccc coccion cc cccc cnn nn ec cceteeeeeeeeeees 1 ABQUEBIOV IZ sicario E Oe adios digitos ys 1 ABOUUTIIS gude ossessi ioe teen e tuba ds nl K EAEEREN aloud lp bed dieron bee 1 Serial Number and Technical Support ooo nn 2 Chapter 2 Getting Started ooo 4 The ChemBioFinder User Interface ooo 4 More WI T6atures lt 4 gt oo nc6 irs stc es sis Se Sus ended Ned So See 10 Opening ChemBioFinder 13 0 0 022 0222 cece cece cece cece cece cece cece cece cece eee aoaaa aaner ionnann 11 Using ChemBioFinder with databases 0 0 2 2 2c eee cece cece cece cece cece cece cece eee ceceeeeceeeeeeeeees 11 Chapter 3 Tutorials cc nn 15 Sample databases cnc 15 Tutorial 1 Creating forms 22 22 2222 c cece cece aoea cece cece cece eee A E Ea aa eanan anann 15 Tutorial 2 Opening a database 2 2 eee 17 Tutorial 3 Creating a database 2 22222 18 Tutorial 4 Searching a database 22 eee 20 Tutorial 5 Reaction searches eesriie kuene anr GRENENE RENEE gus bl lacey riera nina dada 23 Tutorial 6 Creating a BioViz plot 22 e cece cece doado aaner aaran airain nannan 26 Tutorial 7 Working with subforms 222200002222 o cece ccc ccc ccc ccc cece ce cee eee eee eee b ee eeeeeeeeeeeeeeeeeeeees 30 Chapte
109. OR NET_OUTSIDE DISPLAY NET_RXN_CHANGE DISPLAY Chapter 20 CAL Commands DISPLAY DISPLAY PICTURE_BACK GROUND pP PerkinElmer For the Better The default is 100 The color in which sub structure search matches are displayed This param eter can be set manually in the Color tab of the Pref erences dialog box The default is Red Whether or not to move bracketed text to the out side where possible in the display of net reaction Oor1 changes in molecular for mulas and molecular weights The default is 1 move to out side Whether or not to display Oor1 270 of 342 net reaction changes in brackets in molecular for mulas and molecular weights The default is 1 display changes The background color of Pic ture boxes This parameter can be set manually in the Color tab of the Preferences dialog box The default is White ChemBioFinder 13 0 DISPLAY DISPLAY QUERY_BOND_COLOR RXN_CTR_COLOR DISPLAY SHOW_AAMAP SHOW_H_CHARGED _ ATOMS DISPLAY pP PerkinElmer For the Better The color in which bonds with query properties should be displayed This param eter can be set manually in the Color tab of the Pref erences dialog box The default is Green The color in which reaction centers should be high lighted if highlighting is turned on This parameter can be set manually in the Color tab of the Preferences dialog box The default is 33023 pu
110. PerkinElmer For the Better Drag over the points of interest to select them Click Selection to List on the context menu Prevent a plot from a The plot is locked to a given dataset changing when you check the Lock option in the Bio i Note that filters will be locked as select queries or change Viz Plot Properties dialog box well variables y Dragging over a section of the plot Expand the plot to view Select Zoom on Drag on the Bio f enlarges it rather than selecting the individual data points Viz context menu f points In the Queries control select Change Color on the Queries con Change the color of the The data points are displayed in the text menu Note that you cannot data points color you select change the color of the Full List only of daughter lists With the Full List selected click Color on Plot on the Queries con Plot multiple datasets to the query name and the data text menu for each query you want overlay f points are displayed in the color to overlay alternately click the assigned to the query query or the colored box next to it A check mark appears in the box next Tutorial 7 Working with subforms Subforms allow you to display relational data If you have a database containing two or more data tables and these data tables share a common linking field then you can display data from both tables Whenever the value of t
111. Structure Structure Strur abe RXN Formula Text 88 Formula Text O RXN MolwW eight Double MolWeight Dou SS RXN ABSTRA Memo ABSTRACT Men Memo COMMENTS Mer abe RXN ATMOSP Text ATMOSPHERE Text Mabe RXN TEMP Text TEMP Text ESA Text TIME Pa The Import dialog box scans the file to determine what data fields are present and how much space to allow for them in the database The number of records scanned is shown in the status bar If the input file is large the scan may take awhile To interrupt the scan press the Esc key A message box appears to confirm whether you really want to stop The scan continues until you click Yes To abort the scan click Stop scanning 7 Note You should let the scan go to completion so that all needed fields are created in the database before loading Using log files During the import ChemBioFinder 13 0 creates a log file of the actions taken The log file log is a text file that is created alongside the input file and overwrites any previous log file The log records data of your choice form the fol lowing options during the import Errors Errors and warnings Chapter 7 Importing and Exporting Data 89 of 342 ChemBioFinder 13 0 J a PerkinElmer For the Better General data Information about the input file and import process Records processed Logs an entry for each record of the input file Structures registered Logs an entry for each structure stored in the database D
112. Structure registration options To have ChemBioFinder 13 0 present an alert when attempting to enter a structure with an atom in a non standard valence state Click the Check valences check box in the Registration section To have ChemBioFinder 13 0 confirm when you are about to modify data in the database Click the Ask to commit changes check box in the Registration section ChemBioFinder 13 0 opening options You can set ChemBioFinder 13 0 to open with the ChemBioFinder 13 0 Opening dialog box or to open the last form you were using To set the options for what ChemBioFinder 13 0 displays when it starts up 1 On the General preferences tab check the box next to Show startup dialog start with the open ing dialog box Chapter 16 Customizing ChemBioFinder 13 0 203 of 342 ChemBioFinder 13 0 start by opening the last form you used use a default script change which win dow is on top in the Explorer window2 check the box next to Reopen last form check the box next to Check for exter nal scripts select an entry from the Explorer tab drop down menu pP PerkinElmer For the Better select an entry from select a different the Frame style theme drop down menu 2 Click OK Setting the recent file list size You can set the number of files you opened recently that ChemBioFinder 13 0 shows To set the list size for the most recent files opened z Type in a number
113. The hits table is created if it does not already exist 4 A unique ID is assigned to the new list which will result from the search 5 The select statement is wrapped in a larger SQL statement which will cause the results to be deposited directly into the hits table 6 The SQL is executed 7 When the search is complete the results are new rows in the hits table Each row contains the new list ID along side the ID of a record from the searched table 8 The final list is prepared by a join selecting rows from the main table which have record ID s matching those of the new list in the hits table The resulting list is ready to browse save export etc _ Note Text searches in Oracle are case sensitive You will get different hits from the query benz than from wk Benz Sorting Certain sort operations require a ChemBioFinder 13 0 system table CF _SORT that may not exist in your current form If the table does not exist you will be alerted the first time you attempt such a search in an Oracle database Chapter 14 ChemBioFinder Oracle 183 of 342 ChemBioFinder 13 0 PerkinElmer For the Better To create the CF _ SORT table 1 Open anew form then go to File gt Database The Form Properties dialog box opens 2 On the Database tab click Oracle Database 3 Login as the owner of the schema where your ChemBioFinder 13 0 system tables are located Typically this will be ChemBioFinder _ Note If you do
114. This topological parameter is a measure of molecular flexibility Unsaturated bonds and single bonds con nected to hydrogens or terminal atoms single bonds of amides sulphonamides and those connecting two hindered aromatic rings having at least three ortho substituents are considered non rotatable Ovality This refers to a measure of how the shape of a molecule approaches a sphere at one extreme or a cigar shape at the other Ovality is described by a ratio of volume to area O Al Axnx 3xV 4xn Where A is area V is Volume and O is Ovality The ovality of a helium atom is 1 0 and HC H 12 triple bonds is 1 7 equivalent to 1 7 The pKa describes the tendency of compounds or ions to dissociate in solution If B is defined as the conjugate base of the acid HB then pKa is calculated as pKa Log10 Ka where Ka H B HB Polar Surface Area The Polar Surface Area PSA is defined as the surface sum over all polar atoms usually oxygen and nitrogen includ ing attached hydrogens Principal Moment This refers to the principal moments of inertia about the principal axes of a molecule The moments of inertia are com puted for a series of straight lines through the center of mass using the formula I Snad i Where l is the moment of inertia mjs are point masses whose distances from the rotation axis are denoted by d s Chapter 10 Chemical Properties 152 of 342 pP P
115. Will not hit Br Figure 8 31 Results of a link node query Searching more than one substructure A substructure search may contain more than one substructure unit Suppose you want to find all compounds in the CS_Demo database which contain a benzene substructure and another substructure unit containing chlorine bonded to any atom A structure query as drawn in ChemBioDraw would look like Chapter 8 Queries 135 of 342 hemBioFi 13 I ChemBioFinder 13 0 PerkinElmer For the Better A Cl Figure 8 32 Structure query with two substructures You should get five hits Browse the hits By specifying the query as above you obtain hits such as benzyl chloride shown below where the substructure units are not connected H Cl H Figure 8 33 Benzyl chloride hit by query with two substructures The substructure units can overlap they can share a common atom Examples of this overlap are shown below Figure 8 34 Overlapping substructures in the hit list Chapter 8 Queries 136 of 342 hemBioFi 13 I ChemBioFinder 13 0 PerkinElmer For the Better Compound Profiles Compound Profiles a way of visually comparing and ranking structures based on values of selected properties A compound profile is a graph or more typically a series of graphs each of which plots the value of a numerical field in the database on a vertical bar color coded to show regions of cost or undesirability These regions are defined by a
116. YMS field section Using the drop down menu choose MOL_ID for the Link from MOLTABLE field 10 Click OK You have just selected the data source for your subform and linked it to the main form The MOL_ID field links the main form and subform Clicking in either form activates it To test this 1 Click anywhere outside the subform box and browse your database using the Record tools As each molecule rec ord of the MolTable is displayed the subform shows the first matching ID from the Synonyms table 2 Click inside the subform box Now when you browse you are browsing only the entries in the subform To display all of the synonyms 1 Double click in the subform box to switch to Table view Save and close the file a Goto File gt Save b Goto File gt Close Congratulations You have completed the ChemBioFinder 13 0 Tutorials Chapter 3 Tutorials 31 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 Forms You use forms to interact with information in a database A ChemBioFinder 13 0 form is composed of data boxes for viewing or modifying data items such as structures numbers text or pictures A form can also contain subforms for relational access to different data tables and different databases The example below shows a form displaying a single record of information from a database CS_DEMO_backup Structure MoLID Molname 1 Benzene y gt Synonyms S SYN_ID Synonym 1 Ben
117. ab 2 Select a child table from the Child Tables directory 3 Double click the child table The child table appears in the form as a subform 7 Note Not all fields in the child table are necessarily displayed in the subform The subform fields are limited to the same fields you selected in BioSAR and defined in the default form group To add an autolink box automatically 1 Select a child table from the Child Tables directory 2 Inthe child table double click an individual field The child table field appears in the form as an autolink box To create an autolink box manually Assume you have a structure table Moltable with a column of non unique integers Chemist_ID In a separate table Chemists there is a text column to be displayed Name and a column of unique integer record identifiers ID Each Chemist_ID in MolTable matches one ID in Chemists To set up an auto link box on the main form which shows for each structure the name of the associated chemist 1 Create a data box 2 Right click on the data box and connect it to the ID field to be retrieved In this example connect the form box to the Chemist_ID field 3 To connect the box to the ID field right click on the box and choose Properties The Box Properties dialog box appears 4 Check the option With choices or auto link Checking this will automatically bring up the Choices tab Chapter 15 BioSAR 191 0f342 ChemBioFinder 13 0 PerkinElmer For the Better Box
118. ab there are check boxes for full word text matching case insensitive matching for Oracle matching stereochemistry The only box that is checked by default is the Match Stereochemistry box See the figure below Chapter 8 Queries 115 of 342 ChemBioFinder 13 0 Preferences Display Color Search Type Details Tuning General Text Searching Text query matches full word only I Case insensitive match Oracle Stereochemistry M Match stereochemistry Cancel Setting stereochemical search preferences pP PerkinElmer For the Better The Stereochemical Search Preferences dialog box is activated from the Tuning tab of the Preferences dialog box To set Stereochemical preferences 1 Go to File gt Preferences The Preferences dialog box appears 2 Click How on the Tuning tab of the Preferences dialog box The Stereochemical Search Preferences dialog box appears Stereochemical Search Preferences Tetrahedral stereo center hits I Thick bonds represent c a LU relative stereochemisty Double bond hits od sane Fx C aw Cancel Figure 8 21 Stereochemistry search preferences 3 Set the Tetrahedral stereo center hits Chapter 8 Queries 116 of 342 ChemBioFinder 13 0 in Tetrahedral match the target f stereo center hits exactly click Same match same or oppo in Tetrahedral site configuration at the stereo center hits center of the target
119. ade if in a product or broken if in Make amp Change a reactant or whose bond order changes over the course of the reaction target must have a bond here and that bond must Not Center o not participate in the reac tion target must have a bond here and regardless of whether it is part of the Not Modified reaction center or not its order must not change over the course of the reac tion This property is only meaningful when searching a reaction database Chapter 17 Structural Query Features 238 of 342 BioFi 13 I ChemBioFinder 13 0 PerkinElmer For the Better Formula Input Rules In formula queries you are not specifically required to enter symbols in any case This can give rise to ambiguities This appendix describes how ChemBioFinder interprets formulas and resolves these ambiguities For example in a formula query when you type cooh most chemists recognize this as a carboxyl group carbon two oxygens hydrogen However it might be interpreted as cobalt Co oxygen hydrogen Similarly CLI might be carbon lithium or it might be chlorine iodine PHE might be phosphorus helium or since ChemBioFinder allows 3 character amino acid symbols as special atom types it might be phenylalanine Phe One way to avoid this ambiguity is to separate letters with spaces For example the string c o cannot possibly be interpreted as cobalt Another way to avoid ambiguity is to enter formu
120. agram click the table you want to attach then click OK The newly attached table appears in the tree diagram in the Form Properties dialog box 7 Click OK in the Form Properties dialog box The source of the data to display on the form is indicated but the form is still blank To access the data you need to draw some data boxes and indicate what data to show in each of those boxes Creating fields Whether you create a new database or are working in an existing one you can add or remove fields in the selected table You can choose from the following types of fields abc Text field lets you enter text such as names comments and references A text field is fixed in length and you choose the maximum length width for any data item to be stored in the field If you enter a width of 50 then you can t store any item with more than 50 characters in that field You can specify widths of text fields as large as 254 characters If this is insufficient you need to create a Memo Rich Text field instead Chapter 5 Databases 72 of 342 ChemBioFinder 13 0 PerkinEl For the Better Because the text field width cannot be modified after a field is created it is often wise to err on the side of caution and make it longer than you need initially On the other hand larger field widths also create larger files and slower search times Note Non ASCII characters will not display correctly in a data table text field ao Integer field
121. aining one table called MolTable with four fields E Structure Formula w Molecular weight W Mol_ID The Mol_ID field corresponds to a column in the table where a numeric ID is automatically entered as each structure is registered The other fields represent information stored in the structural portion of the database linked to the assigned ID The Formula and Molecular weight data are automatically calculated from a structure These internal fields cannot be edited or deleted After creating a database you can create fields for storing other types of data It is not necessary to create the entire set of fields before working with the database You may add more fields later Creating tables There is no limit to the number of tables a database can contain You may want multiple tables in a database in order to manage relational data or simply to organize different collections of information in the same place A table must contain at least one column When you create a new table ChemBioFinder 13 0 creates a numeric col umn called ID You can use this column to store integer data or delete it and replace it with your own columns Table names must a Begin with a letter Not contain punctuation characters Not be the same as a table already on display To create anew empty table 1 Right click in the form and click Properties The Box Properties dialog box appears 2 Click the Table tab and then click Create Table
122. al reactions Searching for reactants In this tutorial you will learn how to search substructures and text in the Infochem Database This database is included with ChemBioFinder 13 0 and has approximately 250 reaction records Searching for reactants is useful if you have a known starting material and you are interested in learning more about what substances it can produce 1 Goto Search gt Enter Query The form clears 2 Double click in the Structure box The ChemBioDraw toolbar appears 3 Draw the structure below This structure represents a carbon atom bonded to a generic halogen atom x The arrow at the right indicates that you are looking for this substructure as a reactant 4 Select the Search gt Substructure if it is not already selected 5 Deselect the Search gt Similarity if it is selected 6 Go to Search gt Find ChemBioFinder 13 0 begins searching The progress of the search is indicated by counters in the status bar at the bot tom of the window Chapter 3 Tutorials 23 of 342 ChemBioFinder 13 0 PerkinEl For the Better When the search is complete the number of hits is displayed in the Current List Size window of the Status Bar and the form displays the first hit In a substructure search the matched portion of each molecule is highlighted in red Searching for products In this exercise you search for information on a particular reaction product Searching for products of reactions is very common in synth
123. al to the distance between its children where distance is the measure of similarity between two objects Thus the node just above the baseline connects pairs of compounds with very similar in this case usually identical molec ular weights On the right is the cluster window which provides another way of viewing the data The cluster window screen depends on the position of the dotted pink cutoff line across the dendogram Every node directly below the line is represented as a single ball in the cluster window with its size scaled to the number of leaves it contains Thus a large ball represents a large group of compounds with similar molecular weights where the smallest ball is a single compound of a weight all its own By moving the cut off line up and down you vary between a coarse grained view with few clusters to a more detailed view with many To modify the cluster dialog box click the black drop down arrow in the lower right corner See Dendogram Prop erties on page 178 and Cluster Properties on page 179 for more information Chapter 13 Clustering in BioViz 176 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 Clustering on multiple fields To perform clustering on multiple fields you need to create a profile box which contains user defined set of fields and conditions for comparing data records See Creating a compound profile on page 138 After the profile box is created on the form save the form
124. also have a column of unique record identifiers for use in various list handling operations Preferably this column is of type INTEGER and is designated as the pri mary key of the table ChemBioFinder 13 0 provides information about these indexes and allows you to create or recreate them if nec essary To create a structure index 1 Right click on the structure box of an Oracle connected form and choose Properties 2 Go to the Field tab of the dialog box If the selected field is indexed the index name is shown in the properties box Inthe example below the index is named IX50 Form Properties F_HITLISTS A Database Table Field Form Oracle F_SETTINGS SDOHITLIST 8 structure Properties Width Table Native Type 000 J 08 00 MOL_1D Inde 8 STRUCTURE lt E Formula_STRUCT WF Molweight_STRU 2 00 MOLREGNO fabe MOLNAME fhe CORP_ID fabe DATE fabe ACTIVITY Create Index Set As Structure 4 EM TEST x lt Create Index Create Field Index name EET Cancel Figure 14 2 1 Field name 2 Index name _ Note If there is no index or the field is not indexable the Index line does not appear in the list 3 If there is no index click Create Index F Note if this button does not appear itmeans the selected field is not a candidate for indexing 4 Inthe Create Index dialog box provide a name for the new index and click OK The index is created You w
125. ample you might place a frame around a structure field where the label on the frame represents the name of the current structure The label changes every time the structure does You must use Box Properties to set up a live data connection for a frame Creating boxes with frames The Framed Box tool lets you create a data box and a frame simultaneously You name the frame in the Enter the Label dialog box Chapter 4 Forms 36 of 342 ChemBioFinder 13 0 PerkinElme For the Better To create a framed data box 1 Click the Framed Box tool 2 On the form drag to create a box 3 Inthe Enter the Label dialog box type the label you want to attach to the frame and click OK The framed data box is labeled To edit the label of a framed data box 1 Select the frame by carefully right clicking near the edge of the framed box and select Label 2 Inthe Enter Box Label dialog box type the new label The label does not have to match the name of the field dis played in the box 3 Click OK When you create a data box and frame with the Framed Box tool these two items are connected To manipulate them separately Select the Framed box then goto Edit gt Bring to Front Automatic labels You can let ChemBioFinder 13 0 automatically label your framed box with the name of the field from the data tree To automatically label a Framed Box A Right click inside the data box and select the field from the drop down list The data appears in
126. amples Windows 7 C Documents and Settings All Users Application Data CambridgeSoft ChemOffice2012 ChemFinder Samples Win dows XP The CS_Demo database contains 285 structures covering a range of structural types To browse the Cs_Demo data base open the form CS_Demo cfx This is the form used in the tutorials in this guide You may also find the form Demo cfx useful This is a simpler form that displays only the main table of the CS_Demo database amp Caution When you open a sample database file ChemBioFinder gives you the option to create a backup of the file We recommend you make a backup copy of the database before experimenting with it If you change the data or structures in the database the examples in the tutorials may no longer give the documented results Tutorial 1 Creating forms Forms let you view and browse through your data in a display format of your own design To begin building a form first create a new one using the option File gt New or the startup dialog then select the Layout mode button on the Main toolbar For information about each tool see Toolbars Creating data boxes Data and structures from a database are displayed in boxes on the form To create a data box 1 Inthe Form toolbar click the Data Box tool 2 In the form window click drag diagonally to create a box 3 Draw two more boxes in the same way You will edit them in later steps A frame a framed box and a text box are different t
127. and gt where the command is not quoted Example SQL create table mytable id integer CURR_TABLE variable This variable contains the name of the table connected to the current form This works whether or not you are in Oracle Example MSG Current table is CURR_TABLE OPENDB allows change of table Normally this command takes the name of a database followed optionally by the name of a table in angle brackets In ChemBioFinder 13 0 it can now take just the table name and causes the form to become attached to a different table in the current database as if you had brought up Properties and clicked a different table name Example OPENDB lt CHEM STRUCTS gt causes the current form to be connected to the table CHEM _STRUCTS STATMSG command displays a message on the status bar Format STATMSG lt message gt Example STATMSG Search is now in progress SEARCH SAVE LIST RESTORE LIST work with Oracle Normally you can follow either of these commands with the name of a file in ChemBioFinder Oracle you can instead provide a list name Chapter 14 ChemBioFinder Oracle 189 of 342 ChemBioFinder 13 0 PerkinElmer For the Better BioSAR This section explains how to export a data form from BioSAR and view it as an equivalent form in ChemBioFinder Once in ChemBioFinder you can manage the form using a variety of features Starting the BioSAR browser To use BioSAR you must have Internet Explorer 5 5 with SP
128. and lets you select which fields will be exported If you save to an existing file you have the option to replace or append the records The Text Options tab of the dialog box contains options relevant to both text file export and structured text export It also has an option Prefix output filenames relevant to Oracle subform data and an option to select only the fields on the current tab for tabbed ChemBioFinder 13 0 forms To export a file 1 Use the File gt Export submenu to select the output file type The Data Export dialog box appears 2 Type a name and path for the file or click File and browse to an existing file 3 Select deselect the fields you want to export 4 Click the Text Options tab and choose appropriate options _ Note Choosing Comma delimited does not automatically set the file type Text files txt may be either tab delimited or comma delimited If you want to export in the Comma Separated Value csv format you must name your file accordingly either by typing the name or selecting the file type from the Save As dialog box 5 Click Export The file is exported Saving structures Saving structures is similar to exporting them without the fuss To save the structure on display 1 Right click in the structure data box and click the Save Structure context menu command The Save As dialog box appears 2 Choose the destination directory 3 Type the file name and choose a file format 4 Click Save
129. apter 21 CS Oracle Cartridge 297 of 342 ChemBioFinder 13 0 PerkinElme For the Better To designate a BLOB column as a picture column 1 If the CF_SETTINGS table does not exist create it using steps 1 3 of the above procedure 2 Edit the table one of two ways with an Oracle client tool such as SQL Plus OR B by opening it in ChemFinder and creating a form 3 Add a row containing the table name column name and a column of type PICTURE Searching Here s what happens when you present a query to ChemBioFinder Oracle 1 If the query contains a structure it is converted to a text representation and copied to a temporary table _ Note The table is called temp_queries Itis created in the CSCartridge tablespace and removed as soon as the search is finished or interrupted ChemFinder does not yet handle the case of multiple structure boxes where more than one contains a query 2 The query is converted to a SQL select statement Query components in form boxes are ANDed together just as in ChemFinder where the structural parts are calls into the CS Oracle Cartridge structure search functions 3 The hits table is created if it does not already exist 4 A unique ID is assigned to the new list which will result from the search The select statement is wrapped in a larger SQL statement which will cause the results to be deposited directly into the hits table 5 The SQL is executed When the search is complete the results a
130. arching a normal text or memo field a plain text string is taken as an unanchored substring if you are not performing a Full Word search An asterisk is added automatically at each end of the string and the hits include any string containing the search string Thus if you search for benz it becomes benz and returns benzene and flu robenzene When searching a normal text or memo field with wildcard the string is taken as an anchored substring Thus if you search for benz it gets anchored to the left and returns words beginning with benz Text strings may contain wild cards or Boolean operators Standard wild cards are and These characters are equivalent and hit any string Other wild cards are also possible If wildcards are present they override the above defaults _ Note Using wildcards or a in memo fields may lead to unexpected results This is because a memo field may con tain formatting information surrounding the text you see so a search like benz may give no hits Using benz how ever will give the same results in a memo field as in a plain text field A check box in the Search Preferences dialog box lets you request a full word match When this box is checked a hit must contain the query as a complete word not embedded within a larger string Boolean operators are NOT OR and AND They may be used to combine search terms within one field Tip Use NOT to search for empty fiel
131. ariable When you select curve fitting the R squared value also becomes available for display The calculated values appear on the plot You may also display a linear quadratic or cubic least squares fit of the data points with or without a confidence inter val of one to three standard deviations Chapter 3 Tutorials 28 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 5 x s00 i a E 400 Figure 3 4 Plot with statistical analysis The following table describes how to perform various functions in BioViz See which data point cor f navigate to the record using the EO ELAS responds to a particular y The data point is highlighted ChemFinder Record Toolbar record The Structure window displays the View the structure or structure for the data point the data values of a data mouse over the data point Details window displays the values point of selected fields The current record in the form does not change Select a database record S The form displays the matching data click on a data point from the plot record Display plotted var f select or create the query The plot displays the current query iable s for a query On the BioViz context menu Create a query fromthe 4 _ If a check mark appears next The selected points become a new plot to Zoom on Drag click to dese query lect it Chapter 3 Tutorials 29 of 342 hemBioFinder 13 I Dg Order TAg
132. as nine variables called V1 V2 V9 These are temporary storage locations you can use to move information between form boxes and other data sources Variable names can be substituted in any CAL command Any item shown in italics in a command description may be replaced by the name of a variable prefixed with a dollar sign For example MSG message may be either MSG An explicit message a message explicitly coded into the script or Chapter 20 CAL Commands 281 of 342 ChemBioFinder 13 0 PerkinElme For the Better MSG V2 a Message taken from variable 2 at run time You may concatenate variables and variables and literals together in CAL commands You must add both a leading and trailing dollar sign to the variable name For example MSG V25 V1 Displays a message box with the value of V2 immediately followed by the value of V1 Most commands for manipulating variables take an optional variable number as the first argument If the number is omitted it is assumed to be 1 SETVAL puts the specified text into a variable READVAL reads the contents of a text file into a variable WRITEVAL copies the contents of a variable to a file INPUT displays a text input dialog box accepts data from the user and stores it in a variable An optional prompt string is displayed in the box when it appears PASSWORD is the same as INPUT but displays all characters as asterisks GETDATA retrieves the contents of a form box as long as it is not a
133. ata registered Shows each data item stored in the database Database schema Shows input fields found and columns generated The log file for an RDFile import additionally presents an overview of the data table hierarchy within the RDFile You can choose whether to create the log file or not If you choose to create the log file you can save it with a different name or append to an existing log file Importing from a specified location You can start an import from an arbitrary location in an SDFile or RDFile such as a byte or line number To set the location from which to import 1 Click the Advanced tab of the Date Import dialog box 2 Select the appropriate option Data Import Import Logging Form Style Advanced Start reading at beginning C line C byte C record Output database version ChemFinder 9 0 v I Ignore text import structures only Store redundant reagents the beginning of the SDFile or RDFile beginning a specified line line and type the number line number a specified byte byte and type the number byte number record and type the a specified record record number Chapter 7 Importing and Exporting Data 90 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 3 Click Import Reading a structure In addition to importing ChemBioFinder 13 0 can read files of any of the supported structural formats For example if you have structures stored in C
134. atabase At the next level is a field a group of data items defining one type of data Fields are generally set up once and rarely modified Chapter 2 Getting Started 12 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 C21H3004314 462 7305 Lyseroamide Figure 2 7 A data field in a database At the next level is the record a set of data items one for each field defining a single entry YY y C21H3005P62 46 Hydrocortisone AY P Y y AN 0194300228044 Andosterone 00 Ne Hy Y CZIHAOOZ3N4462 Progesterone p yy Figure 2 8 A record in a database A collection of records is a table A table is defined by a set of fields and a set of records which grows as entries are added In spreadsheet terminology A data item is found in a cell A field corresponds to a column A record corresponds to a row A table corresponds to a worksheet A database is a storehouse for one or more tables A database containing only one table is known as a simple or flat database Databases containing multiple tables are called relational For more on relational databases see Relational Data and Subforms on page 156 A form displays data from a single table but may contain subforms that display data from other tables If the tables have a field in common then any record retrieved in the form calls up the related records in the subform Chapter 2 Getting Started 13 of 342 pP Pe
135. ated with a red vertical line Figure 5 11 Moving a column To resize the column widths in the Data Table 1 Place the cursor on the dividers in the top header The cursor changes to the icon shown below Chapter 5 Databases 66 of 342 ChemBioFinder 13 0 PerkinElmer For the Better 157 0079 Figure 5 12 Changing the width of a column 2 Drag to adjust the column width g Note To hide the column right click and choose Hide Column from the context menu To resize the row heights in the Data Table 1 Place the cursor on the dividers in the left header The cursor changes to the icon shown below Structure MOLID Formula MolWeight Molname SYM ID 157 0079 Figure 5 13 Changing the height of a row 2 Click drag to adjust the row height g Note To resize all rows right click in a column header and choose Resize Rows to Fit from the context menu R group tables In Data Table display you can display a substructure search as table of R group substituents 1 Run a substructure search Chapter 5 Databases 67 of 342 hemBioFinder 13 0 I Che oFinde PerkinElmer For the Better _ Note You cannot prepare a table from a full structure or similarity search Figure 5 14 Substructure query to set up R Group table 2 Switch to Data Table view 3 Right click in the Structure column and click R Group Table The following changes occur the topmost structure is replaced with
136. ation see Creating forms automatically on page 32 Chapter 11 Relational Data and Subforms 157 of 342 ChemBioFinder 13 0 PerkinEl For the Better To generate a subform 1 Right click on a blank area of the current form and click the Data Source context menu command The Form Properties dialog box appears Inthe Form Properties dialog box select the Form tab Select the Generate form check box then click Style The Form Generation dialog box appears Click Subforms The Subform Generation dialog box appears a A O N Foreach subform you want to include a Choose afield in the Link from box to specify the linking field of the parent form b Expand the table you want to display in the subform in the Link to box and select the linking field of the sub form c Click Add to append the selected subform to the list being generated 6 When you have added all subform links click OK to close the dialog box and return to the Form Generation dialog box Change existing subform layout You can use the Form Generator to automatically change the overall layout of an existing subform To change the layout of an existing subform 1 Right click on the title bar of the subform data box and click the Properties context menu command The Box Properties dialog box appears 2 Inthe Box Properties dialog box select the Form tab 3 Select the Generate form check box then click Style The Form Generation dialog
137. ation from a Subform different database or a different data table within the same database Contains general purpose commands Main toolbar ns such as copying saving and printing Form toolbar Contains the form creation tools Record toolbar Contains commands from the Record menu Contains commands from the Search menu Search toolbar Reel notes Used to format text in Text and Memo fields toolbar Control box A data box containing an ActiveX control Status bar Displays information about the item opened in Chapter 2 Getting Started 7 of 342 hemBioFinder 13 I me Orea PerkinElmer For the Better the ChemBioFinder window as well as recent actions and user interface elements Displays ADD when you add a new rec ord that has not been committed to the database Read only indi Displays READ if the database is read cator only New Record indi cator Query indicator Displays QRY when you enter a search query aa Displays the position within the current hit list of the record you are viewing Displays the number of records through which you are browsing Might be less than the total database size if you have recently performed a search Current list size Total database Displays the total number of records in the cur size rent table Toolbars The ChemBioFinder 13 0 toolbars help you to create and manage forms and the database records that are displayed Toolbars are normally docked at the top a
138. aw the alternative groups N DO oO FR W Type a title in the alternative Group Title box The title must match the atom label in the parent structure but we ll use R in this example ef Figure 8 6 Adding a title to an alternative group 1 Title box 8 Draw the substructure fragments in the alternative Group box Use the single bond tool to define a fragment and the text tool atom HotKeys or Nicknames to create atom labels for each variable Chapter 8 Queries 105 of 342 ChemBioFinder 13 0 PerkinElmer For the Better Figure 8 7 Adding the alternative groups 9 Add the Attachment Points a Click the diamond shaped Attachment Point tool on the Chemical Symbols palette b Click the open atom position on each substructure fragment Tip altematively the HotKey period can be used to add attachment points A ec R Q CH 0H Figure 8 8 Completed altemative group query _ Note In the above procedure the parent structure was drawn then the R Group table was added In fact the order doesn t matter You may create the R Group table first then draw the parent structure In either case as soon as a generic atom label in the structure matches the group title in the R Group table a hollow attachment point symbol appears next to the label in the parent structure 10 Type CTRL W to return to ChemBioFinder 13 0 The structure and the R Group table appear in the structure win dow 11 Co
139. c cece cece cece ceeeeeceeeeeeeeeeeeeees 181 SON 181 Opening an Oracle database 2 2 oe n nc erann nrrainn 182 Searching 0 000220 cnn 183 Table of Contents iii ChemBioFinder 13 0 I PerkinE For the Better A ee etd E ees ne eet ae 183 Handinq SUS So os oer oe pet ie eee Piece ele Pee ae eee cee eee 184 Setting Oracle preferentes e cece cece cece cece aara naaraana 185 Updating and adding data ooooccccccccccccccccccccccccc cons 185 Korso Lao cc 186 Indexing 5s Ph a e a a e a arches a a ae ee 187 CA e a RNA REE MERE Ee e A 189 Chapter 15 BIOSAR isa 190 Starting the BioSAR browser ooccccccccccccccccccccccccccccccccno nn nn 190 Performing searches in BioSAR 2 eee eee cnn ccoo cece aa aaea aaran annainne 190 Exporting the data form to ChemBioFinder 0 000000 c cece ccc cece cece eee cece eee eeeeeeeeeeeeeeees 190 ChemBioFinder file types 2 222 222 2222 c ccc cece cnn 190 Subforms and autolinks 2 2 4 0 sci soelevewtiesdd ees ao Seabee ote de deg edacs adessbs ee ee sede dedesy sacs Jack cbse ideas 191 Multiple SON acoso a2 5 te cet o les fee tee ate ad Soca ee ee o ce Bo bac o o 192 Query MITNSIS copo ii tie odia e 193 DOMAINS ss 2 2e sce 2i eta anor dotea es R he Nabe Gaaget ener eae 196 Creating an mdb database 22 2 2 eee cc ccc cece ns 197 Chapter 16 Customizing ChemBioFinder 13 0 2 2 20 0 20 0 e cece cececeeeeeeeees 200 Setting Preferences eee eee eee cece cec
140. ce Flags reactions in which the molecular formulae of reactants is different from products Not cor rectable Doubly drawn atoms Flags structures in which two atoms are very close together and at least one of which lacks a label Also to qualify as a doubly drawn pair the combined valence of explicit bonds must not exceed the capacity of either atom You get this sort of structure when attempting to draw a bond from an existing atom but miss and accidentally create a new atom ChemBioDraw flags these cases with a wavy red box 3D not scaled in Angstroms Flags structures with Z coordinates or 3D not scaled in Angstroms Such structures will not be struck in a 3D search Miscellaneous Checks whether isotopic masses are reasonable Chapter 8 Queries 123 of 342 ChemBioFinder 13 0 pP PerkinElmer For the Better False stereomarks Flags stereochemical indicators such as a wedged bond on an atom that is incapable of ster eochemistry because of its geometry In a normal search such indicators are ignored The option lets you find all such stereochemical indications and correct any errors CDX lt gt Mst correspondence Checks whether the chemical interpretation of the original CDX drawing remains same in the latest version of the software It also checks whether the stored internal structures need to be regen erated from the CDX Atom atom maps Checks whether the quality of auto generated maps is satisfactory However use
141. ch atom The default is 0 do not dis play The color of query atoms and other atom types not listed in the Periodic table The default is Purple Whether or not to display bond numbers on each bond The default is 0 do not dis play Spacing between double bonds as a percentage of bond length The default is 12 A correction to the font size of atom labels based on a structure s average bond length More specifically 268 of 342 ChemBioFinder 13 0 DISPLAY FORM_COLOR FRAME_PICTURES DISPLAY DISPLAY GRID_SPACING DISPLAY MAX_BND_LEN Chapter 20 CAL Commands pP PerkinElmer For the Better the font size of atom labels is nominal value FONT_ ADJUSTMENT 100 average bond length The default is 20 The background color of the form This parameter can be set manually inthe Color tab of the Preferences dialog box The default is Grey Whether or not to display borders around pictures This parameter can be set manually in the Display tab of the Preferences dialog box The default is 1 display The spacing in pixels between hash marks on the grid This parameter can be set manually in the Display tab of the Preferences dialog box The default is 10 pixels The scaling factor by which the maximum bond length is modified This value is only applicable when the Fit to box option is deselected 269 of 342 ChemBioFinder 13 0 MOL_HIGHLIGHT_ COL
142. ch see Changing the scope of a search on page 231 Chapter 8 Queries 102 of 342 ChemBioFinder 13 0 PerkinElmer For the Better _ Note In searching substructures ChemBioFinder 13 0 finds the substructure query regardless of its orientation or drawing presentation in the targeted molecules Bonds shown in bold above are highlighted in red in Chem BioFinder 13 0 Full structure searches A full structure search finds structures that completely match the query If you do not specify stereochemistry or use generic atom or bond labels you may get more than one hit You may also get more than one hit if there are duplicates in the database For more information see Stereochemistry on page 104 and Exact searches on page 101 Fragment searches You can draw more than one structure or structure fragment in your substructure search query In the Details tab of the Preferences dialog box you may allow fragments to overlap in the target structure For example if you perform the following substructure query with Query fragments may overlap in target selected OH NY 7 Figure 8 2 Fragment query The hit list will include this structure SS Figure 8 3 Example of substance hit in a fragment query The dot indicates an atom shared between the two fragments The hit list will not include this molecule if the overlap option is deselected _ Note The option Query fragments may overlap in target is useful only in substructure searc
143. ch for an exact match _ Note To search for a list of records using partial text a wildcard search or range of numbers perform a search on the relevant field If the column you search is text use quotes around items that contains commas For example type 1 2 Pyran as 1 2 Pyran You can save a list as a text file and retrieve it later using File To find a list 1 Goto Search gt Find List The Find List dialog box appears 2 Choose a field from the Column menu 3 Paste or type a list of field parameters into the Find List text box 4 Click OK The list of matching records is retrieved Chapter 8 Queries 100 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 Structure searches You can search a ChemBioFinder 13 0 database using sub or full structure queries To refine your search use the query functions in ChemBioDraw These are described in the ChemBioDraw User Manual and in Structural Query Features on page 223 in this manual ChemBioFinder 13 0 matches structures in three ways Search type Normal Exact Similarity Structure mode sub or full structure Tautomerism yes substructure tautomerism no normal structure mode s yes full structure tautomerism no amp Search type K es exact structure mode full structure tautomerism y no substructure similarity structure mode OO full structure Figure 8 1 Structure search tree Search types
144. ches 114 searching 103 frame tool 36 framed box tool 36 framed boxes 36 framed boxes creating 37 framed boxes description 6 frames 36 frames creating 36 framing pictures 201 free sites in queries 234 full structure searching 103 full structure searching see also substructure searching 103 full strucuture searching 103 G G groups see alternative groups 104 general properties 223 general preferences 202 generic groups see alternative groups 104 generics hitting in queries 115 Gibbs free energy 148 go to record command 64 Chapter 22 Index 317 of 342 ChemBioFinder 13 0 I PerkinElmer For the Better grid 35 spacing 201 tool 35 H headers delimited text files 94 heat of formation 149 help CAL 211 Henry s Law constant 149 hiding annotations 201 data boxes 44 histogram plots 27 161 hit any charge on carbon 113 hit any charge on heteroatom 113 hit list merge by drag and drop 131 hit lists boolean operations 131 current 10 intersecting 131 joining 131 merging 130 replacing 131 restoring 130 saving 130 saving as text files 130 hydrogens in queries 225 Chapter 22 Index 318 of 342 ChemBioFinder 13 0 I PerkinE For the Better hydrogens added to structures 81 l ID queries 100 ideal gas thermal capacity 149 identity searching see exact searching 101 implicit hydrogens 235 in queries 235 on metals 203 implicit hydrogens added to structures 81 importing data 87 duplicate reagents from RD or SD
145. ck Enable 2 Click OK The options you choose are applied to the form Disabling security To disable security and reset defaults 1 Right click in the form and click Properties 2 Inthe Form tab of the Form Properties dialog box click Security The Form Security dialog box appears 3 Inthe Form Security dialog box click Disable The Validate Security dialog box appears _ Note This form only appears if you entered a password when you enabled security Setting security options on page 51 4 Enter your password then click OK Security is disabled and the defaults are reset Security Disabled appears in the lower left corner of the Form Security dialog box Overriding security In order to edit security options you must temporarily remove security In this case you should use the Override option rather than the Disable option To temporarily disable security 1 Right click in the form and click Properties 2 Inthe Form tab of the Form Properties dialog box click Security The Form Security dialog box appears 3 Inthe Form Security dialog box click Override Security The Validate Security dialog box appears Note This form only appears if you entered a password when you enabled security Setting security options on page 51 4 Enter your password then click OK You are allowed to edit the security options Security Overridden appears in the lower left corner of the Form Security dialog box Chapter 4 For
146. ck in the Mol_ID field and click the Sort Column gt Ascending context menu command Example Do the following 1 Inthe CS Demo database create a profile with one field Molweight and a cost profile such that values below 100 are ideal and above 100 increasingly bad 2 Browse through the compounds Benzene mw 78 falls in the ideal region so it has a cost of zero and a score of zero Buckyball fullerene mw 800 falls way outside the ideal so it has a high cost and a score of 1 3 Right click in the profile box 4 Click the Compound Profile gt Search Sort gt Sort relative to ideal context menu command 5 Click the Switch to Table icon to make it easier to compare the profiles The compounds are ordered by dist value from 0 00 to 1 00 Note that the score and dist values are the same 6 Browse to bromobenzene mw 157 The score for this compound is not ideal It will be approximately 0 1 depending on how you set the profile Tip You can sort by Molname or MW to find the compound more easily Chapter 9 Compound Profiles 143 of 342 ChemBioFinder 13 0 PerkinEl For the Better 7 Click the Switch to Table icon again to return to form view 8 Right click in the Profile data box then select Compound Profile gt Search Sort gt Sort relative to current from the context menu 9 Switch back to Table View are browse the results Bromobenzene is at the top of the list Other compounds with similar scores follow Note tha
147. cognizes the following operators for addition _ for subtraction for multiplication Chapter 20 CAL Commands 282 of 342 ChemBioFinder 13 0 PerkinElmer For the Better for division SUBSTR extracts a substring from a variable The extracted substring extends from a specified character to the end of the string or from one specified character to another The table below shows examples of Variable Commands SETVAL 3 store text in V1 some text SETVAL 2 other store text in V2 text naa d text f file into V9 paata E read text from file into APPEND ON turn on append mode WRITEVAL append contents of V1 to output txt file SETVAL 2 append text to contents of append me V2 APPEND OFF turn off append mode INPUT 2 enter new data GETDATA 3 copy data from molname molname box to V3 PUTDATA mol name ben zene prompt and get user input to V2 store given string in mol name box sets V3 equal to the value stored in V1 plus the value stored in V4 v4 SUBSTR 2 abcdef 3 5 stores cde in V2 CAL commands SETVAL syntax LET 3 V1 Assigns the specified string to a user variable SETVAL variable text The SETVAL command has the following arguments Chapter 20 CAL Commands 283 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 User variable to which the variable text is assigned String that is assigned to the variable Remarks
148. commands You can enter just enough letters to uniquely identify the menu option For example to execute the Record Next command type rec n Some menu commands open a dialog box and wait for user feedback To avoid this a limited number of menu com mands can take explicit arguments FILE OPEN filename FILE SAVE filename RECORD GO TO RECORD recno The command menu menuitem param executes any menu command as if selected from the menu The menu commands have the following arguments Stringstring_definition con taining the name of the menu in which the com mand resides Stringstring_definition con taining the name of the spe menuitem En ES cific command within the menu Stringstring_definition con taining additional infor param mation required by the command Settings The settings for param vary depending on the specific menu command Most menu commands use no param and ignore it if present The following commands accept a value for param and suppress the appropriate dialog box if it is present File Open Name of the file to open Chapter 20 CAL Commands 244 of 342 hemBioFi r 13 I ad ed PerkinElmer For the Better File Save Name of the file to save Index of the destination rec Record Go to ord within the current list cu rrent_list_definition ON or OFF corresponding Search Sub structure to the checked unchecked state of the menu ON or OFF corresponding Search Sim
149. copy paste use CTRL C CTRL V To undo or redo last change only use CTRL Z Chapter 16 Customizing ChemBioFinder 13 0 212 of 342 ChemBioFinder 13 0 PerkinElmer For the Better The Verify button runs the script through the CAL command parser The parser checks only that lines begin with rec ognized keywords so just because a script is parsed without error does not mean it will run correctly The Properties button displays a dialog box used to specify whether the script is to be stored in an external file or internally and to provide a file path or script name You can assign a script any name you like but the name must be unique among scripts on the current form The OK button saves the script The Run button saves the script and runs it To execute a script not assigned to a button Choose the script from the Scripts menu _ Note To execute a script that does not appear on the menu use the Command line and enter Call lt script file name gt Debugging a script You can step through a script line by line when debugging it To view a script line by line 1 Go to Scripts gt Command Line The Enter CAL Command dialog box appears 2 Type step on and click Execute This turns on the step mode where each step is displayed 3 Run a CAL script by doing one of the following appears in the choose the appro Scripts menu priate script type call and the name of your script in does not appear in
150. corner of the box when you click in the box 5 Click the button to display the menu 6 Select any item on the menu the text appears in the top left corner of the box and the button disappears Click within the data box to make the button reappear Adding scroll bars Scroll bars are used to accommodate lengthy data when there is limited space for the data box To add a scroll bar 1 Right click a data box and click Properties The box properties dialog box appears 2 Inthe Box style section select the With scroll bars check box 3 Click OK The scroll bar appears on the bottom right in the data box Chapter 4 Forms 43 of 342 ChemBioFinder 13 0 PerkinElme For the Better Hiding data boxes You can show or hide boxes when switching between query and browse mode For example you can hide non search able data boxes during query entry or show only those data boxes that display information useful for query entry When you are in form layout mode all boxes are visible regardless of the setting To hide data boxes 1 Right click on the box and click Properties 2 Inthe Box Style area select the Hidden in Browse Mode check box or the Hidden in Query Mode check box 3 Click OK 4 Deselect the Layout Mode to view the results Customizing text Use the Text Format toolbar to customize text fonts sizes styles colors and alignment in form boxes All of the standard text formatting options are available To display the T
151. cost profile associated with the field In the profile costs are normalized to score between 0 and 1 where the ideal is assigned the value of zero and the slope of the deviation to maximum 1 is user defined _ Note The function is a normalizing linear spline Cost Profile high plateau 1050 A ideal value 0 56 Figure 9 1 IC 50 profile The cost profile is designed by the user to reflect their opinion of what constitutes a good value for a property The user can adjust the cost profile to reflect how unhappy they would be when a compound deviates from the ideal value by changing the range of values at zero and the slope of the line to one For example a user might want a drug candidate to have a good solubility in units of mg ml and good biological activ ity in units of nm They might be willing to sacrifice some activity to get better solubility so the cost function for sol ubility would be adjusted to penalize any deviation from some ideal range more severely than the corresponding cost function for activity The default display preference is to have white regions in the bars represent ideal values darker regions increasing deviation from the ideal The normalization function permits properties of different types to be compared A score the total deviation from ideal of all fields is displayed Each property can be assigned a weight to adjust its effect on the overall calculation The score is the
152. cted by default 4 Deselect those fields in the Choose fields to be included section that you want to exclude from the form 5 To have a Structure box in the upper left corner of the form select the Structure in upper left of form check box If you do not select this option the boxes are generated in the order they appear in the list 6 Select the Form style you want Framed Each form field has a label above it and a frame Titled Each form field has a label above and no frame Labeled Each form field has a label to the left and no frame Plain Each form field is displayed without a title or frame 7 Use the Columns scrollbar to select the number of columns you want in your form 8 Use the Grid size drop down list to choose the size and spacing of the boxes and grid 7 Large larger and spaced further apart Medium medium relative to the Large and Small settings Small smaller and spaced closer together 9 Click OK in the Form Generation dialog box Your form settings are saved 10 Click Apply and then click OK in the Form Properties dialog box A warning dialog box appears prompting you to create a new form or replace the existing form Click No to create a new form or Yes to replace the existing form Saving a form In most non database applications including ChemBioDraw and ChemBio3D when you edit data on the screen your changes are not made permanent until you select File gt Save or type CTRL S I
153. ction describes the steps for carrying out clustering operations Clustering on single field 1 Connect your form to the CS_Demo database On the form there are four fields Mol_ID Molname MolWeight Structure and Formula In this section clustering is performed on MolWeight f Note You can perform clustering on any numeric or structure field 2 Perform search on C6 You will get 42 hits Tip Perform analysis on fairly small set of records otherwise the display becomes cumbersome 3 Right click the MolWeight box and then click Cluster by MolWeight Chapter 13 Clustering in BioViz 175 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 It takes few minutes for the operation to perform as it gathers the data perform clustering and data projections then calculates the display co ordinates You will get screen as shown below displaying the results of clustering operation amp CS Clustering Figure 13 1 CS Clustering dialog box In the above figure the display is divided into two parts On the left is the dendogram a standard graph for displaying the results of the clustering operation Each point along the baseline leaf represents one of the input records In the clustering figure you get 42 hits and 42 of them are evenly spaced along the x axis A horizontal line above the base represents a node or a merge of the two objects underneath it The position of the node under y axis is pro portion
154. d Menu Options Toolbars Form Toolbar j Main Toolbar Menu Bar Reset All Record Toolbar Search Toolbar Text Format Toolbar Figure 16 7 2 Click the toolbar you want to return to default settings and then click Reset The toolbar in the ChemBioFinder 13 0 window changes to the default settings To return all the toolbars to the default settings 1 Click the Toolbars tab in the Customize dialog box The Toolbars tab appears and shows all of the toolbars that currently appear in the ChemBioFinder 13 0 window 2 Click Reset All Periodic table ChemBioFinder 13 0 features a periodic table for data display and formula entry Selecting an element displays phys ical and historical data To display the Periodic Table window 1 Go to View gt Periodic Table Periodic Table Mass 15 9994 Electroneg y 3 44 s Discovered by Priestley 1774 Ti Cr Fe elaln z o m Figure 16 8 Chapter 16 Customizing ChemBioFinder 13 0 208 of 342 hemBioFinder 13 0 I Che oFinde PerkinElmer For the Better 2 Click an element to display its name mass and other properties in the top box and to display its symbol in the bot tom edit box By clicking different elements and numbers sequentially you can create a molecular formula in the bottom editable text box You can then paste th
155. d z Display the Data table view and double click on the table header of the field you want to sort Chapter 12 BioViz 169 of 342 hemBioFinder 13 l Che oFinder 13 0 PerkinElmer For the Better Filtering BioViz filters limit the display of a variable by trimming either end of the range that is you can eliminate high points low points or both from the display Filters can be set for either or both plotted variables You may also filter the data set on other variables up to a total of 31 filters per chart x Right click to choose fiterng fhelds 700 94 1004 62 p uS 2 00 Boiling_Point 1004 62 22 939 738 40 LJ mf 22 99 Mobrsecight 9065 31 New filter style I C 278 17 507_3 lt 752 98 1004 62 boing y i a a _ E 2781 657 57 993 152 Ofd filter style Figure 12 8 Filter sliders Filters are set in the filter window If the window is not visible check the box next to Filter Window on the View menu When a filter is set All plots associated with a given form are affected unless the plot is locked before applying the filter Points missing a value for a given field are hidden whenever the filter for that field is visible The range is displayed in black below the slider and the set points in red above the slider Filter name is centered rather than on the right Operation of the sliders is unchanged Chapter 12 BioViz 170 of 342 ChemBioFinder 13 0 Right click to choose filtering fields
156. d and select a new template 7 Click OK to save changes and exit the editor or Cancel to exit without saving Chapter 9 Compound Profiles 141 of 342 ChemBioFinder 13 0 Perkin For the Better Display preferences You can change display characteristics of a profile with the Profile Display Preferences dialog box Changes you make apply only to a selected profile box unless you choose to reset the defaults To change the profile display preferences 1 Right click a profile box and click the Compound Profile gt Preferences context menu command The Profile Display Preferences dialog box appears 2 To change the base color of the cost band default red select a primary color in the Cost Shading Color sec tion 3 To reverse the polarity of the cost band deselect the Ideal white check box When checked light shades are good dark are bad when unchecked the reverse is true 4 To change the color of the value marks and the lines between them click Values and select a color from the color picker Tochange the color of range labels click Labels color and select a color from the color picker 5 6 To turn off the range labels to the right of the cost band deselect the Labels check box 7 Touse the current settings as the defaults for all subsequent profile creations click Use As Defaults 8 When you have finished editing the settings click OK to save the changes or Cancel to discard
157. d names Enter a blank name when complete startinput lif vl exitrecord addputdata molname vlgoto start Chapter 20 CAL Commands 292 of 342 ChemBioFinder 13 0 CAL commands IF syntax Conditionally executes a command depending on the value of an expression IF variable operator value command or IF variable operator value command ELSE command ENDIF The GETDATA command has the following arguments User variable that is the variable basis of the comparison operator Comparison function String that is to be com value pared to the variable Any valid CAL command Settings The settings for operator are Command will be executed if value is less than variable Command will be executed if value is greater than var iable Command will be executed if value is equal to variable Command will be executed if value is not equal to var iable Command will be executed if value is not equal to var iable Chapter 20 CAL Commands pP PerkinElmer For the Better 293 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 Remarks Only one CAL command may be executed by each IF statement However that one command may be a GOTO that skips over many other commands CAL commands LOOP ENDLOOP syntax Executes a block of statements repeatedly LOOP count statements ENDLOOP The LOOP ENDLOOP commands have the following arguments Number of ti
158. data in all fields in the table will be lost To attach a table from another database 1 Click the Table tab 2 Click Attach Table The Attach Table dialog box appears 3 Select the type of database MS Access or Oracle ODBC 4 For MS Access browse to the MDB file containing the table Select a table and click OK Chapter 6 Working with Data 86 of 342 BioFi 13 ChemBioFinder 13 0 PerkinElmer For the Better Importing and Exporting Data You can move data into and out of a database if the data is in a supported file format You can import single files import or export databases or add data to an existing database Supported file formats ChemBioFinder 13 0 lets you work with individual chemical structures and reactions in various file formats The sup ported formats are ChemBioDraw cdx ChemBioDraw XML cdxml Connection Table ct Delimited text csv txt MDL Molfile and V3000 mol MDL RXNfile and Rxn V3000 rxn MDL RDFile rdf MDL SDFile sdf MDL Sketch skc MDL Graphic tf SMD 4 2 smd Supported formats for output files only Bitmap bmp XML cfxml Encapsulated Postscript eps GIF gif Microsoft Word doc TIFF tif Windows metafile wmf For information on the cdx ct and cdxml file formats see the ChemBioDraw Users Guide Importing data ChemBioFinder 13 0 lets you import ChemBioDraw structures Structure Data files SDFile
159. database and one person changes the data in that record the sec ond person will not see the changes immediately The changes will be visible when the second user switches to another record and then back to it Secured access ChemBioFinder 13 0 supports the following types of security Form access ChemBioFinder 13 0 enforces form access security by requiring a user name and password which are stored in the form CFX file Molecule file access ChemBioFinder 13 0 enforces molecule file access security by requiring a user name and password which are stored in the database s MST file Microsoft Jet Relational Database Engine the database engine that underlies Microsoft Access enforces secu rity The user names and passwords are stored in an MS Access Workgroup Administrator database For more information on Form access see Securing forms on page 51 For more information on MS Access secu rity see Opening a secured MS Access database on page 61 When you open a form or database that has security options applied to it you are prompted to enter a username and password to log on When you open a secured MS Access database from within ChemBioFinder 13 0 a username password and work group information file is required Contact your Access Database Administrator for this information To open a secured form 1 Inthe Validate Security dialog box type your username and password and then click OK If the form you access
160. domain you must run a query to define the subset of the database with which you want to work This subset becomes the domain o Tip If you want your domain to have a particular order sort before creating the domain The order will be pre served for all subsequent use To create a domain 1 Select a query by double clicking on it 2 Goto Search gt Domain gt Set Domain to Current List Query control display When you run queries in a domain they will not be displayed as child queries of the domain unless you select Over Current List on the Search menu and specify the domain as the active list Cancelling the domain If you no longer want to use a domain go to Search gt Domain gt Reset to Full Database again to cancel it Creating an mdb database When working with a large Oracle based database on a server it is sometimes convenient to store a subset of the database dataset as a local database ChemBioFinder local databases are Microsoft Access based file extension MDB so the exported dataset must take into account Access naming rules and limitations Access database rules Because ChemBioFinder 13 0 uses the Access Jet database standard names of fields controls and objects must conform to Access rules These are E May be up to 64 characters long z May include any combination of letters numbers spaces and special characters except a period an excla mation point an accent grave or brackets
161. ds Examples of queries Chapter 8 Queries 97 of 342 ChemBioFinder 13 0 PerkinElmer For the Better Benzene Ben benz Bromobenzene zoic acid Benzene Ben benz OR zoic acid Bro 7 e Azobenzene bromo mobenzene Dibromobenzene Benzoic acid benzene Benzene Benzene d Bromobenzene Numeric searches Use numeric searches to find information such as boiling points molecular weights and other properties A numeric query can be either a decimal value or range When you enter a single value the number of significant digits deter mines the precision of the search A hit is any value that rounds off to the query When entering a range enter two values separated by a hyphen Examples of numeric queries values from 89 5 to 90 5 values from 90 05 to 90 15 values from 90 through 100 inclusive values from 90 through gt 90 and lt 100 100 inclusive values from 90 through gt 90 and lt 100 100 exclusive Molecular formula searches Formula searching lets you search molecular compositions Searches can be inclusive exact designated with an equals sign or with an element range you specify ChemBioFinder 13 0 allows formula searching based on special atoms such as A Q X and M The definitions for these atom types can overlap For example the structure BiCI3 will be hit by either the query AX3 or the query A4 Chapter 8 Queries 98 of 342 ChemBioFinder 13 0 PerkinElmer For the Bett
162. ds on page 243 To specify a CAL script 1 Right click on the subform header and select Properties from the context menu The Subform Properties dialog box appears 2 Inthe Table script box type the name of a CAL script or click Edit and select a script 3 Click OK In Table view the entries are blue and underlined indicating that they are hot linked to a script 4 Click any of the hot links to run the script Chapter 11 Relational Data and Subforms 160 of 342 ChemBioFinder 13 0 PerkinEl For the Better BioViz With BioViz you can identify trends and correlations in your data and within subsets of your data without the extra step of exporting to another application You can have as many plot windows as you like each showing a different vis ualization of data from the current form BioViz is designed to be used with the Structure Window and the Queries Tree While not necessary to creating vis ualizations they offer considerable convenience when working with plots Before working with BioViz go to the View menu and activate the Structure and Explorer windows The Structure window gives you a way to display structures without taking up room on the form The Queries Tree in the Explorer Window gives you an easy way to track multiple hit lists To create a new plot view an existing plot or delete a plot use the BioViz Plots submenu of the View menu Plots are saved with the form and will come back when it is opened though
163. e To create multiple structure columns in a table Chapter 5 Databases 74 of 342 ChemBioFinder 13 0 Perkin For the Better Go to File gt Database The Form Properties dialog box appears Create or open a database Click the Field tab Select the Table in which you want to create new structure columns Click Create Field The Create Field dialog box appears Select Structure from the Type drop down list An un editable name is assigned to the field Click OK Four new fields appear in the list and are named to belong to the same set of structure columns ON DO A WD Connect the new fields to boxes by right clicking on the appropriate data box and choosing the field from the con text menu field list Non chemical databases If you open a database that you created using a program other than ChemBioFinder 13 0 and you want to add struc tures to it you can create structure fields in any modifiable non attached table To create a structure field Open a database Right click and select Properties Inthe database tree click the table to which you want to add structures Click the Field tab Click Create Field The Create Field dialog box appears oor O N Choose Structure from the Type drop down list then click OK You do not provide a name or other details when you create Structure columns ChemBioFinder 13 0 automatically creates four columns and names them These columns contain
164. e Users familiar with ChemBioFinder 13 0 will find that ChemBioFinder Oracle operates much the same way You can open a database browse search register load and so forth without worrying about what sort of database you use In practice however there are several visible and invisible differences f Note ChemBioFinde Oracle is available in ChemBioFinder Pro and Ultra versions only When you open an Oracle database in ChemBioFinder Oracle you enter a new body of code which connects directly to Oracle and carries out all searches and transactions on the server This new mode of operation requires a different underlying technology based on Microsoft ActiveX Data Objects and a different philosophy in some aspects of usage such as the handling of lists and new features such as index management All of these are described in this document In ChemBioFinder Oracle a Searches are carried out on the server including structure searches Search results are stored in tables in the Oracle database Hit lists are saved to other tables in Oracle rather than in files Saved lists can be annotated and on restore can be selected from a pick list directory When working with large databases you can choose a new mechanism which eliminates certain slow operations associated with large record sets e g Move Last This is a user choice because there are trade offs involved You cannot create an Oracle database but if you have the privil
165. e Figure 3 2 A reaction type query structure 4 Press ENTER Browse through the search results Each of the reactions shows the transformation of a carbon oxygen double bond to a carbon oxygen single bond This hit list includes reductions of aldehydes acids and ketones Search over list In this example you start with the previous list see Searching by reaction type on page 24 and search again to get only ketone reduction reactions To search over a list 1 If you are not continuing directly from the last example double click the previous query in the Query Tree to make sure it is the active hit list 2 Goto Search gt Over Current List 3 Double click in the Structure box 4 Draw the following O A a Using a selection tool right click on the double bond and set Reaction Center bond properties to Change b Using the Text tool select one of the carbon atoms Type NOT O H all uppercase with brackets as indi cated and press ENTER to replace it c Using the Text tool select the label right click and select Repeat Last Labelfrom the context menu d Double click on the other carbon atom to reproduce the label The structure now looks like this NOT H O NOT O H You have specified a search for ketones by adding the restriction that the atoms adjacent to the carbon must not be oxygen atoms or hydrogen atoms You also specified that the double bond had to change and not be broken 5 Press ENTER The
166. e CTRL F 2 Enter a query in the subform data box See Queries on page 97 for details on entering queries 3 Goto Search gt Find If the subform is linked to the main form the hit list contains the main form records related to the matches in the sub form search You can browse and save this hit list just as you would a hit list from a main form search If the subform is not linked to the main form it behaves independently of the main form and is searched separately Viewing subform data in a table If you have more than one record in the subform associated with a single record in the main form it may be more con venient to view the subform as a table while you browse through the main form The table view shows you the com plete list of related records for each entry in the main form To display a subform in Table view Select the subform and do one of the following Double click on a record in the table Goto View gt Data Table gt In Current Window Type Ctrl T Click the Switch to Table tool A table view of the records in the subform appears To return to the Form view repeat the above action Subform plots A third type of view is the plot view You can use BioViz to create a 1 D 2 D or histogram plot of any numerical field s of the data table connected to the subform To create a subform plot f Note You must be working with a form that has a subform with at least one column of numeric data 1 Cl
167. e ChemBioDraw window by typing CTRL W when you are fin ished 4 Go to Record gt Commit Changes Click the Commit Changes icon or move to a different record The changes are stored To clean up a structure 1 Right click in the box containing the structure and click Clean Structure 2 To save the cleaned up structure do one of the following Goto Record gt Commit Changes Click the Commit Changes icon Working with structures using ChemBioDraw Enter or edit ChemBioDraw structures in data boxes of the Structure field type You can work in ChemBioDraw directly or work in the Structure data box using the ChemBioDraw Control You choose the default in the Structure data box Box Properties To set the preference 1 Right click in the Structure box 2 Click Properties 3 Use the drop down menu in the Box Style section to choose your default ChemBioDraw style to use the ChemBioDraw Control ChemBioFinder style to edit in ChemBioDraw Chapter 6 Working with Data 80 of 342 ChemBioFinder 13 0 PerkinElme For the Better o Tip When ChemBioDraw style is the default you still have the option of editing directly in ChemBioDraw Just right click in the Structure box and choose Edit in ChemBioDraw To edit a structure 1 Double click in the structure data box ChemBioDraw opens or the ChemBioDraw Control appears depending on your default If you already have a structure in a data box that structure appea
168. e Data Source 2 Click Oracle Database and proceed as described under Opening an Oracle database on page 182 It doesn t matter what table you select since you will be creating a new one 3 Click OK to return to the blank form You are now ready to import _ Note When you click OK to dismiss the properties dialog box you will get a warning if the selected table does not have a primary key defined You can ignore this if you are about to create or load a new table Otherwise you should consider using an Oracle tool to define a primary key for the table Choose Import SDFile or Import Structures and select the source file s The Data Import dialog box appears Chapter 14 ChemBioFinder Oracle 186 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 Data Import ogging Form Style Advanced Output database c oraserver EPA TAS 2 Records in file 37 File e Data Fields MS Structure Structure Structure 0 00 MoD Long MoLID abe Formula Text Formula 0 00 Molweight Double Molweight 11 00 MOLREGNO Long MOLREGNO Mabe MOLNAME Text MOLNAME Mahe CORP_ID Text CORP_ID m DATF Text DATF Figure 14 1 1 Import tab 2 Output database text box 4 Inthe Output database box you see the name of the database followed by the table name in brackets To specify the table to load edit the table name by typing between the brackets If you want to create a new table enter the name you wish to give it If yo
169. e Structure Data Box N Cm 2 Search the query You get 103 hits 3 Goto Search gt Save List 4 Save the hit list as c n txt Integrate the two hit lists Goto Search gt Restore List Inthe Open dialog box open the benz txt file Inthe Restore List dialog box click the Replace radio button then click OK You return to your first list of 75 hits Go to Search gt Restore List Inthe Open dialog box open the c n txt file Onh WD Inthe Restore List dialog box click the Subtract radio button then click OK The hit list is reduced to the 60 records with compounds containing a benzene substructure not containing a C N sub structure and having molecular weights between 50 and 200 If you had chosen the Replace option in the last step then only the C N records would be displayed Choosing Inter sect would display those records in either list Finally choosing Union would display all records from both lists Using atom lists Using the text tool in ChemBioDraw you can enter in a structural query a list of possible atom types one of which must match in the target compound If you want to search for molecules containing a benzene ring with an ether amine or phosphane group a query might look like the following Chapter 8 Queries 133 of 342 ChemBioFinder 13 0 PerkinElmer For the Better O N P Figure 8 28 Atom list query Atom types and bond types To broaden or narrow a search query you can defi
170. e at teers gs ee ah iat Sen en eee tido eee at gate 97 NUIMGNIC SCaICheS 220 12 cote co g0t distin otesia dulce celos oil eee ct Sacer 98 Molecular formula searches 2 2 2 2 eee 98 Date searches conoci eet ee ce eee ii 100 PIGS AN ee ote AN 100 Structure Searches oeren nn ee E e RES 101 Reaction Searches on e AS E da 106 Combined searches occ ii A tt 110 JA 111 Query Procedures serere nkau E ge tostada ataco 111 Refining a Sears 118 Special structure searches 2 eee nn c cnn cnnncne 121 Managing queries 0 0000 o coco cece ccc cnn 125 Search examples ns 132 Chapter 9 Compound Profiles 2 2 2 22 2 2 c cocci cece cece cece cence eee eeccceeeeeeeeeeeeeeees 137 Table of Contents ii ChemBioFinder 13 0 I PerkinE For the Better Creating a compound profile 2 222222 2 22 ccc cc ccc cece cece ee cece ee aaea aoa oraraa aaeain 138 Editing a compound profile 0 020222 eee oada aa Aaea cece cece oaoa arrana aeann 140 CUSTOMIZINO ceci da a vied ote deel cede Bed 2h It ested cose 144 Chapter 10 Chemical Properties 2 2 00222 ccc c cece ccc cc ee eee cece cence eccceccceeeeeeeeeeeees 145 ChemBioFinder Chemical Properties 2222222 cece cece cece cece cece cece cc cceeeeceeeececceeteeeeeeeees 145 About Molecular Networks 146 ChemBio3D Chemical Properties 22 22 0020 22222 c cece cece cece ccc cece cece cece eeeeeceeeeceeeeteeeeeeeees 155 ChemBioD
171. e eee e cece eee eeeeeeeeeeeesaeseeeseseeees 200 ICA A 206 TODA ol A tee Seed A e tees 207 Penodictable asii el Parte ot es onto She do a Se eae i tg fe ed 208 Embedding ActiveX controls 2020202222 c cece cece cece cece cece cece cece eee e cece cece ee eeeeeeeeeeeeenes 210 COP ee ee eee peed Ceo oa ee 210 Methods of communication 2 2 2 2 0 22 eee 218 Chapter 17 Structural Query Features 000000000022 c cece cece cece cecceceeeeeeeeees 223 General properties nn 223 Changing the scope of a Search 2 22 22 eee cece cc cece cece ccc cece cece eee e cece eee eeeeteeceeeeceeeereeeeees 231 Atom properties cs 231 Table of Contents iv ChemBioFinder 13 0 I PerkinE For the Better AAA Glasby acne adetoue sone ten ketene dual acece uire rE aa 236 Chapter 18 Formula Input Rules 2 2 22 22 00 2222 conc ccoo 0000000000 020a n cnn 239 A A A A Bode es ete et eat E rs eee tte 239 EXamples tias aora ts Nesta esa te e cee ie e a ie Se Mie cats eee aah CRN 239 Chapter 19 Similarity Rules 220020022 c ccc cece cece eee cnn 241 Complete structure similarity 2 2 0 0 0 00022 c cele eee cece ccc ccc ccc cece nc 241 Substructure similarity 220 000 c cece ccc c cece eee ce cece cece eee e eee ceeeeeeeeeeeeeeeeeeeees 242 Chapter 20 CAL Commands nani 243 CALDEO sae fee te geste oes ee das 243 Menu commands rosene riaa eect dd each lid E id lea a laced E da dagebioe todd 243 Box creation commands 2 2 2
172. e following settings Form is set to form edit mode Form is set to data edit mode Remarks When the form is in form edit mode the SELECT command affects data boxes themselves When the form is in data edit mode the SELECT command affects the data within the data boxes CAL commands SELECT syntax Marks a box on the active formactive_form_definition for further manipulation It is equivalent to clicking in the box with the pointer tool SELECT box The SELECT command has the following argument Chapter 20 CAL Commands 258 of 342 ChemBioFinder 13 0 I ee a PerkinElmer For the Better Box identifier indicating the box to select Remarks The SELECT command acts only on data boxes frames text boxes buttons and picture boxes The similar com mand ACTIVATE is used for subforms The behavior of the SELECT command is modified by the FORMEDIT command When the form is in form edit mode the SELECT command affects data boxes themselves When the form is in data edit mode the SELECT command affects the data within the data boxes CAL commands UNSELECT syntax Reverses the action of the SELECT command making sure that no boxes are marked for further manipulations It is equivalent to clicking in the form background with the pointer tool UNSELECT The UNSELECT command takes no arguments Reverses the action of the ACTIVATE command making sure that the main form is the active form It is equivalen
173. e hit list you want to transmit to Excel If you want to work with the entire data base go to Search gt Retrieve All 3 Execute a short CAL script below which exports the hit list as comma delimited text to a temporary file then instructs Excel with DDE to load that file into a spreadsheet 4 Activate Excel to work with the data in the spreadsheet This procedure takes data one way from ChemBioFinder 13 0 to Excel Retuming modified data from Excel to Chem BioFinder 13 0 can be done using other techniques described in this chapter Here is a script to start up Excel RUNEXCEL CFS script to start Excel EXEC c msoffice excel excel exe If the Excel program is on your search path you can eliminate the complete pathname and just give the executable name exec excel exe if not you may need to modify this script to indicate where EXCEL EXE is located on your system Here is a script to transfer the current hit list from ChemBioFinder 13 0 to Excel TOEXCEL CFS script to send data to Excel WRITETEXT C DATA TMP Chapter 16 Customizing ChemBioFinder 13 0 219 of 342 h BioFi 13 ChemBioFinder 13 0 Perkin For the Better DDE Excel System OPEN C DATA TMP DDE Excel System COLUMN WIDTH 1 C1 C4 3 1 The first line writes out the current ChemBioFinder 13 0 hit list as a temporary delimited ASCII file By default all fields that appear in boxes on the
174. e only available when you select a one variable plot When you select a Histogram plot in the Bio Viz plot properties dialog box the plotting axis switches to X and the Bins section becomes available Each bin in a histogram is labeled with its high low cutoff points Note also that the data for the bin is displayed in the status bar as you mouse over it Chapter 12 BioViz 161 0f 342 pP PerkinElmer For the Better ChemBioFinder 13 0 When you overlay queries the histogram bins display the partial membership of the selected queries within the bars of the histogram epen OS e 118 teie ms arais fou ets Figure 12 1 Histogram display with overlaid queries Plot options BioViz options are available from the BioViz Properties dialog box and from the context right click menu Some of the context menu commands repeat options in the Properties dialog box Chapter 12 BioViz 162 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 General tab Number of variables plotted One and two dimensional plots are currently supported Style Currently supported plot styles are Line Scatter and Histogram By number Sets up n bins evenly spread across the whole range of values n must be lt 500 By size Sets up bins of size n The number of bins will be as many as are necessary to cover the range Log scale Select this option to display a log scale Base Base of the log scale You mus
175. e script if so After the Menu Command Record Add creates a new record the PUTDATA command enters the user s string into the molname field Closing the loop the GOTO command jumps execution back to the start label msg Enter new compound names Enter a blank name when complete startinput lif vl exitrecord addputdata molname vlgoto start Box creation commands DBOX coords fieldname FRAME coords text TEXT coords text PICT coords filename BUTTON coords scriptname SUBFM coords ARROWBOX coords FRAMEDBOX coords fieldname text To create a new box on the form 1 Specify the box type with the appropriate keyword 2 Type four integers giving the rectangular coordinates of the box after the keyword 3 If desired type a text string giving further information appropriate to the box type as shown below Chapter 20 CAL Commands 246 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 name of database field to be Data box j displayed in the box static label for upper left static text pathname of a Windows metafile pathname of a script file or name as it appears on Scripts menu name of database field to be Framedbox displayed in the box and static label for upper left If the text string is omitted you can supply it later using SETFIELD or SETTEXT For a button you must use SET TEXT if you want its visible label to be different from the name of its script Box coo
176. eactions in which bicyclo 2 2 1 heptane or a compound con taining this substructure is produced Chapter 8 Queries 109 of 342 ChemBioFinder 13 0 PerkinElmer For the Better Searching for intermediates Rarely you may be looking for reactions for which you only know something about an intermediate An Intermediate Search is very similar to a normal reaction search except that there are arrows on both sides of the target structure For example consider the query _ R C C 0 Figure 8 18 Sample intermediates query This finds any reactions containing the Ketene structure shown as an intermediate _ Note ChemBioFinder 13 0 cannot predict products or intermediates of reactions It finds this information only if it is already present in the database Combined searches You can combine structure searching with text searching to find a specific class of compounds For example you may want to find all compounds in the database whose names end in mycin and whose structures contain a phenyl ring Because you are entering multiple queries in different data boxes there is an implicit AND condition between data items in different fields To perform a combined search 1 Do one of the following to clear the form Goto Search gt Enter Query Click the Enter Query icon on the Search toolbar 2 Enter the structural query if any 3 Enter the text and or numeric queries in the appropriate boxes 4 Do one of the following
177. ead only mode If the component files extensions CFX MDB LDB MST MSX have read only attributes If the files are on read only media such as CD ROM If you select Read only in the File Open dialog box when you open a form or database When you open a read only database the following conditions apply READ appears in the status line You can not modify data in text or structure boxes _ Note If only the form CFX file is set to read only READ does not appear on the status line and the database can be modified Multi user access If a database resides on a network more than one ChemBioFinder 13 0 user may access it at the same time Each user can view print or modify records independently of the others The following table shows how the type of user affects the other users in the group Multiple readers User actions do not affect in read only each other access All users can read and write A user may see another user s edits If two Multiple writers users try to edit the same in normal access area at the same time one is alerted that the database is temporarily locked The writer in normal access is not affected by One writer mul f the readers The readers in tiple readers read only access may see the writer s edits Chapter 5 Databases 63 of 342 h BioFi 13 I ChemBioFinder 13 0 PerkinElmer For the Better If two people are viewing the same record within a
178. ecord gt Commit Changes create the new record You have now entered the first record in your database The size of your database is indicated in the Status Bar Enter two more records 1 Goto Record gt Add New Record 2 Add a record for n Pentane with boiling point 36 1 3 Repeat step 1 and then add a record for Cyclohexane with boiling point 80 7 _ Note After you have two or more records in your database you can commit changes by moving to a different record using the Record tools 4 Goto File gt Save f Note Choose Save to save the form Choose Commit Changes to save the data in your database Chapter 3 Tutorials 19 of 342 ChemBioFinder 13 0 PerkinElme For the Better Tutorial 4 Searching a database You can often find useful information in smaller databases by browsing through records one at a time However for larger databases you will likely want to enter specific search criteria to find what you want When you search a data base you find only those few records that have the information you want After you have this smaller set of records a hit list you can then browse it much more efficiently than you could the whole database In this tutorial we discuss text and structure searches We will cover reaction searches in Tutorial 5 Reaction searches on page 23 Opening the sample database To open the CS_Demo database 1 Start ChemBioFinder 13 0 and click the Existing tab on the Open dialog box If Ch
179. ecord is displayed _ Note Record numbers are temporary referring only to positions within the current list in its current sort order For example if you have done a search that found ten hits then the only valid record numbers are 1 10 If you want to move to a specific absolute location in a database you must run a search for a value in a field that identifies that location The data table Sometimes browsing through a data record set is more convenient if the data is presented in tabular format f Note You cannot add or modify records while viewing data in a table To display data in a table Goto View gt Data Table gt In Separate Window or type Ctrl T A list window containing the fields and records in the form appears Chapter 5 Databases 65 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 Figure 5 9 Data Table view in a separate window To display a particular record in the form Click the record s entry in the list window By default the fields in the data table are displayed in the order in which they were created To reorder the columns in the Data Table 1 Click one of the column headers to select the column 7 z O C6H6 78 11184 Benzene 2 C6HSBr 157 0079 Bromobend 68 07396 Furan o Figure 5 10 Column selection indicator in the Data Table view 2 Drag the header to a new position The cursor changes to the icon shown below The new position is indic
180. ed You can access data in Oracle databases that do not have the CS Oracle Cartridge installed for example bio logical databases but you cannot search or sort by structure or structure related properties Chem BioFinder Oracle has been developed with CS Oracle Cartridge version 9 or 10 and is not likely to work with earlier versions To display the Cartridge version look in the Database tab of the Properties dialog box The version is listed or None if unavailable Any table containing structures should have a unique primary key Otherwise a warning message will appear You can set up a primary key in ChemBioFinder see Indexing on page 187 As a ChemBioFinder Oracle user you must have sufficient privileges to create tables in your own tablespaces Fast move caching scheme Normally when you open a database or do a search ChemFinder issues a select statement The server then proc esses the statement prepares a set of records and provides a cursor for navigating through them to retrieve the data Unfortunately when the cursor is asked to move to a position N records from the current one it requires all N to be downloaded to the client In the worst case you open a large table and use Move Last to see the last record and the entire table is sent down from the server Chapter 21 CS Oracle Cartridge 296 of 342 ChemBioFinder 13 0 PerkinEl For the Better To get around this problem an alternative mecha
181. ed against the column ID _ Note The columns shown in the drop down menu should match the type of the fields to be linked i e if the ID is numeric then only numeric fields may be linked 8 The form box displays a chemist s name Multiple sort ChemBioFinder s multiple sort feature lets you rearrange the hit list based on one or more form fields you specify For example you can first sort the list by Reg number and then further arrange the list in order of Full reg number Sorting by main form fields To sort the hit list using fields in the main form 1 Goto Record gt Sort The Sort Multiple window appears 2 Inthe Sort Multiple window select from the left pane the field by which you want to sort To sort by multiple fields select the fields in the order you want to sort Chapter 15 BioSAR 192 of 342 ChemBioFinder 13 0 Perkin For the Better 3 By default each field is sorted in ascending order To reverse the order right click the field name in the right pane and click Descending in the pop up menu To remove a field right click the field and select Remove 4 Click OK Sorting by subform fields Just as in the main form you select in the subform the fields you want and the order you want them to be sorted You also indicate which value in each field you want ChemBioFinder to sort by the minimum value the maximum aver age of the values or the sum To sort the main form using subform fields 1 Goto Rec
182. ee steps Clearing the form Adding new data m Committing the new entries Clearing the form To begin adding a new record 1 Create a form and link it to a database For more information see Creating forms manually on page 34 The form should contain all the data boxes you want to view and edit The boxes should be assigned to their appro priate fields 2 Do one of the following Goto Record gt Add New Record Click the Add Record icon on the Record Toolbar 3 All of the boxes in the form are cleared to prepare for entering new data The Status Bar is updated to show that you are in record addition mode AD afl a of Figure 6 1 Status bar in record addition mode Adding new data To add alphanumeric data Click in a box with an alphanumeric field and type the data To add a structure 1 Right click in a box with a structure field 2 Do one of the following 1 Double click in the struc ture box The Chem BioDraw Control draw a struc ture Chem BioDraw mode appears Chapter 6 Working with Data 77 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 Draw the new structure in the Structure box Click outside to box to complete the structure Double click in the struc ture box or Right click and select Edit in Chem BioDraw ChemBioDraw opens draw a struc pe Draw the new structure in the ChemBioDraw win dow Goto File gt Exit and R
183. eges you can create a table within one This causes import operations to work somewhat differently To improve performance you can create indexes on selected columns Other more subtle differences are noted in the sections below Structure search speed is very fast in ChemBioFinder The fast speed comes from two factors improvement of the SQL so that hits are added much faster to the hitlist table and an optimization of certain frequent operations and improved screening efficiency that improves structure search speed in all PerkinElmer Informatics products Setup Before you can make use of the ChemBioFinder Oracle your machine must be configured as an Oracle client If you are already a user of the CS Oracle Cartridge you are probably all set If not you will need to enlist the help of an Oracle administrator to set up the server and set you up as a client For ChemBioFinder 13 0 installation instructions see the readme txt included on the distribution media Ideally ChemBioFinder Oracle should access any existing Oracle database in any format In practice there are some limitations See CS Oracle Cartridge on page 296 for notes and recommendations about preparing an Oracle data base for use with ChemBioFinder Oracle Chapter 14 ChemBioFinder Oracle 181 of 342 ChemBioFinder 13 0 PerkinElme For the Better Opening an Oracle database To open an Oracle database 1 Right click in the form and click the Data Source context
184. egrate the results from the second search with the results from the first Thus you can perform Boolean operations on different searches There are two ways to integrate the results of two searches Browsing to the saved list 1 Perform a search and save the hit list 2 Perform another search 3 Go to Search gt Restore List The Open dialog box appears 4 Browse to the previously saved list you want to integrate with the current hit list and click Open The Restore Merge List dialog box appears Chapter 8 Queries 130 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 Restore Merge List e L1 current list El Replace use L2 2 25 hit eer C Intersect L1 and L2 L2 gt 7 C Subtract L1 L2 C Documents and O Settings zchoo My C Union L1 L2 Documents Models L C Subtract from L2 L1 Figure 8 27 The Restore Merge List dialog box 5 Select the integration option and click OK Replace Discards the current hit list and displays the records from the hit list you chose to open Intersect Displays only those records that appear in both the current hit list and in the saved hit list This is a Boolean AND operation Subtract Displays only those records that are in the current hit list but are not in the saved hit list For example if the current list contains records 1 2 3 4 and 5 and the restored list contains records 4 5 6 and 7 then only records
185. emBio3D perform all of the Browse above options Chapter 4 Forms pP PerkinElmer For the Better 55 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 6 Click the plus sign next to Search to display the options take the appropriate action 3 Query database submit queries records use current hit list for Search over cur searching rent list search the entire data Search over full base database save and manipulate Enable hit list hit lists tools search exact struc ture only search substructures Substructure only search similar struc eae Similarity tures only use all of the above options 7 Click the plus sign next to Update records to display the options take the appropriate action update database rec Update records ords add database records Add new records delete database rec Delete records ords 8 To allow users to import data SDFiles or RDFiles select Import data 9 To allow users to export data including delimited text files select Export data 10 Click the plus sign next to Print to display the options take the appropriate action Chapter 4 Forms 56 of 342 hemBioFi 13 I ChE BIORINGERTAN PerkinElmer For the Better print a single record Single record only Several rec Print several records ords Use print preview mode Print preview perform all of the above functions To complete setting security 1 Cli
186. emBioFinder 13 0 is already run ning goto File gt New to open the dialog box or access CS_Demo directly from the Favorites tab of the Explorer Window 2 Navigate to the samples directory In Windows 7 go toc ProgramData CambridgeSoft ChemOffice2012 ChemFinder Samples In Windows XP or vista gotoC Documents and Settings All Users Application Data Ca mbridgeSoft ChemOffice2012 ChemFinder Samples 3 Inthe Samples directory select CS_demo cfx and click Open The CS_Demo database opens in ChemBioFinder 13 0 Before you begin searching open the Explorer window if it is not already open 4 Go to View gt Explorer Window 5 Click the Queries tab Formula searching To find compounds in the CS_demo database with six carbons and one or two nitrogen atoms 1 Goto Search gt Enter Query The form is cleared so that you can enter a new query 2 Click in the Formula box and type C6N 1 2 3 Click Search The Queries tree in the Explorer window displays one query as a child of the full list Queries can be saved with the form and can be reviewed at any time For more information see Managing queries on page 125 There are three methods for browsing the search results Inthe Form View Use the Record menu commands or toolbar to go through the records Inthe Data Table View Browse the table to view the records Inthe Continuous Forms View view multiple records in their own forms The Explorer wind
187. ement gt OPENDB opens a standard molecule database Specify a pathname to the MDB file or a name from the ODBC Data sources list When connected to an Oracle database OPENDB takes a table name instead of a database name You can specify the mode of database opening a R read only a E E exclusive Chapter 20 CAL Commands 279 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 RE read only and exclusive CRETABLE creates tables in the current database DELTABLE deletes tables in the current database SELTABLE selects a table form the current database and makes it the current working table for subsequent field actions CREFIELD creates fields in the current table in the current database You can specify the field type and width in the CREFIELD command The default text field is 50 characters wide DELFIELD deletes fields in the current table in the current database SORT sorts the database contents on the specified field The default sorts the database in ascending order You can specify descending order with D SQL allows SQL to be passed directly from CAL SQLStatement is a SQL statement that returns no results It is there fore useful for data manipulation operations Available only when connected to an Oracle database SQLSELECT retums a one row recordset It is useful for calculations or lookups v is the name or number of a var iable to receive the results of a Select statement SelectStatem
188. en atoms you exclude hydrocarbons from the hit list By clearly capitalizing the elements and spacing the query you avoid searching ambiguities although there were no ambiguities in this example Link nodes and multivalent Rs A link node is a placeholder for zero or more unspecified atoms It is especially useful when searching for targets with any of several ring sizes or chains substituted in particular ways at either end While link nodes are traditionally diva lent ChemBioFinder 13 0 places no constraints on the upper limit of the range Multi valent R and A atoms are func tionally similar to link nodes They may be thought of as higher valent link nodes Chapter 8 Queries 134 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 a a C ia Figure 8 30 Link nodes The traditional representation of a link node is CH2 but this is misleading because any atom type can substitute for the link node For this reason represents link nodes as R R without a repeat count can match any number of atoms including zero although any atom type of a target atom matches a link node you can impose two restrictions the on the link node Unsaturation Ring topology Using ChemBioDraw s Atom Properties menu to apply either of these properties to the link node restricts the range of target atoms to the specified topology For example specifying the link node to be aromatic would give the following results ZA
189. en the search is complete the number of hits is displayed in the Current List Size window of the Status Bar and the form displays the first hit In a substructure search the matched portion of each molecule is highlighted in red The above mentioned search returns all structures that contain a benzene ring 7 Note You can also set search preferences on the Search tab of the Preferences dialog box For more information see Customizing ChemBioFinder 13 0 on page 200 _ Note If a search gets no hits an alert appears and you are returned to the query mode with the query on display Chapter 3 Tutorials 22 of 342 ChemBioFinder 13 0 PerkinElmer For the Better Combined searching In some cases you may want to combine structure searching with text searching For example you may want to find all compounds in the database that have a benzene substructure and a molecular weight greater than 400 To perform a combined search Goto Search gt Enter Query The form is cleared so that you can enter a new query Double click in the Structure box The ChemBioDraw control appears 1 2 3 Draw benzene 4 Click the Molecular Weight box and type gt 400 5 Press ENTER Your search returns all records that include a benzene ring and have a molecular weight greater than 400 Tutorial 5 Reaction searches In addition to helping you organize information about individual substances ChemBioFinder 13 0 lets you store and search for chemic
190. ent is a SQL Select statement designed to retrieve a single result If vis omitted results go in V1 Available only when connected to an Oracle database If you omit the password from the connection string and you will be prompted for it when running the command The table below shows examples of Database Commands creates a new table E MyTable deletes a new table CAL commands OPENDB syntax Opens a database and assigns it as the Data Source of the active form OPENDB dbname The OPENDB command has the following argument String containing the file name of a database which could be a MDB file or a name from the ODBC Data Sources list Chapter 20 CAL Commands 280 of 342 ChemBioFinder 13 0 PerkinElmer For the Better Remarks If the file to be launched is in ChemBioFinder s standard search path only the actual file name CS_DATA is required Otherwise the complete file path c some long path CS_DATA MDB is necessary OPENDB example This example uses the OPENDB command to assign a new data source to the current form OPENDB c data mydb mdb Variable commands SETVAL v text READVAL v filename WRITEVAL v filename INPUT v prompt PASSWORD v default GETDATA v box PUTDATA box text FROM_SMILES str TO_SMILES v APPEND ON OFF APPENDVAL v text INCREMENT v DECREMENT v LET v vop v SUBSTR v lt str gt lt from gt lt to gt CAL h
191. ent list is indi cated with a frame around the colored box Chapter 8 Queries 125 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 Queries Ful Liss 1 B Q1 16 555 query 5 Q2 24 Molweight E Q4 5 Common E Qs 1 555 query Database Queries Favorites Figure 8 24 The Queries tree 1 Database full list 2 Current List marked with a frame 3 Search over Current list query child list To restore a query Double click a query O Tip Double clicking the root item Full List has the same effect as choosing Retrieve All from the Search menu The Queries context menu When you right click on a query you display a menu with commands to manage the query repeat the search using the selected query This is the same as double clicking on the query Chapter 8 Queries 126 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 merge the hits of the selected query with the current list See Restoring and merging Restore List hit lists on page 130 for details apply the query s color to a plot of the intersection of the Color On selected query with the cur Plot rent list This is the same as single click on the query choose a different query icon i Change color from the color picker i Color dialog box modify the query and or rerun it Restore Query goes to Restore Query mode and displays the Query structure You ma
192. ents are present or quantitative determining how much of each are present Chapter 10 Chemical Properties 147 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 This is the sum of the masses of the individual isotopes in the molecule For example the exact mass of water con taining two hydrogen 1 1H and one oxygen 16 160 is 1 0078 1 0078 15 9994 18 0106 The exact mass of heavy water containing two hydrogen 2 deuterium or 2H and one oxygen 16 160 is 2 014 2 014 15 9994 20 027 Formal Charge This is the charge assigned to an atom in a molecule assuming that electrons ina chemical bond are shared equally between atoms regardless of relative electronegativity The formal charge of any atom in a molecule can be calculated using the formula FC V N B 2 Where V is the number of valence electrons of the atom in isolation atom in ground state N is the number of non bonding electrons on this atom in the molecule and B is the total number of electrons shared in covalent bonds with other atoms in the molecule Gibbs Free Energy Reported in KJ mole Gibbs free energy is defined as G p T U pV TS which is same as G p T H TS Where U is the internal energy SI unit Joule pis pressure SI unit Pascal Vis volume SI unit m3 Tis the temperature SI unit Kelvin S is the entropy SI unit joule per Kelvin H is the enthalpy SI unit Joule f Note Hand
193. ents of a data box into a user variable GETDATA v box The GETDATA command has the following arguments User variable to which the variable 4 E text is assigned Box identifier indicating the source of the text box Remarks GETDATA accepts only boxes that contain text or data that can be represented as text including numbers formulas or dates You cannot GETDATA from a data box containing a structure or a picture If variable is omitted the text will be assigned to V1 CAL commands PUTDATA syntax Copies the contents of a user variable to a data box PUTDATA box text The PUTDATA command has the following arguments Chapter 20 CAL Commands 286 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 Box identifier indicating the destination of the text String containing the text to store Remarks If PUTDATA attempts to store text in a data box that contains a non text data type such as a number date or for mula the text will automatically be converted to the correct type CAL commands APPEND syntax Determines whether data in a user variableuser_variable_definition is kept if other data is being moved there APPEND value The APPEND command has the following argument Value describing whether new data should be added to the end of existing data or whether it should overwrite the existing data Settings The settings for value are New data is added to the end of existi
194. er However it will not be hit by the query A4X3 even though it has four atoms that match A and three atoms that match X This table shows query examples compounds with 6 carbons and 6 hydrogen atoms plus any number of other ele ments compounds with 6 carbons and 6 hydrogen atoms and no other elements compounds with 6 carbons no nitrogens plus any number of other elements compounds with 6 carbons and one to three nitrogen atoms plus any number of other elements Formula queries consist of element symbols and element counts or ranges The following rules apply Symbols may be one or two letters Symbols may be in upper or lower case if there are ambiguities the program resolves them according to rules described in Formula Input Rules on page 239 Capitalize the symbols properly and insert spaces between elements Use the Periodic Table to enter formulas For more information see Periodic table on page 208 and Formula Input Rules on page 239 Element counts are single integers or ranges two integers separated by a hyphen If a count is omitted it is assumed to be 1 If the formula query is preceded by for example C6H6 then the search requires an exact formula match con taining no elements other than those indicated If there is no then the search is a partial match other elements may be present in the hits Symbols may be repeated For example CH3CH3 is interpreted as C2H6 f No
195. er words an atom labeled R in the query must find a matching atom labeled R in the target to produce a hit If the stereochemistry of the query is unspecified it will only hit targets that do not specify stereochemistry The only variable in an exact match search is whether or not it is tautomerically flex ible The Details tab in the Preferences dialog box is unavailable for Exact searches Similarity searches A Similarity search finds targets that look like the query Similarity searches are by their nature fuzzy What looks like means is obviously subject to interpretation and depends on the application In medicinal applications the drug absorption properties are relevant In a toxicological context the metabolism is of interest For database queries the similarity in functional groups is what is measured A quantitative measure of similarity called the Tanimoto algo rithm is calculated For more information see Similarity Rules on page 241 Similarity searches may be either full or substructure In a substructure similarity search there is no penalty if the tar get contains extra non similar aspects In a Full Structure similarity search the results are guaranteed to include all hits you would obtain from a full structure search with the same query Usually they include additional hits For this reason similarity searches are useful if you have a general idea of the types of compounds you are looking for bu
196. erical searching You can perform range searches in ChemBioFinder numeric fields For example to search in the CS_Demo Data base for compounds with molecular weights between 90 and 100 Switch to Form View if you are not already in it Goto Search gt Enter Query The form is cleared so that you can enter a new query Click in the Molecular Weight box and type 90 100 Press ENTER You get all records with molecular weights between 90 and 100 ao A OO N gt Go to View gt Data Table gt In Current Window The Table view appears f Note A molecular weight query is a decimal value or range The precision of the search depends on the number of significant digits entered For more information on molecular weight searching see Numeric searches on page 98 Substructure searching To search for a substructure 1 Goto Search gt Enter Query The form is cleared to allow you to enter your search terms 2 Double click in the Structure box A blue box is displayed around the Structure box and the ChemBioDraw control appears 3 Draw benzene To set the correct options for a substructure search 1 Select the Search gt Substructure menu option if it is not already selected 2 Deselect the Search gt Similarity menu option if it is selected 3 Click Search or go to Search gt Find ChemBioFinder 13 0 begins searching The progress of the search is indicated by counters in the status bar at the bot tom of the window Wh
197. erkinElmer For the Better ChemBioFinder 13 0 Distances are established along each line proportional to the reciprocal of the square root of on either side of the center of mass The locus of these distances forms an ellipsoidal surface The principal moments are associated with the principal axes of the ellipsoid If all three moments are equal the molecule is considered to be a symmetrical top If no moments are equal the molecule is considered to be an unsymmetrical top The eccentricity of an atom is the largest value in its row or column of the distance matrix and represents how far away from the molecular center it resides The diameter D is the maximum such value for all atoms and is held by the most outlying atom s Examples Dia meter of methane 0 ethane 1 propane 2 n butane 3 The radius R is the minimum such value and is held by the most central atom s Examples Radius of methane 0 ethane 1 propane 1 n butane 2 Shape Attribute The shape attribute kappa measures the branching of a molecule and is scaled so as to fall between the minimum and maximum values possible for the given order The first order shape attribute counts the number of one bond paths The second order attribute counts the number of two bond paths and so on The first three orders 1 3 are available Shape Coefficient The shape coefficient is given by I D R IR Where the diameter D is the maximum such val
198. ernately you can make all of your filter adjustments without changing the scale then select Rescale to All Points on the BioViz context menu Zoom The BioViz zoom feature is a toggle activated from the BioViz context menu To expand a portion of a BioViz plot 1 Select Zoom on Drag from the BioViz context menu A check mark appears next to the command when it is selected To deselect click the command again 2 Drag over a section of the plot When you release the mouse button the scale expands to show the points selected While the initial view is the area you selected you may use the scroll bars to view any part of the plot at the expanded scale Clicking either the X or Y Zoom Button will return that axis to the original scale while leaving the other axis at the expanded scale Clicking Unzoom on the BioViz context menu will restore the original scale to both axes simul taneously You may repeat zoom that is zoom in on an area in an already expanded scale If you have performed multiple zooms the Zoom button acts as Undo control reversing one step at a time Statistical analysis You can perform statistical analyses on plots using the Analysis tab on the BioViz Plot Properties dialog box The tab is available only for two variable plots The following statistical parameters may be calculated Minima and maxima of the X or Y variable Mean or median of the X or Y variable Standard deviation of the X or Y v
199. ery mode Automatic frame label updates The label of a framed box is updated if you change the field it displays Resizable dialog boxes The Box Properties Plot Properties Data Import and Data Export dialog boxes and the script editor can be resized allowing you to see more in text windows tree controls and so forth The new position and size is applicable only to the current ChemBioFinder 13 0 session Opening ChemBioFinder 13 0 In default mode ChemBioFinder 13 0 opens with the ChemBioFinder startup dialog The various tabs in the dialog box lets you do the following From the New tab E Blank Form Open a blank form to create your own Database Connection Open a blank form and connect it to a database You can create the form manually or auto matically For more information see Connecting a database to a form on page 17 Database Wizard Helps you set up a database connection From the Existing tab Browse to an existing form in your file system From the Recent tab Open a form on the recently used file list You can choose to display hide the ChemBioFinder 13 0 startup dialog when ChemBioFinder 13 0 opens by doing the following 1 Go to File gt Preferences 2 Inthe Preferences dialog box click the General tab 3 Select or deselect Show startup dialog If you choose to hide the ChemBioFinder 13 0 startup dialog box ChemBioFinder 13 0 will open a new blank form by default when yo
200. es you can add data to your database This tutorial demonstrates the use of the ChemBioDraw control the default structure mode Before you begin to add structures check whether the structure mode is set appropriately To check the current setting 1 Right click on the Structure data box and click Properties 2 Inthe Box Style section of the Box Properties dialog box select ChemBioDraw style When you select ChemBioDraw style ChemBioFinder 13 0 defaults to the ChemBioDraw control This lets you edit structures in the Structure data box in ChemBioFinder 13 0 ChemBioFinder style opens ChemBioDraw in its own window for editing 3 To exit from the Form editor deselect the Layout tool Now you are ready to begin adding records to your database In the steps below we create records for benzene n pen tane and cyclohexane 1 Double click in the Structure box The ChemBioDraw toolbar appears O Tip With ChemBioDraw style selected you can also open ChemBioDraw in ts own window by right clicking in the structure box and selecting Edit gt Edit in ChemBioDraw 2 Select the benzene tool and draw benzene in the structure box 3 Click anywhere outside the Structure data box to finish editing the structure Benzene appears in the Structure Data box ChemBioFinder 13 0 calculates the molecular formula and assigns an ID number of 1 4 Click the MolName box and type Benzene 5 Click the Boiling Point box and type 80 1 6 Goto R
201. es dialog box Plotting a large dataset can be very slow As a safety precaution the default is set to 500 which means that only the first 500 points in the data set will be plotted On most computers this will take no more than a few seconds To plot a larger dataset reset this value as necessary 5 Click OK The Plot appears in a new window 6 Optional Click the Notes button to view additional information For example points will not be plotted if there are missing Y values This is reported in the Notes if any Tip To create a single variable scatter plot right click in a numerical field and select BioViz Plot gt ID Plot Chapter 3 Tutorials 26 of 342 ChemBioFinder 13 0 Perkin For the Better Histogram plots A histogram plot is a variation of a single variable plot where the X coordinate is the variable value and the Y coor dinate shows the count in each histogram bin To create a Histogram plot 1 Go to View gt ChemBioViz Plots gt New 2 Click the One Variable radio button in the Dimension box of the BioViz Plot Properties dialog box 3 Click the Histogram radio button in the Style box 4 Click either the Number or Size radio button in the Bins box and enter a value optional Number sets how many bars will appear in the plot Size sets the range of the values for each bar 5 Select any numerical field from the drop down menu for the X coordinate 6 Enter a name for the plot optional 7
202. eses where you know what you are aiming for but you do not know how to produce it In this exam ple we look for reactions that close a ring alpha to a carbonyl To perform a reaction product search 1 Go to Search gt Enter Query The form is cleared so that you can enter a new query 2 Double click on the Structure data box The ChemBioDraw toolbar appears 3 Draw the following E A Switch to any Selection tool Lasso or Marquee and select the single bond next to the double bond Right click and select Topology gt Ringfrom the context menu Select the remaining single bond NO oO Sf Right click and select Topology gt Ring Right click again and select Reaction Center gt Make Breakfrom the context menu The arrow at the left indicates that you are looking for this substructure as a product 8 Press ENTER The hit list appears An example search result is CI o o _ ON Br Br Figure 3 1 One of the product query hits Searching by reaction type In many cases you have some idea of both your starting materials and your products but are looking for some infor mation on how to get from one to the other For example to search for reactions that reduce a carbonyl to an alcohol 1 Goto Search gt Enter Query The form is cleared 2 Double click in the Structure box 3 Draw the following Chapter 3 Tutorials 24 of 342 pP PerkinE For the Better ChemBioFinder 13 0 O a gt y
203. ess our Technical Support in ChemBioFinder go to Online gt Browse CambridgeSoft Technical Support If you are unable to find a solution on the Web site follow these steps before you contact Technical Support 1 Check the system requirements for the software 2 Read Troubleshooting on page 2 and follow the possible resolution tactics outlined there 3 If all your attempts to resolve a problem fail contact Technical support Try to reproduce the problem before contacting us If you can reproduce the problem please record the exact steps Record the exact wording of any error messages that appear Record what you have tried to correct the problem Additional sources of ChemOffice information are ChemBioFinder 13 0 online Help The PerkinElmer Informatics Web site PerkinElmer Informatics Services Troubleshooting This section describes steps you can take that affect the overall performance of CS ChemBioOffice Applications as well as steps to follow if your computer crashes when using a CS software product Performance Below are some ways you can optimize the performance of ChemBioOffice Applications In the Performance tab in the System control panel allocate more processor time to the application Install more physical RAM The more you have the less ChemBioOffice Applications will have to access your hard disk to use Virtual Memory Increase the Virtual Memory VM Virtual memory extends RAM by allowi
204. eturn to or type CTRL W to return to ChemBioFinder 13 0 and insert the structure ture Chem BioFinder 13 0 mode Right click in the struc import a struc ture box and click Read Structure The Open dialog box appears ture Chem BioFinder 13 0 Browse to a structure file or Chem then click OK The file is BioDraw mode inserted into Chem BioFinder 13 0 7 Note See the ChemBioDraw User s Guide for information about using ChemBioDraw Committing the new data When you finish entering all of the data items do one of the following Click Commit on the Add Record Toolbar Click the Commit Changes icon on the Record Toolbar Goto Record gt Commit Changes Perform another action such as moving to another record or printing The new record is added to the database Chapter 6 Working with Data 78 of 342 ChemBioFinder 13 0 PerkinElme For the Better _ Note Selecting Commit Changes or moving to another record if you have two or more records saves the data to the database Do not use File gt Save clicking File gt Save saves changes to the form layout not changes to data in the database Duplicating records You can create a new record by modifying an existing one To duplicate a record Goto Record gt Duplicate Record You are in Add Mode and the form fills with data from the previously displayed record When you commit the changes you create a new record whose fields conta
205. ext Format toolbar Goto View gt Toolbars gt Text Format The Text Format toolbar appears f Note Text copied from a word processor such as Microsoft Word retains its styles when pasted into a Rich Text box The text format toolbar is active When you are editing a memo field in a rich text box In this case font changes apply only to the current selection within the text When you are editing in a regular data or structure box Font changes apply to the entire contents of the box When you are in form edit mode with the selector tool active and one or more boxes are selected Font changes apply to all selected boxes except frames around data boxes Customizing fonts All labels on ChemBioFinder 13 0 objects can be edited to your specifications You can edit any label s font font style size and color To set the font for a label 1 Click on the label to select it 2 Right click and select Properties 3 On the Box tab of the Box Properties dialog box click Font The Font dialog box appears 4 Set the text font style size and color The sample area previews the font 5 Click OK to commit the changes Chapter 4 Forms 44 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 _ Note To change the color of the atom labels in the structure box you must use the Periodic Table Periodic table on page 208 Customizing numbers Using the Box Properties dialog box you can specify how numeric data
206. f menus toolbars and the form window The central part of the form window contains the work space where you create a form enter query parameters and view query results The ChemBioFinder 13 0 UI is shown below Chapter 2 Getting Started 4 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 yew Jet Jem Becors Sgeti O Figure 2 1 The ChemBioFinder 13 0 user interface A Menu bar B Details window C Main form D Filters window E Output window F Total database size G Current list size H current record I BioViz window J Structure window K Explorer window The table given below describes the components of the ChemBioFinder 13 0 UI Displays data contained in one record of the database To keep the display from getting clut Main form a tered additional tabs may be added for less important data A viewing area in a form linked to a field in the Data box database associated with that form and dis playing data from that field See also Control Chapter 2 Getting Started 5 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 box Picture box Profile box Subform Text box An enclosure around a data box or group of Frame a boxes containing a label Framed data box A data box surrounded by a labeled frame Displays a graphic Picture boxes may be either Fixed that is they remain the same for E all records in the database and are linked to a Picture box ts
207. f those found in the Preferences dialog box and several that cannot be accessed in any other way See the online help for a complete listing of parameters that can be SET CLEAN will atte mpt to standardize the bond lengths and angles of the current molecule It is the same as opening the molecule in ChemDraw and selecting the Clean Up Structure command The arguments are optional HELP displays a list of all valid CAL commands The valid parameter types are listed for each command as is a brief description SET GET functions store data in the Windows registry under HKEY_CURRENT_USER Sof tware C ambridgeSoft ChemFinder 13 0 General Options SOUND plays a wav file you specify SYSMETRIC retrieves the specified system metric into a variable The table below shows examples of General Commands Chapter 20 CAL Commands 264 of 342 ChemBioFinder 13 0 MSG Click OK to con tinue display message wait for click FONT Times 12 1 255 0 change font to red 12 point Times bold 0 place the value of item GET V1 4 5 number 5 in section 4 into the variable V1 SOUND play the sound in the files beep wav beep wav CAL commands MSG syntax Displays a message in a dialog box and waits for the user to dismiss the dialog box MSG message The MSG command has the following argument String displayed as the mes message q k sage in the dialog box CAL commands FONT syntax Changes the current font size style and colo
208. for information on using the Automation interface Scripting CAL ChemBioFinder 13 0 is equipped with its own scripting language the ChemBioFinder Automation Language CAL CAL is used to operate the program from the keyboard or to create custom scripts for automating simple operations such as switching between forms or sending data to Microsoft Excel Chapter 16 Customizing ChemBioFinder 13 0 210 of 342 ChemBioFinder 13 0 PerkinElmer For the Better CAL scripts are stored in text files with their pathnames stored in forms In ChemBioFinder 13 0 you have the option of storing scripts directly in form files Scripts created in ChemBioFinder 13 0 are stored internally by default When you open a form which references external script files you will be prompted to store the script internally If you choose to convert the external script files to internal the scripts will be saved when the form is saved and the original script files may be deleted Scripts originally saved as internal may be also be saved externally Tip You can save the form with a different name and the original will remain untouched in which case deleting the script files would not be a good idea If you choose to leave the form unmodified the alert will continue to show up every time the form is opened To suppress the prompt 1 Go to File gt Preferences 2 Click the General tab 3 Deselect the Check for external scripts check box then click OK
209. form The Menu Command File Open opens the second form or switches to it if it is already open Chapter 20 CAL Commands 245 of 342 ChemBioFinder 13 0 PerkinElmer For the Better Finally the Menu Command Search Enter Query enters search mode the PUTDATA command enters the search string generated earlier in the script and the Menu Command Search Find executes the search append offsetval 1 append ongetdata 1 link fieldappend offfile open d chemfndr otherform cfxsearch enter queryputdata link field vlsearch find Example 3 Saving Compounds Example This example uses the LOOP ENDLOOP commands and the Menu Command Record Next to step through each record in the current list For each record it builds a unique file path based on the current INDEX using SETVAL and APPENDVAL commands Finally it saves each compound to disk with the WRITEMOL command Since the file path ends in cdx this script saves all of the compounds in ChemDraw format append offloopsetval 1 c mydir appendval 1 Sindexappendval 1 cdxwritemol vlrec nextendloop Example 4 GOTO Example This example allows the user to batch enter several new compounds and input one field for each It starts with a MSG command to tell the user what to do Then it has a line starting with a colon that serves as a label to start the loop The INPUT command gets the name of the new entry from the user The IF command tests to see if the user entered a blank string and EXITs th
210. from 0 to 16 or press the up and down arrows to change the current value by one unit in the Recent file list size option on the General preferences tab Changing options with the view menu Several structure display options can be set from the View menu including Atom Numbers Reaction Centers Ster eochemistry and Atom Maps in reactions To display reaction centers Go to View gt Structure gt Reaction Centers 2Explorer window is available in Pro and Ultra versions but not in Standard version Chapter 16 Customizing ChemBioFinder 13 0 204 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 Atom to Atom Map Figure 16 2 Viewing reaction centers With reaction centers shown any bond that changes in the course of a reaction is colored Additionally any atoms that participate in reaction centers are circled if none of their adjacent bonds participate in the reaction center SH H H af O Br E a CH H3C SH Figure 16 3 Visualization of reaction centers To display atom to atom maps Goto View gt Structure gt Atom to Atom Map With atom to atom maps shown equivalent atoms in reactants and products are colored the same o CH3 o c N a Ei HA Sy Ho AS He NS Be anne a 4 Cy gt S O gd 1 H3 Chapter 16 Customizing ChemBioFinder 13 0 205 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 Figure 16 4 Atom to atom maps These two preferences affect only the di
211. functions access to databases OLE Automation file I O program flow control data structures object oriented and struc tured programming and all other features offered by a modern language Python can be developed interactively in the ChemBioFinder 13 0 Script Editor a development environment similar to IDLE PythonWin and others This environment combines line by line execution with program construction con venient for development and debugging Python scripts can operate ActiveX controls that is also available in ChemBioFinder 13 0 form boxes Python communicates with ChemBioFinder 13 0 via OLE Automation allowing it to access documents record sets data form boxes structures CAL commands Chapter 16 Customizing ChemBioFinder 13 0 214 of 342 ChemBioFinder 13 0 PerkinElme For the Better Python in ChemBioFinder 13 0 is integrated with ChemScript the chemical structure processing language from CambridgeSoft ChemScript is an extension to Python which allows carrying out detailed analysis or manipulation of molecules reactions and models Creating a script A ChemBioFinder 13 0 form can contain a collection of scripts both CAL and Python Each is connected to the form in one of three ways depending on how the script will be executed To create a script first decide how it will be called To create a script activated by a button 1 Create a button on the form 2 Right click the button and click the Edit scrip
212. g in BioViz Clustering in ChemBioFinder BioViz is a method for analyzing biological and chemical data It is smoothly integrated with ChemBioFinder databases and forms and presents to the user visually appealing highly interactive display Features One click clustering over current hit list on any numeric field or structure box Multi dimensional clustering via compound profile allows detailed specification of fields and conditions Fast new clustering and projection algorithms from the core chemistry group Resizable zoomable two pane display showing dendrogram and cluster visualization Drop down control panels for display and behavior customization Unique cluster window allows visualization by adjustable partitioning of dendrogram tree Dendrogram tree may be oriented in any direction Sliding adjustment varies dendrogram node spacing between linear and log scale Shaded coloring may be applied to clusters based on value of a selected field User choice of text labels may be applied independently in each pane Tooltips provide full information about nodes and clusters Intuitive highlight and selection mechanisms are synchronized between the two panes Selected set of nodes or clusters can be converted with one click to ChemBioFinder hitlist Pop up structure window displays structures and data of highlighted nodes Structure clustering based on Tanimoto similarity between structure screens Working with Clustering This se
213. g objects You can line up objects relative to each other by aligning them and space objects at an equal distance apart by dis tributing them 7 Note In framed dialog boxes the inner data box is aligned not the frame To line up objects on a form 1 Press SHIFT and click the objects to align 2 Use the Edit gt Align submenu to take the appropriate action top edge of the first object you place on the form middle of an object ee Vertical Center in a vertical line bottom edge of an object left edge of an object middle of an object Horizontal Center in a horizontal line right edge of an object The form objects line up according to your choice To space objects on a form evenly 1 Press SHIFT and click the objects to distribute 2 Use the Edit gt Distribute submenu to take the appropriate action Chapter 4 Forms 50 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 outer boxes of the Vertically form left and right of the form Horizontally The form objects are spaced according to your choice Changing form layout Changing a form layout is the same as automatically creating a new form When you have created a new form you can use it to replace the old form or save it as an alternate form Creating forms automatically on page 32 for details Securing forms You can control the options available to users of your forms by setting the security options Y
214. get must have double Double bond stereo dictated by geometry target must have double Double Either bond any stereochemistry ok target must have triple bond Triple here Substituents In ChemBioFinder a substituent is defined as a non hydrogen atom connected by a bond of any order For example a carbonyl oxygen is a substituent of the carbonyl carbon Chapter 17 Structural Query Features 224 of 342 ChemBioFinder 13 0 PerkinElmer For the Better All unfilled valences in the query may be filled by hydrogen atoms or by non hydrogen substituents The normal valence of an atom is determined from data in the Periodic Table window For example carbon has a valence of 4 while sulfur has valences of 2 4 and 6 Any explicit charges radicals or query properties modify the normal valence For example a carbocation has a valence of 3 Hydrogen atoms in the query may match non hydrogen substituents in the target if the hydrogen in the query is implicit on an unlabeled carbon atom or heteroatom This is the default setting Hydrogen atoms in the query must match hydrogens in the target when the query hydrogen is at the end of an explicit bond The matched hydrogen in the target may be implicit in an unlabeled carbon atom The following query with explicit hydrogens H O H N Finds any of HN y C O om H OH NH2 H Ta Rr Does not find any of OH NH OH E E z o E Chapter 17 Structural Query Features 225
215. h They generally serve to broaden or narrow the scope of the query Special bond types The table below describes the special bond types that ChemBioFinder allows Chapter 17 Structural Query Features 236 of 342 ChemBioFinder 13 0 target bond must be aromatic Aromatic as defined by the H ckel 4n 2 target can have any bond type target must have a single bond l or a double bond here target must have a double bond D A or an aromatic bond here SIA target must have a single bond or an aromatic bond here Topology If Ring or Chain is chosen the target bond must or must not be in a ring respectively Reaction center pP PerkinElmer For the Better The reaction center refers to those bonds that are directly affected by a reaction This property allows you to specify just how a given bond is affected target must have a bond here but the bond can par Unspecified A r ticipate in the reaction in any fashion or not at all target must have a bond here that directly par Center ticipates in the reaction in some way target must have a bond Make Break here that is either made if in a product or broken if in Chapter 17 Structural Query Features 237 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 re target must have a bond here whose bond order changes over the course of the reaction but is not made or broken target must have a bond here that is either m
216. h BioFi 13 I ChemBioFinder 13 0 PerkinElmer For the Better To change the field associated with a profile 1 On the Profile tab click one of the profiles to select it 2 Click the Field tab Change the Source with the drop down menu Change any of the other variables as required 3 Click the Cost Profile tab and select a new profile f Note You must select a new profile when you change the source field If you forget you will be prompted with an error message 4 Click OK The cost profile is displayed and may be edited 5 Click OK to complete the change To change a cost profile 1 On the Profile tab click one of the profiles to select it then click the Cost Profile tab Cost Profile high pites g ideal wiwe Pai d Figure 9 3 Cost profile showing the drag points and ideal value line 2 To change an inflection point drag it to a new location As you drag the X and Y coordinates of the point are displayed on the grid Tip You cannot drag past a neighboring point 3 To add a new inflection point right click on the line segment where you want the new point and click the Add point here context menu command 4 To delete a point right click on the point and click Remove point in the context menu 5 To change the ideal value drag the pink dashed line on the grid to a new location 6 To choose a different template right click anywhere in the editor window click the Choose context menu com man
217. h mode Tautomeric searches In a tautomeric search the location of single and double bonds may vary from query to target A hit occurs if in addi tion to the atom types matching the target possesses a tautomeric form whose bond orders match the query s Which tautomers are recognized is under some degree of control Tautomers of the form XV ZO e gt X YZ Figure 8 4 Tautomeric structure are always recognized when at least one of X and Z is not carbon The lone pair may include a migrating proton It is also possible to include tautomers in which X and Z may both be carbon The choice must be made at the time the database is created or upgraded because it affects how structures are stored Chapter 8 Queries 103 of 342 ChemBioFinder 13 0 PerkinEl For the Better Mesomers resonance structures are also picked up in tautomeric searches Tautomerism involving formation or cleavage of sigma bonds is not currently supported The principal categories are ring chain tautomerism as in the open vs cyclic forms of sugars and valence tautomerism Tautomeric searching is slower than non tautomeric but is the mode of choice when you think the target might have a slightly different layout of double bonds _ Note If the database has not been indexed the tautomer searches may be slow Stereochemistry You can specify whether or not you want a structure search to consider stereochemistry Given a structure with one or more stereocenters
218. he International Union of Pure and Applied Chemistry InChI Material in ChemBioFinder 13 0 is IUPAC 2008 All three commands place the data on the Clipboard allowing it to be copied into other applications To copy a structure as a name or InChI string 1 Click in the Structure box to select it 2 Right click and click Copy As gt Name or Copy As gt InChl submenu command 3 Paste the data into the other application using CTRL V orthe Edit gt Paste menu command Exporting an ASCII file Delimited text files may be the most universal file format used by non chemical applications In a delimited text file each line represents a record and all fields in the record are listed in order from left to right separated by some char acter such as a tab or a comma Individual records are separated by carriage returns ChemBioFinder 13 0 allows you to include a header line at the start of the file that lists the names of all of the fields It also allows you to append to or overwrite existing text files You can import a delimited text file saved by ChemBioFinder 13 0 into many other applications including spread sheets and external database systems Choose the csv file format to export to spreadsheets and the txt format for general export _ Note In delimited text files structures are automatically exported as SMILES strings Exporting a Word file The export to MS Word option is similar to the other export options however a cou
219. he form which contains non structural data The SQL query is not associated with the box in which it is entered Query procedures Searching includes the following steps Setting the search type preferences Structure searches only Entering the query in the form Submitting the query to the search engine To perform a search use the Search menu or the corresponding tools in the Search toolbar Figure 8 19 The Search toolbar 1 Enter Query 2 Find 3 Retrieve All 4 Find Current Molecule 5 Previous Query 6 Save List 7 Restore List 8 Restore Previous List 9 Find List The following procedures describe searching with the Search menu You may use the Search toolbar instead for most procedures Setting search type preferences You can set preferences for the type of structure for which you want to search Chapter 8 Queries 111 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 To set Search Type preferences 1 Select Preferences from the Search menu The Preferences dialog box appears with the Search Type tab dis played Preferences Display Color Search Type Details Tuning General Ad C Subsimolud C Tautomeric A C Ful Structure Nontautomeric A C Normal All C Exact E C Similar E I Search over current list Defaults Figure 8 20 Search type preferences 2 Take the appropriate action find structures containing a common structural com Sub
220. he link ing field changes in the main form the subform only displays those records from its table which have the same value in the linking field You can also use subforms to display data from different databases In this tutorial you open the CS_Demo database and display the MolTable in the main form Then you display the Syn onyms table of the CS_Demo database in a subform By defining the MOL_ID field as the linking field you display the two sets of data relationally Creating a subform To create a subform 1 Open your ChemBioFinder 13 0 form tut1 cfx Opening this form connects you to the CS_Demo mdb database Chapter 3 Tutorials 30 of 342 ChemBioFinder 13 0 PerkinElme For the Better 2 Make some space on the right side of the form by rearranging the data boxes and making them smaller 3 Click the Subform tool 4 Inthe form drag to create a large subform Tip If you cannot make room on the right side of your form you can put the subform at the bottom of the form When you release the mouse button the Subform Properties dialog box appears 5 Click the Form tab then select Synonyms from the hierarchical tree display 6 Click the Generate form check box then click Style 7 Select the Plain form deselect all of the fields to be included except Synonym and click OK You are returned to the Subform Properties dialog box 8 Click the Subform tab 9 SYN_ID already appears as the default in the Link to SYNON
221. he query has not been renamed or marked for saving Saving query lists on page 196 To perform list operations begin by performing a simple search For example you can search the database for all com pounds that have a molecular weight less than 250g mol 1 Click the Enter Query icon on the Search toolbar or menu The form goes into query mode Chapter 15 BioSAR 193 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 2 Enter lt 250 in the MolWeight field of the query form and click Search A query labeled Q1 appears as a child of the Full List BB Queries Wi Full List fA Q1 24715 Molweight lt 250 Database Queries Favorites BioSAR ee Changing the query name If you want you can change the name of a query to one that is more descriptive Renaming a query also ensures that the query is saved with the form Depending on your Preferences settings queries not renamed may be automatically discarded when you save the form To rename a query 1 Point to the query and right click The context menu is displayed 2 Click Rename on the context menu The name Q1 is highlighted 3 Entera new name and press ENTER Changing the display color The color of the box next to the query name is the same color to be used to display the points should you plot the results You may change any query to any color so that the plots look the way you want To change the display color 1 Point to the query
222. he same database as the main form To use a different database as the data source for the subform 1 Click Open Database The Open dialog box appears 2 Choose a database and click Open 3 Select the table to be linked in this case Synonyms 4 Click the Form tab Select the Generate form check box If you want to set the style click Style See Creating forms automatically on page 32 for details on Form style 5 Click the Subform tab The tab should contain reasonable data Link To SYNONYMS subform SYN_ID Title Synonyms based on the choices made so far 6 Choose Mol_ID from the Link from MOLTABLE main form drop down menu 7 Note To use the subform relationally to the main form the two forms must have one field in common This Linking Field must share the same data type text integer real as a field in the main form The fields do not need to have the same name 7 Modify box properties as desired You may want to change the box title font or presence of scrollbars 8 Click OK The new subform appears showing one synonym 9 Optional double click in the subform to switch it to table view The Subform is connected to the database you chose In this example when a record is retrieved in the main form its Molname is used to search the Synonym field of the Synonyms table of CS_ Demo The subform displays the hits from this search Subform generator Automatic subform generation is part of automatic form gener
223. he tools you need to query the database and work with the hit lists that the query produces Figure 2 3 The Search Toolbar 1 Enter Query 2 Find 3 Retrieve All 4 Find Current Molecule 5 Previous Query 6 Save List 7 Restore List 8 Restore Previous List 9 Find List Record toolbar The Record Toolbar contains the tools you need to browse a database or hit list It also has tools for adding deleting and changing records Chapter 2 Getting Started 9 of 342 ChemBioFinder 13 0 PerkinElmer For the Better Figure 2 4 The Record Toolbar 1 First Record 2 Previous Record 3 Go to Record 4 Next Record 5 Last Rec ord 6 Add a Record 7 Undo Changes 8 Commit Changes 9 Delete Record 10 Omit Record Text format toolbar The Text Format Toolbar contains standard text formatting tools that you can use when entering or editing information in data and text fields Text Format Toolbar Arial 10 BZ 1 E ES x w gt 4 5 s D co Figure 2 5 The Text Toolbar 1 Font 2 Point size 3 Bold 4 Italics 5 Underline 6 Subscript 7 Superscript 8 Color 9 Left alignment 10 Center alignment 11 Right alignment 12 Bullets The status bar While you move among records counters in the lower right corner of the window change to indicate the current record the current list size and the total size of the database The lower left corner of the window displays
224. he type of import Overwrite Append or Merge If you have selected Merge click the Merge tab and choose the matching field match options and logging options 6 Select the fields to be imported with the check boxes Optional Double click the field name to change the name of the field field type and width in the Data Field Import dialog box Optional Click the Logging tab to change details of the log file Optional Click the Form Style tab to select the style of boxes that will be created for new fields Optional Click the Advanced tab to set the Advanced options Import only part of a file by setting the starting point You may indicate a starting point by line number byte number or record number Also select the version of the ChemBioFinder database to be created Versions back to 7 0 are supported In addition import structures only by selecting the check box and enter duplicate reagent values by checking the Store redundant reagents check box _ Note In SD and RD files reagents and catalysts are specified in each record ChemBioFinder 13 0 stores them in subtables Thus ifthe same reagent appears in more than one record ChemBioFinder 13 0 only needs to store it once You can over ride this default with the check box 7 When you have finished selecting your options click Import The structures are imported to the specified data base Structure and reaction ChemBioFinder 13 0 lets you import Structure Data files SDFile
225. hemBioDraw format you can open them directly from ChemBioFinder 13 0 without having to import or redraw them To read a structure from a file into a structure box 1 Right click in the structure box and click the Read Structure context menu command The Open dialog box appears 2 Choose the file to read 3 Click Open The structure is read into the structure box The database is not affected by this operation until you choose Commit Changes or move off of the record Drag and drop You can drag certain types of files from the Windows Explorer or Desktop onto ChemBioFinder 13 0 The following table summarizes the ChemBioFinder 13 0 Drag and Drop options Must be dropped Structure into a structure box Must be dropped Graphic into a picture box Does not need to be dropped onto an existing form Multiple files can be dropped at once but you cannot mix types as defined in column 1 of the table If several struc ture or graphic files are dropped at once they are loaded into successive ChemBioFinder 13 0 records If only one is dropped you are asked if you wish to append the structure graphic in a new record or overwrite the existing record If more than five structures graphics are dropped an alert will ask you if you wish to proceed Dropping one or more form files opens the forms without affecting the current form and database Chapter 7 Importing and Exporting Data 91 of 342 ChemBioFinder 13 0 PerkinElme
226. hemBioFinder 13 0 PerkinEl For the Better EXEC to start an application and possibly pass information on the command line DDE to communicate using Dynamic Data Exchange with a DDE ready application Using EXEC is straightforward but limited You can start all Windows applications by this command Most can be passed a filename on the command line such that the specified file is opened or printed on startup A few appli cations can accept more detailed instructions Consult the application s manual for information about how it can be operated using the command line If you have Visual Basic or similar programming language you can extend the power of EXEC You can write an appli cation using the advanced features of Visual Basic and then call the application from within ChemBioFinder 13 0 using the EXEC command Using DDE is more complicated You can operate most Microsoft Office components and many other programs to var ying extents with DDE For example practically every command on the Excel menu can be executed by DDE The syntax is rather difficult but can usually be worked out by experimenting and consulting ChemBioFinder 13 0 help An example is given below DDE is the most direct way of using Excel to view data from ChemBioFinder 13 0 To use MS Excel to view ChemBioFinder 13 0 data 1 Start MS Excel You can start it manually using a CAL script or by starting the application in Windows 2 In ChemBioFinder 13 0 obtain th
227. hemistry Missing Stereochemistry Finds structures with atoms capable of tetrahedral or double bond stereochemistry but drawn as unspecified Charged Finds one or more atoms with a charge Radical Finds one or more atoms with a radical With Isotopic Labels Retrieves records containing a structure with an atom that either has a mass number or has an Isotopic Abundance attribute Query Structures Locates structures with any generic variability such as atom types R A M Q X Alkyl Aliphatic EDG EWG bond types single or double etc variable charge element lists C N O ring bond count etc 3D Locates structures that could be targets in a 3D search These are structures scaled in Angstroms and having Z coordinates Both conditions must be met Structures that meet only one of these conditions can be found by using the Check structures search _ Note The 3D feature is available in both Pro and Ultra 13 0 but notin Standard version Chapter 8 Queries 121 of 342 ChemBioFinder 13 0 I PerkinE For the Better Classes Provides these search options selectable from a submenu Hydrocarbons Finds structures with Carbon and Hydrogen only If there are more than one fragments they must all be hydrocarbons Aliphatics Finds structures with a carbon carbon bond or methane and non aromatic rings Alicyclics Finds structures having a carbocyclic ring that is not aromatic or antiaromatic Aromatics 4n 2
228. her the tables you want to attach are from a file based Access FoxPro dBASE or non file based Oracle database system Attaching files from a file based database To attach a file based database table 1 Right click in the form and click Properties 2 Click the Table tab and then click Attach Table The Attach Table dialog box appears 3 Click Open MS Access Database The Open dialog box appears _ Note The list of file types available in the Attach Table Open dialog box varies from one computer to another The files for which you have drivers installed shown For example if Paradox is not installed you may not have Paradox drivers on your system or in the drop down list lf the database type you wish to access is not on the list it may not be a file based system and you need to connect using ODBC For detailed instructions see Attaching files from a non file based database on page 71 4 Choose the database to access then click OK 5 Inthe tree diagram click the table you want to attach then click OK The newly attached table appears in the tree diagram in the Form Properties dialog box 6 Click OK Attaching files from a non file based database If the database you want to attach is not file based such as Oracle you can attach it using Microsoft s Open Data base Connectivity ODBC Chapter 5 Databases 71 of 342 BioFi 13 I ChemBioFinder 13 0 PerkinElmer For the Better To attach a non file based database
229. hydrogens This atom property may have either of two values Allowed default or Not Allowed If implicit hydrogens are Not Allowed the atom must be fully substituted in the target This property is only meaningful in a substructure search f Note This atom property does not affect the display of implicit hydrogens only their presence in a search For more information about displaying implicit hydrogens see Setting preferences on page 200 Unsaturation Sometimes it is useful to specify that an atom must or must not be attached to unsaturated aromatic double or triple bonds ChemBioFinder allows searches for atoms whose unsaturation Must Be Absent all bonds to the atom are sin gle It also allows searches for atoms with at least one multiple double triple or aromatic bond The default value Undefined finds targets without regard to the hybridization of the atom This property is only meaningful in a substructure search With a substructure search the query Chapter 17 Structural Query Features 235 of 342 ChemBioFinder 13 0 J a PerkinElmer For the Better 0 we l OH Figure 17 6 1 This atom is marked with the atom property Unsaturation must be present Finds any of U OH y Does not find any of da OH T 4 O 0 x o o E Bond properties ChemBioFinder allows special properties to be assigned to bonds in a query These properties usually will only be meaningful during a searc
230. i 13 I ChemBioFinder 13 0 PerkinEl For the Better changing colors 167 changing the display 167 charges and radicals 226 charges in queries 226 check valences 203 checkboxes 39 Chem3D viewing models 82 ChemDraw editing structures 80 ChemDraw format viewing in 41 ChemFinder opening options 203 toolbars 8 Ul 4 chemical name 147 cleaning structures 80 clearing forms 77 117 cluster count 147 color preferences 202 color setting 46 combined searches see searching combined 23 combined searches see searching combined 110 commands add new record 77 bring to front 49 commit changes 78 80 81 current record 8 Chapter 22 Index 306 of 342 ChemBioFinder 13 0 current Record data source delete record enter query Find find current molecule Find List find text first record go to record Intersect with current list last record next record previous record read structure redo replace current list restore list save list Save Structure search over list send to back undo changes commit changes command committing changes vs saving committing new data communicating with other applications using DDE communicating with other applications using OLE automation communicating with other applications using scripts Chapter 22 Index pP PerkinElme For the Better 10 59 71 83 117 118 120 100 73 64 64 131 64 64 64 91 83 131 130 130 93 25 49 79 78 80 81
231. ick the Commit Changes icon Move to a different record _ Note Moving to a different record always commits changes first Chapter 6 Working with Data 79 of 342 ChemBioFinder 13 0 PerkinElme For the Better Editing structures You can edit structures by using the ChemBioDraw drawing tools You can also neaten the appearance of a structure by cleaning it up The Clean Structure command is used to neaten the appearance of molecules by regularizing bond lengths and angles Since the degree of change required cannot be determined a priori the Clean Structure command begins gently You may need to repeat the command to get the changes you wish For more details about how the command works see Structure Clean Up in Chapter 4 Advanced Drawing Techniques of the ChemBioDraw User s Guide Before committing a data entry you can revert to the previous unmodified record by choosing Undo Changes from the Record menu To edit structural data 1 Do one of the following In ChemBioDraw mode Double click the structure box The ChemBioDraw Control appears In ChemBioFinder 13 0 mode Double click the structure box ChemBioDraw opens and the structure appears in the ChemBioFinder 13 0 window In either mode Right click in the structure box and click Edit in ChemBioDraw ChemBioDraw opens and the structure appears in the ChemBioFinder 13 0 window 2 Edit the structure 3 Click in the ChemBioFinder 13 0 form or close th
232. ick the subform box to activate it 2 Goto View gt Subform Plot View The BioViz Plot Properties dialog box appears 3 Set up the plot See Creating a plot on page 161 for more information The plot appears in the subform data box Chapter 11 Relational Data and Subforms 159 of 342 ChemBioFinder 13 0 I PerkinElmer For the Better 4 Note For 2 D plots both numeric fields must be in the data table associated with the subform data box Subform plots have less functionality than regular BioViz plots While mousing over a point will highlight it selection filtering and coloring are disabled Since selection is disabled subform plots are always in Zoom on drag mode Use Control W to toggle between the form table and plot views The Switch to Table tool only toggles between form and table as does double clicking in the subform Tip The subform remains selected until you click the main form so you can only browse in the subform If a plot is displayed browsing does nothing O If you toggle the main form to table view when a subform plot is displayed the plot is displayed as a graphic rather than an active plot Using scripts in subforms You can specify a CAL script to be executed when you click an item in a subform in table view The subform can then be used as alist selection box The script can use CAL commands to retrieve the clicked item and perform an action on it For more information about CAL see CAL Comman
233. ield 0 fmlafield 0 cfrset 0 cfdoc 0 cfapp 0 Chapter 16 Customizing ChemBioFinder 13 0 217 of 342 ChemBioFinder 13 0 PerkinElme For the Better Notes Lines 1 2 Comments beginning with are ignored ChemBioFinder generates lines like these whenever you create anew script Line 3 It s a good idea to add your own comment telling what a script is designed to do Line 4 Import statements are used to declare and execute code from external Python modules This one says we want to use a specific routine GetActiveObject from a module in the Win32 extension library win32com client Lines 5 7 Obtain the currently running ChemBioFinder application object the one from which the script was launched along with its active document and recordset Assign them variable names Lines 8 9 Identify the fields to be included in the report and get corresponding field objects from the document Lines 10 11 Prepare to loop records Calling MoveFirst ensures that you loop the entire list If you omit this or com ment it out the loop begins at the current record Line 12 Begin the loop go until the recordset reaches EOF after the last record A colon at the end of a line indi cates it is the first of acompound statement Lines 13 14 Retrieve data using the Value method of the recordset Line 15 Format and output the record data Our simple example just prints a line to the output window Lines 16 17 Proceed to the
234. ies to refine a search See the ChemBioDraw User s Guide for information on how to add 3D properties to structures Searching with R groups ChemBioFinder 13 0 supports queries using R tables including multiple R tables Queries containing large numbers of R groups or large numbers of R values are not advisable however because ChemBioFinder 13 0 pre processing expands the query substituting all combinations from the R group table s Alternative groups Instead of submitting multiple queries on structures that share a common substructure you can submit a single query with the parent structure and variable functional groups or substructures The parent structure is drawn with attach ment point s that refer to a list of alternative groups that you define Chapter 8 Queries 104 of 342 hemBioFinder 13 I Che oFinder 13 0 PerkinElmer For the Better Figure 8 5 alternative groups Defining an alternative group To define an alternative group 1 Click the query icon to begin the search 2 Right click in the structure window and click the Edit in ChemBioDraw ChemBioDraw opens to a new page Tip You want to open ChemBioDraw because you will need more space than the structure window provides Draw the parent compound Label the atom where the alternate groups will attach with a generic label such as R Click the alternative Group query tool Drag with the tool in an open part of the page to create an area large enough to dr
235. iew omitted points click Notes at the bottom of the chart Plotting queries When you perform queries see Queries on page 97 and have one or more hit lists attached to your form the BioViz plot displays the results of the current hit list You can display overlays by selecting hit lists rather than making them Current For example the following figure shows results of a screening test relative to a control Chapter 12 BioViz 165 of 342 ChemBioFinder 13 0 PerkinElmer j For the Better SDs_Above_Control 0 500 1000 1500 2000 2500 Figure 12 2 Screening test results To remove outliers more than 2 5SD from the control Search for lt 2 5 and gt 2 5 in the SDs Above Control field n The plot displays the results for the hit list 7 Note By default the hits are shown on the same scale as the original list which may cause them to cluster in one sector ofthe window Ifthis happens right click the plot and choose Rescale to All Points or Auto scale Rescale to All Points operates on the current data points only Auto scale sets a switch so that all subsequent searches and list operations will automatically rescale the plot To display the results of an overlay on the full list 1 Open the Queries pane of the Explorer Window 2 Double click on the Full List to make it the current list 3 Click the query to select it for display over the current list Help 00 FRE 4a gt mn
236. ill get an error message from Oracle if You provide an index name which is already in use OR The column already has an index ChemBioFinder Oracle does not provide a direct way to delete or overwrite an index but the CAL SQL command can be used for this purpose To create a primary key index Chapter 14 ChemBioFinder Oracle 188 of 342 ChemBioFinder 13 0 PerkinElmer For the Better The process is the same as for a structure index except that you carry it out on a field of type Long This creates an index on the field and also designates it as the primary key It will fail unless the column already contains unique non null values f Note A new button Set As Structure may appear if you have selected a certain type of column This is an advanced feature described in Configuring via CF_SETTINGS table on page 297 Tip If you want to create a primary key but don t have a column of unique integer values you can create one using a CAL script For example assuming you ve already created a column and form box called ID o loop putdata ID Sindex record commit record next endloop CAL Some new features have been introduced into ChemBioFinder 13 0 Automation Language CAL to support Oracle Some are not specific to Oracle but of general utility SQL command When you are connected to an Oracle database you can pass any SQL command which does not return records The format is simply SQL lt comm
237. in the data displayed Before committing the duplicate you can modify fields or structure and commit changes just as you would with any other new record _ Note When duplicating records only those fields that are visible on the form are duplicated Data in fields present in the database but not visible on the form are not copied into the new record The new record has a new Mol_ID Undoing data entry Before committing a new data entry you can revert the contents of the form to its previous unmodified state To undo your changes do one of the following Goto Record gt Undo Changes Click the Undo Changes icon on the Record Toolbar After you commit the changes they cannot be undone Editing data Modifying the data in a database is performed by directly changing the data items on the form and committing those changes _ Note The Formula and MolWeight fields are automatically calculated by ChemBioFinder 13 0 from the Structure field and cannot be edited by the user The MOL_ID field is also set automatically by ChemBioFinder 13 0 and can not be edited To edit data Click the data box whose data item you want to edit If you click on a Structure data or a picture box it is high lighted If you click on a data box containing alphanumeric data a cursor appears in the data box To edit alphanumeric data 1 Replace it with the text or number you want 2 Do one of the following Goto Record gt Commit Changes Cl
238. includes a secured molecule database the Database Logon dialog box appears ChemFinder Molecule Database Security Enter the Username Password and MS Access Workgroup file required to open this database Usemame Password Workgroup Information File E Figure 5 7 ChemBioFinder 13 0 Molecule Database Security dialog box 2 Type your user name Password and Workgroup Information File name if applicable then click OK The form opens Browsing databases You can browse a database using the buttons on the Record toolbar Chapter 5 Databases 64 of 342 ChemBioFinder 13 0 PerkinElmer For the Better Figure 5 8 Browse functions on the Record toolbar 1 First Record 2 Previous Record 3 Go to Record 4 Next Record 5 Last Record 6 Add a Record 7 Undo Changes 8 Commit Changes 9 Delete Record 10 Omit Rec ord To Browse Click First Record to display the first record in the database Click Previous Record to display the record before the currently shown record Click Next Record to display the record after the currently shown record Click Last Record to display the last record in the database F Note The current record number is displayed in the Status Bar Go directly to a specific record as follows 1 Go to Record gt Go To Record The Record Number dialog box appears 2 Type the number of the record within the current list to display and click OK The specified r
239. inder 13 0 Tip As you click each profile a line of descriptive comments is displayed below the gallery window to aid your selection v 5 On the Cost Profile page you may edit your profile See To change a cost profile on page 141 for details 6 The Profile page of the wizard has an add another field check box that changes the Finish button to a Next but ton Click Next to repeat the procedure for each profile you want to add When you have added all of your profiles click Finish The profiles are displayed in the data box Editing a compound profile You can edit any of the characteristics of a compound profile with the Compound Profile Editor To edit a profile Double click in the profile data box The Compound Profile Editor appears Cost Profile Edit the cost profile To edit drag points or right click points or lines Cost Profile low valley CLOGP 1 57 lt Back Cancel To add a new profile a Right click in the editor window then click the Add Field context menu command To delete a profile 1 On the Profile tab select the required profile 2 Right click in the editor window then click Remove Field in the context menu To change the order of the profiles 1 On the Profile tab click one of the profiles to select it 2 Right click in the editor window then click the lt Move Left or gt Move Right context menu command Chapter 9 Compound Profiles 140 of 342
240. inder 13 0 es Chapter 18 Formula Input Rules 240 of 342 ChemBioFinder 13 0 PerkinElmer For the Better Similarity Rules A common situation is that you are not looking for a specific compound but any compound that is close enough will do ChemBioFinder uses the Tanimoto equation to determine if compounds are similar You can specify how similar in the Searching tab of the Preferences dialog box Exact searching relies on the notion of an atom and bond table a specific set of atoms joined to each other in a certain order by a given set of bonds If some atoms or bonds are missing added or different the query structure and the tar get structure do not match Most similarity searching on the other hand relies instead on the notion of molecular descriptors Each compound can be represented by a collection of qualitative terms that describe general aspects of the structure For example benzoic acid might be described as organic acid contains 6 membered ring contains de localized ring contains C double bond O As you can see the descriptors can be very broad and they can overlap The set of descriptors used by Chem BioFinder is very large When you draw a compound ChemBioFinder compares it against all of the descriptors it knows about Some descrip tors will be present in your compound and some will not Since each descriptor for a given compound is either Present or Not Present they are of
241. ion commands CAL 246 box manipulation commands CAL 255 boxes changing styles 41 creating 36 deleting 48 font 44 hiding or showing 44 moving 48 properties 40 resizing 48 selecting 47 style 40 branching calculating 153 bring to front command 49 browsing databases 64 browsing with the record tool 64 Btrieve 71 buttons creating 39 c CAL box creation commands 246 box manipulation commands 255 environment variables 288 execute with button 39 Chapter 22 Index 303 of 342 ChemBioFinder 13 0 PerkinElmer For the Better file commands 278 general commands 263 help 211 243 menu commands 243 overview 210 program execution commands 259 script only commands 289 variable commands 281 CAL syntax ACTIVATE 258 APPEND 287 APPENDVAL 288 BUTTON 253 CALL 260 CLEAN 278 DBOX 248 DDE 262 DELBOX 256 DOS 261 ENDLOOP 294 EXEC 261 EXIT 295 FONT 265 FORMEDIT 258 FRAME 249 GETDATA 286 GOTO 292 HELP 278 IF 293 Chapter 22 Index 304 of 342 ChemBioFinder 13 0 PerkinElmer For the Better INPUT 285 LOOP 294 MENU 243 MSG 265 OPENDB 280 PASSWORD 285 PAUSE 294 PICT 252 PUTDATA 286 QUIETCLOSE 267 READVAL 284 SEEPTAB 266 SELECT 258 SET 267 SETFIELD 257 SETTEXT 257 SETVAL 283 SUBFM 254 TEXT 250 UNSELECT 259 WRITEVAL 284 CF _SORT table 184 CFS file format 220 CFX file format 34 chain bonds 237 changing box style 41 database scheme 85 layout of an existing subform 158 Chapter 22 Index 305 of 342 h BioF
242. ion queries tutorial 23 Chapter 22 Index 329 of 342 ChemBioFinder 13 0 reaction searches reactions multiple step read only access read only fields READ indicator READ indicator description read structure command reading a structure real fields recent file list size setting record number dialog box record tool record toolbar browsing with description illustration records adding current deleting duplicating moving between redo command redoing changes redundant reagents in RD files refining queries registration preferences relational data and subforms Chapter 22 Index pP PerkinEl For the Better 106 106 63 11 10 91 91 73 204 65 64 64 59 10 77 8 10 83 79 64 49 83 83 88 118 203 156 330 of 342 ChemBioFinder 13 0 relational database definition relational databases relative tetrahedral stereochemistry replace current list command rescale rescale see also autoscale resetting the database resizing boxes objects restore list command restoring changes reversing and restoring changes ring bonds rotatable bonds rules sample databases save command save command effect on changes save dialog box save list command save structure command saving and restoring lists forms hit lists pictures Chapter 22 Index pP PerkinElme For the Better 13 156 117 229 131 28 28 85 48 48 130 49 49 237 152 239 15 78 33 33
243. ions 162 OR operator hit lists 131 OR operator queries 97 Oracle attaching tables 71 case insensitive query matching 115 handling lists in 184 indexing 187 loading 186 opening a database 182 searching in 183 setting preferences 185 setup 181 updating and adding data 185 using CAL with 189 Oracle Cartridge configuration via CF_SETTINGS table 297 Chapter 22 Index 323 of 342 ChemBioFinder 13 0 I PerkinE For the Better fast move caching scheme 296 ordering objects 49 other applications attaching tables from 71 other applications communicating with using DDE 219 other applications communicating with using OLE Automation 220 other applications communicating with using scripts 218 Output window 216 output window description 7 ovality 152 overlay 30 overlay with scatter plots 166 overriding security 57 P Paradox 71 parentheses symbol 100 password for secured forms 64 periodic table 208 225 picture box description 6 picture boxes creating 38 picture fields 73 picture tool 38 pictures 38 framing 201 of structures 81 preferences 201 saving 39 saving ChemDraw drawings as 81 Chapter 22 Index 324 of 342 ChemBioFinder 13 0 I PerkinElmer For the Better searching 81 updating 38 pKa 152 plain text tool 37 plot details 165 plot point description 165 plot single variable 26 plots histogram 27 single variable 26 two variable 27 plots removing 27 plotting options 26 polar surface area 15
244. ipt Chapter 20 CAL Commands 260 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 CALL scriptname The CALL command has the following argument String containing the name scriptname of the CAL script file to execute Remarks If the CAL script file is in ChemBioFinder s standard search path only the actual file name BROWSE is required Otherwise the complete file path c some long path BROWSE CFS is necessary If the CALL command is executed from within another script as opposed to from the Command Line the calling script will continue to execute with its next command after the called script finishes executing A CALLed script inherits all user variables from its calling script The calling script also inherits the user variables back from the called script when it has completed executing CAL commands DOS syntax Executes a standard DOS command line DOS doscommand The DOS command has the following argument Any string that might be doscommand typed at a DOS command prompt Remarks This command may be used to manipulate files execute programs or batch files get directory listings format disks etc During execution aDOS command prompt window appears on the screen when finished the window goes away and control returns to the calling script CAL commands EXEC syntax Starts a Windows program and optionally passes it command line arguments EXEC filename commandargs
245. is displayed in forms you can customize the following properties Currency symbol Decimal position Scientific notation To specify the numeric format 1 Right click in a data box containing numeric data and click Properties The Box properties dialog box appears 2 Click Format The Numeric Format dialog box appears Numeric Format Unformatted C Currency Fixed point 2 decimal places Scientific Sample 123 45 Cancel Figure 4 6 The Numeric Format dialog box 3 Select the appropriate option a varying number of decimal places Unformatted Currency and select the symbol a currency symbol from the drop down menu the currency sym Symbol on right bol to the right of when a currency the number symbol is selected Chapter 4 Forms 45 of 342 ChemBioFinder 13 0 a standard floating point value Fixed point and with a selected select the number number of decimal of decimal places places the numbers dis Scientific and played in scientific select the number notation of decimal places 4 Click OK The format is applied to the current data box Setting color You can set the following color options The form background color The color of the form in query mode The default background for all forms To set the form background and form query colors 1 Right click in a data box and click Properties The Box Properties dialog box appears
246. is formula into the form for a formula query To copy a formula from the Periodic Table to the form 1 Ensure that the cursor is placed in the editable text box 2 Select the text to copy using the SHIFT and left arrow keys of the keyboard or press CTRL A to copy the entire text displayed in the editable text box 3 Press CTRL C 4 Click OK in the Periodic Table window to close it 5 Inthe form click the formula box into which you want to paste the text and press CTRL V To display data about the selected element in the Element Editor do one of the following s Display the desired element and click the display box at the top of the Periodic Table window Double click the desired element button Element Editor Atomic Number Symbol Name Mass daltons Electronegativity Valence State s Melting Point C 1538 _Fevert to defaut Boiling Point C 2861 i 762 5 Cancel loniz Pot kJ mol Density g cm 3 7 874 Discoverer Prehistorie o Figure 16 9 The Element Editor displays properties of the selected element The color of the element is shown in the periodic table for that element and in any structure data boxes in which that element is present To change the color of an element 1 Click the Color button 2 Select a color from the Color dialog box and click OK 3 Click OK in the Element Editor To reset an element s color to the default click Revert to Default in the Element Editor Chap
247. ixels between the left edge of the button and the left edge of the active form Integer value representing the distance in pixels between the top edge of the button and the top edge of the active form Integer value representing the distance in pixels between the right edge of the button and the left edge of the active form Integer value representing the distance in pixels between the bottom edge of the button and the top edge of the active form Name of the CAL script file filename to display in the button Remarks If the CAL script file is in ChemBioFinder s standard search path only the actual file name BROWSE is required Otherwise the complete file path c some long path BROWSE CFS is necessary Chapter 20 CAL Commands 253 of 342 ChemBioFinder 13 0 I ey h PerkinElmer For the Better When a new button is created it adopts the current font settings These settings can be controlled with the FONT command By default the name of the CAL script file for example BROWSE is shown on the button This can be changed with the SETTEXT command BUTTON example This example uses the BUTTON command to create a button near the bottom of the form and assign to it the REG ISTER CFS script in the same directory as the form BUTTON 50 300 200 330 Register CAL commands SUBFM syntax Creates a new subform on the active form SUBFM left top right bottom The SUBFM command has the following argume
248. k the Find icon on the Search Toolbar The search proceeds as with simple structure searching Chapter 8 Queries 120 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 Special structure searches The Find Structures submenu on the Search menu provides for several common types of structure searches can not be efficiently conducted using regular means As with other searches all of these searches operate within the current record set if the Over Current List option is in effect Otherwise the whole list is searched regardless of how many records are currently displayed Special struc ture searches are intended to apply to all data sources including Oracle but presently only work for MST sources The following figure shows the menu options under Find Structures submenu Ele gdt View Tet Search Record Sgipts Opine Window Help Rh a O al a An amp o 6 E D Ready m 1 olaa w 26 Figure 8 22 Find Structure menu These are generic searches made without entering any query information The options are J Empty Structures Locates records containing no structure It is equivalent to specifying a molecular weight of zero in a regular search It is provided because the latter method is a bit obscure Reactions Locates structures that are reactions The same effect can be achieved by entering a bare arrow as a structure query With Stereo Centers Finds structures containing tetrahedral stereoc
249. l value is shown by the line in the middle Click Mext to begin defining Fields Cloge Mw Activity score 2 20 dist 3 30 Define Field dialog box is displayed Chapter 9 Compound Profiles 138 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 Define a field Choose a field enter short name and value range Field Source CLOGP Display As CLOGP Yalue Range Minimum 5 6 Weight 100 ial Maximum 13 79 r lt Back Cancel 3 On the Field page choose a numeric field from the drop down menu of Source You may edit the name automatically entered in the Display As text box You may edit the Value Range The default display is the actual low high values for the first 1000 records in the database You may choose a log scale if no part of the Value Range is negative You may weigh this profile relative to other profiles where 100 is important O is not 4 On the Profile Choose page choose a cost profile Profile Choose Choose a cost template Select a pattern to represent costs across the value range Bottom is ideal top is high cost A FARAH high butte high plateau high valley low butte low plateau Ideal within Y1 Y2 unacceptable above V3 Example CLOGP lt Back Cancel Choosing from this gallery is just for convenience Any pattern you choose can be later modified to any other shape Chapter 9 Compound Profiles 139 of 342 pP PerkinElmer For the Better ChemBioF
250. larity is determined by what you have selected in the Search menu To find the current molecule 1 Browse to the record containing the structure of interest 2 From the Search menu choose the type of structure search you want to perform 3 Do one of the following Goto Search gt Find Current Mol Click the Find Current Molecule icon on the Search Toolbar ChemBioFinder 13 0 begins the search and displays the search status on the lower right corner of the status bar When the search is complete the form displays the first hit and the list you can browse is restricted to the records hit by the query Entering a reaction query The general procedure for creating a reaction query is very similar to creating a structural query 1 Do one of the following to clear the form Goto Search gt Enter Query Click the Enter Query icon on the Search toolbar The form clears 2 Enterthe query Double click in the Structure box The ChemBioDraw Control appears Draw the structure or substructure or reaction in the From ChemBioFinder 13 0 window Click somewhere in the form outside the Structure box 3 Optional enter more query terms in the other data boxes for a combined search 4 Select or deselect the Search gt Substructure menu option as appropriate for your query _ Note The Similarity option is not available for reaction queries 5 Do one of the following to search Goto Search gt Find Clic
251. las using the Periodic Table instead of typing them ChemBioFinder lets free format input and attempts to make the most reasonable interpretations of them by using the rules described below Rules If asymbol is properly capitalized first letter upper case followed by zero one or two lower case letters then the longest valid symbol which matches is preferred Thus Phe matches phenylalanine rather than phosphorus Co matches cobalt Because of this rule if you properly capitalize all symbols no ambiguities will arise If symbols are not properly capitalized such as all lower case then with the exception noted below the shortest symbol which matches is preferred Thus co is taken as carbon oxygen instead of cobalt The exception is if two characters represent a valid two letter symbol and also a valid one letter symbol followed by an invalid one then the two letter symbol is favored Thus cl is not taken as carbon followed by the invalid symbol L but instead is taken as chlorine Examples There is an easy way to experiment with formula interpretation use the Periodic Table Type a formula into the text box at the bottom then click anywhere outside that box ChemBioFinder interprets the formula and redisplays it with correct capitalization ChemBioFinder interprets some ambiguous formulas as follows cooh COOH Chapter 18 Formula Input Rules 239 of 342 pP PerkinElmer For the Better ChemBioF
252. lative and absolute configurations may be registered separately in ChemBioFinder and can be distinguished by var ious search options The basic ChemBioFinder search philosophy can be summarized as follows a more specific query is a more precise request and should get fewer hits than a more general query If the query represents a particular absolute con figuration it should hit only that if it represents a mixture it should hit any of the components If you choose Same in the stereo search choices you are requesting that whatever stereochemistry is specified in the query must match that of the target If the query has relative bonds and RTS is activated a hit must have the same relationship between centers You can use the following three flags in searches based on relative stereochemistry Abs Refers to the Absolute flag It matches the exact stereoisomer as drawn Example gt LLL lt z T Rel Refers to the Relative flag It matches the exact stereoisomer as drawn or its enantiomer Example 8 Rac Refers to the Racemic flag It matches a mixture of the exact stereoisomer as drawn and its enantiomer Example Chapter 17 Structural Query Features 229 of 342 ChemBioFinder 13 0 PerkinElmer For the Better MDL file formats All bond styles available in ChemDraw are retained in CDX files The same is not true of major MDL structure files MolFiles SDFiles and RDFiles In these formats
253. le The Open dialog box appears Chapter 4 Forms 38 of 342 ChemBioFinder 13 0 PerkinElmer For the Better 2 Inthe Open dialog box select the file you want to display in the Picture Data Box then click Open The new pic ture is displayed in the Picture Box 4 Note if the Picture box is linked to a Picture field you must click the Commit changes tool to save the picture in the database To save afile from a Picture Data Box 1 Right click on the Picture Box and select Save File 2 Inthe Save As dialog box type a file name then click the Save The picture is saved Adding a check box The check box tool lets you add check boxes to your form A check box can be assigned to either a Boolean or an Integer field To add a check box 1 Click the check box tool 2 On the form drag an area large enough for the text next to the check box The Enter the label dialog box appears 3 Type in the text and click OK 4 Right click and select a Boolean or Integer field from the field list to assign to the check box Adding a button Buttons on the form are used to activate scripts To place a button on a form 1 Write a script using the ChemBioFinder 13 0 Automation Language CAL 2 Click the Button tool on the Form toolbar 3 On the form drag to draw a button The Enter the Label dialog box appears 4 Enter a label The text can be descriptive Click to browse and does not have to correspond to the name of the
254. les on a single tab Whenever a subform appears on screen ChemBioFinder automatically updates the data from the server If you have alot of subforms ona single tab ChemBioFinder must update all of them at once potentially slowing down your work So if you have subforms you need to see only occasionally put them on other tabs of the form so they will not be updated until you activate those tabs Remove plots that you are not using Plots that are visible all take at least some processing and closing a plot window still doesn t remove it from memory If you have generated plots you no longer need use the View gt BioViz Plots gt Remove menu command to delete them then save the form Chapter 15 BioSAR 199 of 342 hemBioFinder 13 0 I islas armader PerkinElmer For the Better Customizing ChemBioFinder 13 0 You may customize ChemBioFinder 13 0 in the following ways Customize display of your molecules fonts pictures and forms Customize the Favorites tree Design the toolbars to your specifications Perform automated tasks such as interfacing with Microsoft Excel or by using CAL the ChemBioFinder 13 0 Auto mated Scripting Language Setting preferences The Preferences dialog box allows you to customize the display of molecules pictures and forms and set options for searching and exporting General instructions for using the Preferences dialog box 1 Click the tab containing the preferences to set 2
255. lly be executed at the specified event Click OK in the Box Properties dialog box o N DOO A Save the form if you wish to keep the changes Python A Python interpreter is embedded in ChemBioFinder 13 0 the language components reside outside ChemBioFinder 13 0 as well as available from within it and appear to be built in In the same way you can develop complex macros inside Microsoft Word or Excel using Visual Basic you can develop scripts inside ChemBioFinder 13 0 using Python The Output window facilitates Python in ChemBioFinder 13 0 The script editor is used with either CAL or Python It s default configuration is Python interactive About Python Python is a full featured cross platform programming language used to develop applications controls DLLs com mand line utilities and so forth The language is Open Source maintained and supported by a large community of developers Python is available in ChemBioFinder 13 0 in the same ways as CAL In both cases a script can be connected to and activated from a button form trigger event or hyperlink in a subform table T be developed and executed in command mode one line at a time R provide direct access to data in boxes on the ChemBioFinder form be saved to an external file or stored internally in the form But Python is far superior to CAL in many ways Python is a complete programming language not just a set of commands It allows calls to system
256. m 1 Go to File gt Open The Open dialog box appears 2 Select tut1 cfx and click Open The form you created in the previous tutorial appears with its fields blank 3 Select Layout mode on the main toolbar if it is not already selected 4 Right click on the Structure framed box and select Data Source The Box Properties dialog box appears with the Database tab displayed 5 Click Open Database The Open dialog box appears 7 Note The Open and Create Database buttons work with ChemBioFinder 13 0 databases only To access data in other types of databases use the Attach Table or the Oracle button if available For more information about data sources see Attaching tables from other applications on page 71 6 Select CS_demo mdb from the Samples folder ChemOffice 2012 samples folder and click Open The database opens and the Box Properties dialog box appears displaying the Database tab 7 Alist of the tables in the database and the fields in each table are shown The field you select from the table deter mines what type of data appears in the box you selected in step 4 Assigning fields to data boxes To display structures from the CS_ Demo database in the Structure Framed box on your form 1 Right click on the Structure Framed box on your form and select Properties 2 From the list of fields in the Box Properties dialog box select Structure and click OK The Structure field is linked to the Structure Framed box In the St
257. m z N Num Rotatable Bonds O Ovality Topological Diameter Total Connectivity Total Valence Connectivity Vv Vapor Pressure WwW Water Solubility Wiener Index 145 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 About Molecular Networks MOSES pKa MOSES logS and MOSES logP for predicting acid dissociation constants aqueoues solubility and octanol water distribution coefficients of chemical compounds are computational calculator modules based on Molec ular Networks chemoinformatics platform MOSES MOSES is developed maintained and owned by Molecular Net works GmbH Erlangen Germany For further information please visit www molecular networks com moses All rights reserved Molecular Networks GmbH Erlangen Germany www molecular networks com Limitations Only the following atom types and hybridization states are parameterized O U Balaban Index Is represented as J and is defined by the formula J E Y 9 1 2 edgesij Where qis the number of edges in the molecular graph m q n 1 is the cyclomatic number of molecular graph nis the number of atoms in the molecular graph 7 S is the sum of all entries in the it row or column of the topological distance matrix of the molecule The distance matrix stores the shortest path between all pairs of atoms Boiling Point The boiling point is report in Kelvin A solution boils at a slightly higher temperature than the
258. mBioFinder 13 0 LogP Partition Coefficient The partition coefficient is a ratio of concentrations of un ionized compound between two solutions To measure the partition coefficient of ionizable solutes the pH of the aqueous phase is adjusted so that the predominant form of the compound is un ionized The logarithm of the ratio of the concentrations of the un ionized solute in the solvents is called LogP Normally one of the solvents chosen is water the second is hydrophobic such as octanol The formula to calculate logP is log P ot twat solute og solute tano un ionizedwate LogS The logarithm of the solubility of a substance measured in mol liter This is the mass of one molecule of a substance relative to the unified atomic mass unit u equal to 1 12 the mass of one atom of 12C Also called molecular mass Melting Point Is the temperature at which a solid becomes a liquid at standard atmospheric pressure At the melting point the solid and liquid phase exist in equilibrium The formula to calculate melting point is r AZ S Where T is the temperature at the melting point AS is the change in entropy of melting and AH is the change in enthalpy of melting Mol Formula This is the molecular formula of the compound Mol Formula HTML This is the molecular formula written in HTML format You can copy and paste the output to an HTML file Here is an example of the output for a model
259. ments as necessary to fill their lowest acceptable valence The structure above is registered in as methylamine CH NH Structures and reactions drawn with query properties are generally meaningful only in the context of a query Query structures can be stored in a ChemBioFinder 13 0 database but they are not treated as Markush structures and are not guaranteed to be hit by all valid search queries For more information see Structural Query Features on page 223 Chem amp Bio Draw allows you to draw many objects that have no chemical meaning These include boxes circles arrows orbitals and others It also allows you to assign non chemical styles color to objects that have chemical meaning ChemBioFinder 13 0 ignores these properties and stores only objects with chemical meaning in structure fields Chapter 6 Working with Data 81 of 342 ChemBioFinder 13 0 J e PerkinElmer For the Better To store a ChemBioDraw drawing exactly as drawn store it as a picture You can copy and paste a ChemBioDraw drawing into a Picture field Figure 6 2 Form with picture field 7 Note Objects stored in a Picture field have no chemical significance and cannot be searched Viewing models using ChemBio3D ChemBioFinder 13 0 also provides access to the ChemBio3D Control This means a Structure data box can be des ignated as ChemBio3D style To view the molecular model for a structure 1 Inthe Database pane of the Explo
260. mes the state ments are to be repeated Commands that are statements repeated a number of times Remarks If count is omitted the statements will be repeated a number of times equal to the number of records in the current list This command is useful only in a script file and has no effect when entered on the Command Line LOOP example This example uses the LOOP command and the Menu Command Record Next to display all of the records in the cur rent list The PAUSE command keeps each record on screen long enough for people to see it looprec nextpause 2endloop CAL commands PAUSE syntax Temporarily stops the script from executing PAUSE decisecs The PAUSE command has the following argument z Amount of time to sus decisecs a pend script execution Remarks 10 decisec 1 second If the decisecs argument is omitted the script will be suspended for 2 seconds Chapter 20 CAL Commands 294 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 CAL commands EXIT syntax Immediately halts execution of a CAL script EXIT Remarks This command is useful only in a script file and has no effect when entered on the Command Line Chapter 20 CAL Commands 295 of 342 ChemBioFinder 13 0 PerkinElmer For the Better CS Oracle Cartridge Prerequisites for connecting ChemBioFinder Oracle to an Oracle database ChemBioFinder Ultra Oracle Client Oracle OLEDB Provider Oracle
261. mmands are not available from the menu To display the Form tools do one of the following Click the Layout icon on the Main toolbar Goto View gt Toolbars gt Form The Form toolbar appears providing tools for you to create and edit a form Figure 4 4 The Form toolbar 1 Selection tool 2 Data box 3 Frame 4 Framed box 5 Check box 6 Text box 7 Picture 8 Button 9 Subform 10 Profile box 11 Control box 12 Grid Using the grid In anew form the snap grid is turned on by default This grid helps you align boxes on the form Turning on the grid forces objects to snap to the grid as they are drawn To toggle the grid on or off do one of the following Click the Grid tool on the Form toolbar Select deselect the View gt Grid menu option _ Note You can change the grid spacing using the Preferences dialog box See Setting preferences on page 200 Chapter 4 Forms 35 of 342 ChemBioFinder 13 0 PerkinEl For the Better Creating boxes A ChemBioFinder 13 0 form is composed of a collection of boxes that display data from the associated database or other information Each box displays one data item of the current record To create a data box use one of the tools on the Form toolbar _ Note The Form toolbar is not visible unless the Layout button is selected The Data Box displays a data item or structure Use it to display any data from a database including text numbers dates molecules reaction
262. ms 57 of 342 h BioFi 13 I ChemBioFinder 13 0 PerkinElmer For the Better 5 When you have completed your changes click Override Security to toggle security back on Security Enabled appears in the lower left corner of the Form Security dialog box Chapter 4 Forms 58 of 342 ChemBioFinder 13 0 PerkinElmer For the Better Databases You work with data within ChemBioFinder 13 0 by entering it into a database editing it and interfacing with Chem BioDraw and ChemBio3D You can perform all of these functions on data using the commands in the menus or you can use the buttons in the Record toolbar for most of these functions Figure 5 1 Database functions on the Record toolbar 1 First Record 2 Previous Record 3 Go to Record 4 Next Record 5 Last Record 6 Add a Record 7 Undo Changes 8 Commit Changes 9 Delete Record 10 Omit Rec ord Selecting a database A ChemBioFinder 13 0 form does not store data directly but is simply the window through which you look at data When creating a form you need to specify the source of the data to display A form displays data from a single table in a database To specify the data source for a form you must open or create a database and then select a table If you want to view data from more than one table you must create a form for each table Typically you create a main form for one main table and a subform for each other table For more information see Relational Data
263. n a one to many relationship For example you want to view a chemical struc ture together with its physical properties stored in a separate table You are running a stockroom and you want to store package sizes and prices in the same place because they are related Each chemical may be available in lots of package sizes and you wouldn t want to re draw the structure every time you added a new package You can use a subform so the physical property information is entered once in the main form and the package sizes and prices are entered many times in the subform By linking these two data tables with a linking field you can make these tables relational one table can interact with the other The contents of a linking field are not important as long as they are different for each record in the main form Various forms of ID numbers are often used as linking fields As you browse through the main form cor responding records in the subform appear Creating a subform You create a subform place form objects on it and connect the subform to a database just as you do a regular form For detailed information on these procedures see Forms on page 32 For users of version 8 0 and earlier Creating and linking subforms in ChemBioFinder 13 0 was simplified in version 8 5 Users of previous versions should note the following changes There is now a single dialog box which sets properties of both the subform box and its subform You set all
264. n database programs such as ChemBioFinder 13 0 your changes are automatically and permanently saved to the database when you switch records This is known as committing the changes You then have the opportunity to revert to the original data by selecting Record gt Undo Changes The File gt Save menu command refers only to changes made on the form itself such as the position of boxes Choosing the File gt Save menu command has no effect on changes you make to data stored in the database Note Saving a form also saves subforms and changes that you make to subforms Note After you create a form you can save it When you retrieve the saved form it automatically opens a con nection to the database defined in the forms To save a form as cfx file 1 Go to File gt Save To save the form under a new file name go to File gt Save As The Save dialog box appears Chapter 4 Forms 33 of 342 ChemBioFinder 13 0 J e A PerkinElmer For the Better 2 Choose the directory in which you want to save the form type a filename and click Save ChemBioFinder 13 0 saves the form with a CFX extension 7 Note While saving if you select All Files in the Save as type dialog box you will see files with msf and msk extensions A file with the extension msf is a multiple sequence file A file with msk extension is a mask file Creating forms manually You create a form and define it by using the Form tools to create objects and the Box Propertie
265. n in the Password box _ Note Use ofa password is optional 5 To enforce Workgroup Security in an MS Access Workgroup Administrator database you must specify a Work group Information File Take the appropriate action f Note Enforcing workgroup security is optional Type the name of the MS Access Workgroup database in the Work enter a work group file name group Information File box browse for the Click File and select workgroup file the file The following steps refer to the options in the Enable Disable section of the dialog box 1 Click the plus sign next to Database Security to display the options take the appropriate action Chapter 4 Forms 52 of 342 ChemBioFinder 13 0 be prompted to log on with a username password to open a form use a username password to log on to the MS Access database MDB files be prompted to log on to a database with a username password when the form is open use a username password to open the molecule data base MST files be able to access the Form Security dialog box encounter all of the above options 2 Click the plus sign next to Forms to display the options take the appropriate action open or create data bases Chapter 4 Forms Password to open form Logon to MS Access database Prompt for data base logon Protect molecule database Security dialog available Database secu rity Open create data base
266. n the Query Mode box The number of hits is shown in the Status Bar at the lower right corner of the window 7 Note If a search gets no hits or an error occurs an alert appears and you are retumed to Query mode to enter a dif ferent query or modify the current one The hit list is a subset of the complete database You can browse it as you would any database using the Record com mands in the Record menu or toolbar For example to view the hits in tabular form Goto View gt Data Table Stopping a search To stop a structure search in progress press the Esc key The query stops and you return to browse mode _ Note Only queries that involve structural data structure molecular formula and molecular weight searches can be stopped in this manner SQL searches and searches that involved non structural data cannot be aborted Refining a search You can refine a hit list of one or more records by entering a query that searches only the hit list not the entire data base To refine a search 1 Verify that the Search gt Over Current List menu option is selected 2 Do one of the following Goto Search gt Enter Query Click the Enter Query icon on the Search toolbar ChemBioFinder 13 0 searches over the previously retrieved hit list If no hits are found a message appears asking whether to search over the entire database Chapter 8 Queries 118 of 342 hemBioFi 13 I ChemBioFinder 13 0 PerkinElmer For the Better
267. name DATE current date SDTBA_NAME_L database full path Angle bracketed lt item gt is required bracketed item optional 4 lt tect gt four integers left top right bottom lt box gt a point within box x y or a box name Box name a user assigned box name b field name casei y Figure 16 11 CAL help window Tip In ChemBioFinder 13 0 this window is resizable Creating a script To create a script 1 Create a button on a form 2 Label the button 3 Right click and click the Edit Script context menu command The CAL editor appears MM CAL Editor Browse_button Browse script loop mols with short pause if SNUM_RECS lt 1 exit loop rec next pause 2 endloop Import Properties Help Be Figure 16 12 The ChemBioFinder 13 0 script editor 4 Type in your script commands or use the Import button to import an existing script 5 Click OK to create a new file Tip You can still create scripts in Notepad or another text editor if you wish Save the file with extension cfs in the C Documents and Settings All Users Application Data CambridgeSoft ChemOffice 2012 ChemBioFindenSystem windows and C Program Data CambridgeSoft C hem Office 2012 ChemBioFindenSystem Vista subdirectory if you want the name of the script to appear on the Scripts menu v The CAL editor is a simple resizable text entry window It accepts carriage returns and tabs To
268. nd deleting fields appears You are now going to add two new fields to the data table 6 Click Create Field The Create Field dialog box appears 7 Type MolName in the text box change the width to 254 and click OK _ Note You can enter a maximum of 254 characters in a text field If you want a text field to contain more than 254 characters choose Memo Rich Text from the Type drop down list 8 Click Create Field again Type Boiling Point in the text box change the type to Double and click OK The data table tree displays your changes 7 Note Use the field type Double to create a field containing real numbers such as 123 7 and 43 242 9 Click the Form tab The various form options appear 10 Click the Generate form check box Click Style In the Form Generation dialog box make sure the check box for Structure in upper left of form is checked 11 Click OK in the Form Generation dialog box and again in the Form Properties dialog box The Mydb form is gen erated Next check the field assignments in the data boxes 1 Right click in the structure data box There should be a check next to Structure indicating that the Structure field is linked to the structure data box 2 Right click in the Boiling Point data box There should be a check next to Boiling Point Chapter 3 Tutorials 18 of 342 ChemBioFinder 13 0 PerkinElme For the Better Adding records Now that you have created new fields and assigned them to data box
269. nd left side of the Ul but they can be torn off and placed anywhere on the screen for your convenience You can view the toolbars displayed in the ChemBioFinder window through View gt Tool bars submenu You can also use the Toolbars submenu to customize the toolbars A description of toolbar cus tomization is beyond the scope of this manual See Microsoft help for information on customizing toolbars Main toolbar Use the Main toolbar to perform basic functions such as opening and closing forms copying pasting objects and modifying a form Layout Mode switches between Layout Edit Mode and View Mode When you click Layout Mode the Form Toolbar and an alignment grid appear on the form Switch to Table switches between Form View and Table View Database Wizard activates the Database Wizard to connect a database to a form Form toolbar Use the Form Toolbar to add an object to an existing form Chapter 2 Getting Started 8 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 Figure 2 2 The Form Toolbar 1 Selection tool 2 Data box 3 Frame 4 Framed box 5 Check box 6 Text box 7 Picture 8 Button 9 Subform 10 Profile box 11 Control box 12 Grid _ Note The Form Toolbar docks on the left side of the ChemBioFinder 13 0 window by default but can be docked anywhere or torn off as shown The tools are described in Forms on page 32 Search toolbar The Search Toolbar contains t
270. ne the properties of the atoms and bonds in a structural query These properties are definable in ChemBioDraw Pro using the Atom Properties and Bond Properties dialogs acces sible from the Structure menu See Structural Query Features on page 223 for more information Suppose you want to find all molecules that contain a non oxygen chalcogenide bonded to another atom not nec essarily carbon You also want the bond type between the chalcogen and the other atom to be a single or double bond The query drawn in ChemBioDraw Pro may look like this This atom may be any non hydrogen atom A si0 This bond may be single or double S Se Te To This atom must be S Se or Te Figure 8 29 Specifying bond and atom types in a query The A label denotes that the atom may match any atom except hydrogen The indicator near the bond indicates that the bond has been defined in this case in the Bond Properties dialog of ChemBioDraw you specified that the bond type may be single or double S D Finally by entering S Se Te enclosed in brackets you specified that one of these elements must match in the target molecules Searching fullerenes A search of fullerenes can illustrate the restrictions you can place on a formula search Suppose you want to find all fullerenes containing 20 to 80 carbon atoms but you also do not want to include large organic molecules The formula query could be C20 80 HO By designating zero hydrog
271. next record Lines 18 22 Objects created in a script must be freed before leaving Without this you may find it impossible later to exit ChemBioFinder An object can be freed by setting it to zero Rec 1 Name Bromobenzene Formula C6OH5Br Rec 2 Name 3 Bromobenzoic acid Formula C7H5Br02 Rec 3 Name 6 6 Dibromoindigo Formula C16H8Br2N202 Rec 4 Name 3 Bromophenol Formula C6H5Bro Caveats Subforms are not supported by the CF Automation interface If you need to work with subform data you will have to use CAL for the time being Running Python scripts cannot currently be interrupted Be warned before trying the above script on a long hit list Once it starts running it will not stop until finished or until you kill ChemBioFinder in Task Manager We are working on this problem If after you have run a script you try to exit ChemBioFinder and it refuses to exit it means the script created a ChemBioFinder object and failed to release it Methods of communication There are two general methods of communicating with other Windows applications such as Microsoft Excel by using a script within ChemBioFinder 13 0 or by using a Visual Basic procedure within the other application The following is an overview of each method Using scripts A ChemBioFinder 13 0 CAL script can communicate with other Windows applications using either of two com mands Chapter 16 Customizing ChemBioFinder 13 0 218 of 342 C
272. ng containing the data base field name if the target fieldname is a data box or CAL script name if the target is a but ton to assign to the target CAL commands SETTEXT syntax Attaches a text string to a frame text box or button or replaces one already attached SETTEXT box text The SETTEXT command has the following arguments Box identifier indicating the box target String to attach to the tar text get Depending on the box type the text is attached to different places Within the text box data box wrapped to fit On the top border aligned to frame the left Within the text box text box wrapped to fit Centered within the button Chapter 20 CAL Commands 257 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 CAL commands ACTIVATE syntax Marks a subform on the active form to become the new active form It is equivalent to clicking on the subform with the pointer tool ACTIVATE subform The ACTIVATE command has the following argument Box identifier indicating the subform subform to activate _ Note This command will change the active form Remarks The ACTIVATE command acts only on subforms The similar command SELECT is used for data boxes frames text boxes buttons and picture boxes CAL commands FORMEDIT syntax Determines whether the active form is in form edit mode or data edit mode FORMEDIT value The FORMEDIT command has th
273. ng data New data replaces existing data Different form example This example shows how you can use a script to open a second form with some of the same fields as the original form but for example a different layout This same sort of procedure can be used to display related records if you do not want to use an explicit subform Chapter 20 CAL Commands 287 of 342 ChemBioFinder 13 0 I ee a PerkinElmer For the Better The APPEND SETVAL and GETDATA commands build a search string based on the contents of the link_field field on the original form The Menu Command File Open opens the second form or switches to it if it is already open Finally the Menu Command Search Enter Query enters search mode the PUTDATA command enters the search string generated earlier in the script and the Menu Command Search Find executes the search append offsetval 1 append ongetdata 1 link fieldappend offfile open d chemfndr otherform cfx search enter queryputdata link field vlsearch find CAL commands APPENDVAL syntax Concatenates a new string to the end of an existing user variable APPENDVAL v text The APPENDVAL command has the following arguments User variable to which the variable i text is concatenated String that is concatenated to the variable Remarks APPENDVAL is a shortcut designed to make it easier to build string values It is the same as setting APPEND ON doing a SETVAL and then restoring APPEND
274. ng space on your hard disk to be used as RAM However the time for swapping between the application and the hard disk is slower than swapping with physical RAM Chapter 1 About ChemBioFinder 13 0 2 of 342 hemBioFi 13 I ChemBioFinder 13 0 PerkinElme For the Better Applications and Drivers As with most complex software applications there may be unusual circumstances in which ChemBioFinder may become unresponsive Below are some recommended steps for you to follow to try to resolve software and driver issues 1 Restart Windows and try to reproduce the problem If the problem recurs continue with the following steps 2 The most common conflicts concem video drivers printer drivers screen savers and virus protection If you do need to contact us be sure to determine what type and version of drivers you are using Video Driver related problems If you have problems displaying any ChemBioOffice Application try switching to the VGA video driver in the display Control Panel or System Setup and then retest the problems If using a different driver helps your original driver may need to be updated contact the maker of the driver and obtain the most up to date driver If you still have trouble contact us with the relevant details about the original driver and the resulting problem Printer Driver related problems Try using a different printer driver If using a different driver helps your original driver may need to be updated co
275. ngs each of which is fused to at least two others in the group Duplicates Locates records whose structures duplicate at least one other If Clustered List is selected the query will be a list of duplicates only clustered together that is a sorted list This makes duplicates easier to compare but you cannot edit records displayed in a sorted list If Unique Structures Only is selected the query will be the same as the parent list but with only one unique copy of each duplicate structure _ Note The Duplicate search must be performed in Full Structure mode If the Search type is set to Substructure you will get an error message reminding you to reset the search type preference to Full Structure By date modified Locates structures updated recently or some other point in time It applies to structures only not to the other database fields It is not implemented for Oracle at this time Also while it applies to the last time a structure was added or edited it misses deletions The way it works is to read the modification date written within the structure Deleted records have no such date Chapter 8 Queries 122 of 342 ChemBioFinder 13 0 PerkinElmer For the Better T Check structures Locates records by checking the properties specified in the Check structures in database dialog box Depending on the specified properties and whether the database is read only it may be possible to auto matically re register the structu
276. nism is available in ChemFinder Oracle In this scheme instead of requesting complete forms full of data over a list or query ChemBioFinder Oracle retrieves only the ID or primary key field and stores caches the results in an array in memory It then need not rely on the normal recordset cursor When a request is made to move to record N the key for that record is looked up in the array and a new select state ment is issued to retrieve only the corresponding record Thus Move Last takes no more time than Move Next There are tradeoffs between the two schemes The new scheme takes time to retrieve the set of ID s during a database open or after a search or sort Normally this is quite fast even for a large table and steps are taken to avoid repeating the operation unless necessary A message on the status bar indicates when this caching process is taking place In the new scheme moving from one record to the next is somewhat slower since each move involves a fast one hit search This is not very noticeable during list browsing but slows down multi retrieve operations such as filling table view Because of these drawbacks the new caching scheme is OFF by default To turn it ON for an Oracle connected form 1 Go to File gt Database or otherwise bring up the Properties dialog box 2 Go to the Oracle tab of the dialog box 3 Check the Cache ID s for faster moves box 4 Click OK You will get an alert instructing you
277. not have privileges to log in as this user consult a system administrator 4 Click the Oracle tab of the dialog box then click Prepare Schema ChemBioFinder 13 0 will create the one new table needed without modifying any of the others _ Note If this button is dimmed it means you are not logged in as the owner of the current schema 5 Go back to your original form and repeat the sort Tip You may have to click Refresh Session Data on the Oracle tab before the sort will work Subform value aggregate In an Oracle database ChemBioFinder 13 0 allows sorting the main list over subform field aggregate values If for example you have a subform showing a column of test values where there are multiple records in the subform for each main record you can sort the main hit list based on the sum or average of the set of test values for each record To sort by aggregate 1 Go toRecord gt Sort The Sort Multiple dialog box appears 2 Click a subform value in the left hand box to sort by 3 Inthe right hand box right click the Fxn column and choose a function from the popup menu MIN MAX AVG or SUM 4 Click OK The hit list is sorted by the selected value s 7 Note AVG and SUM are available only for numeric fields MIN and MAX can also be used for text fields Handling lists There are differences between ChemBioFinder 13 0 and ChemBioFinder Oracle in working with hit lists Save List does not bring up a file dialog box in
278. nt symbol Button used to create buttons to actuate scripts Buttons display button labels Rich Text displays styled data in multiple lines press CTRL ENTER to start a new line You can format the text with the Text Format toolbar If the data in a field contains rich text markup characters are displayed Structure Chem Bio Draw style displays chemical structures or reactions Reactions are laid out for best fit with the box and the layout may change if the box is reshaped The box defaults to using the ChemBioDraw Control to Chapter 4 Forms 40 of 342 ChemBioFinder 13 0 PerkinElmer For the Better create and edit structures but you can reset the preference For more information Setting preferences on page 200 Structure ChemBioFinder style as above but defaults to opening Chem amp Bio Draw to create and edit structures Structure Chem amp Bio 3D style as above but defaults to display 3D structures To set the box style 1 Right click in the data box you want to change and click Properties The Box Properties dialog box appears 2 Choose the box style from the Box Style drop down list 3 Click OK Viewing structures You can display structures in a structure box in three styles ChemBioFinder ChemBioDraw ChemBio3D In ChemBioFinder style the ChemBioDraw application opens when you want to edit structures or create a query This mode of operation was used in all earlier versions of Chem
279. ntact the maker of the driver and obtain the most up to date driver If you still have trouble contact us with the relevant details about the original driver and the resulting problem 3 Try reinstalling the software Before you reinstall uninstall the software and disable all background applications including screen savers and virus protection See the complete uninstall instructions on the Technical Support web page 4 If the problem still occurs use our online contact form and provide the details of the problem to Technical Support Chapter 1 About ChemBioFinder 13 0 3 of 342 ChemBioFinder 13 0 PerkinElmer For the Better Getting Started In this section we describe the ChemBioFinder 13 0 working environment and introduce the basic features After you become familiar with the fundamental concepts you will be able to perform database queries and review the results Afterwards you will learn to create your own query forms plot data and perform other tasks using ChemBioFinder 13 0 The general steps for performing a query in ChemBioFinder 13 0 are Open or create a form Create or open a database and link it to the form 1 2 3 Enter query parameters in the form 4 Perform a search 5 Browse the search results These steps are described in the ChemBioFinder 13 0 Tutorials and in the detailed reference material in the manual The ChemBioFinder User Interface The ChemBioFinder 13 0 User Interface UI consists o
280. ntinue the query as usual Reaction searches You can search and store reactions In a reaction one or several compounds reactants are transformed into other compounds products Individual reactants or products are separated from each other with plus signs The react ants are separated from the products with an arrow Reactions may have multiple steps for example A gt B gt C gt D Here A is the reactant and D is the product B and C are intermediates for the complete reaction A multi step reaction is actually a shorthand notation for many related reactions In the example above B is an inter mediate for the complete reaction but it is also a reactant relative to C or D It is also a product relative to A The Chapter 8 Queries 106 of 342 ChemBioFinder 13 0 PerkinElme For the Better complete reaction implies many subreactions such as B D and A gt B Reaction centers The most important part of a reaction is the part that changes from the reactants to the products This part which prob ably includes a number of atoms and bonds is called the reaction center For example only the bold bond in the figure below and the two atoms on either side is part of the reaction center The rest of the structure is unchanged from the reactant to the product Figure 8 9 Reaction center example By default ChemBioFinder 13 0 considers reaction centers whenever you search for reactions ChemBioFinder
281. nts Integer value representing the distance in pixels left between the left edge of the subform databox and the left edge of the active form Integer value representing the distance in pixels top between the top edge of the subform databox and the top edge of the active form Integer value representing the distance in pixels right between the right edge of the subform databox and the left edge of the active form Integer value representing the distance in pixels bottom between the bottom edge of the subform databox and the top edge of the active form Chapter 20 CAL Commands 254 of 342 ChemBioFinder 13 0 PerkinElmer For the Better Remarks It is not currently possible to set the data source or link fields of a subform using CAL SUBFM example This example uses the SUBFM command to create a large subform in the middle of the form SUBFM 50 50 600 300 Box manipulation commands FORMEDIT ON OFF SELECT box UNSELECT box DELBOX box SETFIELD box fieldname SETTEXT box text ACTIVATE subform DEACTIVATE SCALE SCALE_TO_FIT To work with a box or subform on the form you specify a keyword followed by a box identifier A box is identified in one of two ways By point Give the coordinates of a point anywhere within the box When coordinates fall in more than one box the most recently created box is used By text The text you enter to identify a box may be The field name if the box con
282. o the file you want to add select it and click Open The item is added to the folder To rearrange items or folders in the tree drag the item to a new location To resort a folder or subfolder alphabetically right click on the folder and click Sort Folder from the context menu Toolbars ChemBioFinder 13 0 lets you format your toolbars You can Customize the toolbars by dragging buttons on or off To open the Customize dialog box Goto View gt Toolbars gt Customize The Customize dialog box appears Customize Commands Toolbars Keyboard Menu Options Categories Commands O New gt Open Close E Save Save As Add to Favorites Description Figure 16 6 Customizing toolbars To add an option to a toolbar that is already in the ChemBioFinder 13 0 window 1 Click the Commands tab in the Customize dialog box 2 Locate the command and drag an option from the Commands window to a toolbar in the ChemBioFinder 13 0 win dow The option appears where you drop it on a toolbar You can delete a button by dragging it off the toolbar To return a toolbar to the default settings Chapter 16 Customizing ChemBioFinder 13 0 207 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 1 Click the Toolbars tab in the Customize dialog box The Toolbars tab appears and shows all of the toolbars that currently appear in the ChemBioFinder 13 0 window Customize Commands Toolbars Keyboar
283. of 342 hemBioFinder 13 0 I j ia PerkinElmer For the Better Charges and radicals Charges or radicals specified on atoms in the query must match those in the target Uncharged atoms in the query may or may not match charged atoms in the target depending on the state of the appropriate check box in the Search tab of the Preferences dialog box The valence of a charged atom is taken to be the valence of the isoelectronic neutral atom With a substructure search the query with charge or radical y Finds any of Pr Does not find any of OH OH E ZE z O E Chapter 17 Structural Query Features 226 of 342 hemBioFi 13 I ChemBioFinder 13 0 PerkinElmer For the Better Isotopes Isotopic labels specified in the query must match the target Unlabeled atoms in the query match unlabeled or iso topically labeled atoms in the target Additionally D is treated interchangeably with 2H and T is treated the same as 3H With a Substructure Search the Isotopic query D oe A O C Finds any of a gt PAN D 2 ae 8CHg D D gt is Does not find any of oN HO SCH e CHa Ho N Stereochemistry Stereochemistry specified on the query must match the target if the relevant Match Stereo item is selected in the Search tab of the Preferences Stereochemistry is specified at a tetrahedral site by using stereo bonds up down either Stereochemistry about a double bond is specified
284. of aniline C lt sub gt 6 lt sub gt H lt sub gt 7 lt sub gt N Chapter 10 Chemical Properties 150 of 342 ChemBioFinder 13 0 PerkinElmer For the Better Mol Refractivity Is a measure of the total polarizability of one mole of a substance It is dependent on the temperature index of refrac tion and pressure The molar refractivity A is expressed as A gt N Where N N is the Avogadro constant and a is the mean polarizability This is the sum of the atomic weights of all atoms in a molecule Molecular Topological Index Is a graph index defined by n MII Y E i 1 Where E are the components of the vector E A D d Where A is the adjacency matrix and D is the graph distance matrix and d is the vector of vertex degrees of a graph _ Note An atom s degree is the number of non hydrogen atoms to which it is adjacent m z The mass to charge ratio is a physical quantity used in the electrodynamics of charged particles Two particles with the same m z ratio move in the same path in a vacuum when subjected to the same electric and magnetic fields Chapter 10 Chemical Properties 151 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 Num Rotatable Bonds Is the number of rotatable bonds in a molecule A rotatable bond is defined as an acyclic bond drawn as a single bond amide C N bonds O C N are rotatable where the atom on each end has at least one other non hydrogen sub stituent
285. of the field are displayed in plain text Adding pictures The Picture tool lets you create a Picture Box to display a bitmap BMP GIF etc or Windows metafile WMF EMF picture It can display a static file or a live one stored in a picture column of a database To create a static picture 1 Click the Picture tool 2 On the form drag to create an area for the picture to occupy The Open dialog appears 3 Inthe Open dialog box select the file you want to display then click Open The picture appears in your form _ Note The file is not actually embedded in the form Only its filename is saved with the form If you move or rename the file the form will not display the corresponding picture However if you make changes to the picture and keep its filename the same the picture in the form will be updated To create a Picture box linked to a field _ Note You must have a picture field in the database See Creating fields on page 72 for more information Click the Picture tool On the form drag to create an area for the picture to occupy The Open dialog appears Click Cancel A blank box appears in the form Right click in the box and click Properties oR OO N Inthe Box Properties dialog box select the picture field you want to link to the box and click OK The picture field item appears in the box To read in a picture file or to replace a picture in a Picture Box 1 Right click a picture and click Read Fi
286. ome situations you might want to merge two lists using drag and drop The result is a new list that has attributes based on the merged lists 1 Select a list and drag it onto another list The Restore Merge List dialog box opens 2 Select the type of merge you want in the Restore Merge List dialog box 3 Click OK A new list is displayed with the merged criteria you selected Restore Merge List oe L1 current list Replace use L2 anni C Intersect L1 andL2 L2 C Subtract L1 L2 aS hasl C Union L1 L2 C Subtract from L2 L1 Cancel Figure 15 4 Restore Merge List dialog box Saving query lists When you transfer data to ChemBioFinder 13 0 from BioSAR Browser ChemBioFinder 13 0 opens a file of type bsbxml and creates a form to simulate the BioSAR setup At the same time it restores whatever hit list was in effect in BioSAR In ChemBioFinder 13 0 the BioSAR hit list is automatically saved when you save close and reopen a file This is different from the default in previous versions Domains The Domain feature in ChemBioFinder lets you create a subset of a database Once created a domain acts as if it is a full database Any database searches you perform are limited to only the domain Any hit lists you create will be added to the query tree as if you are working with the full database Chapter 15 BioSAR 196 of 342 ChemBioFinder 13 0 PerkinElmer For the Better Creating a domain Before you create a
287. ommand starts a program but does not return from it To return to ChemBioFinder you need to use Task Manager or click in the ChemBioFinder frame win dow EXEC_BUTTON transfers execution to the script connected to a particular button where boxname is the button s box name in the Box Properties dialog box usually the same as the text on the button DDE sends a Dynamic Data Exchange message to a specified application Follow the DDE keyword with three argu ments The service name usually the name of the recipient application The topic name a string recognized by the recipient identifying the nature of the message It is typically SYSTEM The command an instruction to the service indicating what you want it to do OUTPUT_STR gives CAL access to the output window used by Python where string writes a string into the output window followed by a new line The command brings the window up on the first call if necessary The string need not be quoted even if it contains multiple words Details of these components depend on the service you are addressing The table below shows examples of Program Execution Commands CALL execute script file located myscript in scripts directory DOS erase execute DOS command to junkfile dat delete a file EXEC notepad e execute Windows program DDE CHEM3D CFWIN open benz mol send DDE message to qual ified service CAL commands CALL syntax Executes the specified CAL scr
288. on 235 unsaturation in queries 235 username for secured forms 64 using atom lists 133 ChemFinder with databases 11 current molecule as a query 119 form tools 35 grids 35 keyboard shortcuts 201 log files 89 periodic table 208 scripts 218 scripts in subforms 160 Visual Basic 220 Chapter 22 Index 340 of 342 ChemBioFinder 13 0 I PerkinElmer For the Better V valence charged atoms 226 checking 203 non standard state 203 unfilled 225 vapor pressure 154 variable commands CAL 281 view format for structures selecting 41 viewing models with Chem3D 82 results 118 structures 41 structures in Chem3D format 42 viewing subform data in a table 159 Visual Basic 220 WwW water solubility 154 Weiner index 154 Windows metafiles 36 38 39 WMF file format 39 Word files exporting 94 working with multiple hit lists 132 subforms tutorial 30 Working with Clustering 175 working with structures using ChemDraw 80 Chapter 22 Index 341 of 342 ChemBioFinder 13 0 PerkinElmer For the Better working with subforms 158 X X halogen special atom type 231 232 Z zoom 167 zoom on drag 164 Chapter 22 Index 342 of 342
289. on the active form PICT left top right bottom filename The PICT command has the following arguments Integer value representing the distance in pixels between the left edge of the box and the left edge of the active form Integer value representing the distance in pixels top between the top edge of the box and the top edge of the active form Integer value representing the distance in pixels between the right edge of the box and the left edge of the active form Integer value representing the distance in pixels bottom between the bottom edge of the box and the top edge of the active form Name of the Windows meta filename file to display in the picture box Remarks If the Windows metafile is in ChemBioFinder s standard search path only the actual file name and extension BUT TRFLY WMEF is required Otherwise the complete file path c some long path BUTTERFLY WMEF is necessary Chapter 20 CAL Commands 252 of 342 ChemBioFinder 13 0 I ee a PerkinElmer For the Better PICT example This example uses the PICT command to create a large picture field toward the right of the form and display in it the BUTTRFLY WMF picture in the ChemBioFinder System directory PICT 300 100 500 300 buttrfly wmf CAL commands BUTTON syntax Creates a new button on the active form BUTTON left top right bottom filename The BUTTON command has the following arguments Integer value representing the distance in p
290. ool is active the Edit menu commands apply to the boxes themselves When the selection tool is not active the Edit Menu commands apply to the contents of the active data box To select an object on a form Click the Selection tool on the Form toolbar then click an object on the form to select it A highlight appears around the object indicating that it is selected To select multiple objects on a form 1 Click the Selection tool on the Form toolbar 2 Do one of the following a Press the SHIFT key and click on the multiple objects Drag the Selection tool around the boxes you want to select Chapter 4 Forms 47 of 342 ChemBioFinder 13 0 PerkinEl For the Better To select all the objects in the form Goto Edit gt Select All Moving objects Use the Selection tool to move data boxes or other objects to a different place on a form To move objects on a form 1 Click the Selection tool on the Form toolbar 2 Select the object to move 3 Dragthe object to a different place 7 Note To move a subform you must drag the title bar of the subform not its contents If an object is nearly in the right place you can nudge it to get it exactly aligned To move an object one pixel at a time 1 Select the object you want to move 2 Press an arrow key in the direction you want to move the objects The objects move one pixel in the direction of the arrow key Resizing objects Use the Selection tool to re
291. ord gt Sort 2 In the Sort Multiple window select from the left pane the subform field by which you want to sort the hit list The subform field is displayed in the format subform name field name To sort the hit list by more than one field select the fields in order of priority 3 To reverse the order in which values will be sorted right click the field name in the right pane and select Descend ing in the pop up menu 4 Also in the pop up menu select the value in the field you want ChemBioFinder to sort by max min average or sum The default is Min 5 Click OK Query hit lists The Queries tab in the Explorer window maintains a list of search queries from the current and previous sessions Que ries are associated with forms So the query hit list is saved when you save the form Viewing the query list When you open an existing form the tree updates to show only the queries for that form The Explorer Window must be visible to view the Queries control If it isn t visible do the following 1 Goto View gt Explorer Window 2 Click the Queries tab to display the Queries tree Query list operations Each time you perform a search or list operation a new query is generated in the tree ChemBioFinder assigns a name to the query and displays it in the tree along with the size of the list number of hits and a brief description The generated name is Q lt n gt where n is a sequential number and indicates that t
292. orm view To retrieve all the records in your database Double click Full List in the Explorer window Name searching The query feature provides several options for searching for text in a database For example to find all compounds in the CS_Demo database with molecular names starting with benz Switch to Form View if you are not already in it Goto Search gt Enter Query The form appears in the Query mode Click the MolName box and type benz Press ENTER All records are returned with names starting with benz ao A OO N gt Go to View gt Data Table gt In Current Window The Table view appears Browse to verify that the molecular names are correct Tip Although the tutorials describe the use of the Search menu you may find using the Search toolbar more con venient The icons on the toolbar match those you have already seen on the Search menu Clicking the Find icon is equivalent to pressing the ENTER key when you are ready to begin your search See Queries on page 97 for information on more advanced use of the Search toolbar Chapter 3 Tutorials 21 of 342 ChemBioFinder 13 0 PerkinEl For the Better F Note Notice that this search gave you benzene but not bromobenzene The query you entered above is an anchored substring and only gives you strings starting with the indicated substring For more information on how to specify text searches see Text searches on page 97 Num
293. ou can also provide the database connection information used to log on to an MS Access database MS Access pro vides a security system that allows the creation and management of usernames and passwords and the assignment of permissions to those usernames MS username password account information is stored in the Workgroup Infor mation file mdw mda For more information about securing an MS Access database Opening a secured MS Access database on page 61 Setting security options To set what ChemBioFinder 13 0 form options are available to users 1 Right click in the form you want to secure and click the Properties The Box Properties dialog box appears with the Form tab displayed 2 Click Security The Form Security dialog box appears 7 Note The Security button does not appear if the security on your form has been set to not allow access to the Secu rity options Chapter 4 Forms 51 of 342 P PerkinElmer For the Better ChemBioFinder 13 0 Form Security 2 Database secunty Forms Y Automation Password V Cut copy paste Y Browse l M Searching Workgroup Information File Y Update records Y Import data Export data Print Figure 4 9 The Form Security dialog box Tip The lower left comer of the dialog box indicates whether security is defined 3 Type the Username to use for logon in the Username box The Enable button becomes available 4 Type the Password to use for logo
294. ow The output window is a dockable window for displaying output from scripts The window comes up automatically the first time it is needed The text in the window is not editable but can be copied to the Windows Clipboard for pasting into other applications Standard keyboard accelerators such as select all CTRL A or copy CTRL C can be used To generate output in the window from a CAL script use the OUTPUT_STR command OUTPUT STR string or phrase which echoes string or phrase into the window followed by a carriage return The string should not be quoted Chapter 16 Customizing ChemBioFinder 13 0 216 of 342 ChemBioFinder 13 0 PerkinElmer For the Better The string goes through the CAL translator and may be modified with regard to spacing or internal quoting To prevent translation and have the string taken verbatim precede it with a backslash character OUTPUT STR use this as written Output from a Python script uses the same mechanism To copy text or clear the output window Right click anywhere in the window and choose the desired command from the context menu Programming in Python Python programming is possible in Pro and Ultra versions but not in Standard version A description of the Python language is beyond the scope of this manual However to learn more about Python you will find numerous books and Internet resources on Python as well as the Python Help file This section covers pro gramming topics with specific a
295. ow is available in Pro and Ultra versions but not in Standard version Chapter 3 Tutorials 20 0f 342 hemBioFi 13 I ChemBioFinder 13 0 PerkinElme For the Better To toggle between the different views go to View gt Switch Views or Ctrl W _ Note As you view the records counters in the Status bar indicate the current record the current list size and the total size of the database To view the database in a table that shows the records in a list do one of the following Goto View gt Data Table gt In Current Window E Click the Switch to Table tool Type CTRL T 7 Note The Switch to Table tool is a toggle Select it again to retum to the Form view The Table view appears and displays all the records of the current list in this case the records that were returned by the search in a table The table view provides several options for you to examine the search results For example You can sort the records by a specific field in Table View For example to sort by the MolWeight field double click on the MolWeight table header You can change the column widths of your table Position the pointer over a table header divider and drag to the width you want You can adjust the height of any form Drag the bar divider on the left To use continuous forms to browse your records Goto View gt Continuous Forms The Continuous Forms view appears By default the Continuous Forms view shows the same form as the F
296. page 170 A toggle which selects the mode of operation when you drag a rectangle on the plot If Zoom On Drag is Zoom on Drag defines the area you want to examine and releasing the drag will cause the plot to zoom in on that area V a rectangle selects the points within it without changing the scale You can use zoom to reset the scale e Rescale to All Unzoom Resets the scale after a zoom or a series of zooms f Scales the plot so that the visible points fill the plot window Points Autoscale Automatically rescales every time you change the list that is perform a search restore a list etc Locked Locks the display See Plot options on page 162 for details Copy Image Copies the plot to the Clipboard allowing it to be pasted into other documents Creates a hit list from selected data points The list is displayed in the Queries Tree and is treated and sa Selection to List QUE Y You cannot use Restore Query on a list selected this way but you can use Restore List to retrieve the rec Chapter 12 BioViz 164 of 342 hemBioFi 13 I ChemBioFinder 13 0 PerkinElmer For the Better Viewing Plots ChemBioFinder provides three windows to view data in a BioViz plot Structure displays structures of data points as you mouse over them used when the form is not visible or is dis playing a different record Details displays data for selected fields either from the database or from child
297. ple of points are worth noting Export to Word is much slower than to other formats For this reason you should probably limit the use of this option to relatively short hit lists You can speed up the export by not exporting the structure field Structures are exported as OLE objects and can be edited in Word with the ChemBioDraw Control If you should by accident begin exporting a large database you can terminate the export by bringing Chem BioFinder 13 0 to the front and pressing the Esc key Chapter 7 Importing and Exporting Data 94 of 342 ChemBioFinder 13 0 PerkinElme For the Better Exporting to SDFile When you export to SDFile you are allowed to export subform fields Each subform field is exported to a separate rec ord in the SDFile but separate subform records are concatenated into a single multi line text block To export subforms 1 Go to File gt Export gt SDFile The Data Export dialog box appears 2 Click the Text Options tab and select the Export subform data check box 3 Return to the Export tab In the Field column of the Data Fields table all subform fields now appear with checks in the check box next to the field name Deselect any subform fields you do not wish to export and select those main form fields you do wish to export 4 Click Export _ Note Re importing a file of this type will not regenerate the original database It will bring back the data but not in the subtables and subforms you
298. pplication to ChemBioFinder Python operates on your data through the ChemBioFinder OLE Automation interface This interface provides external access to a library of the objects you work with in ChemBioFinder application document form recordset fields boxes and others The interface is documented on the ChemBioFinder SDK site You may find it more convenient however to use an object browser to see the library in its current form To illustrate we will develop an example Python script Suppose you have a form open you perform a search and get a hit list You would like to generate a report that contains a set of records in formatted blocks showing specific data items You can perform this task using the script shown below You can copy and paste the script into the Script Editor to try it or use it as a template ChemFinder Python script Generate Report Created Wednesday November 01 2006 10 55 AM Loop records printing name and formula from win32com client import GetActiveObject cfapp GetActiveObject ChemFinderll Application cfdoc cfapp ActiveDocument cfrset cfdoc Recordset namefield cfdoc Fields molname fmlafield cfdoc Fields formula recno 1 cfrset MoveFirst while not cfrset EOF molname cfrset Value namefield index formula cfrset Value fmlafield index print Rec str recno Name molname Formula formula cfrset MoveNext recno recno 1 namef
299. pure solvent The change in boiling point is calculated using the formula AT Kpm Chapter 10 Chemical Properties 146 of 342 ChemBioFinder 13 0 Where K is the molal boiling point constant m is the concentration of the solute expressed as molality and AT is the change in temperature Chemical Name This is the name of the chemical Cluster Count Is the number of paths of a given length in the distance matrix Connolly Accessible Area This is the locus of the center of a spherical probe representing the solvent as it is rolled over the molecular model Connolly Molecular Area This is the contact surface created when a spherical probe representing the solvent is rolled over the molecular model Connolly Solvent Excluded Volume This is the volume of space bounded by the solvent accessible molecular surface Critical Pressure Reported in bars this is the least applied pressure required at the critical temperature to liquefy a gas Critical Temperature Reported in Kelvin this is the temperature above which a gas cannot be liquefied regardless of the pressure applied Critical Volume Reported in cm mol this is the volume occupied by one mole of a substance at the critical temperature and pressure To report the boiling point Elemental Analysis This is a process in which a material is analyzed for its elemental and isotopic composition Elemental analysis can be qualitative determining what elem
300. r subform fields Tips for optimizing performance When working with a large data base or multiple forms you will want to ensure that you can still work efficiently To do so there are a few techniques you can use to improve ChemBioFinder s performance even when you are working with a lot of data Chapter 15 BioSAR 198 of 342 ChemBioFinder 13 0 Perkin For the Better Use domain linked forms Using a domain offers a significant speed advantage compared to working with the full database If you choose Retrieve All after performing some queries you will get only the domain as the full database Since the domain is typ ically much smaller than the database it was created from the query and restore commands are executed much faster Another advantage is that the domain is non volatile that is the view remains on the server until you delete it If you routinely work with a particular subset of a large database creating a domain eliminates the need to perform the initial routine query or create a local database You only need to save the domain information by saving the form The next time you open that form you see only the domain A third advantage is that the sort order at the time of creation is preserved Sorting is a time consuming operation By using a domain you can sort once and save the preferred order To more information including how to create a domain see Saving query lists on page 196 Minimize child tab
301. r plish Whether or not to highlight matching mapped atoms in a reaction in color This parameter can be set man ually in the Display tab of the Preferences dialog box The default is O do not high light Whether or not to display implicit hydrogens on all atoms bearing a charge or radical The default is 1 display DISPLAY SHOW_H_ON_HET Whether or not to display Chapter 20 CAL Commands 271 of 342 ChemBioFinder 13 0 DISPLAY SHOW_H_TERM_C SHOW_RXN_CENTER CFW_METAFILES OPTIONS DDE_TIMEOUT Chapter 20 CAL Commands DISPLAY OPTIONS pP PerkinElmer For the Better implicit hydrogens on all het eroatoms This parameter can be set manually in the Display tab of the Pref erences dialog box The default is 1 display Whether or not to display implicit hydrogens on all ter minal carbons This param eter can be set manually in the Display tab of the Pref erences dialog box The default is 0 do not dis play Whether or not to highlight reaction centers This parameter can be set man ually in the Display tab of the Preferences dialog box The default is O do not high light Whether to generate pic tures using ChemBioFinder or using ChemDraw when copying a structure to the clipboard The default is 0 use ChemDraw to generate Number of seconds to wait for a response to a DDE transaction 272 of 342 ChemBioFinder 13 0 pP PerkinElmer For the
302. r 4 F Onis icc cee ey eects see ee caer e ee BU eI ue ee e 32 Creating forms automatically o 2 002222 c cece cece cece cece cece eee c cece eee eeeeeeeeeteeteeeeees 32 Sa E U el ap ccc 33 Creating forms ManuallY oocccccccccccccccccco coco 34 Selling box properties iio canas dt da a dd cite 40 Editing OMS covevool lotes tetas tees a td Ra e E tiene 47 Chapter 5 Databases nes 59 Selecting a database eee 59 Opening databases eee 62 Table of Contents i ChemBioFinder 13 0 I PerkinE For the Better Browsing databases ieee anaes ete eer eee Wie ede aioe E dete suchen router adas 64 Creating a database 2 eee 70 Creating a portal database 22 22 22 eee 76 Chapter 6 Working with Data 2 22202 c aa raaraa oaa cccceececceeceeeeees 77 Entering data cnn 77 Editing data osteo eerie tse eect ate isos 79 SOMING Caley ne x se Gee se a ee Bg ee oe ee a hse nee cea 84 Resetting the database oo eee 85 Changing the database scheme 2 2 22 eee 85 Chapter 7 Importing and Exporting Data 22202020 c cece cece cece annann annn 87 Supported file formats 0 0 0 0 2022 c cece ec ccc cece ccc ccc cc ne 87 Importing data 2 ccc ccc cc cece cece cece cece cece cece cece eee c cece cece eee ce cece eeeeeeeeeeeeeeeeeees 87 EXPOMING data Seas os Mads sock Sesceniddeeet sess adedesh scice Voebsheslcoseakcs sos cel Videdsdece so ceteunee seeded 93 Chapter 8 Queries 2 2 22 o oo nine 97 TOEXUSCAICNES a2 cretino ee
303. r comments to be displayed on the plot 1 Right click in the plot then click the Properties The BioViz Plot Properties dialog box appears o Tip You must right click either in the plot area or in the top border Clicking any other border brings up different con text menus See Changing the display on page 167 for details 2 On the Display tab enter your legend in the Comment text box You may also enter a font and point size for the legend 3 Click OK to display the legend The default position for the legend is in the upper right comer of the plot After you have created it you may position it where you want by dragging it To remove the legend open the BioViz Plot Properties dialog box and delete the text in the Comment box Background color You can choose any background color you want for a chart A Color button on the Display tab of the BioViz Plot Properties dialog box opens a color picker dialog box Chapter 12 BioViz 173 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 Other changes Extended state saving Filter slider positions and colored by state of plots are now saved with the form Improved Filter display See Filtering on page 170 for details Improved statistical display See Statistical analysis on page 168 for details Improved Histogram bar coloring See Histograms on page 161 for details Chapter 12 BioViz 174 of 342 ChemBioFinder 13 0 PerkinElmer For the Better Clusterin
304. r defined maps are not checked and are considered legitimate Locate deleted structures Identifies structures that have been deleted from structure boxes Representational Drift Checks several invisible aspects of stored chemical structures and ensures that the stored chemical structures are up to date with the latest software version _ Note When the Interactive option is selected the application displays dialog boxes with wamings and errors if any However if you select the To file option you need to provide the path for storing the log file containing warn ings and errors In this case errors and wamings are not displayed in dialog boxes To perform a Check structures search 1 Select the categories of interest 2 Click Scan When a structure is flagged its record is displayed the offending atom or bond if any is flashed and an alert offers the user several choices The options are ignore the error and con tinue checking the same structure rewrite the MST record thus correcting the prob lem Continue the scan from the next structure stop the scan This leaves you on the last record that exhibited a problem flash the problematic atom or bond Chapter 8 Queries Don t know or ignore is specified or has stereo Skip to next struc ture Stop Scanning 124 of 342 ChemBioFinder 13 0 PerkinElmer For the Better This button only appears when the error revolves
305. r used for all subsequent box creation FONT fontname size style r g b The FONT command has the following arguments String containing the name fontname of a font from your Windows font list String containing the size of size the font in points String containing the style in Chapter 20 CAL Commands pP PerkinElmer For the Better 265 of 342 ChemBioFinder 13 0 which to display the font as described in Settings String containing the red component of the font color in the range from 0 to 255 String containing the green component of the font color in the range from 0 to 255 String containing the blue component of the font color in the range from 0 to 255 Settings The settings for style are CAL commands SEEPTAB syntax Displays the Periodic Table window then closes it SEEPTAB decisecs The SEEPTAB command has the following argument Chapter 20 CAL Commands pP PerkinElmer For the Better 266 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 Amount of time to display decisecs the Periodic Table window before closing it Remarks 10 decisec 1 second If the decisecs argument is omitted the Periodic Table window will be displayed for 4 seconds CAL commands QUIETCLOSE syntax Closes the topmost form immediately without checking to see if it has been modified QUIETCLOSE The QUIETCLOSE command takes no arguments
306. raw Properties 2 22 0 0222222 nn nn cnn 155 Chapter 11 Relational Data and Subforms 2 2 0 0222 2 c cee ccceeeeeceeeees 156 Access relational data 2 2 0 2 00 nee nee nee ne cence eee e eee eeeeeeeeeeeeeees 156 Creating a subform 2 2 eee cece eee eee e cece cece cece cece cece cece cece cece DoE Ea aaaea aeann 156 Working with subforms 222222222222 cece eee cece ccc ccc cece ee ce eee ee cece eee eebeeeeeeeeeeeeeeeteeeeeeeeeees 158 Searching a subform cnc 159 Chapter 12 BioViZ 2 2 2 22 0 c cco ccc ccc eee rra 161 Creating a plot cocotero ita 161 MEU AS A IA 165 Plotting queries 2222 22 c cece cece cece ccc nas 165 Changing the display ooooocccccccccccccccccccccccccccccccccn cnn 167 Statistical amalySiS oooooooccccccccccccccccccccccccccccocoooooococococon conocen 168 Customizable Styles cnn cnn ccnncne 173 Chapter 13 Clustering in BioViz oooooccoccccccccccccccccccccnnccncncnonnonncnonoococncccccccccccccio 175 ESAS iii eee 175 Working with ClUSteridg ooooccccccccccccccccccccccccccccccccnc 0000o ea erinra e be eeeeeeeeeeeeeeeeeeeeeeeeeees 175 Modifying Clustering 2 22 2 eee cc cece c cece cece cece cece cece eee e eee AoE ADEA aa nanaonan 177 CS Clustering Dialog features 2 222 222 occ cece ccc ccc ccc eee cece ce cee eee ceeteeceteeeeeeeeeereeeees 179 Chapter 14 ChemBioFinder Oracle 2 2 2 022222 ccc cece cece ccc cc
307. rdinates are specified in this order left top right bottom Units are in pixels the origin is at the upper left with coordinates increasing from left to right and top to bottom so that coordinates will range from left 0 to right 640 or 1024 or whatever fits your screen and from top 0 to bottom 480 or 768 or similar When a new box is created it adopts the current font To specify a particular font for a box use the FONT command prior to creating the box When specifying a script name give one of the following The complete pathname of the script file A simple name without extension if the script is stored in the standard scripts subdirectory with the standard file extension If the script name appears on the Scripts menu you can use the name from the menu The table below shows examples of Box Creation Commands create frame with label at upper left Frame 10 10 Chapter 20 CAL Commands 247 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 300 60 Molec ular Formula DBOX 20 20 create data box for formula 290 50 formula in above frame TEXT 100 100 300 150 A create static text string Label PICT 500 300 600 400 C LOGO WMF put specified picture at lower right BUTTON 500 10 550 40 DEMO create button at upper right to run script DEMO CFS CAL commands DBOX syntax DBOX creates a new data box on the active form DBOX left top right bottom fieldname The DBOX
308. re new rows in the hits table Each row contains the new list ID alongside the ID of a record from the searched table 6 The final list is prepared by a join selecting rows from the main table which have record ID s matching those of the new list in the hits table The resulting list is ready to browse save export etc _ Note Text searches in Oracle are case sensitive You will get different hits from the query benz than from wm Benz Chapter 21 CS Oracle Cartridge 298 of 342 ChemBioFinder 13 0 PerkinElmer For the Better Index iN query 100 in query 111 1 1D plot 26 2 2D plot 27 3 3D properties 104 3D searching 104 3D structure display 42 A A any special atom type 231 Access attaching tables from 71 manipulating MDB files 221 multi user 63 read only 63 secured 64 Access database opening 61 accessing relational data using subforms 156 ADD indicator 17 Chapter 22 Index 299 of 342 ChemBioFinder 13 0 I PerkinElmer For the Better ADD indicator description 8 ADD indicator when displayed 10 add new record command 77 adding buttons 39 checkboxes 39 data 77 data box menu 43 fields 72 menu to a data box 43 pictures 38 plain text 37 records 10 19 77 scroll bars 43 structures T77 tables 85 160 aligning objects 50 aligning and distributing objects 50 alternate groups searching with 104 alternative groups attachment point symbol 106 defining 105 description 104 ancho
309. re with a corrected version By default this scan begins at the currently displayed record and proceeds to the end of the record set or until the scan is aborted You can change this by unchecking the box at the bottom of the dialog box Check structures in database Things to check V Ambiguous stereochemistry MV valence charge Net charge present MV Unrecognized atoms Mass imbalance reactions only MV Doubly drawn atoms I 3D not scaled in Angstroms Y Misc nonsensical isotopes False stereomarks CDX lt gt Mst correspondence Atom atom maps Locate deleted structures Y Representational Drift Defaults Interactive To file a V Scan will begin at current record Figure 8 23 Check structures in database dialog box The following properties can be checked Ambiguous stereochemistry Flags structures with ambiguously drawn tetrahedral or double bond ster eochemistry Not correctable Valence charge Flags structures containing an atom with an impossible valence or charge Sometimes cor rectable Net charge present Flags structures containing a net charge This option is not checked by default because it is not normally useful Not correctable Unrecognized atoms Flags structures containing an atom that was not interpreted by ChemBioFinder 13 0 ChemBioFinder 13 0 Such atoms typically have atom type R with a greyed text label containing question marks Not correctable Mass imbalan
310. red substring text queries 97 AND operator hit lists 131 AND operator queries 97 100 110 annotations showing 201 Chapter 22 Index 300 of 342 ChemBioFinder 13 0 I PerkinElmer For the Better ASCII file exporting 94 assigning fields to data boxes 17 atom lists 133 atom to atom mapping 108 atom lists 232 atom not lists 232 atom properties 231 atom types A any 231 and bond types 134 link node 134 M metal 231 overview 134 Q heteroatom 231 X halogen 231 atoms 223 attaching tables from other applications 71 attachment points defining 106 tool 106 automatic labels 37 autoscale 28 autoscale see also rescale 28 B backing up databases 75 Balaban index 146 Chapter 22 Index 301 of 342 ChemBioFinder 13 0 I PerkinElmer For the Better bin definition 163 BioViz changing fields 167 curve fitting 168 description 7 details window 165 empty points 165 filter sliders 172 histogram plots 161 selecting points 165 setting display range 172 statistical analysis 168 BioViz plot points 165 BioViz about 1 bitscreen 241 boiling point 146 bond length uniform 201 types overview 134 bond properties 236 in queries 236 ring chain 237 bond types double either 224 in queries 224 special 236 bonds 223 boolean field fields boolean 74 Chapter 22 Index 302 of 342 ChemBioFinder 13 0 I PerkinElmer For the Better boolean operations in queries 97 boolean operations on hit lists 131 box creat
311. relative tetrahedral search preferences square planar tetrahedral trigonal bipyrimidal stopping queries Struct gt Name TM structural query features structure display preferences queries registration options searches structure box description structure field structure mode structure window description structures adding as pictures checking chemistry chemically significant text cleaning copying as text strings editing entering Chapter 22 Index pP PerkinElme For the Better 104 227 117 229 116 227 227 227 118 93 223 200 101 203 101 70 74 102 77 81 81 81 80 93 80 80 203 336 of 342 ChemBioFinder 13 0 I PerkinElmer For the Better file formats 87 importing 88 query properties 223 red highlighting in queries 110 119 scaling 201 sorting 84 structures importing only 88 style box changing 41 style definition 163 styled text 83 subform fields exporting 95 subform description 7 subforms changes in ChemFinder 9 156 creating 157 data table 159 linking fields 156 overview 156 searching 159 switching between forms and data tables 159 tutorial 30 using scripts 160 subforms tutorial 30 submitting queries 118 substituents 224 exactly 232 free sites 234 in queries 224 233 up to 233 Chapter 22 Index 337 of 342 ChemBioFinder 13 0 substructure searches substructure searching substructure searching see also full structure searching substructure searching see
312. rence do one of the following Click Find Prev Use the SHIFT F3 key To replace text 1 Right click in a memo or plain text field and select Replace The Find and Replace Text dialog box appears 2 Inthe Text to find text box enter the text to be replaced 3 Inthe Replace with text box enter the text that will replace the text specified in the Text to find text box 4 Click Replace Memo fields can store Styled Text For more information see Styled text on page 83 Date field lets you store dates The dates are displayed according to the settings in the Windows Regional Set tings control panel Chapter 5 Databases 73 of 342 ChemBioFinder 13 0 PerkinEl For the Better El uctu field Consists of four fields a numeric ID stored in the relational database plus three fields Struc ture Formula MolWeight that take data from the ChemBioFinder 13 0 structure database files w Boolean Used with check boxes When searching Boolean fields you can only search for ON This is because ChemBioFinder 13 0 automatically clears all fields when activating the Queries form You can create more than one set of structure fields in a table Each is assigned a unique set of names and each refers to its own ID column in the table although all structural data is taken from the same structure database files To create a field Right click in the form and click Properties The Box Properties dialog box appears Click the
313. rer window double click the Structure field to add another Structure field to the form 2 Right click in the field and click Properties 3 Inthe Box Style section select Structure ChemBio3D style from the drop down menu The Structure field dis plays a 3D structure DEMO_copy cfw molecule name L Aspartic acid formula C4H7NOg moLid E Figure 6 3 Form with 3D structure field To rotate the model or modify the display double click in the field The default tool is the rotation tool but it also can be used to select atoms or bonds If you right click in the field the context menu displayed is the ChemBio3D control context menu giving you access to ChemBio3D commands See the ChemBio3D User s Guide for more information about using ChemBio3D _ Note Unlike interaction with ChemBioDraw changes you make to a model within ChemBio3D are not trans mitted back to ChemBioFinder 13 0 and thus are not saved You can put a picture of the ChemBio3D model into Chapter 6 Working with Data 82 of 342 hemBioFi 13 I ChemBioFinder 13 0 PerkinElmer For the Better adatabase by saving the ChemBio3D model as a bitmap or metafile and inserting it into a Picture field The picture does not retain a connection table and cannot be edited Styled text Make changes to text fonts sizes styles colors and alignment with the tools on the Text menu or the Text Format toolbar To display the Text Format toolbar
314. rkinElme For the Better ChemBioFinder 13 0 Understanding forms and databases A database is where data is stored whereas a form displays but does not store the data The form acts like a window into the database letting you select which fields and tables you want to view You can create more than one form to access the database For example you can create one sample form for working with structural data and another to include literature or lab data By switching between forms you can look at just those fields you want to see While no data is stored in a form some things are saved with it BioViz plots database queries depending on pref erence settings file paths of linked graphics and certain settings are saved with each form Chapter 2 Getting Started 14 of 342 hemBioFi 13 I ChemBioFinder 13 0 PerkinElmer For the Better Tutorials The general steps for using ChemBioFinder 13 0 are 1 Create or open a form 2 Create or open a database and link it to the form 3 Add or manage data 4 Perform a search The tutorials introduce you to ChemBioFinder 13 0 basic functions We recommend performing the tutorials in the sequence they are presented because each tutorial builds on and refers to the previous ones Sample databases The Samples directory contains several small databases forms and sample scripts By default these files are in the Samples folder at C ProgramData CambridgeSoft C hemOffice2012 ChemFinder S
315. rm and its contents SCALE scales all items in the current form by the percentage factor you specify Use this to fit your forms to different size screens See SCALE_TO_FIT below SCALE_TO_FIT scales all elements in the form such that the string you specify will fit in the form at the currently selected font size See FONT below The table below shows examples of Box Manipulation Commands select formula frame created above select formula data box created above change field for formula data A Adl molweight box to molweight CAL commands DELBOX syntax Deletes a data box frame static text box picture box button or subform the active form DELBOX box The DELBOX command has the following argument Box identifier indicating the box to delete Remarks The DELBOX command is a shortcut for FORMEDIT ON followed by SELECT followed by the Menu Command Edit Clear The DELBOX command deletes only the box not its actual contents For example deleting a button does not delete the CAL script file from your disk Chapter 20 CAL Commands 256 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 CAL commands SETFIELD syntax Connects a database field to an existing data box or a CAL script name to an existing button or replaces one already connected SETFIELD box fieldname The SETFIELD command has the following arguments Box indicating the target Stri
316. rs in the edit window You can mod ify and manipulate the structure just like any other ChemBioDraw structure If there is no structure in the Structure data box the edit window is blank You can draw a structure to store in the ChemBioFinder 13 0 database When you have finished do one of the following If you are editing in ChemBioDraw go to File gt Exit and Return to Structure or type CTRL W Ifyou are editing with the ChemBioDraw Control click outside the Structure box The new or edited structure is now displayed but has not yet been added to the database 2 Goto Record gt Commit Changes then click the Commit Changes icon or move to a different record The changes are stored With a few exceptions you can store any chemically meaningful structure or reaction that can be drawn in Chem BioDraw Within ChemBioDraw you can confirm that a structure is chemically meaningful by selecting it and using the Structure gt Check Structure menu command For more information see the Chem amp Bio Draw User s Guide Two exceptions are ChemBioFinder 13 0 does not support importing molecules with multiple or variable points of attachment such as ferrocene ChemBioFinder 13 0 does not recognize bare heteroatoms For example if you draw the following structure N ChemBioDraw reports an illegal valence when you choose the Check Structure command ChemBioFinder 13 0 auto matically infers hydrogen atoms to main group ele
317. ructure data box the data of the Structure field for the first record in the CS _ Demo database appears To assign fields to the other data boxes Chapter 3 Tutorials 17 of 342 ChemBioFinder 13 0 PerkinEl For the Better 1 Right click another box click Properties and select Molname from the properties list Click OK The Molname field in the database is linked to this box and the data for the first record appears in it _ Note After you open a database and table the shortcut menu displays the database fields Right click in another box and click Formula Right click a third box and click the MOL_ID Go to File gt Save As Inthe Save As dialog box save the form as tut2 cfx in the directory of your choice oOo a bh Y N Goto File gt Close Congratulations You have created your own customized form for viewing the CS_Demo database Tutorial 3 Creating a database In this tutorial you will create a new database and use automatic form generation method 1 Create a new form 2 Right click in the form and click Data Source The Form Properties dialog box appears with the Database tab dis played 3 Click Create Database The Save As dialog box appears 4 Type mydb and click Save The name of the database appears in the Properties box ChemBioFinder 13 0 creates one data table MolTable that contains four fields Structure Formula MolWeight and MOL_ID 5 Click the Field tab The options for creating a
318. s and Reaction Data files RDFiles directly into a database In addition you can import text files that are comma or tab delimited Because ChemBioFinder 13 0 uses the Access Jet database standard names of fields controls and objects must conform to Access rules These are May be up to 64 characters long Chapter 7 Importing and Exporting Data 87 of 342 pP PerkinE For the Better ChemBioFinder 13 0 May include any combination of letters numbers spaces and special characters except a period an excla mation point an accent grave or brackets Must not begin with leading spaces Must not include control characters ASCII values 0 through 31 Must not include a double quotation mark in table view or stored procedure names Importing structures ChemBioFinder 13 0 imports structure files directly into a database You can choose to replace the existing records append new records or merge the data eliminating duplicates The general procedure for importing structures is 1 Use the File gt Import submenu to choose the type of structure file to import The Open Chemical Structures dialog box appears 2 Browse to a folder containing structures 3 Select a file or files using Ctrl click or SHIFT click and click Open The Data Import dialog box appears 4 Click File and select a database to import into _ Note You can also type in a name to create a new database file 5 Choose t
319. s and Reaction Data files RDFiles directly into a database Since these files contain both structures and data ChemBioFinder 13 0 creates fields in the database to accommodate the incoming data Chapter 7 Importing and Exporting Data 88 of 342 ChemBioFinder 13 0 J e PerkinElmer For the Better In RDFiles incoming data may be hierarchical and complex When loading RDFiles ChemBioFinder 13 0 converts the data to a relational form creating new tables as necessary and generating linking data _ Note When importing RD files boxes and subforms are created and positioned automatically If you have a blank form when you import ChemBioFinder 13 0 creates boxes on the main form If you have a form with boxes when you import new boxes are created on tabbed forms You can import with a form linked to a database a blank form or no form If you import with no form ChemBioFinder 13 0 creates a new form Selections you make on the Form Style tab of the Data Import dialog box determine what the form will look like To import structure and reaction data files 1 Use the File gt Import submenu to choose the type of structure file to import The Open dialog box appears 2 Choose the file to import and click Open The Data Import dialog box appears Data Import Import Logging Form Style Advanced Input file Scanning input file Stop scanning Data Fields Input Field Type Width Output Column Type MS Structure
320. s or pictures It is the only box that allows you to edit data in the database Data boxes do not have labels but you can label them by adding a Frame or Plain Text You can also use the Data Box to display static data not from a database To draw a Data Box 1 Click the Data Box tool 2 On the form drag diagonally to create a box To specify what type of data is displayed in the box see Setting box properties on page 40 If the form already has a database open you can right click in the data box select Field and choose from a list of the available fields Creating frames The Frame tool lets you create an enclosure with a label surrounding a data box or group of boxes When you draw a new frame you are automatically prompted for a text label to be attached to it To create a frame 1 Click the Frame tool 2 On the form drag diagonally to create a frame A framed box appears with the label Data To change the label 3 Right click on the label and choose Label from the drop down menu The Enter the label dialog box appears 4 Type the label you want to attach to the frame 5 Click OK A fixed label appears on the frame Another way to change a frame s label is in the Box Properties dialog For more information see Setting box prop erties on page 40 You can use a frame to show live data from the database If a frame is connected to a database field it is updated automatically as you browse or search For ex
321. s dialog box to set the form properties To create a new form do one of the following Go to File gt New Click the New File icon on the Main Toolbar The Database Tree is the same tree as in the Database Properties dialog showing the tables or views and columns of the currently open database When you open or activate a form or subform or change databases the tree updates to display the current database and expands to show the columns of the currently selected table To view the Database Tree if it is not visible 1 Go to View gt Explorer Window 2 Click the Database tab To use the Database Tree to build a form 1 Open a new form 2 Right click on the form and select Data Source 3 Click Open Database on the Database tab 4 Browse to a database and click Open 5 Click OK in the Form Properties dialog box The Database Tree displays the database Figure 4 2 Creating a form with the database tree 6 Double click the Structure field in the Database Tree A structure box appears in the upper left of the form Chapter 4 Forms 34 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 w a E Figure 4 3 Structure box created from the database tree 7 Continue double clicking the other fields 8 Use the Selection tool to move the data boxes to where you want them in the form Using the form tools You must use the Form Tools toolbar to design a form Box creation co
322. s in dendogram are highlighted to red and the ball in the Cluster window to blue 2 Click As you move the mouse across the two panes click on any node or ball This click will freeze the selected node or the ball color changes on freeze and you an easily move your mouse across the dialog box To unfreeze the selection click on any empty space in any of the window get original color 3 Drag You can change the shape and size of the dialog box Chapter 13 Clustering in BioViz 179 of 342 hemBioFi 13 I ChemBioFinder 13 0 PerkinElme For the Better 4 Re project cluster When you move the pink dotted line up or down in the left window dendogram pane the cluster window right pane will change the diagram accordingly 5 Show Properties Click the black arrow in the lower right corner of the cluster dialog box You will see the prop erties of the dendogram and the cluster 6 Right click On freezing any node ball you can easily perform actions on that particular node ball Right click on it it shows menu options Zoom Show structure window and Selection to list Zoom It changes the size of the data display beneath the viewing window T Show structure window The highlighted or freezed node ball structure is displayed correspondingly Selection to list It generates a hit list of the selected node ball Chapter 13 Clustering in BioViz 180 of 342 ChemBioFinder 13 0 PerkinElme For the Better ChemBioFinder Oracl
323. s in light grey color Show cutoff line is a pink line It describes the relationship between the dendogram an the cluster window Linear Log scale adjusts the attenuation of the tree by plotting the vertical horizontal node position on the scales In the Label frame click the drop down arrow and select the label to be displayed on the dendogram nodes or leaves Choose the Font for the label display Chapter 13 Clustering in BioViz 178 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 Cluster Properties amp CS Clustering r Ball size C sol ig E Highlight Shaded Labels Shade by mol_1D y None y _ _ M IA OS Dendrogram astes Figure 13 4 Cluster properties Inthe color frame Solid and Shaded specifies how balls to be colored in the display For Shade By select the data type from the drop down menu and choose a range of colors using a button at the end of the color gradient bar Ball Size adjusts relative sizes of the ball In Labels frame click the drop down arrow and select the text to be displayed on the ball Choose the Font for the label display CS Clustering Dialog features The various actions that you can perform on the CS Clustering dialog box to make the dendogram and cluster window look the way you want are as follows 1 Hover As you move mouse across the cluster dialog box the nodes or the balls it touches gets highlighted like the line
324. same for a given compound regardless of whether or not you ve done a sort or where the compound appears within a hit list A bad compound has a high score Chapter 9 Compound Profiles 137 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 7 a MolWeight LogP 1c50 soore 0 18 dist 0 18 Figure 9 2 A compound profile for MW LogP and IC 50 A compound profile is useful as a visual indication of the quality of each compound As such it is most useful in table view where you can see and compare several profiles at once The highest benefit comes from using profiles in sort search operations You can pose one compound as the query and then sort the remaining ones by deviation from that query Creating a compound profile Profiles are displayed on the form in a special data box created with the Profile tool To create a Profile box The database connected to the form or subform you are working with must have at least one numeric field _ Note You can also include structure field in profile 1 Click the Profile tool on the Form toolbar 2 Drag a box on the form The Profile Wizard appears then click Next Profile Wizard ChemBioFinder Compound Profile Wizard Welcome to the Compound Profile Wizard 4 Compound Profile compares values of selected fields with user defined ideal values Each value is shown on a vertical band shaded to indicate regions of cost undesirability The idea
325. se the Verify button to check syntax Run to test the script _ Note To work with CAL interactively do not use the script editor Use the command box that appears when you click the Scripts gt Command Line menu command a Python for editing Python scripts As in CAL mode you can view or edit a script and click Run to test it When you switch into this mode prompts are removed Chapter 16 Customizing ChemBioFinder 13 0 215 of 342 ChemBioFinder 13 0 PerkinEl For the Better m Python Interactive for interactive development of Python scripts In this mode you can ENTxER Python com mands and execute them one at a time or click Run to test the script The buttons on the script editor are as follows Verify checks a CAL script for syntax errors This button does not apply to Python Run executes a script used for testing E Import loads a new script from a text file Properties Opens a dialog box with two options save script internally with the ChemBioFinder 13 0 form or save script as an external text file Help opens the CAL Help window or Python manual Interactive mode The Python Interactive Mode is modelled on standard Python environments such as IDLE and PythonWin In this mode p Type cfhelp for a page of tips and samples of ChemBioFinder 13 0 specific programming At each new line the window shows the Python prompt gt gt gt After the prompt you can ENTXER any P
326. size a data box or any other object on the form _ Note You cannot resize more than one object at a time or simultaneously resize a box and its frame unless you create a framed box using the Framed Box tool For more information see Creating boxes with frames on page 36 To resize objects on a form 1 Click the Selection tool on the Form toolbar 2 Position the pointer over an edge or corner of the object until the pointer is a double headed arrow 3 Drag in the direction you want to resize If an object is nearly the right size you can make small adjustments to get it exactly the size you want To resize objects one pixel at a time 1 Select the object you want to resize 2 Place the mouse pointer over an edge or corner of the object until it is a double headed arrow 3 Press an arrow key in the direction you want to resize the object The edge of the object moves one pixel in the direction of the arrow key Deleting objects Use the Selection tool to remove data boxes and other objects from a form To remove objects from a form 1 Click the Selection toolon the Form toolbar Chapter 4 Forms 48 of 342 hemBioFi 13 I ChemBioFinder 13 0 PerkinElmer For the Better 2 Select the object you want to delete Tip Use SHIFT click to select multiple objects 3 Do one of the following Goto Edit gt Clear a Use the Backspace key The object is removed from the form Reversing and restoring changes Use
327. splay of reactions Not checking the boxes means these types are dis played as all other atoms and bonds Favorites tree The Favorites Tree is a user constructed collection of file system objects It may include folders subfolders Chem BioFinder 13 0 forms structure files and documents of all kinds Its purpose is to allow you to collect organize and access the data and documents you use regularly SE CF_old Exported items C5_DEMO doc C5_DEMO csw Database Queries Favorites Figure 16 5 The Favorites tree You can open items in the Favorites Tree from within ChemBioFinder 13 0 by double clicking them a ChemBioFinder 13 0 form a ChemBioFinder 13 0 script a ChemBioFinder 13 0 query open it in its source any other type of document ee application There are two ways to add items to the Favorites Tree Drag one or more files from Windows Explorer into the Favorites window Use the context menu Chapter 16 Customizing ChemBioFinder 13 0 206 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 To create a new folder in the Favorites Tree 1 Point to the parent folder The new folder will be a subfolder of this folder 2 Right click and click the New Folder context menu command 3 Type in a new name for the folder To add an item to a folder 1 Point to a folder 2 Right click and click the New Item context menu command A File dialog box opens 3 Browse t
328. st character in a line to mark it as a comment This command is useful only in a script file and has no effect when entered on the Command Line command_line_def inition CAL commands syntax Labels a line with the preceding or following text label or label The command has the following argument Text to be used as a label Remarks This command is useful only in a script file and has no effect when entered on the Command Line CAL commands GOTO syntax Unconditionally transfers execution to a specified line in the current script GOTO label The GOTO command has the following argument String indicating the des tination line Remarks The label must be correctly specified with a CAL_ This command is useful only in a script file and has no effect when entered on the Command Line GOTO example This example allows the user to batch enter several new compounds and input one field for each It starts with a MSG command to tell the user what to do Then it has a line starting with a colon that serves as a label to start the loop The INPUT command gets the name of the new entry from the user The IF command tests to see if the user entered a blank string and EXITs the script if so After the Menu Command Record Add creates a new record the PUTDATA command enters the user s string into the molname field Closing the loop the GOTO command jumps execution back to the start label msg Enter new compoun
329. structure ponent find a particular structure oe search with variability in the query search for a precise match Similar and set the degree of similarity find structures having fea 3 Note The tures similar to the query higher the value the fewer hits found Chapter 8 Queries 112 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 find structures that are tautomeric forms of the Tautomeric query match bonds as drawn Non tau without tautomeric forms tomeric 3 Click OK Tip You don t always have to access the Preferences dialog box to change search preferences Switches on the Search menu let you toggle Substructure Full Structure and Normal Similarity Setting search details preferences You can set preferences for the details of each search To set search details preferences 1 Go to File gt Preferences The Preferences dialog box appears 2 Click the Details tab The Details tab appears 3 Take the appropriate action Allow uncharged non car bon atoms in the query to match charged atoms in the target Hit any charge L Note Charged atoms on heteroatom in the query must always match charged atoms in the target regardless of this setting Allow uncharged carbon atoms inthe query to match charged carbon On carbon atoms in the target Chapter 8 Queries 113 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 7 Note Charged a
330. structure into a variable see above for how to identify a box PUTDATA copies specified text into a form box Form names are case sensitive Be sure to use the same case as the form box name into which you want to store data TO_SMILES retrieves the contents of the current structure as a smiles string FROM_SMILES generates a structure from asmiles string APPEND determines whether data in a storage location is kept if other data is being moved there This setting is also consulted when you do a File Export to SD or delimited text file APPEND ON causes any subsequent data movements to append new data to old APPEND OFF causes old data to be overwritten This applies to all variable commands except PUTDATA The default at program startup is APPEND OFF APPENDVAL is a shortcut designed to make it easier to build string values It is the same as setting APPEND ON doing a SETVAL and then restoring APPEND to its original state Tip The difference between APPEND ON and APPENDVAL is that APPENDVAL does not add a carriage return to the string being appended whereas APPEND ON does If you want to insert a carriage retum at the end of the string use APPEND ON INCREMENT adds 1 to the value of a variable Use INCREMENT in loops DECREMENT subtracts 1 from the value of a variable Use DECREMENT in loops LET allows you to perform mathematical operations on variables that contain integer or real number values Only one operator per line is supported It re
331. t don t have an accurate description of the target compound Unlike exact searches similarity searches do not highlight matched portions of the target compounds Similarity searching matches general structural features and not specific atoms and bonds so highlighting specific areas would not be appropriate You can adjust the degree of similarity from 0 to 100 necessary to produce a hit by using the slider on the Search Type tab of the Preferences dialog box Structure modes The structure mode determines whether the query defines a substructure of the compounds in the database being searched or the full structure In this context it is important to note that full structure is not exact When you spec ify the Exact search type the structure mode is always full structure but you may choose the full structure mode with any of the three search types See Full structure searches on page 103 and Exact searches on page 101 for more details Substructure searches A substructure search finds structures that contain the query plus any additional attachments at the open positions This is the default search mode The substructure is highlighted in red in the hit list structures Using the ChemDraw ActiveX toolbar you can attach different features to a query such as atom lists and variable bond types to perform a narrower or broader search For more information about what query features you may use and how they affect a sear
332. t context menu command The script editor window opens for script entry 3 Click OK when you have completed the script The script is executed when the button is clicked Tip You must toggle out of layout mode to use the button To create a script connected to a trigger event 1 Open the Box Properties dialog box and click the Form tab 2 Select an event in the Run script on box by clicking the check box next to it 3 Click Edit The script editor window opens for script entry 4 Click OK when you have completed the script The script is executed when the event occurs To create a script linked to a subform table 1 Right click on the subform name to open the Subform Properties dialog box 2 Enter a name in the Table script text box then click Edit The script editor window opens for script entry 3 Click OK when you have completed the script The subform contents are displayed in hyperlink style blue under lined Clicking any link executes the script The script editor There is a single script editor for all scripts CAL and Python The contents change to match the script being edited This is a change from the CAL editor in earlier versions where you could have a separate window for each script The editor is modeless that is it stays on the screen when you switch to work in ChemBioFinder 13 0 To close the script editor click OK or Cancel The editor has three modes CAL for developing CAL scripts U
333. t enter a number thus for a base e log scale you would enter 2 718281828 BioViz automatically names plots with sequential numbers BioViz1 etc Edit this field if you want to give ferent name Name Locks the display When the display is locked the following have no effect filters changes in the current list Locked list coloring BioViz Plot Properties dialog box options except Name are blocked The Display and Analysis tab optior even though they are not grayed out Selection and mouse overs are not affected Point limit Sets the maximum number of points in the plot Used to limit the plotting time with very large datasets Chapter 12 BioViz 163 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 Point shape Selects the point shape circle square diamond triangle cross or star Point size Selects the point size Values from 2 20 may be dialed in Comment Text box for a comment or legend Background Selects the background color of the plot Label Text box for custom label for both X and Y axes Show grid Option to display a grid X and Y axes may be selected separately Font Selects the font Different fonts may be used for the Comment X and Y axes Q a D lt e D y O O 3 Lal x Cual 3 D 3 o O 5 a Properties Opens the BioViz Properties dialog box Filter Window Opens a filter window See Filtering on
334. t might cause a possible loss of data 7 Note Notes highlight important information Tip Tips are helpful hints that supplemental the main text Shortcut key sequences are indicated with a sign for example Use the command CTRL H to toggle hidden Hydrogens and lone pairs A bold font is used to refer to the User Interface for example Go to File gt Save Chapter 1 About ChemBioFinder 13 0 1 of 342 ChemBioFinder 13 0 PerkinEl For the Better Serial Number and Technical Support The serial number is a unique key that helps you install and activate the ChemBioOffice application on your computer This serial number is displayed on the outside of the original application box This is the same number you entered when you launched your ChemBioOffice application for the first time If you have thrown away your box and lost your installation instructions you can still find the serial number from the application Go to Help gt About lt Chem BioFinder gt The serial number appears in the dialog box For more information on obtaining serial numbers and registration codes see the online Services Web site Technical support is available to registered users through the Internet and our Technical Support department When contacting Technical Support always provide the serial number of your ChemBioOffice application Our Technical Support Web pages contain answers to frequently asked questions FAQs and other information To acc
335. t the score and dist values are no longer equal Customizing The gallery of cost profile templates shown in the Cost Profile Chooser dialog box was designed to help you get started Some are based on user experience other chosen to provide the most common cost profile patterns As you work with the compound profiler you will develop your own templates and may want to substitute them in the chooser The templates are taken from files stored in the ChemBioFinder system profiles folder The files have a CPX exten sion and the name of each file is the name given to the template The Cost Profile Chooser displays all files in this directory having the CPX extension The internal format is XML readable in Notepad To remove a template from the chooser delete the corresponding file or move it to another location or change its extension To add or modify a template Double click in the profile data box to open the Profile Editor then click the Cost Profile tab Edit the profile until it looks the way you want Right click in the edit window then select Save from the context menu When prompted enter a line of descriptive comments to be displayed below the chooser window and click OK ao A OO N gt Type the name you want to appear in the chooser and click Save Chapter 9 Compound Profiles 144 of 342 ChemBioFinder 13 0 PerkinElmer For the Better Chemical Properties ChemBioOffice 2012 lets you determine more
336. t to clicking in the main form background with the pointer tool UNSELECT The UNSELECT command takes no arguments 7 Note This command will change the active form Program execution commands CALL scriptname DOS doscommand EXEC wincommand EXEC_BUTTON boxname DDE ddecommand LAUNCH filename OUTPUT_STR string Program execution commands call up external processes and pass data to them All require an argument which may need multiple components CALL executes a specified CAL script If the call is made from within another script when the called script finishes executing it returns control to the caller CALL must be followed by a scriptname as described above Chapter 20 CAL Commands 259 of 342 ChemBioFinder 13 0 PerkinElmer For the Better DOS executes a DOS command line Follow the DOS keyword with any string you might type at a DOS command prompt If you do not type any arguments after the DOS command you get an interactive command prompt window You can use this feature to manipulate files execute programs or batch files get directory listings format disks etc During execution of the command a command prompt window appears on the screen when finished the window goes away and control returns to the calling script EXEC starts a Windows program and optionally passes it command line arguments Follow the EXEC keyword with any string you might use in the Program Manager s File Run command This c
337. table 1 Right click in the form and click Properties 2 Click the Table tab then click Attach Table The Attach Table dialog box appears 3 Click Open Oracle ODBC Data Source The Select Data Source dialog box appears 4 From the Machine Data Source tab select the ODBC data source to access then click OK Select Data Source File Data Source Machine Data Source Data Source Name Type Description CAMBRIDGESOFT1 User CSUSERS User Oracle database dBASE Files User Excel Files User MS Access Database User New A Machine Data Source is specific to this machine and cannot be shared User data sources are specific to a user on this machine System data sources can be used by all users on this machine or by a system wide service Cancel Help _ Note The ODBC data source dialog box shows all data sources known to ODBC including ChemBioFinder 13 0 Access and other file based data sources If you attempt to open one of these through the ODBC dialog box you get an error message File based data sources must be opened using Open Database as described above Ifthe ODBC data source dialog box does not show the database you seek you may need to create a new data source You can do this using New option For details click Help in the ODBC dialog box 5 If you are prompted for a user name and password enter it If you do not know what name and password to use see your System Administrator 6 Inthe tree di
338. tables as you mouse over data points used when the form is not visible or is displaying a different record Filters displays filter bars for those fields being used to modify the plot Tip To see some of the features you must tile the windows to view the form and the plot simultaneously Displaying plot details The Details Window displays field values other than Structure when viewing a BioViz plot To display the Details window go to View gt Details Window The window floats by default but can be docked with other windows To add new fields to the Details Window 1 Right click in the Details Window 2 Select the field to be displayed A check mark appears next to the selected field Fields appear in the order you select them 3 Toremove afield from the Details Window right click and deselect it Selecting data points Each point on the Bioviz plot represents a record in your database You can select a point in the plot to view data it rep resents When selected the point is displayed as a double hollow red circle When you hover over a point the center circle is solid Points that belong to queries appear as solid colored points without circles Removing empty points A point which has an X value but not a Y value is an empty point on the plot with a distinctive marker If there is a Y value but no X value the point is simply omitted BioViz omits empty X and Y points All omitted points are noted To v
339. tains data from a database The text label if the box contains static text such as frames or text labels The box name assigned in Box Properties For subform boxes the table name In all cases you need not spell out the entire name just enough to be unique Often more than one box matches the text you enter for example a box displaying field molweight within a frame labelled MolWeight In this case preference is given to the box connected to the database FORMEDIT controls the behavior of the SELECT command With FORMEDIT ON SELECT affects boxes With FORMEDIT OFF SELECT affects the contents of those boxes SELECT and UNSELECT choose boxes to be modified by editing operations DELBOX is a shortcut for FORMEDIT ON followed by SELECT followed by Edit Clear SETFIELD connects a database field to an existing box for a but ton it attaches a script name See above regarding script names SETTEXT attaches a text string to a box or Chapter 20 CAL Commands 255 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 replaces the one currently attached see box creation commands above for a list of what the text strings mean for various box types ACTIVATE and DEACTIVATE are the same as SELECT and UNSELECT but work on subforms Following an ACTIVATE command all subsequent commands apply to the active subform and any boxes it contains The DEAC TIVATE command is required to once again refer to the main fo
340. te Formula searches are non structural CH3CH20H matches both dimethyl ether and ethyl alcohol because both compounds have the same condensed formula C2H60 Chapter 8 Queries 99 of 342 ChemBioFinder 13 0 PerkinElmer For the Better Parentheses may be used to group elements and apply a count to the entire group For example CH2 3 is inter preted as C3H6 2 Spaces or non alphanumeric characters other than parentheses are ignored Date searches You can use date searches to track individual reaction runs purchasing histories and so on You specify date ranges using a hyphen between the values at either end of the range Ranges may also be indicated using inequality operators lt gt with the AND operator Dates are always displayed according to the preferences set in the operating system s International control panel but need not be input in that format This table shows query examples the exact date April 11 Apr 11 1971 1971 March 31 1971 any date in the second July 1 1971 quarter of the year 1971 gt 4 11 71 any date after April 11 gt 4 11 71 1971 oron April 11 1971 Find list Use the Find List command to retrieve records having specific values in any non structure field Type parameters into the Find List box as follows a If the column you search is an integer use hyphens to indicate ranges Ifthe column you search is a number or text type hyphens are not allowed you must sear
341. ten stored as bits and another name for a compound s set of descriptors is its bitscreen Consider the following query and target compounds Bisson COI ORE oy fo cme ons faf Qand T E Both have similar numbers of descriptors present the query has 23 while the target has 24 Complete structure similarity One of the hallmarks of a good similarity algorithm is whether it is commutative That is two compounds should have the same similarity value no matter which you compare to which The full structure Tanimoto similarity test is com mutative It compares the number of descriptors they have in common in the intersection of the query and the target Chapter 19 Similarity Rules 241 of 342 ChemBioFinder 13 0 PerkinElmer For the Better to the number of descriptors they have in total in the union of the query or the target The ratio of these two values is known as a Tanimoto coefficient and is always a value between 0 and 100 QAT Tanimoto Coefficient Q UT A For the two compounds above the Tanimoto coefficient is 17 30 or about 57 This is not very similar although ChemBioFinder will allow you to specify any Tanimoto value down to 0 for most cases you will likely be looking for compounds that have Tanimoto coefficients of 90 or higher Substructure similarity Unlike full structure similarity substructure similarity is not commutative you are comparing a portion of one structure against the entire other str
342. ter _ record selected and the next two records If your layout is one per page the default you will print only the selected record Note also that if a subform is selected the entire record with the subform is printed 9 Click OK Chapter 7 Importing and Exporting Data 96 of 342 ChemBioFinder 13 0 PerkinElmer For the Better Queries You can search the database by querying any field or combination of fields You can specify a chemical structure and or text as the query When searching text or numbers you can use wildcards or specify a numerical range When structure searching you can search by sub or full structure search for an exact match similarity or tautomerism and specify how stereochemistry will be matched You can also combine structure searching with text or numerical searching A Find Structure command performs duplicate error isotopic label and other special structure searches The chapter describes the different types of searches and how to set up and manage searches It concludes with some examples of advanced techniques Text searches ChemBioFinder 13 0 lets you search any alphanumeric field for strings of text Use text searching for example to find chemical names or comments in a reference field For text searches ChemBioFinder 13 0 interprets the query then passes it as Structured Query Language SQL to the relational database These rules apply to text searches When se
343. ter 16 Customizing ChemBioFinder 13 0 209 of 342 ChemBioFinder 13 0 PerkinElmer For the Better _ Note The data of the Periodic Table is stored in a tab delimited ASCII file called CS ChemBioFinder 13 0 CS_Iso topes_Table txt in your ChemBioFinder 13 0 system directory You can edit with a text editor or spreadsheet pro gram to change default data values Embedding ActiveX controls You can embed most windowed ActiveX controls on a form For stand alone controls you can embed the control and use it immediately If the control needs programming or if you want the control to manage ChemBioFinder data you will need to customize its behavior using Python scripts To embed a control 1 Select the Control box tool on the Forms toolbar 2 Drag a rectangle on the form The Insert Control dialog box appears 3 Select a control from the list The control appears in the Control box Figure 16 10 Adding a spreadsheet to a form _ Note Not all controls listed are suitable for use in a Control box but appropriate error messages should be displayed in such cases Customizing controls The behavior of an embedded control can be customized by adding Python scripts to the form to perform custom actions at given times The control can be accessed using the Automation interface through the Control property of the corresponding Box object which is obtained from the Boxes collection of the Document object Contact PerkinElmer Informatics support
344. the ADO recordset cache that is the number of records brought to the client for each retrieve operation This value can be adjusted for better performance but in practice it does not have much effect Cache ID s for faster moves Checking this box enables a new record retrieval scheme designed for more efficient browsing of large lists details are given in Fast move caching scheme on page 296 The state of this check box is saved with the formfile Currently when you check or uncheck this box you must save and reopen the form before proceeding SQL Trace to file Check this box to generate a text file of the SQL being sent from ChemBioFinder 13 0 to Oracle To specify an output file enter a pathname or use browse The file is never overwritten new data are always appended Tracing begins when this box is checked and ends when it is unchecked If you exit ChemBioFinder 13 0 with tracing in effect it will be in effect the next time you start up and you will be given a quick warning about it on the status bar 3 Caution The trace file can become very large if you turn on this feature and forget about it Updating and adding data If you have privileges to add update and delete data in the table connected to your form then you should be able to do these operations on records in the database just as in ChemBioFinder 13 0 However there are some cautions Chapter 14 ChemBioFinder Oracle 185 of 342 ChemBioFinder 13 0 PerkinElme For
345. the Better 2 Do one of the following Goto Record gt Delete Record Click the Delete Record icon The record is permanently removed _ Note You can delete multiple records if you use the Table view Sorting data You can sort the database by most types of data in a form Sorting on the Mol_ID field the molecular weight field or any other numeric field arranges the current list in increasing or decreasing numeric order according to that field Sort ing on the structure field arranges the list by increasing number of atoms contained in the structure Implicit hydrogens are not counted Sorting on the formula field orders the records by increasing C H N count for compounds containing carbon followed alphabetically by any other elements Formulas for compounds without carbon are sorted in alpha betical order Sorting by text fields such as molecular name sorts the records alphabetically After sorting the database must be reset to its original state before you can update it _ Note You cannot edit records sorted by formula or molecular weight However if you attempt to sort on one of these fields ChemBioFinder 13 0 offers to set up a database a portal database which allows the operation For details see Attaching tables from other applications on page 71 To sort on a field Inthe Form View right click in the field you want to sort by and go to Sort gt Ascending or Sort gt Descending Inthe Data Table View do
346. the Explorer window b Right click a list and click the Change Color context menu command c Select anew color from the color menu Selection and Zooming to select a part of the plot and zoom in To select part of the plot a Drag a rectangle across a portion of the plot The portion of the plot is displayed in red b To select more than one section use SHIFT drag or CTRL drag To zoom in on part of the plot a Right click in the plot and click the Zoom on Drag context menu command This is a toggle switch choose it again to deselect b Drag a rectangle across a portion of the plot This time when you release the mouse button the plot display zooms in to show only the points selected When the plot is zoomed scrollbars appear Use these to reposition your view of the zoomed plot Click the circled point icon on a scrollbar to restore that axis to the previous zoom Right click and click the Unzoom context menu command to restore to the full view Changing the Style you can change the style of an existing plot For example you can turn a scatter plot into a his togram a Right click in the plot and click the Properties context menu command b Inthe properties dialog box select the style and click OK The plot displays in the new style Changing Fields you can change the field plotted on the X or Y axis with the context menu a Point in the area of the numbers just below or to the left of an axis
347. the data box and the frame label changes to match the field name You cannot automatically label a frame that was created separately from a data box Non data boxes The Form toolbar contains two tools Plain text and Picture to create static displays though they may also be used to display data and three others with special functions Adding plain text The Plain Text tool lets you display text without a box or a frame You can use it to place a static label on the form but like a data box you can also use it to display live data if desired To use the Plain Text tool 1 Click the Plain Text tool 2 On the form drag to create an area to specify where the text will appear The Enter the Text dialog box appears 3 Type the text you want to display 4 Click OK Chapter 4 Forms 37 of 342 ChemBioFinder 13 0 PerkinElme For the Better MoL_ID Formula Structure Molweight This is a demo database Figure 4 5 Creating text on a form To change the font or color of the text select it with the Form toolbar Selection tool Use the text formatting toolbar to customize the text To use plain text to display data 1 With the Select tool right click on the text and select Properties The Box Properties dialog box appears with the Box tab displayed 2 Select a field from the data table The Data text box becomes grayed out and the Data Source selection switches to Field 3 Click OK The contents
348. the hit list Internally however the ChemBioFinder Oracle machinery is quite different There are three types of table involved in handling hit lists All are created in your own tablespace One is global apply ing to all lists saved from any table others are connected to the particular table or view being searched a CF_HITLISTS The directory of all saved lists This table is created the first time any list is saved SAVED_tablename All lists which have been explicitly saved from a given table or view This is created the first time a list is saved HITS_tablename All lists automatically saved after every search over a given table or view This table is created the first time a search or list operation is carried out and is deleted at the end of the session Here s what happens when you present a query to ChemBioFinder Oracle 1 If the query contains a structure it is converted to a text representation and copied to a temporary table g Note The table is called temp_queries Itis created in the CSCartridge tablespace and removed as soon as the search is finished or interrupted ChemBioFinder 13 0 does not yet handle the case of multiple structure boxes where more than one contains a query 2 The query is converted to a SQL select statement Query components in form boxes are ANDed together just as in ChemBioFinder 13 0 where the structural parts are calls into the CS Oracle Cartridge structure search func tions 3
349. the query properties dialog box also accessed from the context menu Mark the query with the Keep command on the context menu Query saved in this way retain their standard name Chapter 8 Queries 129 of 342 hemBioFinder 13 I Che oFinder 13 0 PerkinElmer For the Better Preferences E Display Color Search Type Detads Tuning General a Regitiston Recent fle kst sze 6 o Y Check valences Ask to coment changes Y Use Query Add Window Al Startup Explorer tab Favorites F Show startup dalog I Reopen last form Frame style Wredbey Y 7 Check for extemal serps Query Saving C Save all que es Discard urnamed queres C No save F Open last query on opening foen Caca top Figure 8 26 General preferences Saving a hit list Create a query and perform the search See Entering and submitting a query on page 118 and Entering a structural query on page 119 for more information 1 When you have received the hit list go to Search gt Save List The Save As dialog box appears 2 Type a filename for the hit list and click Save The file consists of a list of values of the primary key of each record in the hit list If there is no primary key the mole cule ID is used To edit a saved hit list open the text file with a text editor such as Notepad and edit the values you want changed Restoring and merging hit lists Once you have saved a hit list you can perform another search and then int
350. to 5 Save the form close it and reopen it This is currently necessary in order to reinitialize the database connection with the caching scheme Configuring via CF_SETTINGS table When you select a table in an Oracle database ChemBioFinder determines and displays the types of columns in the table Here s how it decides whether a particular column contains structures The column must be of type CLOB or BLOB If the column has been indexed by the CS Oracle Cartridge then it is a structure column If there is no index then ChemBioFinder Oracle looks for a table of configuration info called CF_SETTINGS If the column is listed in that table as being of type STRUCTURE then it is a structure column The CF_SETTINGS table is also used to determine whether a particular column of type BLOB contains ChemFinder pic tures Windows metafiles To designate an unindexed column as a structure column 1 Inthe Field tab of the Properties dialog box select a column of type BLOB or CLOB 2 Click Set As Structure If the CF_SETTINGS table has not yet been created an alert indicates that it is about to be created 3 Click OK to proceed and create the table or Cancel to abort without creating If the table already exists and there is already an entry for the selected column you are given an alert and a chance to cancel 4 Click OK to proceed A new entry is created in the table marking the selected column as a structure column Ch
351. to its original state If variable is omitted the text will be assigned to V1 Saving compounds example This example uses the LOOP ENDLOOP commands and the Menu Command Record Next to step through each record in the current list For each record it builds a unique file path based on the current INDEX using SETVAL and APPENDVAL commands Finally it saves each compound to disk with the WRITEMOL command Since the file path ends in cdx this script saves all of the compounds in ChemDraw format append offloopsetval 1 c mydir appendval 1 Sindexappendval 1 cdxwritemol vlrec nextendloop Environment variables SINDEX RECNO NUM_RECS DTBA_NAME_LONG DTBA_NAME_SHORT FORM_NAME_LONG Chapter 20 CAL Commands 288 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 FORM_NAME_SHORT CFW_DIR FORM_DIR SYSTEM_DIR f Note To view a complete list of variables click Help on the Enter Cal Command dialog box ChemBioFinder provides several variables to allow you to retrieve information about the current ChemBioFinder envi ronment They cannot be set directly but are modified as a consequence of other commands For example the menu command Record Next increments the current RECNO by 1 The table below shows examples of Environment Variables V1 now equals the number of the current record V1 now equals total number of records in the current list V1 now equals for example c
352. toms in the query must always match charged atoms in the target regardless of this setting Allow hits to contain Permit extra molecular fragments in neous fragments addition to the structure in full structure searches hit by the query Ignore salts and solvents Hit any charge Run a search that ignores on heteroatom differences merely due to On carbon salt state and presence of Permit extra solvents neous frag ments in full structure searches Allow fragments in the Query fragments can overlap in tar get query to overlap share one or more atoms in the target Require that any reaction center present in the query overlap with reac Reaction query tion centers in the target must hit reaction This preference applies center only to reaction search ing Chapter 8 Queries 114 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 Prohibit generic struc tures from hitting any Generics hit only other structures in a generics query Require full word text matching If you do not check this box the query will hit any matching text Text Match full word only fragment Match ster Require that the ster eochemistry and eochemistry of the target click How to set structure match that of how the ster the query structure eochemistry is matched Tuning The Tuning tab of the Preferences dialog box has settings for special query conditions On this t
353. ts 103 multiple substructures 135 no highlighting 119 numbers in 98 overlapping fragments 114 plotting with BioViz 29 precision 98 products 109 progress display 110 119 radicals 226 Chapter 22 Index 327 of 342 ChemBioFinder 13 0 I PerkinElmer For the Better ranges 98 100 reactants 109 reactions 106 red highlighting 110 119 refining 118 similarity 102 similarity rules 241 special atom types in 231 special bond types 236 SQL 111 stereochemistry 104 227 stopping 118 structural similarity 102 structures 101 subforms 159 submitting 118 substituents 224 233 tuning 115 unsaturation 235 using current structure 119 query operators 111 equals 99 greater than gt 100 less than 100 minus 100 parentheses 100 query properties conflicting 223 Chapter 22 Index 328 of 342 ChemBioFinder 13 0 I PerkinElmer For the Better overview 223 Questel F1D files 87 Questel F1Q files 87 R R group tables 67 R group tables persistence 68 R group tables sorting 68 r groups see alternative groups 104 R special atom type 232 radicals in queries 226 radius 153 ranges in queries 98 RDFiles 56 88 93 reactants in queries 109 reactants searching for 106 reaction centers 107 237 bond type 241 bond types 238 239 display preferences 204 overview 107 reaction queries 106 atom atom mapping 108 creating 120 hitting reaction centers 107 114 intermediates 110 products 109 reactants 109 react
354. u can create or remove fields or tables in an existing or new database if the database is not read only and you have permission to modify it You may also attach or link tables from external data sources Use the Box Properties dialog box to perform the following procedures Do one of the following Goto File gt Database Right click any empty space in the form window and click Data Source The Box Properties dialog box appears with the Database tab displayed To add afield 1 Click the Field tab 2 If there is more than one table select the table that will contain the new field 3 Click Create Field The Create Field dialog box appears 4 Replace the default name New_Field select a data type and adjust the field width optional Click OK To delete an existing field 1 Select a field 2 Click Delete Field A warning box comes up asking if you really mean to delete a field 3 Click Yes to delete the field 1 Caution All data entered in the field will be lost as soon as you click YES To add a table 1 Click the Table tab Do one of the following 2 Click Create Table 3 Enter a name in the Create Table dialog box The new table is created with a default field named ID Chapter 6 Working with Data 85 of 342 hemBioFi 13 I ChemBioFinder 13 0 PerkinElmer For the Better To remove a table 1 Select a table 2 Click Delete Table 3 Click YES in the warning box 2 Caution All
355. u open the application To open the ChemBioFinder 13 0 startup dialog box when the preference is set to hide go to File gt New Using ChemBioFinder with databases ChemBioFinder 13 0 comes with the Microsoft Jet database engine ChemBioFinder 13 0 maintains its own table of chemical information structure formula and molecular weight and relies on Jet to create a database for managing Chapter 2 Getting Started 11 of 342 hemBioFinder 13 l Che oFinder 13 0 PerkinElmer For the Better the rest of the data The data created by Jet is stored in an MS Access database file MDB file If you have MS Access installed you can use it with the relational part of the database You can use ChemBioFinder 13 0 to add chemical structures to a database you have already developed in Microsoft Access The database model A database is a collection of information In ChemBioFinder 13 0 the information is organized into levels of increasing complexity At the simplest level is the data item itself for example a molecular weight value as shown in the table below MOL_I Structure Formula MolWeight Molname 157 Ro cmo Hydrocortisone ANAL As 158 moe C19H3002 290 44 Andiosterone Mi 159 y K C21H3002314 462 Progesterone OL al x y 160 WY CIGHI7N3 267 326 Lysergamide HA 161 Q9 EHUNA 263 31 Lysergic acid IA al y 163 f CI7H20N4 375354 Riboflavine uy 164 LX DO YAM ssas thisnine Figure 2 6 A data item in the d
356. u want to append to an existing table enter its name 5 Set other options as desired and click Import to begin the process Tip for text fields being imported make them wider than the value determined by the input scan To do this dou ble click the name under Input Field and enter a larger Width value Otherwise you might have problems if you append more records later 6 Afterimporting you should create a primary key and index see Indexing on page 187 To append to an existing table follow the procedure above except Step 1 You can start with an existing form instead of a blank one Step 2 You should select the target table When you do there will be no need to edit the table name in Step 5 Indexing As every Oracle administrator knows a key to good performance is to index certain columns so that searches over them become fast lookups If you intend to create load or manage tables then you are an administrator and need to know something about indexing ChemBioFinder Oracle provides a few tools to assist you There are two types of index of interest to ChemBioFinder Oracle Chapter 14 ChemBioFinder Oracle 187 of 342 hemBioFinder 13 I me Orea PerkinElmer For the Better Structure indexes Any column containing structures should have an index created by the CS Oracle Cartridge If there is no index searching is still possible but very slow Primary keys A table containing a column of structures should
357. ually in the Search tab of the Pref erences dialog box The default is 1 require in center Whether or not to stop searching after the max imum number of hits have been found If this pref erence is turned off Chem BioFinder will report the total number of hits but will still display only the max imum number The default is 1 stop 277 of 342 ChemBioFinder 13 0 CAL commands CLEAN syntax Attempts to standardize the bond lengths and angles of the current molecule CLEAN param The CLEAN command takes the following optional arguments default Progressively deanup stronger drawing modes starting with Tidy until something changes Minimum redrawing if any License to redesign rings Complete redesign from denovo scratch Remarks pP PerkinElmer For the Better This command is equivalent to opening the structure in ChemDraw selecting the Clean Up Structure command and returning to ChemBioFinder CAL commands HELP syntax Displays a list of all valid CAL commands The valid parameter types are listed for each command as is a brief description HELP Remarks This command is not of much use during the execution of a CAL script but can be a quick syntax aid when entered into the ChemBioFinder Command Line File commands READMOL filename READPICT boxname filename WRITEMOL filename WRITEPICT boxname filename WRITETEXT filename Chapter 20 CAL Commands 27
358. uble click on the table header of the field you want to sort by The table is sorted in ascending order by the column you selected Double clicking again will sort in descending order O Tip There is also a context menu option for sorting in Data Table view Right click in a column and choose Sort Column Sorting in languages other than English Text that you sort must be in the same language as the default language of the system on which the database was created or an incorrect sort order can occur The ChemBioFinder 13 0 sample databases created in English can be sorted correctly using the following lan guages English German French Portuguese Italian Modern Spanish Chapter 6 Working with Data 84 of 342 ChemBioFinder 13 0 PerkinElmer For the Better If you want to sort text in a different language than the one in which the database was created perform the following procedure 1 On a computer using the same language as the text you want to sort open MS Access 2 Open the MDB file you want to sort 3 Compact the database Go to Tools gt Database Utilities gt Compact Database 4 Afterthe database is compacted close MS Access The correct sort information is written into the database When you perform a sort in ChemBioFinder 13 0 the sort order will be correct Resetting the database To reset the database to its original state Goto Search gt Retrieve All Changing the database scheme Yo
359. ucture and so it does matter which you compare to which In considering substructure sim ilarity ChemBioFinder finds what percentage of descriptors in the query are also present in the target This value will always be at least as large as the complete structure Tanimoto coefficient for the same two com pounds and usually it will be larger The two compounds above are 17 23 or about 74 similar by substructure sim ilarity For a given coefficient value a substructure similarity search will always return all of the hits in a full structure similarity search and will often return additional ones as well Chapter 19 Similarity Rules 242 of 342 hemBioFi 13 I ChemBioFinder 13 0 PerkinElmer For the Better CAL Commands ChemBioFinder Automation Language CAL is a set of commands that control many ChemBioFinder operations You invoke CAL commands in either of two ways Interactively Type commands and execute them one at a time on a command line Scripts Use ASCII files containing a series of CAL commands to be executed automatically in sequence Arguments to commands consist of numbers and text strings You can enter a text string without punctuation unless the argument is not the last one on the command line and contains multiple words or spaces In this case you must enclose the argument in quotation marks CAL help Information about the CAL command and variables is available in the CAL Scripting Help window To access CAL Help
360. ue for all atoms and is held by the most outlying atom s The radius R is the minimum such value and is held by the most central atom s Examples values for D methane 0 ethane 1 propane 2 n butane 3 Example values for R Radius methane 0 ethane 1 propane 1 n butane 2 Sum Of Degrees Is the sum of degrees of every atom An atom s degree is the number of nonhydrogen atoms to which it is bonded Sum of Valence Degrees Is the sum of degrees of every atom An atom s valence degree is equal to the sum of its adjacent bonds orders including hydrogens Chapter 10 Chemical Properties 153 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 Topological Diameter Is the longest dimension of a molecule Total Connectivity Is the connectivity considered over all the heteroatoms Total Valence Connectivity Is the valence connectivity considered over all the heteroatoms Vapor Pressure Is the pressure exerted by a vapor in equilibrium with its solid or liquid phase Vapor pressure measures the con centration of solvent molecules in the gas phase Vapor pressure can be calculated using Raoult s law The formula to calculate vapor pressure is Prot T SPX i Where p is vapor pressure i is a component index and y is a mole fraction Water Solubility Is the maximum amount of a substance that can be dissolved in water at equilibrium at a given temperature and pres
361. uery structures For more information about the structure drawing and query capabilities of ChemDraw please consult the ChemDraw User s Guide ChemBioFinder does its best to follow your instructions even if those instructions are contradictory For example you can create a query such as the following 1 Chn Figure 17 1 1 This bond must not be in ring That bond is already in a ring so ChemBioFinder returns no hits for this query General properties ChemBioFinder allows the following general properties to be assigned to a query Atom Bond Substituents Charges and radicals Isotopes Stereochemistry Normalization Atoms Atom types specified in the query must match atoms at corresponding positions in the target Hydrogen is an excep tion see Substituents on page 224 Bonds All bonds explicitly drawn in the query must match in the target For certain caveats see Stereochemistry on page 227 and Normalization on page 230 ChemBioFinder recognizes the following standard bond types Chapter 17 Structural Query Features 223 of 342 hemBioFinder 13 I Che oFinder 13 0 PerkinElmer For the Better target must have single bond Single here specifies stereochemistry Wedged i down from the point end to Hashed the wide end specifies stereochemistry up Wedged from the point end to the wide end specifies stereochemistry Wavy TS i either at both ends Hollow same as Wedged Wedged tar
362. ve as many plots as you like each showing a different visualization of data from the current form ChemBioFinder 13 0 amp BioViz is integrated with these applications ChemBioDraw Lets you draw two dimensional structures and reactions ChemBio3D Lets you view three dimensional structures ChemBioDraw Excel Lets you export data to Excel About this guide The topics in this user guide are organized by task They are intended to help you familiarize yourself with the Chem BioFinder applications and start using them as quickly and efficiently as possible New users should read the Getting started chapter for an overview of the product and how it works The Tutorials chapter demonstrates most of the fea tures of the application Perform the tutorials in the order they are presented Experienced users can skip to sub sequent chapters which provide more detailed information This guide assumes that you are familiar with the basics of your Windows operating system If you are not refer to your system manual Some of the material describes tasks that must be performed in conjunction with other integrated ChemBioOffice 13 0 products The material on the addins describes tasks that must be performed in conjunction with Microsoft Excel or Word If you are not familiar with these applications consult the relevant user s manual Conventions The following notations are used throughout this guide amp Caution Cautions warn you of situations tha
363. w color 3 Click OK Tip Some users prefer not to see red highlighting because it masks the atom colors You can change the highlight color on the Color tab of the Preferences dialog box Selecting black will effectively cancel highlighting leaving atoms to display in their normal colors Structural query matching Search Type Search Details and Tuning help you define a query to give the kind of hits you are looking for The set tings are discussed in the chapter on queries under Search types on page 101 Setting search details preferences on page 113 and Tuning on page 115 General preferences The general preferences let you set Recent file list size Startup defaults Frame styles Query save defaults To set the general preferences 1 Go to File gt Preferences The Preferences dialog box appears 2 Click the General tab The General tab appears Chapter 16 Customizing ChemBioFinder 13 0 202 of 342 ChemBioFinder 13 0 PerkinElmer For the Better Preferences e Display Color Search Type Detads Tuning General Regatiation Check valences T Atk to coment changes Recent He kst sze 6 I Use Queey Add Window Al Startup Explorer tab Favcetes D Show startup dialog I Reopen bast fom Fiame style Whedbey Check for etemal scripts Query Saving C Save all que es Discard urnamed queres No save Figure 16 1 Setting general preferences
364. with a slightly larger frame DBOX 10 20 210 50 FormulaFRAME 5 5 215 55 Formula CAL commands FRAME syntax Creates a new frame on the active form FRAME left top right bottom text The FRAME command has the following arguments Integer value representing the distance in pixels Chapter 20 CAL Commands 249 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 between the left edge of the frame and the left edge of the active form Integer value representing the distance in pixels top between the top edge of the frame and the top edge of the active form Integer value representing the distance in pixels right between the right edge of the frame and the left edge of the active form Integer value representing the distance in pixels bottom between the bottom edge of the frame and the top edge of the active form String displayed as a label text on the top left corner of the frame Remarks When a new frame is created it adopts the current font settings These settings can be controlled with the FONT com mand After a frame is created its label can be changed with the SETTEXT command CAL commands TEXT syntax Creates a new static text box on the active form TEXT left top right bottom text The TEXT command has the following arguments Chapter 20 CAL Commands 250 of 342 hemBioFinder 13 I Che oFinder 13 0 PerkinElmer For the Better Integer value representing the
365. x 1 Inthe Boxtab select the field to associate and then click the Field radio button 2 Click OK The box display updates as you change records To specify fixed data for a data box 1 Inthe Box tab select the field to associate and click the Fixed radio button 2 Type a label in the text box If you choose a structure or picture field click the browse tool to browse to the file to display 3 Click OK The box display is fixed Chapter 4 Forms 42 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 Adding a data box menu You can add a menu containing a list of choices to a data box so you can choose an item from it to appear in the data box To add a menu 1 Right click on a data box and click Properties The Box Properties dialog box appears 2 On the Box tab click the With choices or auto link check box The Choices tab appears 3 Take the appropriate action From table and fol low the instructions at the bottom of the dialog box use alist from a database table as the data box menu Fixed list of create your own list choices and follow for the data box menu use a list from a database table and the instructions at the bottom of the dialog box a From table A list appears b Click Fixed list of choices and edit the list add your own items to the data box menu 4 Click OK to close the dialog box then click in the data box A button appears in the lower right
366. xactly how a bond participates in a reaction center For more information about these properties see Setting search details preferences on page TE Atom to atom mapping The second most important part of reaction searching is the atom to atom map You can specify maps in Chem BioDraw where they are stored as part of the data about a reaction Maps are used during searching to resolve certain types of structure search hits Atom to Atom mapping does not affect the search result when a query reaction is done with or without reaction map Consider a simple esterification reaction OH Jl OY _ H20 Figure 8 13 Esterification example Does the ester oxygen come from the acid or the alcohol You specify the fate of individual atoms through an atom to atom map In reality the ester oxygen in this reaction originates in the alcohol so the atom to atom map looks like this Figure 8 14 Atom map of esterification By matching numbers across the arrow you can see where atoms move during the course of the reaction The other reaction not observed experimentally where the ester oxygen comes from the acid would be mapped like this on sn iii oe f 1 08 Chapter 8 Queries 108 of 342 ChemBioFinder 13 0 PerkinElme For the Better Figure 8 15 alternate possible atom map for esterification ChemBioFinder 13 0 uses atom to atom map information to determine reacting centers for reactions If only some atoms are mapped Chem
367. y modify the query then rerun it man ually save the query to a separate Save file with extension cfq Query Chapter 8 Queries 127 of 342 pP PerkinElmer For the Better ChemBioFinder 13 0 mark the query so it will be saved as named when the form is saved This has no effect unless the Query Saving preference has been set to Discard unnamed queries See Sav ing and restoring lists on page 129 delete the selected query from the tree The next time you save the form this query will be lost If Remove you delete by mistake you can close and reopen the form without saving rename the query When the Query Saving pref erence has been set to Dis Rename card unnamed queries this has the same effect as Keep for all queries at the same depth in the tree sort alpha Sort Folder betically by name You also use the context menu to display the Query Properties dialog box In this dialog box you can modify the query name add a comment or change the color used in plots Text entered in the Comments box will replace the standard description displayed along with the number of hits Chapter 8 Queries 128 of 342 ChemBioFinder 13 0 PerkinElmer For the Better Query Properties ES Name SSS query CSH10 Commerts KE rm lt Hits 235 Tabie MolT able SELECT Molname Mol JO Structure A OK Query FROM MolT able WHERE Mol_ID IN 46 483 086 93 94 108 116 119 121
368. ypes of boxes and require a label To draw a Framed Box 1 Click the Framed Box tool and drag diagonally to create a framed box A box labeled Data is created Chapter 3 Tutorials 15 of 342 ChemBioFinder 13 0 PerkinElmer For the Better 2 Right click on the Data label and select Label The Box Text or Label dialog box appears In the Box Text or Label dialog box type Frame Box and click OK The label appears above the Framed Box To draw a frame around several existing boxes 1 Click the Frame tool 2 Place the pointer at the comer of the upper left data box and drag to create a border around the group of three data boxes The Enter the Label dialog box appears 3 Inthe Enter the Label dialog box type Frame and click OK The label appears above the box To place a picture in your form 1 Click the Picture tool and drag in the form The Open dialog box appears 2 Browse to a graphic file then click Open The picture appears in the area you dragged in the form f Note ChemBioFinder 13 0 supports EMF WMF BMP GIF JPG PNG and TIF formats Editing data boxes To edit one or more data boxes you must first select them 1 Click the Selection tool in the Form toolbar 2 To select the upper left box click it A selected data box is designated by four black squares at its corners Note To de select the box click an empty space in the form with the Selection tool To select multiple boxes press SHIFT
369. ython com mand then press ENTER The command is executed immediately and a new prompt is displayed on the next line The first time you execute a command in the window there is a short delay while Python is initialized If it is not already visible the Output Window then opens showing a ChemBioFinder header and the output of your com mand If the line you ENTXER ends with a colon then it is taken as the beginning of a compound multi line statement After you press ENTER the next line begins with the continuation prompt and is indented The statement is not executed until you press ENTER twice in a row that is you must ENTXER a blank line to terminate the compound statement You can execute commands other than the one you just typed Position the cursor on any line and press ENTER The command under the cursor is executed If the line is part of acompound statement the entire statement executes Afterwards you are not given a new prompt and the cursor does not move unless it was positioned at the end of the line in which case it inserts a new line and moves to it If you copy text into the window it is not automatically executed You can execute pasted code a line at a time by positioning the cursor on each line and pressing ENTER If you switch from interactive to standard Python mode all prompts are removed and the text is shifted left Line by line execution is then disabled and you can edit the text freely The output wind
370. zene Formula Molweight Gets gt 06 gt Figure 4 1 A form showing a single record You can create a form any of three ways E Automatically using the Form Generator dialog box Manually using the Form tools With the Database Tree Creating a form consists of creating a layout See Creating forms manually on page 34 and setting box properties see Setting box properties on page 40 tabs see Creating and editing tabs on page 40 and security See Secur ing forms on page 51 You can edit your form at any time see Editing forms on page 47 and Changing form layout on page 51 To begin designing a form you first select the database and deciding which fields to include Creating forms automatically Use the Form Generation dialog box to create a form or change the layout of an existing form You can choose prede fined form style and properties To create a form 1 Right click a blank area of the current form and select Data Source Chapter 4 Forms 32 of 342 ChemBioFinder 13 0 PerkinEl For the Better 2 Inthe Form Properties dialog box select the Form tab _ Note If the Generate form check box and Style button are disabled you must connect your current form to a database For more information see Connecting a database to a form on page 17 3 Select the Generate form check box then click Style The Form Generation dialog box appears In the left panel all the fields are sele

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