BIOVIA Draw Configuration Guide

CONFIGURATION GUIDEBIOVIA DRAW 2016

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ContentsBIOVIA Draw Configuration ivTasks ivConfiguration Tasks ivConfiguration Outside AccelrysDraw-net.xml vEditing the XML Configuration File v

Specify XML Configuration Files viSpecify the Path to Custom XMLConfiguration Files viiBefore: include= Points to Compiled ClassResources viiAfter: include= Points to Custom XMLConfiguration File vii

Setting a Startup Structure viiBiopolymers viiiBiopolymers: Sequence Tools viiiCase-sensitive Sequence Residues viiiDisabling the Feature viii

Customize Draw for Biopolymer Searches andRegistration ixProviding Standard Biopolymer Templatesto Users ixCustomizing the Standard AbbreviationDefinitions File xCustomizing BIOVIA Draw for Users xiCustomizing BIOVIA Draw forAdministrators xiiiCreating Additional Abbreviations xiv

Standard Abbreviation XML Reference xviiiEnhanced Stereochemistry xxDisable the Stereochemistry Dialog xxDisable Stereochemistry Actions xxExpose the Purity Section xxiHiding OR and AND Stereogroups xxiiCustomize Stereogroup Labels xxiii

Enabling the Data Sgroup Tool to ControlSgroup Data xxiiiExample for Data Sgroup Tool xxivCustomizing Draw for Attached Data xxvAttached Data in BiopolymerRepresentation xxvOther Attached Data xxvData Validation, Registration, and theAttached Data Dialog xxviiCleaning Data Sgroups xxvii

Enabling or Disabling Rgroup Atom andBuilding Block Tools xxix

Specify a Custom Ptable and CustomWeights xxix

Templates xxxAdding Templates to the Toolbar Manager xxxAdd a Directory to the Template Directory xxxiTemplate Security xxxii

Removing Template Toolbars xxxiiSpecify Display of Templates ContainingAbbreviated Structures xxxii

Display Preference Settings xxxiiiSpecify Display Preferences xxxiiiExample: AromaticRingCircles,AtomHighlightDotWidth xxxiii

Synchronize Display Settings xxxvdefault.xml with Custom Settings forDisplay Preferences xxxv

Removing a Feature xxxvExample: Removing the Data SgroupFeature xxxviExample: Removing from the Chemistrymenu xxxvi

Show Explicit Carbon Label xxxviiiDisabling Arrow Toolbar Autohide xxxixRemoving a Menu Item xxxixRemoving the Insert Option from the FileMenu xxxixRemoving the Formatting Toolbar Itemfrom theWindowMenu xli

ChemCheck Configuration xliiMigrating Custom Toolbars xlivCommand-line Image File Conversion xlviOnline Help on the ImageGenerator xlviConverting Single File Examples xlviConvert a Batch of Files Example xlvii

Creating a Custom Ptable xlviiiCustom Ptable Example xlviiiCustom Ptable Path xlviiiRunning the Example xlix

Add-Ins lCheshire Actions liSpecify a Custom Ptable and CustomWeights liAccelrysDraw-net.xml liiiAbout the Draw XML Configuration Files liiiHow to Edit XML Tags in the XML ConfigurationFiles liiiSample Screens liiiMain Screen livDrop-down Menu lviDialog box lvi

Attached Data Dialog lviiAttributes lviiParent Element lviiChild Elements lviiiExample lviii

Hierarchy of Elements lviiiXML Configuration Elements lixAlphabetic List of Elements lxiiDescription of Elements lxivabbreviationtoolbar lxivaction lxvbutton lxviiicheckbox lxviiicombobox lxixdialog lxxiDisplayPreferences lxxiidonetoolbar lxxiiifieldname lxxiiifolder lxxvilabel lxxvilistvalue lxxviimenu lxxviiimenuitem lxxixmenustrip lxxxmodule lxxximultitool lxxxiiioperator lxxxvpalette lxxxvpalettebar lxxxvipanel lxxxviipopup lxxxviiiradiobutton lxxxixradiogroup xciseparator xcishortcut xciishortcuts xciiselection xciiispace xciiitemplatedirectory xcivtemplatetoolbar xcvitemplatetoolbarmanager xcvitool xcviitoolbar c

Trigger Table ci

BIOVIA Draw ConfigurationXML tags define themenus, tools, toolbars, and other items that display inDraw. The AccelrysDraw-net.xml file is the primary XML configuration file and specifies the secondary class resources or XMLconfiguration files that affect Draw.

The AccelrysDraw-net.xml file is located in the installation directory. The AccelrysDraw-net.xmlfile points to secondary XML configuration files located in:

BIOVIA\BIOVIA Draw <version>\XmlConfig\

The menustrip.xml, a secondary configuration file, points to tertiary XML Configuration files thataffect each menu on themenu bar. The following are a list of affected menus:

n menubar-file.xmln menubar-edit.xmln menubar-object.xmln menubar-chemistry.xmln menubar-window.xmln menubar-help.xml

The XML parser in Draw does not validate parent-child tag relationships. However, if a relationship is notvalid, the object defined by the tags do not display.

Tasks iv

Biopolymers viii

Standard Abbreviation XML Reference xviii

Enhanced Stereochemistry xx

Enabling the Data Sgroup Tool to Control Sgroup Data xxiii

Enabling or Disabling Rgroup Atom and Building Block Tools xxix

Templates xxx

Display Preference Settings xxxiii

ChemCheck Configuration xlii

Migrating Custom Toolbars xliv

Command-line Image File Conversion xlvi

Tasks

Configuration TasksYou can configure Drawwithout writing applications or using the DrawAPI by updating theAccelrysDraw-net.xml configuation file or setting a custom start-up structure. The XMLconfiguration file affects the initial loading of BIOVIA Drawwhen a user opens the application. When aDraw application user changes one or more display settings, using Options > Settings, those localsettings override the default or custom values defined in the configuration file, AccelrysDraw-net.xml.

You must have administrator privileges to edit Draw, the AccelrysDraw-net.xml.

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Always back up the AccelrysDraw-net.xml beforemaking any changes in the configuration file. Theelements and attributes in the XML files are case-sensitive, for example, Dog, and not the same as dog inan XML file.

You can update the Action, Tool, and ContextMenu elements in the AccelrysDraw-net.xml file. Ifyou are editing the AccelrysDraw-net.xml configuration file to add the functionality of a third-partyadd-in, you should not make the add-in available from more than one location such as context menu,toolbar, or as a menu option in Draw.

You can make the following edits:

n Change the default value for a settingn Customize chemical drawingn Enforce business rules for biopolymer representationn Specify a custom Ptablen Enable or disable the Data Sgroup tool (attached data)n Hide enhanced stereochemistryn Enable or disable the Rgroup Atom and building block toolsn Add more templates to the toolbarn Edit display text or imagesn Remove certain actions or toolsn Edit dialog boxesn Migrate custom toolbars created in previous versions of Draw

Configuration Outside AccelrysDraw-net.xmlMost tasks described in the BIOVIA Draw Configuration Guide consist of edits inside the configurationfile, AccelrysDraw-net.xml and the XML Configuration files to which it points. The exceptions are:

n Writing one or more batch files that cause BIOVIA Draw to start up in association with a particularXML configuration file. See Specifying XML Configuration Files.

n Safeguarding and administering the central set of templates at your site. See Templates: Customizing.n Command-line conversion of structure files into image files. See Command-line Image File

Conversion: ImageGenerator.

Notes:

n BIOVIA Draw can be the structure editor for ISIS/Base (Options > Structure Editor).

Editing the XML Configuration FileTo customize the BIOVIA Draw graphical user interface, edit the primary XML Configuration file and theXML Configuration files it points to. See Specify the Path to Your Custom XML Configuration Files. Thedefault name of the primary XML Configuration file is AccelrysDraw-net.xml, which is installed inthe root directory of the BIOVIA Draw installation, which this document refers to as <draw_home>.

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IMPORTANT!

n Keep a backup copy of the original versions of any XML Configuration files undergoing edits. It isvery easy to break the XML and not always easy to fix, so it is good to be able to revert to a versionthat works.

n Do NOT change entries in the AccelrysDraw-net.xml file (or the XML Configuration files itpoints to) except according to the product documentation and the instructions included in thecomments of the default AccelrysDraw-net.xml file and the XML Configuration files it pointsto. Any other changes might cause unexpected results. Only the BIOVIA Administrator shouldmake changes on behalf of the end-users. End-users should not alter the XML files.

n For each configuration task, make the change in only one of the following areas of the XML: Action,Tool, or ContextMenu. Unexpected results might occur, for example, if you make an add-inavailable in more than one of the following ways: from themenu bar (action), from the verticaltoolbar (tool), or from the right-click context menu.

n The entries in the XML files are case-sensitive. Be careful that the spelling of elements andattributes is exactly correct, including the case.

Specify XML Configuration FilesYou can specify the XML configuration file using the following methods:

At start up the BIOVIADraw.exe looks for the XML configuration file, AccelrysDraw-net.xmllocated in the installation directory. If Draw does not find AccelrysDraw-net.xml in the rootdirectory of the installation, it loads an internal XML configuration file.

If you launch Drawwith a batch file, the batch file can specify the primary XML configuration file. Theprimary XML configuration file and the secondary XML configuration files it points to implement thegraphical user interface, including which features are visible and enabled.

You can usemore than one XML configuration files, as follows:

n A file that points to palettebarStereochemistryEnable.xmlwith stereochemistry enabledn A file that points to palettebarStereochemistryDisable.xmlwith stereochemistry disabled.n A batch file that specifies a structure file to load at start-up.

Use the command line after launching Drawwith from a command-line console prompt. You can specifythe XML configuration file, the following as showing in the example:

n The simple path:C:\myFolder>BIOVIADraw.exe Alt_Config\MyConfig.xml

n A Path with spaces and quotation marks:\\"Program Files (x86)\BIOVIA\BIOVIA Draw<version number>\BIOVIADraw.exe"c:\myFolder\myAccelrysDraw-net.xml

n The UNC_path:\\Program Files (x86)\BIOVIA\<version_number>\BIOVIADraw.exe

\\myServer\sharedfolder\AccelrysDraw-net.xml

You can change the properties of the start menu shortcut to point to a custom target location for Draw.

Use the DrawAPI to set the primary XML configuration file. Always backup the original versions of anyXML configuration files that you plan to edit.

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Specify the Path to Custom XML Configuration FilesSome of the XML Configuration files point by default to compiled class resources, but you can makethem point to your custom XML Configuration files. To do so, give the full path after include=.

For complete step-by-step examples, see Adding a set of templates to the Toolbar Manager andRemoving a Menu Item.

For an explanation of which XML Configuration files can specify other XML Configuration files, see Aboutthe BIOVIA Draw XML Configuration Files.

Before: include= Points to Compiled Class ResourcesThe primary XML Configuration file, AccelrysDraw-net.xml, points to compiled class resources thatyou cannot edit.

<menustrip include="MDL.Draw.Editor.XmlConfig.menustrip.xml" /><maintoolstrip include="MDL.Draw.Editor.XmlConfig.maintoolstrip.xml"/><toolbar include="MDL.Draw.Editor.XmlConfig.templatetoolstrip.xml" /><palettestrip include="MDL.Draw.Editor.XmlConfig.palettestrip.xml" />

After: include= Points to Custom XML Configuration FileTo specify the XML Configuration files that contain your custom configuration, change the include=assignment for the element to point to the full path of your new XML configuration file(s).

In this example, we specify custom XML Configuration files with the full path for the my-menustrip.xml, my-maintoolstrip.xml, and my-templatetoolstrip.xml, but continue to usethe compile class resource for the palettestrip.xml.

<menustrip include="C:\Program Files (x86)\BIOVIA\BIOVIA Draw2016\XmlConfig\my-menustrip.xml" /><maintoolstrip include="C:\Program Files (x86)\BIOVIA\BIOVIA Draw2016\XmlConfig\my-maintoolstrip.xml" /><toolbar include="C:\Program Files (x86)\BIOVIA\BIOVIA Draw2016\XmlConfig\my-templatetoolstrip.xml" /><palettestrip include="MDL.Draw.Editor.XmlConfig.palettestrip.xml" />

Setting a Startup StructureFor testing purposes, you might want BIOVIA Draw to open with the display of a particular structure.The following example illustrates how to open a molfile when BIOVIA Draw starts up:

1. Close all open versions of BIOVIA Draw and navigate to the root directory of your BIOVIA Drawinstallation.

2. Make a copy of AccelrysDraw-net.xml and name it myXmlConfigFile.xml.

IMPORTANT! BIOVIA recommends that you always keep a backup copy of the original XMLconfiguration files.

3. Navigate to the Examples\C#\GettingStarted directory of your installation and copy test.molto the root directory of your Draw installation.

4. Make a batch file called MyDraw.bat file in the root directory of your BIOVIA Draw installation thatcontains the following text:BIOVIADraw.exe myXMLConfigFile.xml test.mol

5. Run MyDraw.bat to start the BIOVIA Draw Editor with the specified structure already loaded and thefile name in the title bar.

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Biopolymers

Biopolymers: Sequence ToolsYou can configure Draw and your company’s databases to comply with the business rules for searchingand registering biopolymers, by:

n Customizing the standard abbreviation definitions file, std_abbrev_defs.xml, to providebiopolymer templates for the Draw Sequence tools. The std_abbrev_defs.xml file is located in theinstallation directory.

n Customizing Draw to enforce your company’s business rules biopolymer representation.n Implementing subsequence searching in applications that access databases that contain

biopolymers.

For more information, see Biopolymer Representation in the BIOVIA Chemical Representation Guidelocated in the Draw installation directory's docs folder.

The Draw Sequence tools use the templates that are specified in the version of std_abbrev_defs.xmlthat is located in the BIOVIA Draw installation directory. BIOVIA recommends that you do not allowusers to modify the default Sequence tools.

Case-sensitive Sequence ResiduesThe default setting in BIOVIA Draw displays D- sequence residues with a single lower-case letter, and L-sequence residues with a single uppercase letter.

For example, "a" creates D-alanine and "A" creates L-alanine.

When this feature is enabled, the D- form also precedes the L- form for 3-letter residues.

Disabling the FeatureIn the Settings, dialog, setMake sequence residue case sensitive to Off.

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Customize Draw for Biopolymer Searches and RegistrationTo customize Draw so chemists can illustrate biopolymers to comply with business rules for biopolymerrepresentation, do the following:

n Provide standard templates for biopolymer residues, protecting groups, and polyethylene glycolgroups (PEG).

n Provide a read-only directory of templates on the company network.n Configure the standard abbreviation definitions file to reference the templates in the read-only

directory.n Edit the Draw configuration file to include customizations for your enterprise.n Distribute the customized version of Draw.

When Draw users start the customized application, the toolbars for each Sequence tool displays thebiopolymer templates in the write-protected directory. End-users cannot create their own residuetemplates. However, users can create templates for protecting groups in their personal templatedirectories.

Providing Standard Biopolymer Templates to UsersBIOVIA Draw supports four different conventions for representation of biopolymers. To enforce yourchosen structure convention, ensure that all chemists use the same set of write-protected templates forbiopolymer residues, protecting groups, and PEG groups:

1. Provide a directory for the templates that is visible in the corporate network. End-users should haveread-only privileges to this directory. Administrators should have write and delete privileges.

2. Install BIOVIA Draw on your workstation.3. Copy the directory that contains the biopolymer templates from your local hard drive to the

directory that you created in Step 1.

Notes:

Biopolymer templates are located in the following directory and its subdirectories in the BIOVIADraw installation on your local hard drive:<draw_home>\StdAbbreviations

4. Configure the standard abbreviation definitions file to reference the templates in the directory thatyou created in Step 1. See Customizing the standard abbreviation definitions file.

5. Copy the standard abbreviation definitions file that you edited in Step 3 to the directory that youcreated in Step 1.

6. Edit the BIOVIA Draw XML configuration file as needed. See Customizing BIOVIA Draw for end users.7. Provide your end users with a customized BIOVIA Draw that uses the edited BIOVIA Draw

configuration file that you created in Step 5.

When your users start the customized version of BIOVIA Draw, the toolbars for each Sequence Tool willdisplay the biopolymer templates in the write-protected directory. End-users will not be able to create

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their own residue templates, but they can create templates for protecting groups in their personaltemplate directories.

Customizing the Standard Abbreviation Definitions FileThe standard abbreviation definitions file, std_abbrev_defs.xml, specifies the biopolymer templatesthat display on the toolbar for each sequence tool.

Entries in the standard abbreviation definitions file specify the structure convention for eachabbreviation (full, *atom, or pseudoatom), the full structure that the abbreviation represents, and otherinformation. For more information see Standard Abbreviation XML Reference.

BIOVIA Draw provides four example versions of the standard abbreviation definitions file, eachcorresponding to one of the conventions for representation of biopolymers. Each file contains thefollowing abbreviations:

n Standard 1-letter abbreviations for 21 of the 22 naturally occurring amino acids, and for DNA and RNAnucleotides

n Abbreviations for widely used protecting groups for amino acids.n Example abbreviations for PEG structures

BIOVIA recommends that you use one of these files as the basis for creating your own standardabbreviation definitions file. You can customize this file to add your own abbreviations.

Note: The version of std_abbrev_defs.xml that is located in the BIOVIA Draw installation directoryis the same as std_abbrev_defs_fullctab.xml in the examples directory, except that the file inthe BIOVIA Draw installation directory references the <draw_home>\StdAbbreviations directory on your local hard drive. Therefore, BIOVIA recommends using std_abbrev_defs_fullctab.xmlinstead.

To configure the standard abbreviation definitions file:

1. Use the following table to choose the example standard abbreviation definitions file thatcorresponds to the biopolymer structure convention that you want to use in your database.

StructureConvention

File Name

Full <draw_home>\Examples\SequenceTool\std_abbrev_defs_fullctab.xml

*Atoms alone(condensed)

<draw_home>\Examples\SequenceTool\std_abbrev_defs_staratom.xml

Pseudoatomsalone(condensed)

<draw_home>\Examples\SequenceTool\std_abbrev_defs_pseudoatom.xml

*Atoms andpseudoatoms(condensed)

<draw_home>\Examples\SequenceTool\std_abbrev_defs_staratomPlusPseudoatom.xml

2. Copy the selected file to the location where the standard abbreviation templates are stored (seeStep 1 in Providing standard biopolymer templates to users).

3. Rename the copied file std_abbrev_defs.xml.4. Edit the directory specifications at the beginning of your std_abbrev_defs.xml to point to the

location where the biopolymer template files are stored.

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For example, if the biopolymer template files are on a network drive named “x” in the directoryMyMolfiles/StdAbbrevs, change the text from the original:<!ENTITY ABBREVROOT "CompanyMolTemplates/StdAbbreviations/"><!ENTITY AADir "&ABBREVROOT;Sequence-AA/"><!ENTITY DNADir "&ABBREVROOT;Sequence-DNA/"><!ENTITY RNADir "&ABBREVROOT;Sequence-RNA/"><!ENTITY SAGDir "&ABBREVROOT;Sequence-SAG/">

To the following (changes are in bold):<!ENTITY ABBREVROOT "x:/MyMolfiles/StdAbbreviations/"><!ENTITY AADir "&ABBREVROOT;Sequence-AA/"><!ENTITY DNADir "&ABBREVROOT;Sequence-DNA/"><!ENTITY RNADir "&ABBREVROOT;Sequence-RNA/"><!ENTITY SAGDir "&ABBREVROOT;Sequence-SAG/">

where:

n ABBREVROOT defines the root directory that contains the biopolymer templates.n AADir, DNADir, and RNADir specify the locations of the directories that contain residue templates

for amino acid, DNA, and RNA sequences.n SAGDir specifies the directory that contains templates for single-attachment groups such as

protecting groups and PEG groups.

If the template files are on aWeb server called CompanyServer, you can specify ABBREVROOT asfollows:<!ENTITY ABBREVROOT "http://CompanyServer/StdAbbreviations/">

5. Customize the file as needed to provide additional abbreviation. See Creating additionalabbreviations.

Customizing BIOVIA Draw for UsersTo ensure that users create polymers that use the templates that you specify in your standardabbreviation definitions file, provide users with a customized version of BIOVIA Draw. To customizeBIOVIA Draw, you must edit the BIOVIA Draw XML configuration files, and provide them to your users.

To configure a custom toolbar:

1. Make a copy of AccelrysDraw-net.xml in your Draw installation folder. The version will appearas follows:<mdldraw width="950" height="700" name="BIOVIA Draw 2016">

<module class="MDL.Draw.Modules.Editor.EditorModule"><shortcuts>

<shortcut char=" " method="SwapTool"/></shortcuts>



<menustrip include="MDL.Draw.Editor.XmlConfig.menustrip.xml"/>

<maintoolstrip include="MDL.Draw.Editor.XmlConfig.maintoolstrip.xml"/>



<palettestrip include="XmlConfig\palettestrip.xml"/>

<atomtoolbar name="Atoms" direction="Horizontal"/><bondtoolbar name="Bonds" direction="Horizontal"/><arrowtoolbar name="Arrows" direction="Horizontal" autohide="true"/>

</module></mdldraw>

It references palettestrip.xml in subfolder XmlConfig.

2. Make a copy of XmlConfig/palettstrip and place the following version in the Draw installationfolder. It has 2 lines modified lines:

Line 1190was added:

<abbreviationtoolbar name="Modified Amino Acids" path="%MDLDRAW%std_abbrev_defs.xml" sequence="true" toolbarType="Modified"/>

In line 1206 the toolbar type “modified” was added:<sequencetoolbutton name="Amino Acid Sequences" image="SeqToolAA1.png"toolbarType="AA,dAA,Modified,SAG,LINKER,ASM"/>

3. Make a copy of std_abbrev_defs and place it in your Draw installation folder.

The block with themodified residues and their location was added:<toolbarType name="Modified" class="AA">

<abbreviation displayName="Met_m" oneLetterDisplayName="M*" fullName="L-methionine_modified" isQueryOnly="no">

<molfile>%MDLDRAW%AADir;Methionine1.mol</molfile></abbreviation><abbreviation displayName="Phe-M" oneLetterDisplayName="F*" fullName="L-

phenylalanine_modified" isQueryOnly="no"><molfile>%MDLDRAW%AADir;phehylalnine1.mol</molfile></abbreviation><abbreviation displayName="Pro_M" oneLetterDisplayName="P*" fullName="L-

proline_modified" isQueryOnly="no"><molfile>%MDLDRAW%AADir;proline1.mol</molfile>

</abbreviation></toolbarType>

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The 3 .mol files were placed in the following folder:C:\Program Files \BIOVIA\BIOVIA Draw 4.2\StdAbbreviations\Sequence-AA

You can define an alternate folder and create a path variable in std_abbrev_defs.xml.

Customizing BIOVIA Draw for AdministratorsAdministrators are responsible for creating and maintaining the biopolymer template files that theSequence Tools use. To perform this task, administrators require access to the Enhanced TemplateEditor dialog, which allows you to edit attachment atoms on the structures of biopolymer residues. Thisdialog is hidden so that end users cannot accidentally alter the templates. Creating and editingbiopolymer templates requires additional settings that differ from the BIOVIA Draw defaults:

n Display explicit hydrogen leaving groups on non-terminal attachment atoms in contracted amino acidresidues. These groups are hidden by default.n For information on why explicit hydrogen leaving groups are necessary, see BIOVIA Chemical

Representation, Biopolymer Representation, “Explicit hydrogen leaving groups on attachmentatoms of reactive side chains”. This document is installed as:<draw_home>\docs\Draw\devguide\BIOVIAChemicalRepresentation.pdf

n Use right-click, rather than double-click, to start the Template Editor.n By default, clicking an abbreviation on a any template toolbar adds the corresponding structure to

the drawing area, while double-clicking displays the Template Editor. Using right-click avoids avoidaccidentally adding templates to the drawing area while you create and edit biopolymer templatefiles.

n Use the following procedure to customize BIOVIA Draw for administrator users:1. Create a settings file, biopolymer.xml, that contains the recommended settings for editing

biopolymer templates. See To create the settings file.2. Edit a copy of the BIOVIA Draw XML configuration files to provide access to the Advanced

Template Editor and to the settings file that you created in the previous step. See To edit theBIOVIA Draw configuration files.

3. Distribute the edited copy of the XML configuration and the settings file biopolymer.xml toadministrator users. Instruct each user to copy biopolymer.xml to the Preferences subdirectoryon their local hard drive:C:\Users\<user_name>\AppData\Roaming\BIOVIA\BIOVIA Draw\Preferences\

Create the Settings File

Two settings that administrator users require are available on the Settings dialog in BIOVIA Draw. Thesetting to display non-terminal leaving groups is hidden and therefore not available on the Settingsdialog. To specify the value of a hidden setting, you must edit the settings file manually. Use thefollowing procedure to create the settings file biopolymer.xml:

1. Start BIOVIA Draw using the customized version of the XML configuration that you created for endusers. For more information, see Customizing BIOVIA Draw for end users.

2. ChooseOptions > Settings from themenu. The Settings dialog opens.3. Change the General setting Invoke Template Editorwith from Double Click to Right-Click.4. (Optional) Change any other settings that administrator users require.5. On the Settings dialog, click Save As.6. Enter biopolymer.xml as the file name, click Save, and then click Cancel to exit the Settings dialog.7. Exit BIOVIA Draw.

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8. Navigate to the directory on your hard drive that contains your personal settings:C:\Users\<user_name>\AppData\Roaming\BIOVIA\BIOVIA Draw\Preferences\

9. Edit biopolymer.xml to add the hidden setting that enables display of internal leaving groups:<DisplayInternalLeavingGroup>true</DisplayInternalLeavingGroup>

The following example shows a portion of biopolymer.xml, with the added setting in bold:<DisplayPreferences xmlns:xsd="http://www.w3.org/2001/XMLSchema"

xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">

<TemplateEditorInvokingGesture>RightClick</TemplateEditorInvokingGesture><DisplayInternalLeavingGroup>true</DisplayInternalLeavingGroup>...(additional settings)...</DisplayPreferences>

10. Save the edited biopolymer.xml file.

Edit the Configuration Files

Use the following procedure to enable the Advanced Template Editor and specify biopolymer.xml as thedefault settings file:

1. Create a copy of the version of the XML configurations that you customized for end users. For moreinformation, see Customizing BIOVIA Draw for end users. Edit this copy as described in the stepsthat follow.

2. To enable the Enhanced Template Editor dialog, edit the value forMDL.Draw.Modules.Editor.EditorModule. The following example shows the default XML:<mdldraw width="950" height="640" name="MDL Draw"><module class="MDL.Draw.Modules.Splitter"orientation="horizontal" percentage="70"><module class="MDL.Draw.Modules.Editor.EditorModule">

The following example shows the XML after editing (changes are in bold):<mdldraw width="950" height="640" name="MDL Draw"><module class="MDL.Draw.Modules.Splitter"orientation="horizontal" percentage="70"><module class="MDL.Draw.Modules.Editor.EditorModule"enableMultipleAttachmentTemplateMode="true">

3. To specify biopolymer.xml as the default settings file, change the name of the default settings file,default.xml, to biopolymer.xml. For example:<DisplayPreferences file="biopolymer.xml" />

IMPORTANT! The settings file must be located in the user’s personal settings directory, as shownin this example. You cannot use a different path for the file.

4. Save the edited copy of the XML configuration.

Creating Additional AbbreviationsYou can provide your users with additional abbreviations for biopolymer residues, protecting groups,and PEG groups. For example, you can provide abbreviations for non-natural amino acids like 2-aminoisobutyric acid (Aib), or PEG groups of differing molecular weights. All of these procedures involveadding entries to the standard abbreviations file. When you add new entries to the standardabbreviation file, the templates display on the sequence toolbars as soon as you restart BIOVIA Draw.

BIOVIA Draw Configuration | Page xiv

http://www.w3.org/2001/XMLSchema

http://www.w3.org/2001/XMLSchema-instance

The sections that follow give procedures for each category of biopolymer abbreviation: biopolymerresidues, protecting groups, and PEG groups.

Note: To understand how to create new entries in your standard abbreviation definitions file, BIOVIArecommends that you study the entries in the example standard abbreviation definitions files and thecomments for the entries.

Creating Abbreviations for Biopolymer Residues

Creating abbreviations for additional biopolymer residues uses procedures necessary to ensure thatend-users cannot alter the templates. For example:

n BIOVIA Draw prevents users from accessing the Enhanced Template Editor, which must be used todefine attachment atoms and leaving groups on residue templates. If you want to add more residueabbreviations, you must edit your copy of the BIOVIA Draw XML configuration file to allow editing ofbiopolymer residues. See Customizing BIOVIA Draw for end users and Customizing BIOVIA Draw foradministrators.

n A biopolymer template does not display on the top toolbar of any sequence tool until you add anentry for that template to the appropriate section of the standard abbreviation definitions file.Consequently, creating a biopolymer residue template involves not only creating and editing thestructure in BIOVIA Draw, but also editing the standard abbreviation definitions file.

The complete procedure for creating a residue template consists of the following steps:

1. Use BIOVIA Draw to create the underlying structure of the residue, contract the structure to anabbreviation, and save the structure to a molfile in the directory where other residue templates arelocated.

For detailed instructions, see the following index entry in the BIOVIA DrawOnline Help: “biopolymeradministration, creating residue templates”.

2. Edit the standard abbreviation definitions file to add entries for each template that you created inStep 1. Add the entry to the section of the standard abbreviation file that corresponds to theabbreviation class of the residue:a. Use copy/paste to create a duplicate of an existing entry of the same abbreviation class. For

example, to create an abbreviation for an amino acid residue, duplicate the entry for L-alanine.b. Change the displayName attribute of the duplicate entry to the symbol that you want to

display on the toolbar.c. Change the molfile attribute in the duplicate entry so that it refers to the file that contains

the structure of the new residue.d. Change the fullName attribute of the duplicate entry.e. Change any other attributes that are required for full structure, *atom, or pseudoatom

representation. For information on which attributes to edit, see the examples of edited entrieslater in this section.

f. Repeat Steps a through e for additional abbreviations.3. Restart BIOVIA Draw and use the Enhanced Template Editor to define attachment atoms and leaving

groups, as described in the following index entry in the BIOVIA DrawOnline Help: “biopolymeradministration, creating residue templates.”

Full Structure Representation

The following example shows duplicate entries for the full structure representation of L-alanine:<abbreviation displayName="Ala" oneLetterDisplayName="A"fullName="L-alanine" isQueryOnly="No"><molfile>&AADir;alanine.mol</molfile>

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</abbreviation><abbreviation displayName="Ala" oneLetterDisplayName="A"fullName="L-alanine" isQueryOnly="No"><molfile>&AADir;alanine.mol</molfile></abbreviation>

The following example shows how the second entry has been edited to refer to the non-natural aminoacid 2-aminoisobutyric acid (Aib). The structure of the residue is in themolfile aib.mol, which is located inthe same directory as the structures of other amino acids. Aib lacks a 1-letter abbreviation, so thedisplayName appears in both 1-letter and 3-letter mode (changes are in bold):

<abbreviation displayName="Ala" oneLetterDisplayName="A"fullName="L-alanine" isQueryOnly="No"><molfile>&AADir;alanine.mol</molfile></abbreviation><abbreviation displayName="Aib"fullName="2-aminoisobutyric acid (Aib)" isQueryOnly="No"><molfile>&AADir;aib.mol</molfile></abbreviation>

*Atom Representation

The following example shows duplicate entries for the *atom representation of L-alanine:<abbreviation starAtomName="AA-Ala" displayName="Ala"

oneLetterDisplayName="A"fullName="L-alanine" isQueryOnly="No"><molfile>&AADir;alanine.mol</molfile>

</abbreviation><abbreviation starAtomName="AA-Ala" displayName="Ala"

oneLetterDisplayName="A"fullName="L-alanine" isQueryOnly="No"><molfile>&AADir;alanine.mol</molfile>

</abbreviation>

The following example shows how the second entry has been edited to refer to the non-natural aminoacid 2-aminoisobutyric acid (Aib). The structure of the residue is in the molfile aib.mol, which islocated in the same directory as the structures of other amino acids. Aib lacks a 1-letter abbreviation, sothe displayName appears in both 1-letter and 3-letter mode (changes are in bold):

<abbreviation starAtomName="AA-Ala" displayName="Ala"oneLetterDisplayName="A"fullName= “L-alanine” isQueryOnly="No"><molfile>&AADir;alanine.mol </molfile>

</abbreviation><abbreviation starAtomName="AA-Aib" displayName="Aib"

fullName="2-aminoisobutyric acid (Aib)" isQueryOnly="No"><molfile>&AADir;aib.mol</molfile>

</abbreviation>

Creating Abbreviations for Protecting Groups

1. Draw the abbreviated structures in BIOVIA Draw and add them to a personal toolbar on your localhard drive.

For detailed instructions, see the following index entry in the BIOVIA DrawOnline Help: biopolymeradministration, creating protecting groups.

BIOVIA Draw Configuration | Page xvi

2. After creating the new template files, copy the files from your local hard drive to the directory wheresingle-attachment groups are stored.

3. Edit the standard abbreviation definitions file to add entries for each template that you created inStep 1. Add the entry to the section of the standard abbreviation definitions file that containsprotecting groups:a. Use copy/paste to create a duplicate of an existing entry.b. Change the displayName attribute of the duplicate entry.c. Change themolfile attribute in the duplicate entry so that it refers to the file that contains the

structure of the new protecting group.d. Change the fullName attribute of the duplicate entry.e. Repeat Steps a through d for additional abbreviations.

Creating Abbreviations for PEG Groups

Templates for PEG groups contain solely a single *atom or pseudoatom. To create new PEG groups, youneed to duplicate an existing template and then edit the template in BIOVIA Draw.

Use the procedure that follows to create abbreviations for PEG groups:

1. Draw the abbreviated structures in BIOVIA Draw and add them to a personal toolbar on your localhard drive.

For detailed instructions, see the following index entry in the BIOVIA DrawOnline Help: "biopolymeradministration, creating PEG groups".

2. After creating the new template files, copy the files from your local hard drive to the directory wheresingle-attachment groups are stored.

3. Edit the standard abbreviation definitions file to add entries for each template that you created inStep 1. Add the entry to the section of the standard abbreviation definitions file that containsprotecting groups:a. Use copy/paste to create a duplicate of an existing entry.b. Change the displayName attribute of the duplicate entry to the symbol that you want to

display on the toolbar.c. Change themolfile attribute in the duplicate entry so that it refers to the file that contains the

structure of the new PEG group.d. Change the fullName attribute of the duplicate entry.e. Change the formulaWeight attribute of the duplicate entry to the desired averagemolecular

weight.f. Repeat Steps a through e for additional PEG groups.

The examples in the following sections show how to create an abbreviation for a PEG group with anaveragemolecular weight of 5,000 in both the *atom and pseudoatom representations.

*Atom Representation of PEG Groups

The following example shows duplicate entries for PEG-20000:<abbreviation displayName="PEG20000"

fullName="Polyethylene glycol, average molecular weight = 20,000"starAtomName="MPEG-20000" formulaWeight="20000.0000"isQueryOnly="No"><molfile>&SAGDir;PEG20000.mol</molfile>

</abbreviation><abbreviation displayName="PEG20000"

fullName="Polyethylene glycol, average molecular weight = 20,000"

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starAtomName="MPEG-20000" formulaWeight="20000.0000"isQueryOnly="No"><molfile>&SAGDir;PEG20000.mol</molfile>

</abbreviation>

The following example shows how the second entry has been edited to represent PEG-5000 (changes arein bold):

<abbreviation displayName="PEG20000"fullName="Polyethylene glycol, average molecular weight = 20,000"starAtomName="MPEG-20000" formulaWeight="20000.0000"isQueryOnly="No">

<molfile>&SAGDir;PEG20000.mol</molfile></abbreviation><abbreviation displayName="PEG5000"

fullName="Polyethylene glycol, average molecular weight = 5,000"starAtomName="MPEG-5000" formulaWeight="5000.0000" isQueryOnly="No"><molfile>&SAGDir;PEG5000.mol</molfile>

</abbreviation>

Pseudoatom Representation of PEG Groups

The following example shows duplicate entries for PEG-20000:<abbreviation displayName="PEG20000" pseudoatomName="PDB"

fullName=" Polyethylene glycol, average molecular weight = 20,000”formulaWeight="20000.00000" isQueryOnly="No"><molfile>&SAGDir;PDB.mol</molfile>

</abbreviation><abbreviation displayName="PEG20000" pseudoatomName="PDB"

fullName=" Polyethylene glycol, average molecular weight = 20,000”formulaWeight="20000.00000" isQueryOnly="No"><molfile>&SAGDir;PDB.mol</molfile>

</abbreviation>

The following example shows how the second entry has been edited to represent PEG-5000, which isrepresented as the pseudoatom “PXY” in the Ptable (changes are in bold):

<abbreviation displayName="PEG20000" pseudoatomName="PDB"fullName=" Polyethylene glycol, average molecular weight = 20,000”formulaWeight="20000.00000" isQueryOnly="No"><molfile>&SAGDir;PDB.mol</molfile>

</abbreviation><abbreviation displayName="PEG5000" pseudoatomName="PXY"

fullName="Polyethylene glycol, average molecular weight = 5,000”formulaWeight="5000.00000" isQueryOnly="No"><molfile>&SAGDir;PXY.mol</molfile>

</abbreviation>

Standard Abbreviation XML ReferenceThe table describes the elements in the standard abbreviation definitions file, and specifies the followinginformation for each abbreviation.

BIOVIA Draw Configuration | Page xviii

Element Description

displayName (Required) Residue symbol. For amino acid sequences, this is the 3-letterabbreviation that displays in 3-letter mode. For DNA and RNA residues, this isthe 1-letter abbreviation that displays in the toolbars of the DNA and RNASequence Tools, respectively.

oneLetterDisplayName (Optional) For structures that have both 1-letter and multi-letter symbols (forexample, amino acid and nucleic acid residues), the 1-letter symbol. The 1-letter symbol displays when in amino acid 1-letter mode. One-letter symbolsmust be the standard symbols approved by International Union of Pure andApplied Chemistry and the International Union of Biochemistry andMolecular Biology,IUPAC-IUB Joint Commission on BiochemicalNomenclature (JCBN). For more information, see the Nomenclature andSymbolism for Amino Acids and Peptides .

starAtomName (Optional) The Sgroup data that is attached to the *atom representation ofthe residue and that uniquely identifies each residue. Required forabbreviations that use the *atom representation.

pseudoatomName (Optional) If the residue is to be represented as a pseudoatom rather than a*atom, the pseudoatom name.

formulaWeight (Optional) The formula weight of the residue or group. Use this for fragmentswhosemolfiles lack the full connection tables, such as the *atom andpseudoatom representations of PEG groups. The Chemistry > Calculatorcommand in Draw also uses this value in calculating molecular weight.

fullName (Optional, but recommended) Specifies the full name of the residue, forexample L-glutamine. The fullName displays as the tooltip for the template onthe top toolbar of the Sequence Tool.

isQueryOnly (Optional)Indicates whether the structure is usable only for queries. The validvalues are as follows:n Yes, use only for queries and do not register to a database.n No, the structure is usable in queries, and can be registered to a database.

comment (Optional) Comment

molfile (Required) Path to templatemolfile that contains the underlying structure ofthe abbreviation. This molfile contains the structure that displays when youright-click the structure and choose Expand. The Chemistry > Calculatorcommand in BIOVIA Draw also uses this structure to calculatemolecularweight and other values.

The starAtomName and pseudoatomName elements are optional. These three element names havethe following precedence:pseudoatomName > starAtomName > displayName

Element name precedence:

n If an entry in std_abbrev_defs.xml does not contain a pseudoatomName or starAtomName buthas displayName, then the structure of the corresponding abbreviation is saved as a fully definedstructure (full connection table or ctab) in a sequence.

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http://www.chem.qmul.ac.uk/iupac/AminoAcid/

http://www.chem.qmul.ac.uk/iupac/AminoAcid/

n If an entry in std_abbrev_defs.xml has both starAtomName and displayName, but does nothave a pseudoatomName, then the structure of the corresponding abbreviation is saved as a *atomin a sequence.

n If an entry in std_abbrev_defs.xml has both pseudoatomName and displayName, but does nothave starAtomName, then the structure of the corresponding abbreviation is saved as apseudoatom in a sequence.

n If an entry in std_abbrev_defs.xml has all three names (pseudoatomName, starAtomName, anddisplayName), then the structure of the corresponding abbreviation is saved as pseudoatom in asequence because pseudoatomName has the highest priority.

Enhanced StereochemistryYou can edit the XML Configuration for stereochemistry. For more information, see Specify the Path toCustom XML Configuration Files.

The Stereochemistry dialog and actions in BIOVIA Draw enable users to create structures withstereochemistry features. The original (classic) stereochemical representation is a subset of the current(enhanced) stereochemical representation.

For more information on stereochemical representation, see the following in BIOVIA ChemicalRepresentation, which is installed as <draw_home>\docs\Draw\devguide\BIOVIAChemicalRepresentation.pdf

Your users can continue to register structures that use your existing business rules until you adapt yourbusiness rules to the enhanced representation. If you have not yet upgraded your business rules, youcan customize BIOVIA Draw to hide the stereochemistry dialog and actions.

End-users can also change their own Stereochemistry preferences. Select theOptions > Settings >Stereochemistry > Label display at stereogenic centers > Classic instead of the default value of IUPACStyle.

Disable the Stereochemistry DialogTo disable the Stereochemistry dialog:

n Use comment notation () to remove all the lines related to StereoChemTool in theBIOVIA\BIOVIA Draw <version>\XmlConfig\palettestrip.xml file.

n Some tools havemultiple XML entries. The tool element looks similar to the following in thepalettestrip.xml"<tool class="MDL.Draw.Modules.Editor.Tools.StereoChemTool"

With comment notation:

Disable Stereochemistry ActionsTo disable the stereochemistry actions:

BIOVIA Draw Configuration | Page xx

n Use comment notation () to remove all the lines in the BIOVIA\BIOVIA Draw

<version>\XmlConfig\\XmlConfig\palettestrip.xml file that are related to actions.

For example use comment notation as follows:

Expose the Purity SectionIn Draw, the Purity section for unspecified stereocenters is disabled by default.

You can enable or disable sections to provide or hide functionality from end users. The following sectionof BIOVIA\BIOVIA Draw <version>\XmlConfig\\XmlConfig\palettestrip.xml file exposesthe Purity section.<panel margin="3">

<label text="Purity (optional):" style="bold" width="250" height="25" />

</panel>

<radiogroup>

<radiobutton text="Unknown / unimportant" command="unknown"update="T" width="250" />

<radiobutton text="Pure" command="pure" update="T" width="250" />

<radiobutton text="Partially resolved" command="partial"layout="horizontal" listener="MDL.Draw.Gui.GrayOutChildren" update="T"width="130">

<combobox command="puritycombo" editable="T" update="T" enabled="F"select="3" width="50">

<selection text="50%" />






</combobox>

<label text=" ee" enabled="F" />

</radiobutton>

</radiogroup>



In the example above, the default value is the third selection as set by the value 3 in the select="3"attribute, making the default value 70%.

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Hiding OR and AND StereogroupsBoth the OR stereogroups button and the AND stereogroups button are enabled in the [draw-home]

\XmlConfig\palettestrip.xml file. To hide these buttons, look in the XML palettebar.xml forthis comment:

. For example,the following example is of a section that is not commented out:

...

Here, the same section that is commented out:

In the following section, the OR stereogroups is not commented out:<space height="10" /><panel border="T" layout="horizontal">

<panel margin="4"><panel>

<radiobutton text="Add to OR# group" command="or#" variable="T"update="T" width="162" />

</panel><radiobutton text="Create new OR group" command="createor#"

width="162" /></panel><panel margin="3">

<label image="StereoOr.png" /></panel>

</panel>

The following AND stereogroups section has been commented out.

BIOVIA Draw Configuration | Page xxii

Customize Stereogroup LabelsYou can customize the appearance of stereogroup labels such as for ABS, OR, or AND stereogroups bymanually editing the default.xml. You can find the user preferences default.xml file in a locationsimilar to the following:\\Users\<user_name>\AppData\Roaming\BIOVIA\BIOVIA Draw <version_number>\Preferences

The following example of a default.xml file shows an user’s custom settings for the display ofstereochemistry preferences, which are set using Options > Settings, and setting the label options in theStereochemistry group.<?xml version="1.0"?>

<DisplayPreferences xmlns:xsd="http://www.w3.org/2001/XMLSchema"xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">

<DisplayChiralStereoLabels>Enhanced</DisplayChiralStereoLabels>

<StereoAbsLabel>*</StereoAbsLabel>

<StereoAndLabel>#</StereoAndLabel>

<StereoGroupDisplay>LabelsAndBonds</StereoGroupDisplay>

</DisplayPreferences>

The resulting StereoAndLabel display uses the following pattern: #1, #2, #3. You cannot change &1 into #

because the numeric part is appended automatically when used with StereoAndLabel or StereoOrLabel.

Enabling the Data Sgroup Tool to Control Sgroup DataOrganizations have different business rules for chemically-significant data (attached data or Sgroupdata) that end-users attach to targets, such as atoms, bond, fragments, or entire structures. BIOVIAallows you to control the vocabulary for data Sgroups.

By default, <draw_home>\XmlConfig\palettestrip.xml enables the SimpleDataSgroupTool thatallows end-users to specify a database field, search operator, and data that might or might not be valid.

However, if you enable the DataSgroupTool, you can "pre-populate" picklists to control the dataSgroup choices available to end-users.

To specify the types of attached data and targets that your organization requires, edit the examples inthe comments for DataSgroupTool in <draw_home>\XmlConfig\palettestrip.xml.

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Notes:

n Keep a backup copy of the original versions of any XML Configuration files undergoing edits. It isvery easy to break the XML and not always easy to fix, so it is good to be able to revert to a versionthat works.

n If your company’s business rules require attached data, you need to customize BIOVIA Draw andcreate Sgroup fields in your databases. For complete information on the procedures that arerequired to implement business rules for attached data, see the "Attached Data" chapter in BIOVIAChemical Representation, which is installed as<draw_home>\docs\Draw\devguide\BIOVIAChemicalRepresentation.pdf

n If you enable the DataSgroupTool, you should disable the SimpleDataSgroupTool.

See also

n Comments in <draw_home>\XmlConfig\palettebar.xml on DataSgroupTool, which provide:n Procedures for disabling or enabling the DataSgroupTooln XML code for examples of attached data for various targets, with explanatory comments. To

specify the types of attached data and targets that your company’s business rules require, editthese examples.

n fieldname in the XML referencen Attached Data dialog (data Sgroups) in Sample Screens, which shows an example of a dialog box for

end-users.n Specify the Path to Custom XML Configuration Files.

Example for Data Sgroup ToolThere aremany examples and many places to either comment out or uncomment.

Before (commented out) - disabled

After (exposed) - enabled

The following snippet is one ofmany places where the comments are removed.

BIOVIA Draw Configuration | Page xxiv

Vocabulary of allowed values: R, S, P, M, E, Z, none. --><fieldname readablename="Non-tetrahedral chirality" name="CHIRAL_NONTETRAHEDRAL" target="sketch"

type="text" unit="" value="list"><listvalue value="(none)" /><listvalue value="R" /><listvalue value="S" /><listvalue value="P" /><listvalue value="M" /><listvalue value="E" /><listvalue value="Z" />

</fieldname>...

Note: In this context, "sketch"means any structure drawn on the canvas, not the sketch file formatwith the .skc extension.

Customizing Draw for Attached DataUsers have access to the Data Sgroup Properties dialog that allows them to type in a Field Description,which might or might not be the correct database Field Name. However, you can:

n Hide the Data Sgroup Properties dialog by commenting out its appearances in the XML configurationfile.

n Make available the Attached Data dialog, which can have a drop-down list for Field Name, so thatend-users choose from a standard set of field names that you establish.

Attached Data in Biopolymer RepresentationTo enable your users to create biopolymers that contain the correct types of attached data, seeCustomizing BIOVIA Draw for Registration and Searching of Biopolymers.

Note: The attached data required for biopolymer representation is invisible to end users. See BIOVIAChemical Representation > Biopolymer Representation. This document is installed as:<draw_home>\docs\Draw\devguide\BIOVIAChemicalRepresentation.pdf

Other Attached DataIf you have incorporated additional categories of attached data into your business rules for chemicalsubstance representation, enable the Attached Data dialog in BIOVIA Draw to allow your users to createand edit attached data. For information on enabling this dialog, see Data Validation, Registration, andthe Attached Data dialog.

The dialog is hidden in BIOVIA Draw. To make the dialog available, customize the BIOVIA Draw XMLconfiguration.

1. Add the required Sgroup fields to your database.2. Make a backup copy of the XML configuration files.3. Use a text editor or XML editor to open and locate the section that contains examples of attached

data. You can do this by searching for the text string "Examples of Attached Data".4. Follow the instructions in the comments to adapt relevant examples to the categories of attached

data that you have defined. Two elements are associated with the definition of attached data,operator and fieldname:n Each occurrence of the element operator specifies a comparison operator that is available for

searching numeric data.

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n Each occurrence of the element fieldname in the XML configuration defines a type of attacheddata that the user can select in the Attached Data dialog box, and that is associated with aparticular Sgroup field.

For each category of attached data, you can optionally use the listvalue element to provide aset of allowed values (vocabulary) for user to choose from.

IMPORTANT! BIOVIA Draw does not check the name, type, or other attributes against informationin the database. If you enter incorrect values for these attributes, the attached data can be savedto a molfile but cannot be registered to the target database or used in a search. For example, if theSgroup field name is incorrect, the data is not registered to the database. If a search operator thatyou specify is not available in the target database, queries that use that operator will be invalid. Toensure that these attributes are correct, you need to test the customized XML configuration asdescribed in Step 7 below.

5. For each type of target for which you specified attached data in Step 4, remove the comments fromthe associated menu command.

Each menu command has the following format:<menuitem command="<target>" text="Attach data..."/></popup>

6. Save the edited XML configuration.7. Test the edited XML configuration:

a. Start BIOVIA Draw and open a structure file.b. Select the Properties Tool [X] from the palettebar.c. Select the target that you specified in Step 4.d. Select Attach data from the popup menu. The dialog, as defined in the XML file, appears.e. Save the file with the structure and its attached data to a molfile.f. Register the structure to a test database.

BIOVIA Draw Configuration | Page xxvi

g. Use the structure as a query to retrieve the structure that you registered in the previous step.h. Conduct additional searches to ensure that the customized XML configuration is valid. For

example, to ensure users can use search operators.8. Distribute the customized version of the XML configuration to end-users.

Data Validation, Registration, and the Attached Data DialogBIOVIA Draw does not validate attached data. For example, BIOVIA Draw provides no mechanism forlimiting the range of numeric data that end-users enter. Therefore, BIOVIA Draw cannot enforce thatattached data that represents a percentage lie between 0 to 100. Your searching or registrationapplication should therefore check the validity of attached data against your company’s business rules.

For text data, BIOVIA recommends that you provide a set of allowed values in the Attached Data dialog.If scientists want to find structures with more than one value for the attached data, they can runmultiple queries and then apply list logic to merge the result sets.

Use search operators in substructure-search queries. If you are customizing BIOVIA Draw for use in aregistration application, you can prevent users from adding operators to attached data by commentingout the operator values in the XML configuration. For example:



For information on using attached data in substructure search queries, see BIOVIA ChemicalRepresentation, Substructure Search (SSS), “Substructure Search of Attached Data”. The document isinstalled as:<draw_home>\docs\Draw\devguide\BIOVIAChemicalRepresentation.pdf

For examples of customizing BIOVIA Draw for attached data, see the <draw_home>\XmlConfig\palettestrip.xml file. For reference information on the XML elements in theexamples, see the AccelrysDraw-net.xml chapter.

Cleaning Data SgroupsThe end-user can click Chemistry > Clean to improve the appearance of one or more selected structuresby giving them uniform bond lengths and angles. In so doing, Clean changes the x- and y-coordinates ofthe atoms, bonds, and attached data (Sgroup data).

Relative Coordinates

An Sgroup basis is the atoms and bonds with which the attached data is associated. BIOVIA Draw usesthe version of the internal Cheshire Clean script that ensures that each Sgroup datum is located in thesame position relative to its Sgroup basis.

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Absolute Coordinates

You might want Clean to lock the attached data position at the original location in the drawing area(absolute coordinates), regardless of the location of the associated atom or bond. For example, yourorganization might have a business rule that requires all attached data to be in the lower right corner.

ISIS/Draw creates data Sgroups with absolute coordinates, and BIOVIA Draw creates data Sgroups withrelative coordinates. One structure can have both kinds of attached data if the structure was created inISIS/Draw (absolute coordinates), and gets a second data Sgroup in BIOVIA Draw (relative coordinates).BIOVIA Draw’s Clean operation converts the absolute coordinates of data Sgroups into relativecoordinates. You can configure BIOVIA Draw to preserve the absolute coordinates of attached datacreated in ISIS/Draw. This change does not affect the rule that BIOVIA Draw creates data Sgroups withrelative coordinates.

IMPORTANT!

n Preserving absolute coordinates for attached data means that the Clean operation might relocatethe atoms and bonds of the Sgroup basis at coordinates that are distant from their attached data.

To configure BIOVIA Draw to use the version of Clean that preserves the absolute coordinates ofattached data, perform the following two steps in <draw_home>\XmlConfig\menubar-chemistry.xml.

1. Comment out the default Clean that positions attached data relative to the structure (relativecoordinates):<action name="Cl&ean"class="MDL.Draw.Modules.Editor.Actions.Calcs.RelativeCleanAction"/>

2. Uncomment the Clean that preserves the original coordinates of the attached data (absolutecoordinates).<action name="C&lean"class="MDL.Draw.Modules.Editor.Actions.Calcs.CleanAction"/>

BIOVIA Draw Configuration | Page xxviii

Enabling or Disabling Rgroup Atom and Building Block ToolsThe Rgroup Atom and Building Block tools are enabled so that users of BIOVIA Draw can createMarkushstructures for registration into library and/or building blocks database.

Notes:

Although superficially similar to Markush queries, Markush structures differ in important ways. Toavoid confusion between the different types of Rgroup structures, BIOVIA Draw supplies a separatepalette of tools for drawing generic structures and building blocks.

The default setting for the Rgroup Query tool is enabled.

See also

Specify the Path to Your Custom XML Configuration Files

Rgroup Atom Tool and Building Block Tool in <draw_home>XmlConfig\palettestrip.xml

Specifying the Custom Ptable and CustomWeights

Markush structure in the BIOVIA DrawOnline Help

For more information about generic databases and building-blocks database, see the documentationfor Relational-Chemical Database Administration, such as the Relational-Chemical DatabaseAdministration Command Reference, which gives the syntax for the CREATE DATABASE command.

Specify a Custom Ptable and Custom WeightsBefore specifying a custom periodic table, review the information in Custom Ptable Example and CustomPtable Path.

If Draw is using a custom Ptable with custom weights, the BIOVIA Cheshire scripts must also use thecustom Ptable with custom weights. You can edit the Ptable and weights file to match any customelements and weights for your organization.

Although the Ptable contains a weight for each element, the custom weights file determines the weightfor calculations within Draw. Other BIOVIA products, such as BIOVIA Direct, might interpret the formatof the atomic weight as Fortran format F10more strictly leading to different results.If your businessrules require Ptable customization, you must customize Draw and set the chemical environment at yoursite for all products that interact with Draw to use the same Ptable.

Note: The bold format indicates updates you make to the configuration file.

To specify a custom Ptable and customWeights:

1. Close Draw.2. Navigate to the BIOVIA\BIOVIA Draw <version>\Examples\CheshireAction directory.3. Make a backup copy of CheshireActionExample.xml.4. Edit the following line in the CheshireActionExample.xml file to specify the custom Ptable for

Draw.<module class="MDL.Draw.Modules.Editor.EditorModule" ptable="BIOVIA\BIOVIADraw <version>\Examples\Ptable\MyPtable.txt">

5. Modify the line to look similar to the following:<module class="MDL.Draw.Modules.Editor.EditorModule" ptable="<draw_

home>\Examples\Ptable\MyPtable.txt">

The BIOVIA\BIOVIA Draw <version> represents the absolute path to the root directory of your

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BIOVIA Draw installation.6. Edit the following line in the CheshireActionExample.xml file to make the calculations available

as options on the Draw Chemistrymenu use the custom weights associated with the custom Ptable.<menustripitem text="&Chemistry"> <action name="&Calculator..."class="MDL.Draw.Modules.Editor.Actions.Calcs.MolValuesAction">

7. Modify the line to look similar to the following:<menustripitem text="&Chemistry"> <action name="&Calculator..."class="MDL.Draw.Modules.Editor.Actions.Calcs.MolValuesAction"weights="custom" weightsscript="..\Ptable\MyWeights.cct">

To verify the implementation of the custom Ptable and weights:

1. Run the batch file, CheshireActionExample.bat.2. Open the CheshireAction.mol file.3. In Draw, select Chemistry > Cheshire Scripts > Rotate Molecule.

The Cheshire script rotates and cleans themolecule.

4. Right-click an atom and select Atom Symbol.

The three custom elements (PC1, PC2, PC3) of the custom Ptable are available.

5. Click PC1.6. Select Chemistry > Calculator.

The custom weight displays.

7. Paste the calculated values onto the canvas.

TemplatesYou can customize the structure templates by editing the XML configuration file. End-users cannotcreate or edit biopolymer sequence templates.

See also

Biopolymers: Sequence Tools


Adding Templates to the Toolbar ManagerIn this example, we add two directories that contain structure files.

n myNitrogens is the default template directory (selected="true"), and has the display name ofmyNitrogens

n MySugarTemplates is specified with an absolute directory, and has the display name of mySugars1. Copy <draw_home>\XmlConfig\templatetoolstrip.xml and rename it to <draw_

home>\XmlConfig\myTemplatetoolstrip.xml.

BIOVIA Draw Configuration | Page xxx

2. In <draw_home>\XmlConfig\myTemplatetoolstrip.xml add entries:<templatetoolbarmanagerclass="MDL.Draw.Modules.Editor.Tools.ConfigTemplateTool"...>

...<templatetoolbar name="Rings" path="%MDLDRAW%Templates\Template

Sets\Rings\"/><templatetoolbar name="myNitrogens" path="%MDLDRAW%mynitrogens\"

selected="true"/><templatetoolbar name="mySugars" path="C:\MySugarTemplates\"

readonly="true" /></templatetoolbarmanager>

3. Copy <draw_home>\AccelrysDraw-net.xml and rename it to <draw_home>\MyTemplateToolbarPrimary.xml.

4. In <draw_home>\MyTemplateToolbarPrimary.xml, change the reference to the new XMLConfiguration file for the toolbar.

Before, with a reference to a compiled class resource.<toolbar include="MDL.Draw.Editor.XmlConfig.toolbar.xml"/>

After, with an absolute path to an XML file.<toolbar include="C:\Program Files (x86)\BIOVIA\BIOVIA Draw2016\XmlConfig\myToolbar.xml"/>

5. To test, create a batch file that uses the new XML Configuration.BIOVIADraw.exe MyTemplateToolbarPrimary.xml

6. Start the batch file.7. Open the templatetoolbar dropdown list.

For XML reference details, see templatetoolbarmanager.

Add a Directory to the Template DirectoryTo display a particular folder under the Imported Templates directory in the Template Directorywindow, add a corresponding folder element under the templatedirectory element in the XMLconfiguration file, in<draw_home>\XmlConfig\toolbar.xml:

<templatedirectory . . .><folder name="myNewTemplateDirectory" path="d:\test\mytest\"

readonly="true" /></templatedirectory>

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For XML reference details, see templatedirectory and folder in the XML Reference.

See also

Template Security

Template SecurityBIOVIA recommends that you set the user permissions to the directories with your corporate templatesfiles to be read-only. This precaution is to safeguard the templates from being overwritten. Be awarethat blocking write permissions on corporate templates does not prevent end-users from changing fileson their local machines.

Removing Template ToolbarsWhen a new version of BIOVIA Draw is installed, the user’s access to any custom template toolbars ispreserved. To remove access to any custom template toolbars, follow these steps:

1. Use Add/Remove Programs on theWindows Control Panel to uninstall the current version of BIOVIADraw.

2. Delete the following directories and all the files within them:n C:\Users\<user_name>\AppData\Roaming\BIOVIA\BIOVIA Drawn <draw_home>

where C: represents the drive on which BIOVIA Draw is installed, <user_name> represents thesubdirectory with the name of the computer user, and <draw_home> represents the directory inwhich BIOVIA Draw is installed, such as C:\Program Files (x86)\BIOVIA\BIOVIA Draw2016\

Specify Display of Templates Containing Abbreviated StructuresThe abbreviation display file, displayAbbreviations.xml, enables you to control the display of thetext label (abbreviation name) of individual abbreviated structures. You can use this file to:

n Apply formatting such as Greek letters, italics, subscripts, superscripts, and large or small fonts, toabbreviated structures that you save as templates.

When you create an abbreviated structure to save as a template, you cannot apply special formats tothe abbreviation name, because the abbreviation name is identical with the template filename. Theformatting instructions (markup) specify characters that cannot be used in filenames.

n Override formula recognition for specific cases where formula recognition is not appropriate.

BIOVIA Draw automatically applies appropriate formatting to any abbreviation name that can beinterpreted as a formula, and displays these formulas appropriately when you reorient the structure.For example, if you enter the text string "C2H5" as the abbreviation for an ethyl group, Draw textrecognizes the text "C2H5" as a formula and subscripts the numbers. Draw also recognizes "C" as the

BIOVIA Draw Configuration | Page xxxii

character that should attach to other structures (attachment character), so that the abbreviationname flips when you re-orient the structure.

Automatic formula recognition is not appropriate for all templates, however. For example, thetemplate for N-bromosuccinimide is named NBS. BIOVIA Draw displays the abbreviation as either"NBS" or "SBN", depending on whether the abbreviation is on the left or right side of the structure.You can override formula recognition by specifying "N" as the attachment character, so that theabbreviation name always displays as "NBS".

Each user of BIOVIA Draw has an abbreviation display file at the following location on the local harddrive:

C:\Users\<user_name>\AppData\Roaming\BIOVIA\BIOVIADraw\DrawdisplayAbbreviations.xml

This file contains any necessary markup for all templates that are supplied with BIOVIA Draw. If you havecustomized BIOVIA Draw to provide additional template directories and/or template toolbars, use thefollowing procedure to provide a customized version of the abbreviation display file to your users:

1. Edit the XML configuration file using the instructions in the section, Adding a set of templates to theToolbar Manager and/or To add a directory to the Template Directory.

2. Use an XML or text editor to edit the copy of displayAbbreviations.xml on your local hard drive toadd formatting instructions for all custom templates that need it.

For a detailed instructions on creating entries in the abbreviation display file, see the following indexentry in the BIOVIA DrawOnline help: "abbreviation display file".

3. Distribute the edited displayAbbreviations.xml to your users. Instruct each user to replacethe default abbreviation display file with the one that you provide.

Display Preference Settings

Specify Display PreferencesYou can set values for display preferences (display settings) in <draw_home>\XmlConfig\Menubar-options.xml. For XML reference details, see Display Preferences.

These values can also be set programmatically. See the API Reference forMDL.Draw.Renderer.Preferences.DisplayPreferences.

IMPORTANT!

n Preferences set by the end-user in the GUI (Options > Settings) override the values specified inDisplayPreferences.

See also

Specify the Path to Custom XML Configuration Files

Synchronizing Display Settings with default.xml

Example: AromaticRingCircles, AtomHighlightDotWidthAccelrysDraw-net.xml points to menubar-options.xml, which resides in <draw_

home>\XmlConfig.

Before you edit menubar-options.xml to add preference settings:<separator /><action name="&Settings..."class="MDL.Draw.Modules.Editor.Actions.PreferencesAction"><DisplayPreferences file="default.xml" />

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Example rendering with default display settings:

After you edit menubar-options.xml to add preference settings:<separator /><action name="&Settings..."class="MDL.Draw.Modules.Editor.Actions.PreferencesAction"><DisplayPreferences file="default.xml" >

<AromaticRingCircles>true</AromaticRingCircles><BackColor>yellow</BackColor><AtomHighlightDotWidth>0.1</AtomHighlightDotWidth><HighlightColor>Red</HighlightColor><ForceV3000>true</ForceV3000>


Example rendering with changed display settings:

Note:Preferences can also be set using the API, for example,MDL.Draw.Renderer.Preferences.AtomHighlightDotWidth.Preferences set by the end-user in the GUI override the values specified in DisplayPreferences.

See also

Synchronizing Display Settings with default.xml

BIOVIA Draw Configuration | Page xxxiv

Synchronize Display SettingsIf your company has corporate standards for display settings, you can define the standard in the XMLConfiguration files.

End-users can always locally set their own display settings for their copy of Draw by clicking Options >Settings to open the Settings dialog.

The local preference setting are stored in a file called default.xml located in \\Users\<user_name>\AppData\Roaming\BIOVIA\BIOVIA Draw \Preferences directory.

Software developers can synchronize the display settings ofmultiple renditors programmatically. Formore informaiton, see DrawDeveloper's Guide, DemoRenditorMulti Example.

The XML file for local preference settings that correspond to ISIS/Draw and earlier versions of BIOVIADraw is

IsisDraw.xml file. The IsisDraw.xml file is located in the same directory as default.xml file.

See also

Specify Display Preference Value

default.xml with Custom Settings for Display PreferencesThe following is sample content of default.xml indicating that aromatic rings are displayed as circles.

<?xml version="1.0"?><DisplayPreferences xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"xmlns:xsd="http://www.w3.org/2001/XMLSchema">

<molPrefs><PiBondWriting>0</PiBondWriting>

</molPrefs><LabelHeight>0.45</LabelHeight><AromaticRingCircles>true</AromaticRingCircles><AppsNeedingAuxThreading>iexplore.exe</AppsNeedingAuxThreading><AndStereoLabelText>custom text 1</AndStereoLabelText><OrStereoLabelText>custom text 2</OrStereoLabelText><DefaultAngleRangeVal>10</DefaultAngleRangeVal><PreferencesPath>C:\Users\<user_name>\AppData\Roaming\BIOVIA\BIOVIA

Draw\Preferences\</PreferencesPath>


where smith is the <user>.

To synchronize Display Settings, default.xmlmust be removed from every local machine.Alternatively, you can distribute your organization’s standard version of default.xml to each localmachine as C:\Users\<user_name>\AppData\Roaming\BIOVIA\BIOVIADraw\Preferences\default.xml

Some changes to default.xml cannot bemade through the Settings dialog. For an example, seeCustom Display of Stereogroup Labels such as abs, or, and.

Removing a FeatureTo remove a feature by editing the XML configuration file, comment out each and every occurrence ofthe feature in the appropriate XML Configuration file.

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http://www.w3.org/2001/XMLSchema

See also

Specify the Path to Custom XML Configuration Files

Example: Removing the Data Sgroup FeatureTo disable a data Sgroup feature, comment out all the references in <draw_home>\XmlConfig\palettestrip.xml to DataSgroupTool. Items that are commented out arewithin the open and close comments: 

Enabled:

<popup><menuitem command="attachMol" text="Attach Data..." />

</popup>

</tool> -->

Disabled:

</tool> -->

Similarly, to re-enable a feature you have commented, remove the comments of each of the references.

Note: For developers, it is possible to remove the Chem Check feature that occurs when a user clicksthe Transfer button in an application that uses a Renditor. See the Developer’s Guide, “DisablingChem Check from Transfer back to Renditor”.

Example: Removing from the Chemistry menuTo hide part of the Chemistry menu, such as the section for Generate Text from Structure and GenerateStructure from Text (highlighted in yellow), complete the following steps.

BIOVIA Draw Configuration | Page xxxvi

Three XML Configuration files must bemodified: <draw_home>\AccelrysDraw-net.xml points toxmlConfig\menustrip.xml, which points to XmlConfig\menubar-chemistry.xml.

1. Make a copy of <draw_home>\XmlConfig\menubar-chemistry.xml and name the copymyMenubar-chemistry.xml

2. Locate the item (or section) that you want to remove in <draw_home>\XmlConfig\myMenubar-chemistry.xml

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In the example above, a complete section was commented out, but you can comment out a singleaction. When you comment out a section, remove any nested comments.

3. Save myMenubar-chemistry.xml4. Make a copy of <draw_home>\XmlConfig\menustrip.xml and name the copy

myMenustrip.xml

5. Edit myMenustrip.xml to point to myMenubar-chemistry.xml

Replaceinclude="MDL.Draw.Editor.XmlConfig.menubar-chemistry.xml"/>

withinclude="<draw_home>\XmlConfig\myMenubar-chemistry.xml"/>

where <draw_home> represents the installation directory, such as C:\Program Files(x86)\BIOVIA\Draw 2016

6. Make a copy of <draw_home>\AccelrysDraw-net.xml and name the copyMyAccelrysDraw-net.xml

7. Edit MyAccelrysDraw-net.xml to give the path and name of the edited file.<menustrip include="<draw_home>\XmlConfig\myMenustrip.xml"/>

where <draw_home> represents the installation directory, such as C:\Program Files(x86)\BIOVIA\BIOVIA Draw 2016

8. Write a batch file that points to your custom primary XML Configuration file.BIOVIADraw.exe MyAccelrysDraw-net.xml

9. To view the customized Chemistry menu, start Draw by launching the batch file.

Show Explicit Carbon LabelAn example of a Display Preference you can configure is the context menu item, Show explicit Carbonlabel, which is governed by the XMLConfig\palettestrip.xml file.

<tool class="MDL.Draw.Modules.Editor.Tools.CExplicitTool"><popup>

<menu command="cshow" text="Show explicit Carbon label"/><menu command="chide" text="Hide explicit Carbon label"/>

</popup></tool>

BIOVIA Draw Configuration | Page xxxviii

Disabling Arrow Toolbar AutohideThe Arrow toolbar displays itself only when you are using the Arrow tool.

To force the Arrow toolbar to display at all times, edit AccelrysDraw-net.xml as follows.

Before<arrowtoolbar name="Arrows" direction="Horizontal" autohide="true"/>

After<arrowtoolbar name="Arrows" direction="Horizontal" autohide="false"/>

Removing a Menu Item

Removing the Insert Option from the File MenuComplete the following steps to remove the Insert option from the Filemenu of the Draw Editor andmodify the title bar.

1. Close any open versions of Draw.2. Make a copy of <draw_home>\XmlConfig\menubar-file.xml, and rename it <draw_

home>\XmlConfig\myMenubar-file.xml

3. Edit the myMenubar-file.xml file.

Find the Insert action by searching for "&Insert" and comment out the entire section:

4. Make a copy of <draw_home>\AccelrysDraw-net.xml and rename it <draw_home>\NoInsert-AccelrysDraw-net.xml

5. In NoInsert-AccelrysDraw-net.xml, change the name attribute of the MDLDraw element (online 6) so that it reads as follows:

<mdldraw width="950" height="700" name="My Draw - No Insert">

6. Edit NoInsert-AccelrysDraw-net.xml to point to a custom myMenustrip.xml that you willcreate.

<menustrip include="<draw_home>\XmlConfig\myMenustrip.xml"/>

Page xxxix | BIOVIA Draw • Configuration Guide

where <draw_home> represents the installation directory, such as C:\Program Files(x86)

\BIOVIA\Draw 2016

7. Make a copy of <draw_home>\XmlConfig\menustrip.xml and name the copymyMenustrip.xml

8. In myMenustrip.xml, assure that include= gives the full path to the custom XML configurationfile.



<menu text="&File" include="<draw_home>\XmlConfig\myMenubar-file.xml"/>

where <draw_home> represents the installation directory, such as C:\Program Files (x86)\BIOVIA\BIOVIA Draw 2016

9. Create a batch file called NoInsert-Draw.bat that starts Draw by pointing to <draw_home>\NoInsertAccelrysDraw-net.xml. The content of the batch file is:

BIOVIADraw.exe NoInsert-AccelrysDraw-net.xml

10. Verify the result.

Before, with the Insertmenu item under the Open menu item:

After, with no Insertmenu item:

The title bar now says "My Draw - No Insert" and there is no longer an "Insert" action under theOpen menu item.

See also


BIOVIA Draw Configuration | Page xl

Removing the Formatting Toolbar Item from the WindowMenu1. Disable the Formatting Toolbar.

a. Open theWindows Registry Editor.b. Navigate to HKEY_CURRENT_USER\Software\BIOVIA\BIOVIADraw\Client\2016c. Set the value for Persistency.ShowFormattingToolbar to False.d. Exit theWindows Registry Editor.

If you do not want the user to be able to enable the Formatting Toolbar from theWindowmenu,you must also hide themenu item.

2. Hide themenu item.a. Edit <draw-home>\XmlConfig\menubar-window.xml by adding the 

b. Edit <draw-home>\XmlConfig\menustrip.xml to point to the file the you edited in theprevious step.

BEFORE<menu text="&Window"include="MDL.Draw.Editor.XmlConfig.menubar-window.xml"/>

AFTER

<menu text="&Window" include="C:\Program Files (x86)\BIOVIA\BIOVIADraw 2016\XmlConfig\menubar-window.xml"/>

where C:\Program Files (x86)\BIOVIA\BIOVIA Draw 20162\XmlConfig\ representsthe absolute path to your Draw home directory.

c. Edit <draw-home>\AccelrysDraw-net.xml to point to the file you edited in the previousstep.

BEFORE<menustrip include="MDL.Draw.Editor.XmlConfig.menustrip.xml"/>

AFTER<menustrip include="C:\Program Files (x86)\BIOVIA\BIOVIA Draw2016\XmlConfig\menustrip.xml"/>

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where C:\Program Files (x86)\BIOVIA\BIOVIA Draw 2016\XmlConfig\ representsthe absolute path to your Draw home directory.

3. Test the result.

ChemCheck ConfigurationYou can configure the Chemistry > Run ChemCheck dialog for your end-users.

After (customized XML):

Copy menubar-chemistry.xml in the <draw_home>\XmlConfig folder, rename the copymyMenubar-chemistry.xml, and edit it to set add to true for options you want visible.

Before:class="MDL.Draw.Modules.Editor.Actions.Calcs.ConfigurableChemInspectorAction">

<checktypes><checktype text="for query (SSSQUERY/RSSQUERY)" type="SSSQUERY"

add="true"/><checktype text="for registration (RCG_SPECIFIC/RXNCARTRIDGE)"

type="RCG_SPECIFIC" add="true"/><checktype text="for transform (TRANSFORM)" type="TRANSFORM"

add="false"/><checktype text="for registration to Direct (DIRECT_SPECIFIC_2D)"

type="DIRECT_SPECIFIC_2D" add="false"/><checktype text="for registration to Direct (DIRECT_SPECIFIC_3D)"

type="DIRECT_SPECIFIC_3D" add="false"/><checktype text="for registration to Direct (DIRECT_REACTION)"

type="DIRECT_REACTION" add="false"/></checktypes><checks>

BIOVIA Draw Configuration | Page xlii

<check text="Reaction has Rgroup definition"command="RxnWithRgroup" add="true"/>

<check text="Valence Check" command="Valence Check" add="true"/><check text="Atoms are overlapped" command="Atom Overlap"

add="true"/><check text="Bonds are overlapped" command="Bond Overlap"

add="true"/><check text="Structure needs V3000 molfile format"

command="V3000Check" add="false"/></checks>

</action>

After (with changes in bold):class="MDL.Draw.Modules.Editor.Actions.Calcs.ConfigurableChemInspectorAction">

<checktypes><checktype text="for query (SSSQUERY/RSSQUERY)" type="SSSQUERY"

add="true"/><checktype text="for registration (RCG_SPECIFIC/RXNCARTRIDGE)"

type="RCG_SPECIFIC" add="true"/><checktype text="for transform (TRANSFORM)" type="TRANSFORM"

add="true"/><checktype text="for registration to Direct (DIRECT_SPECIFIC_2D)"

type="DIRECT_SPECIFIC_2D" add="true"/><checktype text="for registration to Direct (DIRECT_SPECIFIC_3D)"

type="DIRECT_SPECIFIC_3D" add="false"/><checktype text="for registration to Direct (DIRECT_REACTION)"

type="DIRECT_REACTION" add="false"/></checktypes><checks>

<check text="Reaction has Rgroup definition"command="RxnWithRgroup" add="false"/>

<check text="Valence Check" command="Valence Check" add="true"/><check text="Atoms are overlapped" command="Atom Overlap"

add="true"/><check text="Bonds are overlapped" command="Bond Overlap"

add="true"/><--! <check text="Structure needs V3000 molfile format"command="V3000Check" add="false"/> -->

</checks></action>

1. In the <draw_home>\XmlConfig\myMenuStrip.xml file, specify the path to myMenubar-chemistry.xml:

<menu text="&Chemistry" include="<draw_home>\XmlConfig\myMenubar-chemistry.xml"/>


2. In the <draw_home> directory, copy AccelrysDraw-net.xml as myAccelrysDraw-net.xml,and edit it to specify the path to myMenuStrip.xml

<menustrip include="<draw_home>\XmlConfig\myMenustrip.xml"/>

Page xliii | BIOVIA Draw • Configuration Guide


3. Write a batch file:"<draw_home>\BIOVIADraw.exe" "<draw_home>\myAccelrysDraw-net.xml"

where <draw_home> represents the installation directory, such as C:\Program Files(x86)

\BIOVIA\Draw 2016

4. Run the batch file to verify your changes.

Migrating Custom ToolbarsTo migrate custom toolbars from an earlier version, such as 3.3, to the current version, be aware of thefollowing differences.

Installation directory 4.0 or 4.1 3.3

AccelrysDraw-net.xml for 4.1and SymyxDraw-net.xml for 4.0

<arrowtoolbar name="Arrows"direction="Horizontal"autohide="true"/>

<arrowtoolbarname="Arrows"direction="Horizontal"/>

XmlConfigfile

4.0 or 4.1 3.3

atomtoolstrip.xml

Note: this file is not in 4.0 or 4.1 <atomtoolbar name="Atoms"direction="Horizontal" />

maintoolstrip.xml

<control type="SandBarButton"command="new" image="mtb_new.png"tooltip="New"/>

<control type="toolstripbutton"command="new" image="mtb_new.png" tooltip="New"/>

menubar-chemistry.xml

menubar-edit.xml

menubar-file.xml

filefilter="All structure files(*.skc;*.mol;*.rxn;*.smi;*.cdx;*.xml)|*.skc;*.mol;*.rx n;*.smi;*.cdx;*.xml|sketchfiles (*.skc)|*.skc|molfiles (*.mol)|*.mol|rxnfiles(*.rxn)|*.rxn|SMILES files (*.smi)|*.smi|ChemDraw files (*.cdx)|*.cdx|Uniprotxml files (*.xml)|*.xml"/>

filefilter="All structure files(*.skc;*.mol;*.rxn;*.smi;*.cdx)|*.skc;*.mol;*.rxn;*.smi;*.cdx|sketch files (*.skc)|*.skc|molfiles (*.mol)|*.mol|rxnfiles (*.rxn)|*.rxn|SMILESfiles (*.smi)|*.smi|ChemDraw files(*.cdx)|*.cdx"/>

menubar-help.xml

menubar-object.xml

BIOVIA Draw Configuration | Page xliv

XmlConfigfile

4.0 or 4.1 3.3

menubar-options.xml

<action name="&Small Buttons (16)"class="MDL.Draw.Modules.Editor.Actions.ButtonS izeAction" size="16" />

<action name="&Medium Buttons (24)"class="MDL.Draw.Modules.Editor.Actions.ButtonS izeAction" size="24" />

<action name="&Large Buttons (32)"class="MDL.Draw.Modules.Editor.Actions.ButtonS izeAction" size="32" />

<action name="&Custom Buttons"class="MDL.Draw.Modules.Editor.Actions.ButtonSizeAction" size="custom" />

<action name="&Smallbuttons"class="MDL.Draw.Modules.Editor.Actions.ButtonSizeAction" size="16" />

<action name="&Mediumbuttons"class="MDL.Draw.Modules.Editor.Actions.ButtonSizeAction" size="24" />

<action name="&Largebuttons"class="MDL.Draw.Modules.Editor.Actions.ButtonSizeAction" size="32" />

menubar-window.xml

[Note: support for tabbed windows]

<action name="Windows"class="MDL.Draw.Modules.Editor.Actions.TabMen uAction" />

<action name="&TranslucentToolWindows"class="MDL.Draw.Modules.Editor.Actions.TransluscentWindowsAction"/>

<action name="&Arrange"class="MDL.Draw.Modules.Editor.Actions.Til eWindowMenuAction"/>

<action name="Tile &Vertical"class="MDL.Draw.Modules.Editor.Actions.Til eWindowMenuAction"orientation="Vertical"/>

<action name="Tile&Horizontal"class="MDL.Draw.Modules.Editor.Actions.Til eWindowMenuAction"orientation="Horizontal" />

<action name="Windows"class="MDL.Draw.Modules.Editor.Actions.Wi ndowMenuAction" />

menustrip.xml

Page xlv | BIOVIA Draw • Configuration Guide

XmlConfigfile

4.0 or 4.1 3.3

palettestrip.xml

<toolclass="MDL.Draw.Modules.Editor.Tools.CExplicit Tool">

<popup>

<menu command="cshow" text="Showexplicit Carbon label"/>

<menu command="chide" text="Hideexplicit Carbon label"/>

</popup>

</tool>

templatetoolstrip.xml

Command-line Image File ConversionBIOVIA Draw includes the ImageGenerator command-line utility, which outputs image files thatcorrespond to structure files.The input formats aremolfile (mol), reaction files (rxn), sketch (skc), SMILES(smi), and ChemDraw Exchange (cdx). The output formats are: bmp (default), gif, png, and tif, true colorwhen possible, otherwise black structure on white backaground.

The ImageGenerator executable resides in the Tools subdirectory of your BIOVIA Draw installation.

The API provides programmatic access to convert to image files formats bmp, gif, png, tif or wmfwithMDL.Draw.Renderer.HeadlessRenderer.SaveMoleculeAsImage.

When you "convert" structure files to imagine files, the original files remain unaltered.

For conversion of MolfileString, SketchData, Smiles, StructureHandle, or Metafile, see theAPI Reference on MDL.Draw.StructureConversion.StructureConverter.

Online Help on the ImageGeneratorInvoke the ImageGenerator executable, which resides in the Tools subdirectory of your BIOVIA Drawinstallation.ImageGenerator

Usage information is printed to the screen.

Converting Single File ExamplesTo interactively convert the specified molfile to a bmp, the default format, use the following:

1. Run the ImageGenerator.exe located in the Tools subdirectory of your BIOVIA\BIOVIA Draw

<version>.2. ImageGenerator -i test001.mol

To interactively convert the specified molfile to a specified format, use the following:n BIOVIA\BIOVIA Draw <version>\Tools\ImageGenerator -i test001.mol -f png

where BIOVIA\BIOVIA Draw <version> represents the installation directory that is similar to thefollowing: \\Program Files (x86)\BIOVIA\BIOVIA Draw 2016>

The output file is put in the same directory as the input file, if you use the following:

BIOVIA Draw Configuration | Page xlvi

BIOVIA\BIOVIA Draw <version>\Tools>ImageGenerator -i "C:\myDir\objects.cdx" -f tif

The utility displays the following message:C:\myDir\objects.cdx converted to C:\myDir\objects.tif

To interactively convert the image using a specified width and height in pixels, use the following:n ImageGenerator -i test001.mol -w 300 -h 350

Convert a Batch of Files ExampleTo interactively convert a batch of files, use the following:

1. Create a list of the files in the directory using a DOC command such asdir/b > list.txt

2. Run the ImageGenerator.exe located in the Tools subdirectory of your BIOVIA\BIOVIA Draw

<version>.3. Use the following command to generate a batch of gif images from the list of files:

ImageGenerator -l list.txt -f gif

4. (Optional) Specify additional options such as foreground and background color using the followingcommand:ImageGenerator -l list.txt -f gif -fg purple -bg gold

Page xlvii | BIOVIA Draw • Configuration Guide

Creating a Custom Ptable

Custom Ptable ExampleTo specify a custom periodic table (Ptable), do one of the following:

Use PtableDemo.xml to understand Draw XML configuration for themodule element. The ptableattribute specifies the path and name of the Ptable.

n Before: module class="MDL.Draw.Modules.Editor.EditorModule"n After: module class="MDL.Draw.Modules.Editor.EditorModule" ptable="MyPtable.txt"

For an overview of the Ptable, see the "Customizing the BIOVIA Ptable" in BIOVIA ChemicalRepresentation Guide. You can find a copy at:

\\docs\Draw\devguide\BIOVIAChemicalRepresentation.pdf.

If you are developing a Java application and want to use a custom Ptable, see the DrawDevelopersGuide, custom Ptable for a JMolRendererCom Java application.

Custom Ptable PathThe custom Ptable, MyPtable.txt includes three elements that are not in the standard periodic table:PC1, PC2, and PC3.

The Ptable example includes batch file that specifies that Draw loads a specific XML configuration file thatidentifies the custom Ptable and provides its location.

You can specify relative, absolute, or a URL path to the Ptable. The following examples show thedifferent path:

n Relative<module class="MDL.Draw.Modules.Editor.EditorModule"

ptable="MyPtable.txt">

n Absolute<module class="MDL.Draw.Modules.Editor.EditorModule"

ptable="<BIOVIA Draw installation directory>\Examples\Ptable\MyPtable.txt">

where <BIOVIA Draw installation directory> represents the absolute path to the rootdirectory of your BIOVIA Draw installation.

n URL<moduleclass="MDL.Draw.Modules.Editor.EditorModule"ptable="http://myDir/MyPtable.txt">

To run the Ptable example:

1. Close Draw.2. Double-click the batch file in the Examples\Ptable directory in BIOVIA\BIOVIA Draw <version>.3. In the canvas, type the name of a custom element in the Ptable.

The custom elements in this Ptable are PC1, PC2, and PC3.

The keyboard sprouting feature places the custom element on the Draw canvas.The custom elementsalso appear in the list of available elements if the Show Extended Table check box is enabled.

Creating a Custom Ptable | Page xlviii

Running the ExampleFollow these steps to run the example:

1. Close any open versions of BIOVIA Draw.2. Start BIOVIA Draw by double-clicking the batch file in the Examples\Ptable directory of your

BIOVIA Draw installation.3. In the canvas, type the name of a custom element in the Ptable. The custom elements in this Ptable

are PC1, PC2, and PC3.4. The keyboard sprouting feature places the custom element on the BIOVIA Draw canvas.

The custom elements also appear in the list of available elements if the Show Extended Table checkbox isenabled.

Setting a Custom Ptable

Page xlix | BIOVIA Draw • Configuration Guide

Notes:

n See also Specifying the Custom Ptable and CustomWeights.n PC1 is a pseudoatom, which is different from an abbreviated structure (abbreviation Sgroup), such

as COOH.

Abbreviated structures can be expanded to reveal the underlying structure. Pseudatoms cannot beexpanded and do not have underlying structure.

Add-InsSoftware add-ins such as add-ins for ACD/Labs, Bioavailability (Rule of 5), and Isotopomer Distributionplace options on menus inDraw. After installing the add-ins and configuring Draw, you can access theadded functionality from within Draw.

Access these functions by selecting the newmenu item from the Chemistry menu.

To make Add-ins available to all users, load Add-ins to <Draw_Home>/AddIns.

To load Add-ins to the user's personal profile:

n Create the folder AddIns:C:\users\<user_name>\AppData\Roaming\BIOVIA\BIOVIA Draw 2016\

For example:

1. Go to <DRAW_HOME>/Examples/C#/AddInActionExample2. Create folder AddIns under C:\users\<user_name>\AppData\Roaming\BIOVIA\BIOVIA

Draw 2016\

3. Copy XML Document (DisplaySmilesString) andbin/Release/MDL.Draw.AddIn.DisplaySmilesString.dll file to AddIns Folder

4. Launch BIOVIA Draw.5. Draw any structure on the canvas.6. Select Chemistry > Display SMILES String.

Creating a Custom Ptable | Page l

Cheshire ActionsBIOVIA Draw contains the functionality of Accelrys Cheshire in an embedded version to support featuressuch as such Clean and Uniprot file conversion.

See also

Specify a Custom Ptable and CustomWeights

Specify a Custom Ptable and Custom WeightsBefore specifying a custom periodic table, review the information in Custom Ptable Example and CustomPtable Path.

If Draw is using a custom Ptable with custom weights, the BIOVIA Cheshire scripts must also use thecustom Ptable with custom weights. You can edit the Ptable and weights file to match any customelements and weights for your organization.

Although the Ptable contains a weight for each element, the custom weights file determines the weightfor calculations within Draw. Other BIOVIA products, such as BIOVIA Direct, might interpret the formatof the atomic weight as Fortran format F10more strictly leading to different results.If your businessrules require Ptable customization, you must customize Draw and set the chemical environment at yoursite for all products that interact with Draw to use the same Ptable.

Note: The bold format indicates updates you make to the configuration file.

To specify a custom Ptable and customWeights:

1. Close Draw.2. Navigate to the BIOVIA\BIOVIA Draw <version>\Examples\CheshireAction directory.3. Make a backup copy of CheshireActionExample.xml.4. Edit the following line in the CheshireActionExample.xml file to specify the custom Ptable for

Draw.<module class="MDL.Draw.Modules.Editor.EditorModule" ptable="BIOVIA\BIOVIADraw <version>\Examples\Ptable\MyPtable.txt">

5. Modify the line to look similar to the following:<module class="MDL.Draw.Modules.Editor.EditorModule" ptable="<draw_

home>\Examples\Ptable\MyPtable.txt">

The BIOVIA\BIOVIA Draw <version> represents the absolute path to the root directory of yourBIOVIA Draw installation.

6. Edit the following line in the CheshireActionExample.xml file to make the calculations availableas options on the Draw Chemistrymenu use the custom weights associated with the custom Ptable.<menustripitem text="&Chemistry"> <action name="&Calculator..."class="MDL.Draw.Modules.Editor.Actions.Calcs.MolValuesAction">

7. Modify the line to look similar to the following:<menustripitem text="&Chemistry"> <action name="&Calculator..."class="MDL.Draw.Modules.Editor.Actions.Calcs.MolValuesAction"weights="custom" weightsscript="..\Ptable\MyWeights.cct">

To verify the implementation of the custom Ptable and weights:

1. Run the batch file, CheshireActionExample.bat.2. Open the CheshireAction.mol file.

Page li | BIOVIA Draw • Configuration Guide

3. In Draw, select Chemistry > Cheshire Scripts > Rotate Molecule.

The Cheshire script rotates and cleans themolecule.

4. Right-click an atom and select Atom Symbol.

The three custom elements (PC1, PC2, PC3) of the custom Ptable are available.

5. Click PC1.6. Select Chemistry > Calculator.

The custom weight displays.

7. Paste the calculated values onto the canvas.

Cheshire Actions | Page lii

AccelrysDraw-net.xml

About the Draw XML Configuration Files liii

How to Edit XML Tags in the XML Configuration Files liii

Hierarchy of Elements lviii

XML Configuration Elements lix

Alphabetic List of Elements lxii

Description of Elements lxiv

Trigger Table ci

About the Draw XML Configuration FilesXML tags define themenus, tools, toolbars, and other items that display in the Draw interface.

The AccelrysDraw-net.xml file:

n Is the primary XML Configuration filen Specifies the secondary class resources or XML Configuration files that affect the BIOVIA Draw Editorn Is located in the installation directory, <draw_home>n The secondary XML Configuration files that AccelrysDraw-net.xml points to are in <draw_

home>\XmlConfig\

n One of the secondary XML Configuration files, menustrip.xml, points to tertiary XML Configurationfiles that affect each menu on themenubar: menubar-file.xml, menubar-edit.xml, menubar-object.xml, menubar-options.xml, menubar-chemistry.xml, menubar-window.xml, and menubar-help.xml

n The Draw XML parser does not verify that parent-child tag relationships are valid. However, if arelationship is not valid, the object defined by the tags will not display. The valid parent-child taghierarchies are documented in the Descriptions of Elements section.

See also

BIOVIA Draw Configuration Tasks

Specifying XML Configuration Files

Specify the Path to Your Custom XML Configuration Files.

How to Edit XML Tags in the XML Configuration FilesYou can customize the BIOVIA Draw Editor user interface for your end-users by editing theAccelrysDraw-net.xml file and the files to which it points . For a list of typical tasks and associatedXML tags, see Configuration Tasks.

Sample Screens

See also

Hierarchy of Elements

Alphabetic List of Elements.

Page liii | BIOVIA Draw • Configuration Guide

Main Screen

The following shows a splitter, which divides the screen into two spaces. One possibler use of a splitter is to display a module that contains buttons.

AccelrysDraw-net.xml | Page liv

Page lv | BIOVIA Draw • Configuration Guide

Drop-downMenu

Note: Whereas a tool persists for reuse, an action is a one-time event, such as Save, Open, or Print. Theitems on a menu are actions.

Dialog boxTo view the sMolecular Value dialog box, open or draw a molecule and select Calculator in theChemistrymenu.

AccelrysDraw-net.xml | Page lvi

Attached Data DialogWhen the user right-clicks an atom and selects Attach Data, theData Sgroup Properties dialog displays.

AttributesThe data type of all attributes is CDATA.

Attribute Required Description

name No Specifies the name displayed in the title.

height No Specifies the height of the dialog in pixels.

width No Specifies the width of the dialog in pixels.

Parent ElementNone

Page lvii | BIOVIA Draw • Configuration Guide

Child Elements

Element Required Description

module No Specifies a component or sub-application within themain window.

ExampleNone

See also


XML Configuration Elements

Hierarchy of ElementsThe element attributes are omitted to show the structure of the XML.<mdldraw>

<module class="MDL.Draw.Modules.Splitter" orientation="horizontal"percentage="70">

<module class="MDL.Draw.Modules.Editor.EditorModule">

<menustrip>

<menu>

<action />

...

<separator />

<action />

...

</menu>

<menu>

...

<actionclass="MDL.Draw.Modules.Editor.Actions.PreferencesAction">

<DisplayPreferences />

</action>

</menu>

<menu>

<action>

<dialog>

<panel>

<label />

<button />

</panel>

...

AccelrysDraw-net.xml | Page lviii

</dialog>

</action>

</menu>

...

</menustrip>

<donetoolbar>

<action>

</donetoolbar>

<toolbar>

<action>

...

<templatedirectory>

<folder />

</templatedirectory>

<templatetoolbarmanager>

<templatetoolbar />

</templatetoolbarmanager>

</toolbar>

<palettebar>

<palette>

<multitool>

<tool />

<abbreviationtoolbar />

<tool />

<abbreviationtoolbar />

</multitool>

...

</palette>

...

</palettebar>

</module>

</module>

</mdldraw>

XML Configuration ElementsThe table alphabetically lists the elements in the AccelrysDraw-net.xml configuration file. Theelements definemenus, tools, toolbars, and other items that display in the Draw user interface.

Page lix | BIOVIA Draw • Configuration Guide

Element Parents Brief Description

abbreviationtoolbar tool Specifies the location of the standard abbreviationdefinitions file that provides the abbreviations thatdisplay in the top toolbar of the Abbreviation SequenceTool.

action menu, toolbar,donetoolbar,palettebar

Specifies a menu item and the class that performs theaction when that item is selected

button panel, radiobutton,dialog

Specifies a push button control.

checkbox panel, dialog Specifies a check box control that allows the user toselect a true or false condition.

combobox panel, dialog,radiobutton, button

Specifies a dropdown selection box.

dialog action, menuitem,tool, button

Specifies a dialog box that opens when the parentmenu item or toolbar item is selected.

DisplayPreferences action Specifies the file that stores the changes the usermakes to display preference settings, and allows you toset values for display preferences.

donetoolbar module (Editor) Specifies a toolbar that goes in the upper left corner ofthe Editor window. In the default configuration, itcontains a button that transfers themolecule back tothe application that passed it.

fieldname tool (Data Sgroup tool only) Specifies that each occurrenceof field name defines a type of attached data (Sgroupdata) that the user can select in the Attached Datadialog box.

folder templatedirectory Specifies the display name and path of a directory thatcontains template files such as molfiles, rxnfiles, sketchfiles, or SMILES files. A sketch file means entirestructure.

label panel, radiobutton,dialog

Specifies a control that displays text.

listvalue fieldname (Data Sgroup tool only) Specifies a value that the usercan select in a list in the Attach Data dialog box for theparent type of attached data.

mdldraw None Specifies the root element.

menu menustrip, popup Specifies a menu such as a pull-down menu to displayon themenu bar or a sub-menu.

AccelrysDraw-net.xml | Page lx


menustrip module (Editor) Specifies themenu bar at the top of the Editor window,contains all the primary menus.

menuitem menu, popup, tool Specifies a menu item.

module mdldraw Specifies a component or sub-application within themain window.

multitool toolbar, palette,palettebar

Specifies a control that can contain multiple toolcontrols within it.

operator tool (Data Sgroup tool only) Specifies an operator that theuser can select in the Attach Data dialog box whencreating a query molecule, for example, ’>’.

palette palettebar, toolbar Specifies a container for tools that allows only one ofthe contained tools to be visible at a time.

palettebar module Specifies a vertical bar that runs down the left side ofthe Editor window, that contains palettes, tools, andmulti-tools

panel dialog, radiogroup Specifies a container for other controls, such as labels,buttons, checkboxes, and radio buttons.

popup tool Specifies a popup menu that is opened when theparent tool is selected.

radiobutton panel, radiogroup,dialog

Specifies a radio button control.

radiogroup dialog, panel Specifies a container for grouping radio buttons.

selection combobox Specifies one of the items available for selection in acombo-box list.

separator menu, toolbar,palettebar, popup

Inserts a line in a menu, or a space between elementsin a toolbar or palette bar.

shortcut shortcuts Specifies the key assignment for keyboard shortcuts.

shortcuts module (Editor) Contains one or more keyboard shortcuts.

space dialog, panel Inserts a space between components.

templatedirectory toolbar Specifies a control on the toolbar that opens theTemplate Directory dialog box.

templatetoolbar templatetoolbarmanager

Specifies a directory that contains template groups.

templatetoolbarmanager

toolbar Specifies a control to add to a toolbar that enables auser to select the group of templates available on thetoolbar.

Page lxi | BIOVIA Draw • Configuration Guide


tool multitool, palette,palettebar, toolbar

Specifies a control that, when selected, causes theDraw to call a specified class to handle events thatoccur in the drawing area such as mouse drags, mousemoves, key pressed, mouse pressed, and mousereleased.

toolbar module (Editor) Specifies a horizontal bar across the top of the Editor.Usually contains tools and actions.

Alphabetic List of Elements

Element Parents Description

abbreviationtoolbar tool Specifies the location of the standard abbreviationdefinitions file that provides the abbreviations thatdisplay in the top toolbar of this Sequence Tool.

action menu, toolbar,donetoolbar,palettebar

Specifies a menu item and the class that performs theaction when that item is selected

button panel, radiobutton,dialog

A push button control

checkbox panel, dialog A check box control that allows the user to select a trueor false condition

combobox panel, dialog,radiobutton, button

A dropdown selection box

dialog action, menuitem,tool, button

A dialog box that opens when the parent menu item ortoolbar item is selected

DisplayPreferences action Specifies the file that stores the changes the usermakes to display preference settings, and allows you toset values for display preferences

donetoolbar module (Editor) A toolbar that goes in the upper left corner of theEditor window. In the default configuration, it containsa button that transfers themolecule back to theapplication that passed it.

fieldname tool (Data Sgroup tool only) Each occurrence of fieldnamedefines a type of attached data (Sgroup data) which theuser can select in the "Attached Data" dialog box

folder templatedirectory Specifies the display name and path of a directory thatcontains template files (molfiles, rxnfiles, sketch files, orSMILES files). Note: In this context, sketch means entirestructure.

AccelrysDraw-net.xml | Page lxii


label panel, radiobutton,dialog

A control that displays text

listvalue fieldname (Data Sgroup tool only) Specifies a value that the userwill be offered in a drop-down list in the "Attach Data"dialog box for the parent type of attached data

mdldraw None The root element

menu menustrip, popup Amenu, such as a pull-down menu to display on themenu bar or a submenu

menustrip module (Editor) Themenu bar at the top of the Editor window.Contains all the primary menus

menuitem menu, popup, tool Amenu item

module mdldraw A component or subapplication within themainwindow

multitool toolbar, palette,palettebar

A control that can contain multiple tool controls withinit

operator tool (Data Sgroup tool only) Specifies an operator that theuser can select in the "Attach Data" dialog box whenthe user is creating a query molecule, for example, ’>’

palette palettebar, toolbar A container for tools that allows only one of thecontained tools to be visible at a time

palettebar module A vertical bar, which runs down the left side of theEditor window, that contains palettes, tools, andmultitools

panel dialog, radiogroup A container for other controls, such as labels, buttons,checkboxes, and radiobuttons

popup tool A popup menu that is opened when the parent tool isselected

radiobutton panel, radiogroup,dialog

A radio button control

radiogroup dialog, panel A container for grouping radiobuttons

selection combobox One of the items available for selection in a comboboxdrop down list

separator menu, toolbar,palettebar, popup

Inserts a line in a menu, or a space between elementsin a toolbar or palettebar

shortcut shortcuts A keyboard shorcut key assignment

shortcuts module (Editor) Contains one or more keyboard shortcuts

Page lxiii | BIOVIA Draw • Configuration Guide


space dialog, panel Inserts a space between components

templatedirectory toolbar A control on the toolbar that opens the "TemplateDirectory" dialog box

templatetoolbar templatetoolbarmanager

Specifies a directory that contains template groups


toolbar A control, which can be added to the toolbar, thatallows a user to select which group of templates will beavailable on the toolbar

tool multitool, palette,palettebar, toolbar

A control that, when selected, causes the BIOVIA DrawEditor to call a specified class to handle events thatoccur in the drawing area (for example, mouse drags,mousemoves, key pressed, mouse pressed, mousereleased, etc.)

toolbar module (Editor) A horizontal bar across the top of the Editor. Usuallycontains tools and actions.

See also

Sample Screens


Description of Elements

abbreviationtoolbarSpecifies the location of the standard abbreviation definitions file that provides the abbreviations thatdisplay in the top toolbar of this Sequence Tool.

Attributes

The data type of all attributes is CDATA.

AttributeRequired

Description

name Yes The tooltip for the sequence tool.

path Yes The path to the standard abbreviation definitions file. For example:

path="x:/MyMolfiles/StdAbbrevs/std_abbrev_defs.xml"

where x:/MyMolfiles/ is the location of the standard abbreviationdefinitions file.

AccelrysDraw-net.xml | Page lxiv

AttributeRequired

Description

toolbarType Yes Specifies the name of the section of the standard abbreviation file thatcontains templates for this sequence tool.

Allowed values are: AA, DNA, RNA

extraTemplates No (Optional) Specifies the location of additional templates (for example,protecting groups and PEG groups) in the standard abbreviations file.

sequence No (Optional) Specifies how abbreviations are arranged on the top toolbar ofthe sequence tool.

If True, BIOVIA Draw arranges abbreviations on the toolbar in the followingorder:

(1) templates from toolbarType

(2) templates from extraTemplates if available. Within each group, thetemplates are listed in alphabetical order.

If False, (the default), BIOVIA Draw arranges abbreviations on the toolbar inalphabetical order without differentiating templates from toolbarType orextraTemplates.

Parent Element

tool

Child Elements

None

Example<multitool name="SequenceToolAA1" image="SeqToolAA124.gif" tooltip="1-letter amino acid sequence">

<tool class="MDL.Draw.Modules.Editor.Tools.SequenceTool">

<abbreviationtoolbar name="Peptide Sequences 1-letter"path="%MDLDRAW%std_abbrev_defs.xml" sequence="true" toolbarType="AA"extraTemplates="SAG" />

</tool>

<tool class="MDL.Draw.Modules.Editor.Tools.SequenceLassoTool" />

<tool class="MDL.Draw.Modules.Editor.Tools.AbbreviationBondTool" />

<multitool name="MenuTool" trigger="rmro,rmr" />

</multitool>

See also



actionSpecifies the class associated with a particular action. An action added to a menu appears as a menuitem. An action added to a toolbar appears as a button, if an image file is specified. Defined in thetoolbar.xml, donetoolbar.xml, and menubar configuration files.

Page lxv | BIOVIA Draw • Configuration Guide

When an action is selected, the function is performed a single time. Once the action is done, it has nocontinuing effect on the Draw environment. When a tool is selected,it remains active until another toolis selected. The save operation is an example of an action. The save operation is performed once eachtime Save is selected.

Attributes



name Yes Specifies the text that displays for themenu item.

Begin the namewith & to enable keyboard selectionof the item, when viewed on themenu, for example,&Open enables the Draw user to open themenu bytyping alt-o.

class Yes Specifies the fully qualified name of the class associatedwith the action.

shortcut No Specifies a shortcut key combination such as Ctrl+O forOpen.

image No Specifies the name of the image file for the image to displayof the action is added to the toolbar.

tooltip No Specifies the tooltip that displays when the cursor hoversover the button.

file No Specifies the path to and name of the file used as input oroutput.

listener No Specifies the fully qualified name of the class listening for anevent on the widget, for example, the radio button mightuse a listener such aslistener="MDL.Draw.Gui.GrayOutChildren".

enabled No Indicates if the action in enabled. When set to True theaction is enabled. The default value is True.

weight No Do not use; for internal use only.

Parent Element

menu, toolbar, donetoolbar, palettebar

Child Elements

ElementRequired

Description

dialog No Defines a dialog box that is opened when this item is selected

AccelrysDraw-net.xml | Page lxvi

ElementRequired

Description

DisplayPreferences

No When the action class is:class="MDL.Draw.Modules.Editor.Actions.PreferencesAction"

Specifies the file that stores changes in the display preferences. Youcan also use DisplayPreferences to specify values for particularpreferences.

Example<action name="&Open..." shortcut="CtrlO" image="Load.gif"class="MDL.Draw.Modules.Editor.Actions.LoadAction"/>

Calculator Example with Exact Mass<actionname="&Calculator..."class="MDL.Draw.Modules.Editor.Actions.Calcs.MolValuesAction">

<dialog title="Molecular Values" command="calDialog">

<panel height="40">

<label text="" command="error" update="T" height="20"/>

</panel>

<panel layout="horizontal" width="300" height="35">

<checkbox text="Formula Weight" command="weightcheck" value="selected"update="T" width="150"/>

<label text="" command="weight" update="T" width="150"/>

</panel>


<checkbox text="Exact Mass" command="exactmasscheck" value="selected"update="T" width="150"/>

<label text="" command="exactmass" update="T" width="150"/>

</panel>


<checkbox text="Molecular Formula" command="formulacheck"value="selected" update="T" width="150"/>

<label text="" command="formula" update="T" width="150"/>

</panel>


<checkbox text="Molecular Composition" command="compositioncheck"value="selected" update="T" width="150"/>

<label text="" command="composition" update="T" width="150"/>

<label text="" command="composition" update="T" height="40">

</panel>

<panel layout="horizontal" align="center" width="280" command="ok"/>

<button text="Paste" command="paste"/><button text="OK"

Page lxvii | BIOVIA Draw • Configuration Guide

</panel>

</dialog>

</action>

See also



Menu

buttonA push button control.

Attributes


Attribute Require d Description

text Yes The text that displays for the button.

command Yes Specifies a value that is passed to the button widget

update No If "true", the button can be updated dynamically. Default is "false".

style No Sets the style for the font. Possible values: "bold", "italic", or

"bolditalic".

Parent Element

panel, radiobutton, dialog

Child Elements

Element Require d Description

dialog No Defines a dialog box that is opened when the button is clicked.

Example

See the Example for dialog.

See also



checkboxSpecifies a check box control that allows the user to select a true or false condition. The check boxelement is defined in the menubar-chemistry.xml configuration file.

Attributes



text Yes Specifies the text that displays for the check box.

AccelrysDraw-net.xml | Page lxviii


command Yes Specifies a value that is passed to the check box widget

value No Indicates if the value="selected", the check box is checked.

update No Indicates true or "T" means that BIOVIA Draw should dynamically provide avalue. For more information, see the Example.

width No Specifies the width of the check box in pixels.

height No Specifies the height of the check box in pixels.

style No Sets the style for the font. The valid values are bold, italic, or

bolditalic.

Parent Element

panel, dialog

Child Elements

None

Example<panel layout="horizontal" width="300" height="35">

<checkbox text="Molecular Formula" command="formulacheck"value="selected" update="T" width="150" />

<label text="" command="formula" update="T" width="150" />

</panel>

See also



comboboxA dropdown selection box. If editable="true", the user will also be allowed to type in text.

Attributes


AttributeRequired

Description

command Yes Specifies a value that is passed to the combobox widget

editable No If "true" (or "T"), this combobox can be edited.

update No If "true", the button can be updated dynamically. Default is "false".

enabled No If "true" (or "T"), this combobox is enabled. If this attribute is not specified, thedefault is enabled.

Page lxix | BIOVIA Draw • Configuration Guide

AttributeRequired

Description

select No Specify a number that indicates which of the items specified in the selection childelements should be selected by default. For example, if select="1", the first itemwill appear in the combobox. If select is not specified, the combobox will initiallybe empty.

width No Width of the combobox in pixels

height No Height of the combobox in pixels

tooltip No Tooltip to display when mouse cursor is over this combobox

listener No The fully qualified name of an action class that is listening for an event on thiswidget.


"bolditalic".

Parent Element

panel, dialog, radiobutton, button

Child Elements


selection No Preset value offered in a combobox

Example<dialog title="Molecular Values" command="calDialog" width="300"height="300">

<panel height="60">

<combobox command="puritycombo" editable="T" update="T" enabled="T"select="3" width="100">







</combobox>

</panel>

</dialog>

See also



AccelrysDraw-net.xml | Page lxx

dialogDefines a dialog box that opens when the parent menu item or toolbar item is selected or the parentbutton is clicked. The child elements specify the controls in the dialog box.

Attributes


AttributeRequired

Description

title Yes Title that displays at the top of the dialog box

command Yes Specifies a value that is passed to the dialog widget

update No Alerts the dialog widget that elements in the dialog box can be updated atruntime

Parent Element

action, menuitem, tool, button

Child Elements


panel No Inserts a panel of a specified size in the dialog box. Various GUI

elements can be added to the panel.

space No Inserts a blank space of a specified size between panels. Value is in pixels.

radiogroup No Inserts a container for radio buttons

radiobutton Yes A radio button control

button No A push button control

label No A control that displays text

combobox No A dropdown selection box control that also allows text to be typed in

checkbox No A check box control that allows the user to select a true or false condition

Example<dialog title="Valence Check" command="valencecheck" width="175"height="200">

<space height="7" />

<panel width="175">

<label text="# atom(s) has exceeded valence." command="exceedText"update="T" align="center" width="175" />

<label text="Every atom has correct valence." command="correctText"update="T" align="center" width="175" />

<label text="Not available for reaction." command="rxnerror"update="T" align="center" width="175" />

</panel>


Page lxxi | BIOVIA Draw • Configuration Guide

<panel layout="horizontal" align="center" width="175" height="40">

<button text="OK" command="ok" />

</panel>

</dialog>

See also



DisplayPreferencesSpecifies the file that stores changes Draw users make to display preference settings, and enables settingvalues for display preferences. Preferences set by the user in Draw override the values specified inDisplayPreferences.

For information on property names, types, and possible values, see the DisplayPreference class inthe API Reference.

Data Types

The following tables describes the format of data types used in DisplayPreferences.

Data typeFormats / possiblevalues

Example

Boolean true or false <AromaticRingCircles>true</AromaticRingCircles>

Color Pre-defined names in theColor class

<Background>LightGray</Background>

RGB triplets <Background>211,211,211</Background>

Enumeration Name of an enumeratedvalue

<HydrogenDisplayMode>Hetero</HydrogenDisplayMode>

Example

The following example sets several properties and specifies the default.xml as the file that overrides theXML Configuration files. The user preferences are located in a directory similar to the following:\\Users\<username>\AppData\Roaming\BIOVIA\BIOVIA Draw\Preferences.<action name="&Preferences"class="MDL.Draw.Modules.Editor.Actions.PreferencesAction">

<DisplayPreferences file="default.xml" >

<AromaticRingCircles>true</AromaticRingCircles>

<BackColor>yellow</BackColor>

<AtomHighlightDotWidth>0.1</AtomHighlightDotWidth>

<HighlightColor>Red</HighlightColor>

<ForceV3000>true</ForceV3000>


</action>

See also

Synchronizing Display Settings

AccelrysDraw-net.xml | Page lxxii

donetoolbarA toolbar that goes in the upper left corner of the Editor window.

When BIOVIA Draw is called from another program, the donetoolbar contains a button that transfersthemolecule back to the application that passed it.

Attributes

None

Parent Element

module (where class="MDL.Draw.Modules.Editor.EditorModule")

Child Elements


action Yes Adds a button to the toolbar that performs a specified action when it is clicked

Example<menubar>

<donetoolbar>

<action image="Done.gif"class="MDL.Draw.Modules.Editor.Actions.DoneAction" tooltip="Transferto the Web"></action>

</donetoolbar>

</menubar>

See also


XML Configuration Element

fieldname(Data Sgroup tool only) Each occurrence of fieldname defines a type of attached data (Sgroup data)which the user can select in the "Attached Data" dialog box. The user can associate attached data with allor part of a structure. Each "type" of attached data:

n Has a display namen Is associated with a particular kind of object such as "atom", "bond", "collection"n Has an associated database field, called an Sgroup field. An Sgroup field is a special kind of database

field that assigns meaning to a specific type of attached data (Sgroup data) that is stored with thestructure. The Sgroup field specifies whether the attached data is text or numeric and, for numericdata, the units. The data in Sgroup fields is accessible solely through a graphical search query; youcannot display data from an Sgroup field in a form box.

n Might have a particular numeric or non-numeric data type for the data to be stored. See Examples forSgroup data.

n Might have display units

The "Attached Data" dialog box is displayed when the user selects some or all of a structure and thenchooses "Attach data..." from the popup menu.

n To enable the end-user to register a molecule with attached data, the exact name of the databasefield, which, you, the BIOVIA DrawAdministrator, has created for this type of attached data must be

entered into the name attribute.n The data Sgroup tool is commented out in the <draw_home>\XmlConfig\palettebar.xml file.

To enable this dialog box to display, you must uncomment out all the lines in the XML file that arerelated to the data Sgroup tool. To disable it later, you can comment out those same lines.

n To represent that there is no operator, you can use <listvalue value="(none)" />n Additional information is available at Enabling the Data Sgroup Tool to Control Sgroup Data.

Attributes


AttributeRequired

Description

readablename Yes The display name for this type of attached data. This name appears in the"Sgroup Field Name" drop-down in the "Attach Data" dialog box.

Attribute Required

Description

target Yes The kind of object with which this attached data is associated. Possiblevalues are:

n atomn bondn sketchn fragmentn collectionn file

In this context, sketch means entire structure.

name Yes The name of the database field in which this attached data will be stored. Inorder to register molecules, this namemust match the name of the fieldthat the Administrator has created. The name can be up to 30 characterslong.

type No Data type of the attached data. For example, numerical data might be int ordouble, and non-numeric data might be text.

CAUTION: BIOVIA Draw does NOT validate the type of data.

unit No Units to display in the "Attach Data" dialog box

value No Value to display in the "Attach Data" dialog box

Parent Element

tool (where class="MDL.Draw.Modules.Editor.Tools.DataSGroupTool")

Child Elements


listvalue No; zeroor more

Specifies a value that the user will be offered in a drop-down list in the "AttachData" dialog box for this type of attached data

Examples for Sgroup data

Note: BIOVIA Draw does not validate the data type of Sgroup data.

The following example show using data of type text, integer, and double. This example involves thetype of data as text.





<fieldname readablename="Non-tetrahedral chirality" name="CHIRAL_NONTETRAHEDRAL"

target="sketch"

type="text" unit="" value="list">

<listvalue value="(none)"/>

<listvalue value="R"/>

<listvalue value="S"/>

<listvalue value="P"/>

<listvalue value="M"/>

<listvalue value="E"/>

<listvalue value="Z"/>

</fieldname>

This example specifies the type of data as double or integer.

<fieldname readablename="Fraction of E (trans) bond"

name="FRACTION_E_CONFIG"

target="bond"

type="double"

unit="E"

value=""

/>



<fieldname readablename="Coefficient of ion"

name="COUNTERION_COEFF"

target="fragment"

type="int"

unit="" value=""

/>

See also



folderSpecifies the display name and path of a directory that contains template files (molfiles, rxnfiles, or

SMILES files). Use folder to define what displays in the "Template Directory" dialog box.

Attributes


AttributeRequired

Description

name Yes The display name of the template folder that displays in the left column of the"Template Directory" dialog box.

path Yes The path to the template folder. For example:

path="%MDLDRAW%Templates\Template Sets\"

where %MDLDRAW% represents the BIOVIA Draw installation directory (notethat the constant includes the ending backslash).

readonly No If "true", the user cannot update this directory.

Parent Element

templatedirectory

Child Elements

None

Example

See the Example for templatedirectory.

See also



labelA control that displays text. A label can also be used as a placeholder to display values that are to befilled in by BIOVIA Draw. To do this:

n Set the text attribute to "" (empty string) or insert a wild-card symbol for a number ("#") as a placeholder

n Set the update attribute to "true" (or "T")

Attributes


AttributeRequired

Description

text Yes The text the label displays.

To have BIOVIA Draw dynamically fill in the value, set the text attribute to ""(empty string) or insert a wild-card symbol (’#’) as a place holder. Note: Youmust also set the update attribute to "true".

command Yes Specifies a value that is passed to the label widget

update No "true" (or "T")means that BIOVIA Draw should dynamically provide the value forthe label

height No Height of the label in pixels

width No Width of the label in pixels

align Positioning in parent container. Possible values: "left", "center", or

"right". Default is "left".

variable No If "true", allows a "#" symbol in the value of the text attribute to be replaced bya variable at run time. Default is "false".


"bolditalic".

Parent Element

panel, radiobutton, dialog

Child Elements

None

Example

See the Example for dialog.

See also



listvalueSpecifies one of the values that the user will be offered in a drop-down list in the "Attach Data" dialogbox for the parent type of attached data.

Attributes



value Yes Specify a value to include in the drop-down list

Parent Element

fieldname

Child Elements

None

Example

See the Examples for Sgroup data for fieldname.

See also



menuSpecifies a menu such as a pull-down menu that is available from themenu bar. If menu is a child ofanother menu, it specifies a sub-menu. Defined in the menustrip.xml, palettebar.xml, and

the AccelrysDraw-net.xml configuration files.

Attributes



text Yes Specifies the keyboard key that initiates theaction, for example, pressing char = "1"

,representing the number 1 key on the keyboard,initiates the action.

Command No Specifies a value passed to the executing classwhen an item on themenu is selected.

Parent Element

menustrip, popup, tool, menu

Child Elements

ElementRequired

Description

action No Specifies a menu item

menu No Specifies a sub-menu, for example, use the menu element if a menu item hasseveral sub-choices.

separator No Inserts a separator line in themenu

menuitem No Specifies a menu item and the command to pass to the executing class whenthemenu item is selected.

Examples

Drop-down menu example<menustripitem text="&File">

<action name="&New Molecule" shortcut="Alt5" image="New.gif"class="MDL.Draw.Modules.Editor.Actions.NewStructureAction" />

<action name="&Open..." shortcut="CtrlO" image="Load.gif"class="MDL.Draw.Modules.Editor.Actions.LoadAction" />

<action name="&Insert..." shortcut="CtrlI" image="Load.gif"class="MDL.Draw.Modules.Editor.Actions.InsertAction" />

<separator />

<action name="&Save" shortcut="CtrlS" image="Save.gif"class="MDL.Draw.Modules.Editor.Actions.SaveStructureAction" />

<action name="Save As..." image="Save.gif"class="MDL.Draw.Modules.Editor.Actions.SaveStructureAsAction" />

<action name="Save As Image..." image="Save.gif"class="MDL.Draw.Modules.Editor.Actions.SaveAsImageAction" />

<separator />

<action name="&Print..." shortcut="CtrlP"class="MDL.Draw.Modules.Editor.Actions.PrintAction" />

<action name="Print Pre&view..."class="MDL.Draw.Modules.Editor.Actions.PrintPreviewAction" />

<action name="E&xit"class="MDL.Draw.Modules.Editor.Actions.ExitAction" />

</menu>



</menubar>

Popup menu example<tool class="MDL.Draw.Modules.Editor.Tools.RadicalTool">

<popup>

<menu command="radical" text="Radical">



<menuitem command="mono" text="Monoradical" />

<menuitem command="di" text="Diradical(Singlet)" />

<menuitem command="di-triple" text="Diradical(Triplet)" />

<menuitem command="radicaloff" text="Off" />

</menu>

</popup>

</tool>

See also



menuitemSpecifies a menu item and the command to pass to the executing class when this item is selected. Theclass that is executed is specified in the tool element under which this menuitem resides.

Attributes


AttributeRequired

Description

text Yes The name of this menu item, for example "Atom symbol...".

command Yes A value passed to the executing class when this item is selected. If you createyour own widget you can use a command attribute to pass a value that youneed to have.

state No state="title" is the only possible value. Specify this attribute if the function ofthis menuitem is to specify a menu title for a popup menu.

Parent Element

menu, popup, tool

Child Elements


dialog No Defines a dialog box that is opened when themenu item is selected.

Example<tool class="MDL.Draw.Modules.Editor.Tools.RadicalTool">

<popup>

<menu command="radical" text="Radical">



<menuitem command="mono" text="Monoradical" />

<menuitem command="di" text="Diradical(Singlet)" />

<menuitem command="di-triple" text="Diradical(Triplet)" />

<menuitem command="radicaloff" text="Off" />

</menu>

</popup>

</tool>

See also



menustripSpecifies themenu bar at the top of the Draw user interface. Contains all the primary menus. Defined inthe menustrip.xml configuration file.

Attributes

None

Parent Element

module where class="MDL.Draw.Modules.Editor.EditorModule"

Child Elements


menu Yes Specifies one or moremenus.

Example

menu

See also



moduleSpecifies a component or sub-application that runs in the Drawwindow. You can use themoduleelement to add your own components to the Draw framework. Modules are found in theMDL.Draw.Modules namespace. Defined in the AccelrysDraw-net.xml configuration file.

Draw provides two types ofmodules listed in the following table.

Module Description Class Attributes

Splitter Divides themainwindow into tworesizable panes.

MDL.Draw.Modules.Splitter class,orientation,percentage

Editor Enables renderingand editing structures

MDL.Draw.Modules.Editor.EditorModule class,ptable

Attributes


Attribute Required Description Module

class Yes The class that implements the functionality for this module. SeeExample for Editor module.

All

orientation Yes,splitteronly

The orientation of the windows created by a splitter. The validvalues are as follows:

n horizontal - windows are next to each other; splitter is verticaln vertical - windows are on top of each other; splitter is

horizontal

See Example for Splitter module.

Splitter

percentage Yes,splitteronly

Specifies the percentage ofmain window occupied by the firstwindow created by a splitter. See Example for Splitter module.

Splitter

Attribute Required Description Module

ptable No Specifies the path and name of a Ptable to use instead of theinternal Ptable. You can specify a URL that points to the Ptable.The path is relative to the directory from which the BIOVIA Drawexecutable is launched, for example: <moduleclass="MDL.Draw.Modules.Editor.EditorModule"ptable="myptable.txt"></module>

Editor

Parent Element

mdldraw

Child Elements

Element Required Description Module

module No Specifies a Splitter module can have child modules, forexample, an Editor or ButtonModule.

Splitter

shortcuts No Contains one or more keyboard shortcuts. Editor

menustrip No Defines themenu bar at the top of the Editor window. Editor

donetoolbar No Specifies a toolbar that displays in the upper left corner ofthe Editor window. In the default configuration, it contains abutton that transfers themolecule back to the applicationthat passed it.

Editor

toolbar No Inserts a horizontal bar across the top of the Editor orButtonModule, and can contain tools and actions. Only onetoolbar is allowed in a module.

Editor

palettebar No Specifies a vertical bar, which runs down the left side of theEditor window, that contains palettes, tools, and multi-tools.

Editor

Examples

Module Element Example<module class="MDL.Draw.Modules.Editor.EditorModule">

<shortcuts>

<shortcut char=" " method="SwapTool" />

</shortcuts>

<menubar>

<menu text="&File">

<action name="&New Structure" shortcut="CtrlN" image="New.gif"

class="MDL.Draw.Modules.Editor.Actions.NewStructureAction" />

...

</menu>

...

</menubar>

<donetoolbar>

<action image="Done.gif"class="MDL.Draw.Modules.Editor.Actions.DoneAction" tooltip="Transfer to theWeb">

</action>

</donetoolbar>

<toolbar file="HorizontalToolbar.xml" allowdrop="true">

<action image="Clear.gif"class="MDL.Draw.Modules.Editor.Actions.ClearAllAction" tooltip="Clear All" />

...

</toolbar>

<palettebar>

<palette>

<multitool name="SingleBondTool" image="SingleBond24.gif"tooltip="SingleBond Tool">

<tool class="MDL.Draw.Modules.Editor.Tools.BondTool" />

<tool class="MDL.Draw.Modules.Editor.Tools.RingBondTool" />

<tool class="MDL.Draw.Modules.Editor.Tools.KeyboardTool" />

<multitool name="MenuTool" trigger="rmro,rmr" /

</multitool>

</palette>

...

</palettebar>

</module>

Splitter Module Example<module class="MDL.Draw.Modules.Splitter" orientation="horizontal"percentage="70">

<module class="MDL.Draw.Modules.Editor.EditorModule">

...

</module>

<module class="MDL.Draw.Modules.ButtonModule">

...

</module>

</module>

See also



multitoolSpecifies a control that can contain multiple tool controls. Each tool adds functionality to themultitool.When themultitool control is selected, the Draw calls a class specified in one of the child tools to handleevents that occur in the drawing area such as mouse drags, mousemoves, and mouse pressed. Themultitool element is defined in the palettebar.xml configuration file.

You can create a multitool by combing the Bond tool and an associated keyboard shortcut tool.

Attributes



image Yes Specifies the image file name containing the imagethat displays on the button. For moreinformation, see Image Specification.

name No Specifies a name for themulti-tool. If you specify aname, you can reference the definition for thatmultitool in the BIOVIA\BIOVIA Draw<version>\XmlConfig\palettebar.xml file, byspecifying another multitool that has the samename, helpful if you need to reuse a multi-toolthat has a very long definition. For moreinformation, seeMenuTool in palettebar.xmlexample.

tooltip No Specifies text to display in the tool tip.

default No If "true", this tool is selected when BIOVIA Drawstarts up. Only one tool or multitool in the XMLconfiguration file can be specified as the default.The BIOVIA Draw default is the LassoTool.

trigger No A comma delimited list of tool events that willtrigger this object

(example: trigger = "mdo, mpo, rmpo") (seeTrigger Table)

customfile No The name of a file in which BIOVIA Drawwill savethe changes if the user customizes this multitool.

button No Specify your own button class to be used in themain toolbar instead of the regular toolbarbutton. For example:button="MDL.Draw.Gui.TemplateSelectorButton"

file No Specifies a the path and name of a file that can beused as input or output.

Parent Element

toolbar, palette, palettebar, multitool

Child Elements


tool No Specifies a tool participating as part of themultiple tool combination.

multitool No Specifies a child multitool.

Example

<multitool name="DoubleBondTool" image="DoubleBond24.gif" tooltip="DoubleBond Tool">

<tool class="MDL.Draw.Modules.Editor.Tools.DoubleBondTool" />



</multitool>

See also



operatorSpecifies an operator that the user can select in the Attach Data dialog when the user creates a querymolecule, for example, ’>’ to indicate that the target value is greater than the attached data value. Theoperator element is defined in the palettebar.xml configuration file.

Note: There is onemaster list of operators that is used for all types of attached data.

Attributes



value Yes An operator to offer in the Attach Data dialog.

Parent Element

tool where class="MDL.Draw.Modules.Editor.Tools.DataSGroupTool".

Child Elements

None

Example

See the Examples for Sgroup data for fieldname.

See also



paletteSpecifies a container for tools that:

n Allows only one of the contained tools to be visible at a timen Allows the user to open the palette to view all contained tools and to select a different one

The palette element is defined in the palettebar.xml configuration file.

A palette is indicated by a black triangle to the right of the displayed tool icon (button). Click on the blacktriangle to open the palette and view the other choices.

Attributes


Attribute RequiredDescription

default No Indicates whether the tool is active at start up and is used when the userchanges tools.

Parent Element

palettebar, toolbar

Child Elements

A tool or multi-tool must exists.


tool No Specifies a control that causes the BIOVIA Draw Editor tocall the specified class to handle events that occur in thecanvas.

multitool No Specifies a control that can contain multiple toolcontrols.

Example<palette>

<tool name="Rotate/Flip Tool" image="RotateTool24.gif"tooltip="Rotate/Flip Tool" class="MDL.Draw.Modules.Editor.Tools.RotateTool"/>

<tool name="Flip/Rotate Tool" image="FlipTool24.gif" tooltip="Flip/RotateTool" class="MDL.Draw.Modules.Editor.Tools.FlipTool" />

</palette>

See also



palettebarSpecifies a vertical bar located down the left side of the Draw user interface. The palettebar elementcontains palettes, tools, multi-tools, or actions. Draw only allows one palette bar. The palettebarelement is defined in the palettebar.xml configuration file.

Attributes


Attribute RequiredDescription

name No Specifies a string that contains a name for the palettebar.

visible No Indicates the visibility of the palette bar. If this attribute is set to false, thepalette does not display. The default value is true.

Parent Element

module where class="MDL.Draw.Modules.Editor.EditorModule".

Child Elements


palette No, can occurmultiple times

Specifies a container for tools and multi-tools.

tool No, can occurmultiple times

Specifies a control that causes the Draw to call a specified class tohandle events that occur in the canvas.

multitool No, can occurmultiple times

Specifies a control that can contain multiple tool controls.

separator No Inserts a space between elements in a palette bar.

action No Adds a button to the toolbar that performs a specified action when itis clicked.

Example<palettebar>

<palette>

<multitool name="RotateTool" image="RotateTool24.gif"tooltip="Rotate/FlipTool">

<tool class="MDL.Draw.Modules.Editor.Tools.RotateTool"/>


</multitool>

<multitool name="Flip/Rotate Tool" image="FlipTool24.gif"tooltip="Flip/RotateTool">

<tool class="MDL.Draw.Modules.Editor.Tools.FlipTool" />


</multitool>

</palette>

</palettebar>

See also



panelSpecifies a container for other controls such as labels, buttons, check boxes, and radio buttons. Panelsare used to group controls in a dialog. The panel element is defined in the palettebar.xml, toolbar.xml,donetoolbar.xml, menubar-chemistry.xml, mainpanel.xml configuration files.

Attributes



height No Specifies the height in pixels.

width No Specifies the width in pixels.

layout No Specifies the orientation of the panel. The valid valuesare horizontal or vertical. The default value is vertical.

align No Specifies the positioning in parent container. The validvalues are left, center, or right. The default value is left.

border No Indicates if a border is displayed. When set to T or true ,the panel is displayed with a border.

margin No Specifies the size of themargin within the panel in pixels

Parent Element

dialog, radiogroup

Child Elements


label No Specifies a control that displays text.

checkbox No Specifies a check box control that enables selecting a true or falsecondition.

button No Specifies a button control.

radiobutton No Specifies a radio button control.

panel No Specifies a panel within the current panel.

space No Inserts a blank space of a specified size between components. Thespace value is defined in pixels.

Example

For more information, see the dialog example.

See also



popupDefines a popup menu that is opened when the parent tool is selected. The popup can also be

"triggered" by mouse or keyboard activity (see the trigger attribute).

Attributes


AttributeRequired

Description

trigger A comma delimited list of tool events that will trigger this object

(example: trigger = "mdo, mpo, rmpo") (see Trigger Table)

Note: Triggers can also be specified for the parent tool or grandparent multitool.The actual triggers for this popup menu is the intersection of the three sets oftriggers.

Parent Element

tool

Child Elements

One of the following elements is required:


menu No Defines a menu, such as a pull-down menu to display on themenu bar

menuitem No Specifies a menu item and the value to pass to the executing class identifyingthis menu item

separator No Inserts a line in a popup menu

Example<tool class="MDL.Draw.Modules.Editor.Tools.IsotopeTool">

<popup>

<menu command="isotope" text="Isotope">





<menuitem command="specific" text="Specific value..." />

<menuitem command="isotopeoff" text="Off" />

</menu>

</popup>

</tool>

See also



radiobuttonSpecifies a radio button control. Place radio buttons in the same panel or in the same radiogroup. Theradiobutton element is defined in menubar-chemistry.xml and palettebar.xml configurationfiles.

Attributes


AttributeRequired

Description

text Yes Specifies the text that displays with the radio button.

command Yes Specifies a value that is passed to the radio button widget.

variable No Indicates if a pound (#) symbol can replace a variable. If the attribute is set totrue, a pound (#) symbol in the value of the text attribute to be replaced by avariable at run time. Default is "false".

update No Indicates if "true" (or "T")means that BIOVIA Draw should dynamically provideupdates.

listener No Specifies the fully qualified name of an action class that is listening for an eventon this widget, for example,listener="MDL.Draw.Gui.GrayOutChildren".

layout No Use horizontal to lay out the child elements horizontally and vertical tolayout the child elements vertically. The default is vertical.

width No Specifies the width of the radio button in pixels.

height No Specifies the height of the radio button in pixels.

style No Sets the style for the font. The valid values are bold, italic, or bolditalic.

Parent Element

panel, radiogroup, dialog

Child Elements

ElementRequired

Description

combobox No Specifies a drop-down selection box control that also enables adding text tothe list of choices.

button No Specifies a push button control.

label No Specifies a control that displays text.

Example<dialog title="Chemistry Check" command="cheminspector" width="300"height="300">

<panel width="300" height="80">

<radiobutton text="Validate structure query (SSSQUERY)"command="sssquery" update="T" width="280" height="40"/>

<radiobutton text="Validate structure for registration (RCG_SPECIFIC)"command="rcgspecific" update="T" width="280" height="40"/>

</panel>


<label text="no result yet" command="result" update="T" align="center"width="280" />

</panel>


<button text="OK" command="ok" update="T" />

<button text="Cancel" command="cancel" update="T" />

</panel>

</dialog>

See also



radiogroupA container for grouping radiobuttons. Only one button in a radiogroup can be selected at one time.

Attributes

None

Parent Element

dialog, panel

Child Elements


radiobutton Yes A radio button control

panel No Inserts a panel in a dialog box

See also



separator(palettebar.xml, toolbar.xml, menubar- files) Inserts a line in a menu or popup menu, or a spacebetween elements in a toolbar, palette or palettebar.

Attributes

AttributeRequired

Description

target No Specifies themenu to which the separator applies. Needed when adding aseparator to a popup menu. For example, <separator target="atom" /> appliesthe separator to the "Atom Properties" popup menu. Possible values: "atom","bond", and "fragment".

Parent Element

menu, palettebar, toolbar, popup

Child Elements

None

Example

See the Example for menu.

See also



shortcutSpecifies a keyboard shortcut key assignment. Defined in the AccelrysDraw-net.xml configurationfile.

Attributes



char Yes Specifies the keyboard key that initiates the action, for example, pressing char= "1" ,representing the number 1 key on the keyboard, initiates the action.

class No Specifies the fully qualified name of the class that contains themethod thatperforms the action. MDL.Draw.Modules.Editor.EditorModule is thedefault class if no class is specified.

method Yes Specifies themethod that performs the action. Only use with methods that donot have parameters or a return value.

Parent Element

shortcuts

Child Elements

None

Example

The example implements a keyboard shortcut that uses the zero (0) key to resize themolecule to fit thescreen.<shorcuts>

<shortcut char="0" class="MDL.Draw.Modules.Editor.Actions.ZoomAction"method="FitMolToScreen" />

</shorcuts>

See also



shortcutsSpecifies one or more keyboard shortcuts. Defined in the AccelrysDraw-net.xml configuration file.

Attributes

None

Parent Element

module where class="MDL.Draw.Modules.Editor.EditorModule"

Child Elements


shortcut Yes Specifies a Keyboard shortcut.

Example

Shortcut

See also



selectionSpecifies one of the items available for selection in a combobox drop down list.

Attributes



text Yes The value to display for this item.

visible No If "false", does not display. Default is "true".

Parent Element

combobox

Child Elements

None

Example

See the Example for combobox.

See also



spaceInserts a blank space of a specified size between components. Value is in pixels.

Attributes



height No Specifies vertical space to insert in pixels

width No Specifies horizontal space to insert in pixels

Parent Element

dialog, panel

Child Elements

None

Example<dialog title="Valence Check" command="valencecheck" width="175"height="200">


<panel width="175">

<label text="# atom(s) has exceeded valence." command="exceedText"update="T" align="center"

width="175" />

<label text="Every atom has correct valence." command="correctText"update="T" align="center"

width="175" />

<label text="Not available for reaction." command="rxnerror"update="T" align="center"

width="175" />

</panel>



<button text="OK" command="ok" />

</panel>

</dialog>

See also



templatedirectoryA control on the toolbar that opens the "Template Directory" dialog box. Using this dialog box, a usercan add structural fragments to their structure (for example, atoms, rings, chains, or larger structures).

Use folder to define which templates are offered in the “Template Directory" dialog box.

Personal templates that are under the directory C:\Users\<user_name>\AppData\Roaming\BIOVIA\BIOVIA Draw\Personal Templates\ (in Windows 7) willappear in the "Template Directory" window.

Attributes


AttributeRequired

Description

class Yes The fully qualified name of the class that manages template selection

AttributeRequired

Description

button Yes The button class that is used in themain toolbar

(button="MDL.Draw.Gui.TemplateSelectorButton")

customfile Yes The name of a file in which BIOVIA Drawwill save the changes if the usercustomizes the Template Directory

tooltip No Text to display in the tooltip

image No The name of the image file that contains the image to display on the toolbar forthe template group selector. See Image Specification.

Parent Element

toolbar

Child Elements

ElementRequired

Description

folder No Specifies the display name and path of a directory that contains template files(molfiles, rxnfiles, or SMILES files)

Example<toolbar file="HorizontalToolbar.xml">

...

<templatedirectory tooltip="Template Directory"

class="MDL.Draw.Modules.Editor.Tools.TemplateSelectorTool"

customfile="templateselector.xml"

image="TempDir24.gif"

button="MDL.Draw.Gui.TemplateSelectorButton">




<templatetoolbarmanagerclass="MDL.Draw.Modules.Editor.Tools.ConfigTemplateTool" tooltip="Dragmolecule onto button to change template."button="MDL.Draw.Gui.MoleculeButton" image="TempGroup24.gif"customfile="templategroupselector.xml">



<templatetoolbar name="Default" path="%MDLDRAW%Templates\TemplateSets\Default\" selected="true" />

<templatetoolbar name="ISIS Draw Templates"path="%MDLDRAW%Templates\Template Sets\ISIS Draw Templates\" />

<templatetoolbar name="Carbonyls"path="%MDLDRAW%Templates\Carbonyls\" />

<templatetoolbar name="Nitrogen"path="%MDLDRAW%Templates\Nitrogen\" />


</toolbar>

See also



templatetoolbarSpecifies a folder that contains the templates included in this template toolbar.

Attributes


AttributeRequired

Description

name Yes The display name for this template toolbar

path Yes The path to the template toolbar folder. For example:

path="%MDLDRAW%Templates\Template

Sets\Default\"

where %MDLDRAW% represents the BIOVIA Draw installation directory (notethat the constant includes the ending backslash).

selected No If "true" (or "T"), this is the active template toolbar

Parent Element


Child Elements

None

Example


See also



templatetoolbarmanagerA toolbar manager control, which can be added to themain toolbar, that allows a user to select whichtemplate toolbars will be available on themain toolbar.

Attributes


AttributeRequired

Description

class Yes The fully qualified name of the class that manages template toolbars

button Yes The button class that is used in themain toolbar

(button="MDL.Draw.Gui.MoleculeButton")

customfile Yes The name of a file in which BIOVIA Drawwill save the changes if the usercustomizes this toolbar

image No The name of the image file that contains the image to display on the toolbar forthe template group selector. See Image Specification.

tooltip No Text to display in the tooltip

Parent Element

toolbar

Child Elements


templatetoolbar Yes The name and path of a folder that contains template groups.

Example


See also



toolSpecifies a control that causes BIOVIA Draw to call a class to handle events occuring in the canvas suchas mouse drags, mousemoves, and key pressed. The tool element is defined in the palettebar.xml,donetoolbar.xml, mainpanel.xml, and donetoolbar.xml configuration files.

Attributes


AttributeRequired

Description

class Yes Specifies the fully qualified name of the class executes when the toolis activated.

name No Specifies the name of the tool.

default No Indicates if a default tool is selected when Draw starts. If set to true,the tool is selected when BIOVIA Draw starts up. Specify only onetool or multi-tool in the XML configuration file as the default. TheBIOVIA Draw default is the LassoTool.

image No Specifies the name of image that displays for the tool. For moreinformation, see Image Specification.

AttributeRequired

Description

enabled No Indicates if the Draw user can select the tool. When set to true or "T", the user can select the tool. The default value is true.

tooltip No Specifies the text to display as the tooltip.

trigger No Specifies a comma delimited list of tool events that triggers theobject, for example, trigger = "mdo, mpo, rmpo". For moreinformation, see the Trigger Table.

customfile No Specifies he name of a file Draw saves the changes if the usercustomizes the tool.

button No Specifies your own button class to be used in themain toolbarinstead of the regular toolbar button, for example,button="MDL.Draw.Gui.TemplateSelectorButton".

file No Specifies a the path and name of a file to use as source for inputs oroutputs.

initialshortlist No Specifies the list of elements to display when the end-user clicks onthe canvas. Separate each element with the pipe (|) character.

additionallistsize No Specifies the number of elements added to the element list when theDraw user clicksMore... , and adds an additional element. When thelimit is exceeded, the least-recent addition is replaced by a morerecent addition.

displayMDLIsotopes No For the IsotopeTool, if set to true, the end-user can set the isotope ’smass value to any value within the range of +12 to -18 relative to thenon-isotopic mass value. The default value is set to false limiting theDraw user’s choice to a mass value in the set of well-known,published mass values.

Parent Element

multitool, palette, palettebar, toolbar

Child Elements

ElementRequired

Description

popup No Defines a popup menu.

menuitem No Specifies a menu item and a value to pass to the class specified in the parenttool.

Note: To improve readability, insert a popup element under tool and makethemenuitems children of the popup.

dialog No Defines a dialog box that is opened when the button for the parent tool isclicked.

ElementRequired

Description

fieldname No, zeroor more

(Data Sgroup tool only) Each occurrence of field name defines a type ofattached data (Sgroup data) which the user can select in the Attached Datadialog.

operator No, zeroor more

(Data Sgroup tool only) Specifies an operator that the user can select in theAttach Data dialog when the user is creating a query molecule, for example,’>’.

Examples

The following example defines the Zoom Tool.<palette>

<tool name="ZoomTool" image="ZoomTool.gif" tooltip="Zoom Tool"class="MDL.Draw.Modules.Editor.Tools.ZoomTool" />

<tool name="PanTool" image="Pan24.gif" tooltip="Pan Tool"class="MDL.Draw.Modules.Editor.Tools.PanTool" />

</palette>



<palette>

<multitool name="ChainTool" image="ChainTool24.gif" tooltip="Chain Tool">

<tool class="MDL.Draw.Modules.Editor.Tools.ChainTool" />



</multitool>

<multitool name="MultiBondTool" image="MultiBondTool24.gif"tooltip="MultibondTool">

<tool class="MDL.Draw.Modules.Editor.Tools.MultiBondTool" />



</multitool>

</palette>

Change Atom Type tool example<multitool name="PeriodicTableTool" image="ChangeAtom24.gif" tooltip="ChangeAtomType Tool">

<tool class="MDL.Draw.Modules.Editor.Tools.AtomTool"initialshortlist="F|Cl|Br|I|" additionallistsize="2" />

See also



toolbarInserts a horizontal bar across the top of the Draw user interface or another module. The toolbarelement usually contains tools and actions. You can only define one toolbar in a module. The toolbarelement is defined in the donetoolbar.xml, mainpanel.xml, palettebar.xml, and toolbar.xmlconfiguration files.

Attributes



name No A string that contains a name for the toolbar

visible No If "false", does not display. Default is "true".

Parent Element

modulewhere class="MDL.Draw.Modules.Editor.EditorModule"

Child Elements

ElementRequired

Description

action No Adds a button to the toolbar that performs a specified actionwhen it is clicked

tool No Adds a control that, when selected, causes the BIOVIA DrawEditor to call a specified class to handle events that occur in thedrawing area

multitool No Specifies a control that can contain multiple tool controls withinit

templatedirectory No Adds a control that opens the Template Directory dialog toenable adding structural fragments to structures such asatoms, rings, chains, or larger structures.

templatetoolbarmanager No Adds a control that allows an end-user to select which group oftemplates to make available on the toolbar

separator No Inserts a space between elements in a toolbar

palette No Specifies a container for tools and multi-tools.

Example<toolbar file="HorizontalToolbar.xml">

<action image="Clear.gif"class="MDL.Draw.Modules.Editor.Actions.ClearAllAction" tooltip="Clear All" />

<action image="Undo.gif"class="MDL.Draw.Modules.Editor.Actions.UndoAction" tooltip="Undoes the lastedit" />

<action image="Redo.gif"class="MDL.Draw.Modules.Editor.Actions.RedoAction" tooltip="Returns drawingto the state before Undo" />

<separator />

<templatedirectory tooltip="Template Directory"class="MDL.Draw.Modules.Editor.Tools.TemplateSelectorTool"

button="MDL.Draw.Gui.TemplateSelectorButton"file="%MDLDRAW%Templates/Rings/ring6.mol"

selectiongroup="true" customfile="templateselector.xml">

<folder name="Predefined Templates (Read-Only)"path="%MDLDRAW%Templates\" readonly="true" />

<folder name="Predefined Template Sets (Read-Only)"path="%MDLDRAW%Templates\Template Sets\" readonly="true" />


<separator />

<templatetoolbarmanagerclass="MDL.Draw.Modules.Editor.Tools.ConfigTemplateTool" tooltip="Dragmolecule onto button to change template."

button="MDL.Draw.Gui.MoleculeButton" selectiongroup="true"image="TempGroup24.gif" customfile="templategroupselector.xml">

<templatetoolbar name="Default"path="%MDLDRAW%Templates\TemplateSets\Default\" selected="true" />

<templatetoolbar name="ISIS/Draw Templates"path="%MDLDRAW%Templates\TemplateSets\ISIS Draw Templates\" />

<templatetoolbar name="Carbonyls" path="%MDLDRAW%Templates\Carbonyls\" />

<templatetoolbar name="Nitrogen" path="%MDLDRAW%Templates\Nitrogen\" />


</toolbar>

See also



Trigger TableList of possible values for the trigger attribute.

Trigger name Description of trigger Elements

always ALWAYS tool, multitool

mpo LEFT_MOUSEPRESSED_ON_OBJECT tool, multitool, dialog, popup

rmpo RIGHT_MOUSEPRESSED_ON_OBJECT tool, multitool, dialog, popup

kpo KEYPRESSED_ON_OBJECT tool, multitool, dialog, popup

mro LEFT_MOUSERELEASED_ON_OBJECT tool, multitool, dialog, popup

rmro RIGHT_MOUSERELEASED_ON_OBJECT tool, multitool, dialog, popup

kro KEYRELEASED_ON_OBJECT tool, multitool, dialog, popup

mmo MOUSEMOVED_ON_OBJECT tool, multitool

Trigger name Description of trigger Elements

mdo MOUSEDRAGGED_ON_OBJECT tool, multitool

oen OBJECTENTERED tool, multitool

oex OBJECTEXITED tool, multitool

mp LEFT_MOUSEPRESSED_ON_CANVAS tool, multitool, dialog, popup

rmp RIGHT_MOUSEPRESSED_ON_CANVAS tool, multitool, dialog, popup

kp KEYPRESSED_ON_CANVAS tool, multitool, dialog, popup

mr LEFT_MOUSERELEASED_ON_CANVAS tool, multitool, dialog, popup

rmr RIGHT_MOUSERELEASED_ON_CANVAS tool, multitool, dialog, popup

kr KEYRELEASED_ON_CANVAS tool, multitool, dialog, popup

mm MOUSEMOVED_ON_CANVAS tool, multitool

md MOUSEDRAGGED_ON_CANVAS tool, multitool

Documents

BIOVIA Draw Configuration Guide