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Lead Discovery 5.2
User Guide
Last Modified: July 26, 2013
Powered by TIBCO Spotfire®
Lead Discovery 5.2
© Copyright 1998-2013 CambridgeSoft Corporation, a subsidiary of PerkinElmer, Inc. All rights reserved. 2 of 93
Table of Contents
1. Introduction ....................................................................................................................................................... 5
2. Loading Data .................................................................................................................................................... 6
2.1. Opening an SDFile ................................................................................................................................... 6
2.2. Importing a ChemDraw for Excel File ...................................................................................................... 6
2.3. Auto Detection of Structure Column and Content Type .......................................................................... 8
3. Exporting Data ................................................................................................................................................ 13
3.1. Exporting Data to an SDFile .................................................................................................................. 13
3.2. Details on Export to SDFile Dialog ......................................................................................................... 14
3.3. Exporting Data to a ChemDraw for Excel file ........................................................................................ 17
3.4. Details on Export to ChemDraw for Excel Dialog .................................................................................. 18
4. Working with Structures .................................................................................................................................. 22
4.1. About the Structure Viewer .................................................................................................................... 22
4.2. Using the Structure Viewer .................................................................................................................... 23
4.3. About the Structure Viewer Toolbar ....................................................................................................... 24
4.4. About the Structure Viewer List Content Pane ...................................................................................... 24
4.5. About the Structure Viewer Structure Viewer Pane ............................................................................... 26
4.6. Configuring Structure Connections ........................................................................................................ 27
5. Working with ID Lists ...................................................................................................................................... 28
5.1. About ID Lists in the Structure Viewer ................................................................................................... 28
5.2. About Manage Lists in the Structure Viewer .......................................................................................... 30
5.3. About New Lists Dialog .......................................................................................................................... 31
6. Searching Structures ...................................................................................................................................... 32
6.1. Searching for Compounds using Structure Search ............................................................................... 32
6.2. About the Structure Search Dialog ........................................................................................................ 33
6.3. Viewing Structures in Virtual Columns ................................................................................................... 35
6.4. Viewing Structures in Labels or Tooltips ................................................................................................ 35
7. Calculation of Chemical Properties ................................................................................................................ 38
8. Structural Clustering ....................................................................................................................................... 48
9. Structure Filtering ........................................................................................................................................... 50
9.1. About the Structure Filter ....................................................................................................................... 50
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9.2. Accessing the Structure Filter ................................................................................................................ 51
9.3. About the Structure Filter Toolbar .......................................................................................................... 51
9.4. Search Types ......................................................................................................................................... 52
9.5. Performing a Structure Filter .................................................................................................................. 53
9.6. Editing a Filter ........................................................................................................................................ 58
9.7. Clearing a Filter ...................................................................................................................................... 59
9.8. Viewing Historical Structure Filters ........................................................................................................ 59
9.9. Saving Structure Filters .......................................................................................................................... 60
10. R-Group Decomposition ............................................................................................................................ 62
10.1. Setting the R-Group Decomposition Threshold Preference .............................................................. 62
10.2. Performing an R-Group Decomposition Analysis .............................................................................. 67
11. Structure Alignment ................................................................................................................................... 72
12. Settings ...................................................................................................................................................... 78
12.1. Supported Renderers ......................................................................................................................... 78
12.2. Renderer Settings .............................................................................................................................. 80
13. Glossary ..................................................................................................................................................... 83
14. Chemical Property Calculations ................................................................................................................. 86
14.1. Balaban Index .................................................................................................................................... 86
14.2. Boiling Point ....................................................................................................................................... 86
14.3. Cluster Count ..................................................................................................................................... 86
14.4. Critical Pressure ................................................................................................................................. 86
14.5. Critical Temperature........................................................................................................................... 86
14.6. Critical Volume ................................................................................................................................... 87
14.7. Elemental Analysis ............................................................................................................................. 87
14.8. Exact Mass ......................................................................................................................................... 87
14.9. Formal Charge ................................................................................................................................... 87
14.10. Gibbs Free Energy ............................................................................................................................. 87
14.11. Heat of Forma tion ............................................................................................................................. 88
14.12. Henry’s Constant Law ........................................................................................................................ 88
14.13. Ideal Gas Thermal Capacity .............................................................................................................. 88
14.14. m/z...................................................................................................................................................... 89
14.15. Mass ................................................................................................................................................... 89
14.16. Melting Point ...................................................................................................................................... 89
14.17. Mol Formula ....................................................................................................................................... 89
14.18. Mol Formula HTML ............................................................................................................................ 89
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14.19. Mol Refractivity ................................................................................................................................... 90
14.20. Molecular Topological Index .............................................................................................................. 90
14.21. Mol Weight ......................................................................................................................................... 90
14.22. Number of HBond Acceptors ............................................................................................................. 90
14.23. Number of HBond Donors .................................................................................................................. 90
14.24. Number of Rotable Bonds .................................................................................................................. 91
14.25. Polar Surface Area ............................................................................................................................. 91
14.26. Principal Moment ............................................................................................................................... 91
14.27. Radius ................................................................................................................................................ 91
14.28. Shape Attribute .................................................................................................................................. 92
14.29. Shape Coefficient ............................................................................................................................... 92
14.30. Sum of Degrees ................................................................................................................................. 92
14.31. Sum of Valence Degrees ................................................................................................................... 92
14.32. Topological Diameter ......................................................................................................................... 92
14.33. Total Connectivity ............................................................................................................................... 92
14.34. Total Valence Connectivity ................................................................................................................ 92
14.35. Vapour Pressure ................................................................................................................................ 92
14.36. Water Solubility .................................................................................................................................. 93
14.37. Wiener Index ...................................................................................................................................... 93
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1. Introduction
Lead Discovery powered by TIBCO Spotfire empowers scientific professionals to freely analyze data and create
analytic applications and dashboards. It puts scientists in control, which speeds the time to insight while
reducing typical technical bottlenecks to understanding data.
Layered on top of the core TIBCO Spotfire feature set, Lead Discovery adds chemical intelligence to an
analysis. Visualize chemical structures alongside other data in the creation of SAR tables and interactive
dashboards. TIBCO Spotfire supports the use of most chemical renderers able to interpret molfile, SMILES or
CDX including the PerkinElmer ChemDraw® software.
This Guide provides a description of the chemical structure display, interpretation and search functionality available in Lead Discovery. With Lead Discovery, you can:
Render Chemical Structures (SMILES, Molfile, ChemDraw) alongside text, numbers and dates in TIBCO Spotfire tables.
Open an SDFile and view its fields in the table visualization, including the molecular structures.
Load chemical structures from a database in molfile, smiles or ChemDraw formats.
Export data to an SDFile or ChemDraw for Excel file format, preserving the structure data.
Use the Structure Viewer to view chemical structures, and to create, export, and import ID lists.
Search on structures in a database using similarity and substructure search.
Set a ChemDraw template (.cds) to be used for visualizing structures.
Filter the contents of a data table based on structure.
Access Structure Filter history – the last ten structure filters applied are saved for re-use.
Save structure filter definitions with a user defined name. This allows for manipulation on multiple structure filters at once resulting in dynamic toggling between structures in the filter.
Highlight the query molecule when using the Structure filter.
Perform an R-Group decomposition analysis on the results of a substructure filter. R-Group columns are created as real SMILES columns allowing you to use the text representation in plot axes, legends etc.
Export of R-Groups to ChemDraw for Excel
Import a ChemDraw for Excel file with specified columns including structure columns.
Calculation of Chemical Properties based on a molecular structure
Clustering by Chemical Structure – linked dendrogram, 2D scatter plot and 3D scatter plot are created.
Calculation of Similarity Score based on similarity search
Structure Alignment – chemical structures in a dataset can be aligned to a user selected structure in the existing dataset or to a scaffold drawn in the structure filter.
The following features are supported in the Web Player:
Rendering of Chemical Structures in tables and tooltips
Export data to an SDFile
Export Data to a ChemDraw for Excel file format
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Structure Alignment
Copy Structure
2. Loading Data
2.1. Opening an SDFile
You can open an SDFile to view in the table visualization.
To open an SDFile:
1. Click on Open on the toolbar, or select File > Open from the File menu.
2. Browse to the SDFile you want to open and click Open. An initial visualization using the fields of the
SDFile appears.
3. If your initial visualization is not a table, create a new Table visualization. The table containing the fields
of the SDFile, including the chemical structures appears.
As with any table visualization, you can:
Save this analysis to file or library (see the "Saving an Analysis file in the Library" topic of the Spotfire
online help).
Change the column order, column width, or row height; add, remove, sort, or mark rows (see the "How
to Use the Table" topic of the Spotfire online help).
Change the table appearance and settings using the Table Properties Dialog.
You can export the contents of table visualization to an SDFile or a ChemDraw for Excel file.
Note: When an SDFile containing structures is opened, the row height will automatically default to 10.
Tip: You can change the default initial visualization to be a table by going to the Document page, and changing
the Initial visualization when loading data to Table.
2.2. Importing a ChemDraw for Excel File
You can import a ChemDraw for Excel File (*.xlsx), containing structures, to view in the table visualization.
Only one Worksheet can be imported at a time. You can select the columns to import including multiple
structure columns.
Note: Files from ChemDraw for Excel v12 and v13 are supported as well as files exported to ChemDraw for
Excel from Lead Discovery.
To import a ChemDraw for Excel file:
1. Click on Open on the toolbar, or select File > Open from the File menu.
2. Browse to the ChemDraw for Excel File you want to open and click Open.
The ChemDraw for Excel Import dialog opens. From here, you can select the Worksheet to import as well as the
specific columns to import.
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Note: If the selected file is found to contain standard Excel Worksheets in addition to ChemDraw for Excel
Worksheets, you will be prompted if you want to continue to import the ChemDraw for Excel Worksheets. If not,
the Worksheets will be imported into Lead Discovery using Spotfire’s standard Excel Import functionality.
3. Once the Worksheet and columns to import have been selected, click OK. An initial visualization using
the selected columns to import appears.
Note: When a ChemDraw for Excel file containing structures is opened, the row height will automatically default
to 10.
The following table explains the fields displayed in the ChemDraw for Excel Import window, as shown above.
Option Description
ChemDraw for Excel
Worksheet
Lists the available Worksheets for the selected file. Only
one Worksheet can be imported at a time.
Available columns Lists the columns of the data table that are currently not
selected for exporting to the ChemDraw for Excel File.
Columns to Import Lists the columns of the Worksheet that are currently
selected for importing.
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Add > Adds the selected column to the list of columns to import.
< Remove Removes the selected column from the list of columns to
import and returns it to the list of available columns.
Remove All Removes all columns from the list of columns to include in
the import and returns them to the list of available
columns.
Move Up Moves the selected items in the Columns to import list up
one step. The order of the columns in this list determines
the order of the columns in the imported file.
Move Down Moves the selected items in the Columns to import list
down one step. The order of the columns in this list
determines the order of the columns in the imported file.
2.3. Auto Detection of Structure Column and Content Type
Structure column(s) and the content type for each structure column are automatically detected when data is
imported into Spotfire.
If the content type is mistakenly identified, you can change the content type through the Column Properties for a
data table. Additionally if a structure column was not identified as such, you can set the content type through the
Column Properties.
To identify the content type for a column:
1. Select Edit > Column Properties from the Edit menu.
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2. Select the column for which you want to specify the content type. If there is more than one table, you may
have to choose the table first.
3. Select the Properties tab. Select the Content Type property.
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4. Click on the Edit button to open the Edit Property dialog.
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.
5. Edit the value to reflect the correct content type.
Note: The content type you enter can be an arbitrary string, but it is recommended that you use the MIME types
defined for molfiles, CHIME, SMILES and CDX strings as shown in the table below.
Structure Format Content Type
MDL molfile chemical/x-mdl-molfile
MDL Chime string chemical/x-mdl-chime
Daylight SMILEs string
chemical/x-daylight-smiles
ChemDraw Chemical Structure Exchange
chemical/x-cdx
6. Click ‘OK’ to return to the Column Properties dialog. The value field is updated with the content type.
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7. Click ‘OK’.
Note: Chemical structures loaded into Spotfire in ChemDraw’s native file format (CDX, CDMXL) are supported
for chemical rendering, chemical searching and exporting. This content in data tables will be displayed natively
in renderers that support the format (ChemDraw) or converted to MOLfiles or SMILES for renderers that do not
offer support. Query molecules will be extracted from renderers that support the format (ChemDraw) and sent
unchanged to cartridges that support the format or converted to MOLfiles or SMILES for cartridges that do not.
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3. Exporting Data
You can export data from Lead Discovery to an SDFile or to a ChemDraw for Excel file.
Note: It is possible to include data in a table visualization (or labels and tooltips of some other visualizations)
that is not part of the original data table. A virtual column connects to a remote data source and collects data
from there.
The virtual column is only part of the table visualization and not part of the data table. Exporting of the data table
does not include the virtual columns. To export the data contained in the virtual columns, you must export the
visualization data for all items.
3.1. Exporting Data to an SDFile
To export data from visualization table to an SDFile:
1. Right-click on the table and select Export to SDFile.
2. Select whether to export Visualization data for all items or Data table.
Visualization data for all items – Exports all items from current visualization table.
Data table – Exports the data table from current visualization table.
3. If Data table is selected, specify whether to export all rows, marked rows, or filtered rows only:
All rows - Exports every row in the data table regardless of filtering.
Marked rows - Exports the marked rows of the table only.
Filtered rows - Exports the rows remaining after filtering only.
4. Select the Structure column from the drop-down list. If Visualization data for all items is selected, all
virtual structure columns will be available for selection here.
Comment: The SDFile format supports only one structure per record. You can select any column in the
table that contains Molfile or SMILES structures. The first column containing structures displays as the
default choice.
5. If Data table is selected, use Add >, < Remove, and Remove All to select the columns to export with
the structure. Use Move Up and Move Down to specify the order of columns in the SDFile.
6. Click OK.
7. In the Save As dialog, specify a filename, browse to the location where you want to save the file.
8. Click Save.
Tip: You can export data to an SDFile by selecting File > Export > Data from the main menu and choosing
Save as type: SDFile (*.sd;*.sdf). However, you will not be able to change the columns to include in the export if
you use this method.
To export data from the Structure Viewer to an SDFile:
1. Select the IDs you want to export in the List Content pane of the Structure Viewer panel or popover.
2. Right-click on any of the selected IDs and select Export Selection to SDFile.
3. Select the Structure column from the drop-down list.
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Comment: The SDFile format supports only one structure per record. You can select any column in the table
that contains Molfile or SMILES structures. The first column containing structures is displayed as the default
choice.
4. Use Add >, < Remove, and Remove All to select the columns to be exported with the structure.
5. Use Move Up and Move Down to specify the order of columns in the SDFile.
6. Click OK.
7. In the Save As dialog, specify a filename, browse to the location where you want to save the file.
8. Click Save.
3.2. Details on Export to SDFile Dialog
To navigate to the Export to SDFile dialog:
1. Right-click on the table and select Export to SDFile.
Comment: If the table does not contain any structures, the Export to SDFile menu item will be
unavailable.
OR
2. Select the IDs you want to export in the List Content pane of the Structure Viewer panel or popover.
3. Right-click on any of the selected IDs and select Export Selection to SDFile.
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The following table explains the fields displayed in the Export to SDFile window, as shown above.
Option Description
Export data from: Note: If you exported data from the Structure Viewer,
these options will not be available since you have already
selected which rows to export.
Visualization data for all
items
Exports all data from the current visualization.
Data Table
All rows
Marked rows
Filtered rows
Exports data from current data table.
Exports all rows in the selected data table.
Exports data for the marked rows only.
Exports data for the filtered rows only.
Structure column Specify the column in the data table that contains
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molecular structures.
Displays the available structure columns. Select the one
you wish to export. If no structure column is available in
the actual data set (for example, if structures are shown in
a virtual column) you will not be able to export the
structures using this tool.
Note: If Visualization data for all items is selected, all
virtual structure columns will be available for selection
here.
The following options are only available if Export data from ‘Data Table’ is selected.
Available columns Lists the columns of the data table that are currently not
selected for exporting to the SDFile.
Columns to include in
SDFile
Lists the columns of the table that are currently selected
for exporting to the SDFile.
Add > Adds the selected column to the list of columns to include
in the SDFile.
< Remove Removes the selected column from the list of columns to
include in the SDFile and returns it to the list of available
columns.
Remove All Removes all columns from the list of columns to include in
the SDFile and returns them to the list of available
columns.
Move Up Moves the selected items in the Columns to include in
SDFile list up one step. The order of the columns in this
list determines the order of the columns in the resulting
SDFile.
Move Down Moves the selected items in the Columns to include in
SDFile list down one step. The order of the columns in
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this list determines the order of the columns in the
resulting SDFile.
3.3. Exporting Data to a ChemDraw for Excel file
Note: The Export to ChemDraw for Excel menu item is available on all clients, regardless of the presence of
ChemDraw for Excel. Lead Discovery does not need ChemDraw for Excel present in order to produce an Excel
file that is compatible with ChemDraw for Excel. The user will need the ChemDraw/Excel Add-In to open the file,
but not to export it.
The file produced by Lead Discovery is saved in Excel’s *.xlsx format.
The file that can be opened by Excel, regardless of whether it is equipped with the ChemDrawExcel Add-In.
However, the chemical structures will only be converted into pictures when the ChemDrawExcel Add-In is
present.
After successfully opening in Excel, the file, if re-saved, will contain the chemical structure pictures. It will display
structure systems in Excel (without ChemDrawExcel Add-In); however, the structures will not be searchable or
editable in Excel.
Note: Chemical structures loaded into Spotfire in ChemDraw’s native file format (CDX) can also be exported to
ChemDraw for Excel.
Note: The File > Export > Data feature in Spotfire is not the same as the Export to ChemDraw for Excel feature.
Any results exported into Excel using the native Spotfire export feature may vary depending on how the
structure data was imported into Spotfire. It is recommended that you use the Export to ChemDraw for Excel
option.
To export data from visualization table to ChemDraw for Excel file:
1. Right-click on the table and select Export to ChemDraw for Excel.
2. Select whether to export Visualization data for all items or Data table.
Visualization data for all items – Exports all items from current visualization table.
Include virtual structure columns – if enabled, includes virtual structure columns for export.
Data table – Exports the data table from current visualization table.
3. If Data table is selected, specify whether to export all rows, marked rows, or filtered rows only:
All rows - Exports every row in the data table regardless of filtering.
Marked rows - Exports the marked rows of the table only.
Filtered rows - Exports the rows remaining after filtering only.
4. Select the Structure column from the drop-down list. If Visualization data for all items is selected,
and Include virtual structure columns is enabled, all virtual structure columns will be available for
selection here.
Comment: The Export to ChemDraw for Excel feature supports the export of one structure column per
record. You can select any column in the table that contains Molfile, SMILES, and CDX structures. The
first column containing structures displays as the default choice.
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5. If Data table is selected, use Add >, < Remove, and Remove All to select the columns to export with
the structure. Use Move Up and Move Down to specify the order of columns in the ChemDraw for Excel
file.
6. Click OK.
7. In the Save As dialog, specify a filename, browse to the location where you want to save the file.
8. Click Save.
Tip: You can export data to a ChemDraw Excel File by selecting File > Export > Data from the main menu and
choosing Save as type: ChemDraw for Excel File (*.xlsx). However, you will not be able to change the columns
to include in the export if you use this method.
To export data from the Structure Viewer to a ChemDraw for Excel File:
1. Select the IDs you want to export in the List Content pane of the Structure Viewer panel or popover.
2. Right-click on any of the selected IDs and select Export Selection to ChemDraw for Excel.
3. Select the Structure column from the drop-down list.
Comment: The ChemDraw Excel File format supports only one structure per record. You can select any
column in the table that contains Molfile, SMILES, and CDX structures. The first column containing
structures displays as the default choice.
4. Use Add >, < Remove, and Remove All to select the columns to be exported with the structure.
5. Use Move Up and Move Down to specify the order of columns in the ChemDraw Excel File.
6. Click OK.
7. In the Save As dialog, specify a filename, browse to the location where you want to save the file.
8. Click Save.
3.4. Details on Export to ChemDraw for Excel Dialog
To navigate to the Export to ChemDraw for Excel dialog:
1. Right-click on the table and select Export to ChemDraw for Excel.
Comment: If the table does not contain any structures, the Export to ChemDraw for Excel menu item
will be unavailable.
OR
2. Select the IDs you want to export in the List Content pane of the Structure Viewer panel or popover.
3. Right-click on any of the selected IDs and select Export Selection to ChemDraw for Excel.
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The following table explains the fields displayed in the Export to ChemDraw Excel File window, as shown
above.
Option Description
Export data from: Note: If you exported data from the Structure Viewer,
these options will not be available since you have already
selected which rows to export.
Visualization data for all
items
Include virtual
structure columns
Exports all data from the current visualization
Exports all virtual columns containing molecular
structures when this checkbox is enabled.
Data table
All rows
Marked rows
Filtered rows
Exports data from current data table.
Exports all rows in the selected data table.
Exports data for the marked rows only.
Exports data for the filtered rows only.
Structure column Specify the column in the data table that contains
molecular structures.
Displays the available structure columns. Select the one
you wish to export. If no structure column is available in
the actual data set (for example, if structures are shown in
a virtual column) you will not be able to export the
structures using this tool.
The following options are only available if Export Data from ‘Data table’ is selected.
Available columns Lists the columns of the data table that are currently not
selected for exporting to ChemDraw for Excel.
Columns to include in Lists the columns of the table that are currently selected
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ChemDraw for Excel for exporting to ChemDraw for Excel.
Add > Adds the selected column to the list of columns to include
in the ChemDraw Excel File.
< Remove Removes the selected column from the list of columns to
include in the ChemDraw Excel File and returns it to the
list of available columns.
Remove All Removes all columns from the list of columns to include in
the ChemDraw Excel File and returns them to the list of
available columns.
Move Up Moves the selected items in the Columns to include in
ChemDraw Excel File list up one step. The order of the
columns in this list determines the order of the columns in
the resulting ChemDraw Excel File.
Move Down Moves the selected items in the Columns to include in
ChemDraw Excel File list down one step. The order of the
columns in this list determines the order of the columns in
the resulting ChemDraw Excel File.
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4. Working with Structures
4.1. About the Structure Viewer
The Structure Viewer is used to:
View the structures marked in the visualization or to display structure search results.
View, create, import, and export ID lists.
The key elements of the Structure Viewer are:
Toolbar and lists drop-down
List Content pane
Structure Viewer pane
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The following table describes the fields in the Structure Viewer window, as shown above.
Option Description
Toolbar Contains the buttons that allow you to export, import, rename
and delete ID lists, and to edit list settings.
Lists You can select an existing list in the Lists drop-down. The
Structure Viewer maintains a dynamic list called Marked Rows
that contains the marked rows in the active visualization.
The number of items in each list is displayed within parentheses
after the name of the list.
List Content
pane
Displays the list of identifiers for the list selected in the Lists drop-
down. The values in this pane are taken from the ID column you
selected when opening the Structure Viewer.
Structure Viewer
pane
Displays the chemical structures for the list selected in the Lists
drop-down. The structures in this pane are taken from the
structure column you selected when opening the Structure
Viewer, or from the results of a structure query.
4.2. Using the Structure Viewer
To navigate to the Structure Viewer:
1. Open data in Lead Discovery.
2. Click the Structure Viewer button in the toolbar.
Comment: You can also select View > Structure Viewer from the menu. The Configure Structure Connection
dialog displays.
3. Select the columns in the visualization containing molecular structures and identifiers.
4. Click OK. The Structure Viewer displays.
Mark or highlight compounds in a visualization. When there are no marked rows, the structure from the currently
highlighted row in the data table is displayed in the Structure Viewer pane of the Structure Viewer, and its
identifier is displayed in the List Content pane. When there are marked rows, the structures from the marked
rows are displayed in the Structure Viewer pane and their identifiers are displayed in the List Content pane.
When you highlight a marked row, its corresponding identifier and structure will be highlighted in the Viewer and
List Content panes.
Note: The Structure Viewer automatically becomes active when you perform a structure search.
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4.3. About the Structure Viewer Toolbar
The image below shows the toolbar for the Structure Viewer.
The following table explains the icons found on the Structure Viewer toolbar, as shown in the image above.
Button / Control Description
Imports an ID list file to Structure Viewer.
Exports the ID list currently selected in the Lists drop-down to an LST file.
Displays the structures with the IDs from the active ID list in separate data table visualizations.
Creates a new data table containing the structures and IDs from the current list. If additional data is available, it is included in the new table. Additional data may be drawn from the linked rows in the active data table or from an information link, depending on the source of the list.
Opens the Structure Connection dialog where you can re-configure the mapping of ID and structure columns between data tables and Structure Viewer.
Opens the Manage Lists dialog where you can change the name and description for previously created lists, as well as delete lists.
Displays the name of the selected list followed by the number of items in the list within parentheses. The elements of the selected list are displayed in the List Content and Viewer panes. Use this drop-down to select a different list.
4.4. About the Structure Viewer List Content Pane
In the List Content pane of the Structure Viewer, you can view the identifiers of the molecular structures from the
ID list currently selected in the Lists drop-down. This can represent:
The marked rows in the active data table.
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A previously-created or imported ID list.
The results of a structure search.
The List Content pane displays the identifiers of the rows in the list. The identifiers are taken from the column
you selected as the ID column when the Structure Viewer was first opened. If the result of a structure query is
shown, the metadata supplied by the information link are used.
The right-click pop-up menu of the List Content pane contains a number of options. These options are explained
in the table below.
Right-click Menu Option
Description
Mark Selection in Active Visualization
Marks the rows with the selected IDs in the active visualization.
Create New List from Selection
Creates a new ID list from the IDs selected in the List Content pane.
Export Selection to SDFile
Export Selection to ChemDraw for Excel
Opens the Export to SDFile dialog where you can export the selected IDs to an SDFile.
Opens the Export to ChemDraw for Excel dialog where you can export the selected IDs to a ChemDraw for Excel file.
Copy IDs Copies the selected IDs to the clipboard.
Select All Selects all IDs in the List Content pane.
Invert Selection Inverts the selection in the List Content pane.
Remove IDs from List Removes the selected IDs from the list in the List Content pane.
Manage Lists Opens the Manage Lists dialog where you can change the names and descriptions of all previously added lists. You can also remove unwanted lists from Structure Viewer.
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4.5. About the Structure Viewer Structure Viewer Pane
In the Structure Viewer pane, you can see the structures of either the marked rows of the data table, or of the
currently active ID list. This pane also displays the structures of the search results after you run a Structure
Search.
The right-click context menu of the Structure Viewer pane contains a number of options. These options are
explained in the table below:
Right-click Menu Option
Description
Structure Search Displays the Structure Search dialog.
Copy Copies information from the Structure Viewer to the Windows clipboard:
Structure - Copies the selected structure as a structure which can be edited in the structure renderer.
Image - Copies the selected structure as an image.
Image with All Visible Structures - Copies the visible contents of the Structure Viewer pane as an image.
Renderer
Use this option to select the default renderer used in the Structure Viewer pane (see Supported Renderers for more information). You can also change the renderer settings in the Renderer Settings dialog.
Print All - When selected, specifies that all structures from the current list will be printed.
Visible Structures - When selected, specifies that only those structures from the current list that are visible in the Structure Viewer pane will be printed.
Print - Prints the structures according to the print settings
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4.6. Configuring Structure Connections
In the Configure Structure Connection dialog, you specify the columns of the table which will be treated by the
Structure Viewer as the columns containing structures and IDs. The structure connection can be different for
different lists.
To navigate to the structure connection dialog:
1. Click on the Structure Viewer button on the toolbar. The Configure Structure Connection dialog
displays.
Comment: You can also select View > Structure Viewer from the menu.
2. In Structure Viewer, you can also click on the Configure Structure Connection button, to open the
dialog again.
The following table explains the fields found in the Configure Structure Connection dialog, as shown above.
Option Description
ID column Select the column from the data table which you want to use as the identifier of the structure. The values from this column will be displayed in the List Contents pane of the Structure Viewer panel. Also, the Structure Viewer will use the IDs from this column for creating, exporting, and importing the ID lists.
(All or Visible Structures).
Print Preview - Displays the Print Preview window.
Show IDs Shows or hides the molecule IDs for the structures displayed in the Structure Viewer pane.
Layout Specifies the number of columns to be shown in the Structure Viewer pane.
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Structure
Column
Select a column that contains structures from those available in the active table visualization. The contents of this column will be rendered in the Structure Viewer pane.
Displays the content type for the structure column. This field is read-only.
Link Select an information link that contains structures from those available in the drop-down list. The structures from this link display in the Structure Viewer pane. The information links that are available here are configured using Information Designer. See the TIBCO Spotfire Lead Discovery - Installation Manual for more information.
5. Working with ID Lists
5.1. About ID Lists in the Structure Viewer
The ID lists in the Structure Viewer let you keep track of groups of compounds. Each time you conduct a
structure search, the result is added as a new list in the List Content pane of the Structure Viewer. All the lists
that you create are stored locally and appear in the Lists drop-down of the Structure Viewer.
The Structure Viewer also maintains a dynamic list called "Marked Rows", which contains the current set of
marked rows. To save the results of a structure query or the set of marked rows more permanently, create a new
list and convert the list to a data table, or export a list file or an SDFile.
To display the Structure Viewer:
1. Select Tools > Structure Viewer, or, click on the Structure Viewer button on the toolbar.
Comment: Another way to launch the Structure Viewer is to perform a structure search by right-clicking on a
table column containing structures and selecting Structure Search. The Structure Viewer appears and the
search results are displayed in the List Content and Structure Viewer panes.
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The following table explains the actions you can perform from the Structure Viewer.
Action Instruction
Create a list Do either one of:
Perform a search using the Structure Search tool.
Select the IDs in the current list, right-click and select Create New List from Selection
Change list settings Click the Manage Lists button, , on the Structure Viewer toolbar. You can also right-click and select Manage Lists from the pop-up menu. In the Manage Lists dialog, you can change the list name and description. In the Structure Connection dialog, reached
from the Configure Structure Connection button, you can re-map the ID and structure columns, if necessary.
Rename a list Click the Manage Lists button , on the Structure Viewer toolbar. You can also right-click and select Manage Lists from the pop-up menu. In the Manage Lists dialog, click to select the list you want to rename, then click Rename.
Export the list as an LST file
Select the list in the Lists drop-down and click the Export
button, , on the Structure Viewer toolbar.
Import a list Click the Import button, , on the Structure Viewer toolbar and select the list file to import in the Open File dialog.
Export selected IDs to an SDFile
Export selected IDs to a ChemDraw for Excel file
Right-click on any of the selected IDs and select Export Selection to SDFile from the pop-up menu to open the Export to SDFile dialog.
Right-click on any of the selected IDs and select Export Selection to ChemDraw for Excel from the pop-up menu to open the Export to ChemDraw for Excel dialog.
Display structure for a compound ID
Click on one or more identifiers in the List Content pane. The Structure Viewer pane will display the structures corresponding to the selected identifiers.
Create a new data table with the compounds from the current list
Select the list in the Lists drop-down and click the Create
Table button, , on the Structure Viewer toolbar. A new data table will be created with the ID, structure, and any related data for the compounds in the list.
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Mark compounds from the list
In the list, select the desired identifiers. Right-click and select Mark Selection in Active Visualization.
Copy a list In the list, select the desired identifiers. Right-click and select Copy IDs.
Select all identifiers in a list
Right-click in the List Content pane and select Select All.
Invert the selection in the list
In the list, select the desired identifiers. Right-click and select Invert Selection.
Remove identifiers from the list
In the list, select the desired identifiers. Right-click and select Remove IDs from List.
5.2. About Manage Lists in the Structure Viewer
In the Manage Lists dialog, you can specify the list name and description of all available lists. See an image of
the Manage Lists dialog below.
To open to the Manage Lists dialog:
1. Click the Manage Lists button, , on the Structure Viewer toolbar or right-click in the List Content
pane and select Manage Lists.
The following table explains the fields found in the Manage Lists dialog.
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Option Description
ID Lists Lists all currently available ID Lists in Structure Viewer.
Rename Click on a list in the ID Lists pane and then click Rename to change the name of the selected list.
Delete Click on a list in the ID Lists pane and then click Delete to remove the selected list from the Structure Viewer.
Description Optional. Type a description of the contents of the selected list.
5.3. About New Lists Dialog
New lists are automatically created when you perform a structure search.
To create a new list from a selection in another list:
1. Ensure that the IDs are selected in the List Contents pane of the Structure Viewer. See Working with ID
Lists for more information.
2. Right-click in the List Contents pane and select Create New List from Selection. The New List dialog
displays.
The following table describes the fields found in the New List dialog, as shown in the image above.
Option Description
Name Type a suitable name for the new list.
Description Optional. Type a description of the contents of the list.
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6. Searching Structures
6.1. Searching for Compounds using Structure Search
The Structure Search tool allows you to perform substructure and similarity searches. See Details on Structure
Search for more information regarding the individual search methods. The search returns a list of identifiers that
is displayed in the Structure Viewer.
To search for compounds in a structure database:
1. In the Structure Viewer or in a table visualization with structures, click to activate the compound on
which you want to base the search. The Structure Search dialog displays.
2. Right-click on the structure and select Structure Search from the pop-up menu.
Comment: You can also select Tools > Structure Search from the main menu.
3. Select one of the alternatives under Search for.
Comment: You can search for Substructure or Similarity.
4. If the Parameters button becomes available, click on it to edit the parameters available for the selected
search method.
Comment: If you select Similarity search, you must enter a range of similarity values in the Similarity Search
Parameters dialog. Similarity values range from 0 (least similar) to 100 (most similar).
5. If you want to import a structure from a file, click Import Structure. The Open File dialog appears.
Select the file you want to import and click Open. The structure from the file will be displayed in the
Structure Search dialog.
6. If required, click Edit. If more than one structure editor is available, you can choose which editor to use
from a drop-down list. Your selected structure editor is launched. Edit the structure and click the button
that returns the structure to Spotfire (in ChemDraw: OK, in Symyx® Draw (MDL): Transfer). Please refer
to the documentation of your current structure editor for more details.
7. Select an information link in the Search in drop-down.
Comment: See Configuring Information Links in the Lead Discovery Installation Guide for more information
about how to configure information links.
8. If required, limit the search to the current list of identifiers.
Comment: This option is only available when performing the search from the Structure Viewer and when any list
except for the Marked Rows list is selected in the Lists drop-down of the Structure Viewer. When you start a
structure search from table visualization without activating the Structure Viewer, or, if the Marked Rows list is
selected, the Data Source option will be the only one available.
9. Specify the name for the resulting list.
10. Click OK. Structures in the database that match the search criteria are displayed in the Structure
Viewer (Viewer pane). A new ID list is added and displayed in the List Content pane. To show the
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search results as a separate data table, select the search results list in the Lists drop-down and click the
button on the Structure Viewer toolbar.
Note: Using Information Links, configured through the Information Designer, structures can be returned with the
query molecule highlighted when performing a chemical substructure search as shown in the following example.
This capability is only available with the CSCartridge. Refer to the Lead Discovery Installation Guide for
instructions on how to configure these information links.
6.2. About the Structure Search Dialog
To open the Structure Search dialog:
1. Select Tools > Structure Search, or right-click on a structure in a table, or the Structure Viewer and
select Structure Search from the pop-up menu. The Structure Search dialog appears.
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Note: Structures searches can also be performed in Lead Discovery without opening a file first (Tools >
Structure Search). The following table explains the fields found in the Structure Search dialog, as shown in the
image above.
Option Description
Search for Substructure
Performs a search for structures containing the specified substructure.
Similarity Performs a search for structures similar to the specified master structure. Open the Similarity Search Parameters dialog and specify a range of values between 0 (least similar) and 100 (most similar).
Parameters Launches the Parameters dialog where you can provide search parameters for similarity search.
Import Structure Launches the Open dialog where you can select a structure file to use in the search.
Edit... Launches your current structure editor where you can edit the structure before performing the search. The same thing is achieved by double-clicking the structure. If more than one structure editor is available, you can choose which editor to use from a drop-down list.
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6.3. Viewing Structures in Virtual Columns
In the table visualization, you can view structures from remote data sources using virtual columns. You can
connect to a virtual column and collect structure data from the remote data source both when showing structures
in table visualization and when structures are shown in the Structure Viewer.
To add a virtual column:
1. Right-click on a table visualization and select Properties.
2. Select Virtual Columns and click Add > Structure Column.
3. In the Structure Column Settings dialog, select the key column, for example, the column that contains
the IDs of the structures in your visualization.
4. Click Browse. The Open from Library dialog displays.
5. Select the information link that contains the data you want to retrieve in your virtual columns and click
Open.
Note: Ensure the columns containing the key column data (in our example - structure IDs) and the data you
would like to view in the virtual column (for example, molecular structures) are included in the information link.
6. Click OK. The virtual Structure column is displayed in the active table visualization.
6.4. Viewing Structures in Labels or Tooltips
You can display structures and other images in the labels or tooltips of visualizations.
To show structures from the loaded data in labels:
1. Open the Properties dialog for the visualization.
After editing the structure and sending it back, the Structure Search dialog is updated with the edited structure.
Search in Specifies the information link (predefined query) to the data source in which the search will be performed.
See chapter 2.4 of the TIBCO Spotfire Lead Discovery - Installation Manual for more information about Configuring Information Links. See Information Links topics in the TIBCO Spotfire online help for general information about information links.
Limit search to Allows you to limit the search to a set of identifiers from the list currently selected in the Lists drop-down. This option is only available when any (not empty) list except for the Marked Rows list is selected.
Name of resulting list
Allows you to give the resulting structure search list a name of your choice.
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Comment: This is done by right-clicking on the visualization and selecting Properties from the pop-up
menu.
2. Click on the Labels page in the list on the left. The Labels page displays.
Note: Not all visualizations support labels.
3. Select the structure column under Label By.
Comment: This is possible if the loaded data contains the structure information directly (e.g., if the
loaded data is an SDFile). For example, select "Structure <MOLFILE>". If you want to retrieve the
structures from an information link instead, see below.
4. Specify whether to Show labels for: All or Marked rows.
5. Ensure that Get content from is set to (Selected column).
6. Ensure that Show as is set to your current structure renderer. For example, Symyx® Draw (MDL).
7. If desired, change the Size of the structures using the slider.
8. Click Close.
To show structures from an information link in labels:
1. Open the Properties dialog for the visualization.
Comment: This is done by right-clicking on the visualization and selecting Properties from the pop-up
menu.
2. Click on the Labels page in the list on the left. The Labels page displays.
Note: Not all visualizations support labels.
3. Select an identifier column under Label By.
Comment: Here you select the identifier column in your data table that will be used to match the
identifier in the information link from which structures are to be retrieved.
4. Specify whether to Show labels for: All or Marked rows.
5. Select Get content from: Structure Column.
Comment: This specifies that rather than displaying the information from the selected Label by column
directly, the selected column will be used as an identifier when retrieving data from an information link.
6. Click on the Settings button next to Get content from. The Structure Column Settings dialog displays.
7. Ensure that the correct Key column is selected, and click Browse. The Open from Library dialog
displays.
8. Click to select the information link containing your structures and click Open.
Note: Ensure columns containing the key column data (in our example - structure IDs) and the data you
would like to view in the virtual column (for example, molecular structures) are included in the
information link.
9. Click OK.
10. Ensure that Show as is set to your current structure renderer. For example, Symyx® Draw (MDL).
11. Click Close.
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To show structures from the loaded data in tooltips:
Most visualizations can display images from a binary image column, a shape file, or chemical structures in
tooltips.
1. Open the Properties dialog for the visualization.
Comment: This is done by right-clicking on the visualization and selecting Properties from the pop-up
menu.
2. Click on the Tooltip page in the list on the left. The Tooltip page displays.
3. Click on Add. The Add Tooltip Value dialog displays.
4. Select the structure Column of interest.
5. Type a Name to display.
Comment: This is the text shown together with the expression value in the tooltip, and also will be
shown in the list of available tooltip values.
6. Ensure that Get content from is set to (Selected column).
Comment: Make sure that Show as is set to your current structure renderer.
7. If desired, change the Size of the tooltip image by moving the slider,
8. Clear the Include value name in tooltip check box if you only want to display the image in the tooltip
and not the name.
9. Click OK. The Add Tooltip Value dialog closes and the newly added value is shown in the Tooltip
property page.
10. Click Close.
To show structures from an information link in tooltips:
1. Open the Properties dialog for the visualization.
Comment: This is done by right-clicking on the visualization and selecting Properties from the pop-up
menu.
2. Click on the Tooltip page in the list on the left. The Tooltip page displays.
3. Click Add. The Add Tooltip Value dialog displays.
4. Select an identifier Column.
Comment: Here you select the identifier column in your data table used to match the identifier in the
information link from which structures are to be retrieved.
5. Type a Name to display.
Comment: This is the text that will be shown together with the expression value in the tooltip, and also
will be shown in the list of available tooltip values.
6. Select Get content from: Structure Column.
Comment: This specifies that rather than displaying the information from the selected Label by column
directly, the selected column will be used as an identifier when retrieving data from an information link.
7. Click on the Settings button next to Get content from. The Structure Column Settings dialog displays.
8. Ensure the correct Key column is selected, click Browse. The Open from Library dialog displays.
9. Click to select the information link containing your structures and click Open.
Note: Ensure sure that columns containing the key column data (in our example - structure IDs) and the
data you would like to view in the virtual column (for example, molecular structures) are included in the
information link.
10. Click OK.
11. Ensure that Show as is set to your current structure renderer.
12. If desired, change the Size of the tooltip image by moving the slider,
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13. Clear the Include value name in tooltip check box if you only want to display the image in the tooltip
and not the name.
14. Click OK. The Add Tooltip Value dialog closes and the newly added value is shown in the Tooltip
property page.
15. Click Close.
7. Calculation of Chemical Properties
Lead Discovery allows you to determine different chemical, topological, physical, and thermodynamic properties
based on a chemical structure. Once calculations are complete, they can be used in other visualizations.
You can insert chemical properties, based on a selected structure column, into the data table as new columns.
This provides a quick interface for you to generate multiple chemical property columns simultaneously.
In this case, the calculations are performed via custom Data Function(s). The column type of the new chemical
property column inserted is Result type.
You can also insert chemical properties using Calculated Columns in Spotfire. In this case, the column type of
the new chemical property column is Calculated type.
Only calculated columns support expression editing. The chemical property expression can be combined with
other expressions allowing for customization of expressions. Chemical Properties are available anywhere
expressions are available within Spotfire.
Note: Overall, higher performance is seen when using Data Functions for the calculation of chemical properties.
Calculating chemical properties for a structure column:
1. Right click on a structure column in the table visualization and select Insert Chemical Properties.
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Note: If the selected column is not a valid structure column, the Insert Chemical Properties option is not
displayed in the right click context menu.
The Insert Chemical Properties window opens.
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2. From the Structure column list, select the Structure column on which to perform the chemical property
calculations. The first structure column, detected by Lead Discovery, is listed by default.
3. Select the chemical properties to calculate.
Note: You can search for a Chemical property by entering a chemical property in the search field. The text
box supports ‘smart search’ and an abbreviated list of Chemical property matches is displayed for selection
as you are typing. Clearing the search field will re-populate the list with all Chemical properties.
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4. Click ‘OK’.
New columns are generated in the table for each calculated chemical property. If there is a row that does
not contain a structure, a calculation is not shown for that row.
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In addition to the column name containing the name of the chemical property, it also displays the structure
column and the units for the calculated property.
5. Via Edit > Column Properties, you can re-name the column.
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Additional complex computations, using Spotfire functionality, can be performed on the newly added
columns.
Inserting a Chemical Property using Calculated Columns
1. From the main menu, select Insert > Calculated Column.
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2. From the Functions drop down list, select Chemical Properties.
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3. Select a Chemical Property from the list, or type a chemical property name in the Search field.
4. Double click on the Chemical Property, or use the Insert Function button to insert the selected function
(chemical property) at the current cursor position in the Expression field.
5. Select a structure column from the Available Columns list, and click on the Insert Column button.
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6. Specify a Column Name.
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7. Click on the OK button.
A new column is generated based on the calculated chemical property.
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Note: Refer to the Chemical Properties Calculation section for a description of each calculation.
8. Structural Clustering
Hierarchical clustering can be performed through a one-click operation on a structure or numerical column. It is
available as a tool on the right-click menu on the table visualization. Clustering can be performed on tables with
a maximum of 1000 rows. Clustering results dynamically reflect the filtered rows of the source table.
The Hierarchical Structure clustering is based on the Tanimoto similarity between the chemical fingerprint of the
structures in the selected column.
Upon performing clustering, a new page (“Cluster by <column name>”) is generated containing 4 visualizations
to display the results:
A table visualization: containing the source data table upon which the clustering was performed.
A dendrogram: displaying the clustering results in a tree-structured graph.
2D and 3D Scatter Plots: providing a visual representation of the clusters (indicating cluster size and
similarity distance between clusters) present at the pruning line currently selected in the dendrogram.
Note: To support the construction of the dendrogram, a column (“ClusteringMatch”) is added to the source data
table and a new data table (“Clustering”) is added to the analysis.
On each visualization, the appearance can be customized through the standard Spotfire visualization properties.
However, it is not recommended to change the axes in the cluster plots, as doing so will invalidate the data
displayed in the visualization.
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To perform a clustering analysis:
1. Right click on a structure or numeric column in the table visualization and select Cluster By.
Note: If the table has more than 1000 rows, you will be notified that the selected column has more than 1000
rows and that this exceeds the maximum row limit for clustering.
A new page (“Cluster by <column name>”) is generated containing 4 visualizations to display the results:
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The scatter plots depend on the position of the dotted red cutoff line across the dendrogram (pruning line). Every
node directly below the line is represented as a single ball in the scatter plot, with its size scaled to the number
of leaves it contains. By moving the cut off line up and down, you vary between a coarse-grained view with few
clusters, to a more detailed view with many.
The clustering analysis can be removed by deleting the page containing the clustering results.
9. Structure Filtering
9.1. About the Structure Filter
The Structure Filter is used to:
Draw a chemical structure on which to filter the contents of a data table.
Filter the contents based on full structure, substructure or similarity.
Perform an R-Group decomposition analysis on the results of a substructure filter.
Chemical structures loaded into Spotfire in ChemDraw’s native file format (CDX) are supported in the Structure
Filter provided ChemDraw is being used as the renderer and/or editor. The content is converted to MOLfiles or
SMILES for renderers/editors that do not offer support.
Note: The Structure Filter does not support all advanced query features, including variable attachment points
when drawn in the ChemDraw editor.
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9.2. Accessing the Structure Filter
To navigate to the Structure Filter:
1. Open data in Lead Discovery.
2. Click the Structure Filter button in the main toolbar.
3. The Structure Filter opens. By default, the Structure Filter opens above the Filters panel.
Note: You can also select View > Structure Filter from the main menu to open the Structure Filter.
9.3. About the Structure Filter Toolbar
The image below shows the toolbar for the Structure Filter.
The following table explains the icons found on the Structure Filter toolbar, as shown in the image above.
Button / Control Description
Opens the Structure Editor to edit the current structure filter.
Clears the current filter.
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Opens the Settings dialog for the selected renderer. Refer to Settings section.
Opens the Historical Search drop down list.
Insert/Remove R-Group Columns
9.4. Search Types
The Structure Filter supports three structure search types:
Full Structure
Substructure
Similarity
A Full structure search finds a particular structure.
A Substructure search finds structures containing a common structural component, plus any additional
attachments at the open positions. An R-Group decomposition analysis can be performed on a data table
following a substructure filter. Refer to the following section on R-Group Decomposition. Similarity searches are
useful if you have a general idea of the types of compounds you are looking for, but do not have an accurate
description of the target compound.
Similarity searches find structures having features similar to the query structure. By default, a similarity search is
performed based on a 90% degree of similarity. You can adjust the degree of similarity (from 0 to 100%) using
the slider. The higher the value, the fewer hits found.
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Adding Similarity Score to the Table
When performing a similarity search, you have to option to add Similarity Score to the table.
If this option is enabled, an additional column will be added with the value of the similarity score of each
matching row.
The Similarity Score column is added to the table as a real column, and therefore you are able to sort or plot the
Similarity Score column.
9.5. Performing a Structure Filter
There are three different means by which you can filter a data table based on chemical structure:
1. Using a structure editor, draw the chemical structure in the Structure Filter pane, and specify the search type.
Alternatively, you can copy and paste it into the Structure Editor window.
2. Filter directly from the current table visualization by selecting a chemical structure within the table, and
specify the search type.
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3. Filter directly from the current scatter plot visualization by selecting a chemical structure within the scatter
plot, and specify the search type. Each of these options is described below.
A column named ‘Structure Match’ is added to the data table after filtering is performed. This column contains
the tags ‘true’ and false’ If the structure matches the defined filtering criteria, then it will be tagged as ‘true’; if not,
it will be tagged as ‘false’.
This column appears at the bottom of the applicable data table on the Spotfire Filters panel. By default, the tags
are set to display the matches (true). You can select to view the structures that do not match the filter criteria
(false), or both (true and false).
In the case of a similarity search with the option to add similarity score to table enabled, an additional column will
be added with the value of the similarity score of each matching row.
Show Highlighting when Filtering
When using the Structure Filter with the ChemDraw renderer, structures will be returned, by default, with the
query molecule highlighted when performing a chemical substructure search.
When the filter is cleared, the molecules are re-rendered without the highilighting.
This feature can be enabled/disabled for each visualization via the Renderer Settings window. Refer to the
Settings section.
Monitoring Indexing and Filtering Progress
Prior to filtering a data table for the first time, the structures undergo an indexing operation which may be time
consuming depending on the number of structures. A progress bar is displayed indicating the indexing status.
Similarly when filtering a data table, a similar progress bar may be displayed.
In both cases, the Structure Filter panel is disabled.
Note: If a data table is embedded in the analysis, when loading a saved Spotfire analysis (*.dxp file) which
contains a filter, the index for that data table is persisted and therefore indexing is not performed again upon
loading.
The index is not persisted if the data is linked to the original data source when saved. Therefore, if the data is
not embedded in the analysis, when loading a saved Spotfire analysis (*.dxp file) which contains a filter, the
indexing will be performed again upon loading.
Filtering a Data Set with multiple structure columns
If the data file contains more than one structure column, you can select the column on which to filter.
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When the structure column is changed, the current filter is cleared.
If there are no structure columns defined in a data table, the Structure Filter panel is disabled. A message will
appear in the Structure Filter pane that no structure columns have been identified for the active data table.
However, if there are columns containing structure strings in the data table, a column can be defined as a
structure column by setting its content type property. At this point, the Structure Filter panel will be enabled.
Filtering using the Structure Filter pane
To create a new filter:
1. Open the Structure Filter.
2. Select the Filter Type from the drop down list. By default, Substructure is selected. If Similarity is selected,
use the slider to specify the degree of similarity. Note that the filter operation is triggered upon release of the
mouse button when using the slider bar. Also, if Similarity is selected, you can specify to add similarity score
to the table.
3. Double click in the Structure Filter pane to open the Structure Editor. By default, the ChemDraw Structure
Editor opens.
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Note: To select a different Structure Editor, close the ChemDraw Structure Editor, and click on the Edit filter
button in the toolbar. A list of available editors is presented. The selection is then saved as a user
preference, and will be opened by default the next time you double click on the Structure Filter pane.
4. Draw the query structure in the Structure Editor window using appropriate tools.
You can also copy and paste a structure into the Structure Editor window. For example, a structure can be
copied from the Structure Viewer, a table, or the Details-on-Demand panel, and paste it into the Structure
Editor.
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5. Click OK to initiate the filter.
Filtering directly from a table visualization
Structures can be rather large and complex to draw. Existing structures in the current visualization table can be
selected as the filter structure.
To filter directly from a table:
1. Mark the row in the data table containing the structure on which to filter.
2. Right click on the row in the table visualization and select Structure Filter. Select the Filter Type (Full
Structure, Substructure, and Similarity).
If Similarity is selected as the Search Type, a 90% degree of similarity is used by default. You can adjust the
degree of similarity (from 0 to 100%) using the slider in the Structure Filter panel. The filter operation is triggered
upon release of the mouse button. Also, if Similarity is selected, you can specify to add similarity score to the
table.
Note: Filtering can be performed on only one row at a time. If more than one row is marked, or no rows are
marked at all, then the filtering search types will not be available for selection.
Filtering directly from a scatter plot
Existing structures in the current scatter plot visualization can be selected as the filter structure.
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To filter directly from a scatter plot:
1. Mark the data point in the scatter plot representing the structure on which to filter.
2. Right click on the data point and select Structure Filter. Select the Filter Type (Full Structure, Sub-Structure,
and Similarity).
If Similarity is selected as the Search Type, a 90% degree of similarity is used by default. You can adjust the
degree of similarity (from 0 to 100%) using the slider in the Structure Filter panel. The filter operation is
triggered upon release of the mouse button. Also, if Similarity is selected, you can specify to add similarity score
to the table.
Note: Filtering can be performed on only one data point at a time. If more than one data point is marked, or no
data points are marked, then the filtering search types will not be available for selection.
9.6. Editing a Filter
To edit a filter:
1. Click on the Edit filter button in the toolbar to open the Structure Editor. If applicable, select the editor to
edit the current structure. Alternatively, you can also double click in the Structure pane to open the editor for
the current structure.
2. Edit the query structure in the Structure Editor window using appropriate tools.
3. Click OK to initiate the filter.
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Note: When editing a filter, all visualizations associated with the data table will be affected.
9.7. Clearing a Filter
To clear a filter:
1. Click on the Clear filter button in the toolbar. The current filter is cleared and the Structure Match column
is removed from the data table. .
Note: The filter applies to the data table, therefore clearing a filter will clear the results for all visualizations
associated with the data table. Clearing a filter does not clear the results of an R-Group decomposition.
9.8. Viewing Historical Structure Filters
Lead Discovery retains the previous ten filters allowing you to re-do a previous filter without having to re-draw
the chemical structure or set the filter conditions.
These filters are accessible by clicking on the Previous Filters button in the toolbar. A drop down displaying
the last ten searches is displayed similar to the example shown here.
The structure, search type, date and time stamp and the structure column on which the filter was initially
performed are displayed.
Selecting a filter from this list re-populates the query structure, resets the filter conditions, and sets the
associated filter column to display matching rows.
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9.9. Saving Structure Filters
Structure filter definitions can be saved with a user defined names, persisting the tag column used to define the
filter matches. This allows manipulation of multiple structure filters at once resulting in dynamic toggling between
structures in the filter.
Saving a structure filter
1. Perform a structure filter.
2. Enter a unique name for the filter search in the Structure Filter panel. If the name already exists, you will
be prompted if you want to overwrite the existing filter name.
3. Click on the Save Filter button.
All current filter settings are saved with the filter. The ‘Structure Match’ column (tag column), added to the data
table after filtering is performed, is re-named to the saved filter name.
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In addition, the column added to the applicable data table on the Spotfire Filters panel is also re-named to the
saved filter name.
The re-named tag column is not removed from the table when the filter is cleared. To remove this column, you
need to delete the saved filter.
Re-naming a saved structure filter
An existing filter can be re-named by selecting the filter name from the list, and entering a new name for the
filter. Click on the Save Filter button to save the newly named filter.
Executing a saved structure filter
When a saved filter is selected from the drop down list, the filter panel is updated with the filter settings of the
saved filter. The table is filtered to reflect the saved structure filter settings.
Note: If a structure filter was already in place at the time the saved search was selected, the saved filter will
replace the other structure filter. However, the replaced filter (if not a previously saved filter) will still be available
as part of the Historical Search list.
Once a saved filter has been selected, further changes to the filter settings will create an additional Structure
Match column to be added to table. If you want to save the new filter settings, you would need to create a saved
filter.
Using the Spotfire Filter panel, filter results can be combined for further analyses.
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Deleting a saved structure filter
Saved filters can be deleted from the list by selecting the filter to delete and clicking on the Delete Filter
button. You will be prompted to confirm the deletion.
The tag column is removed from the data table.
10. R-Group Decomposition
An R-Group decomposition analysis separates out the functional groups attached to a variable point of a
specified substructure.
Following a substructure filter on a data table, you can perform an R-Group decomposition on the filtered data.
Note: You cannot perform an R-Group decomposition from a full structure or similarity search.
The resultant R-Group template structure or scaffold is displayed in the Structure Filter panel under the R-Group
Decomposition tab.
Whether the functional group found at each Rn position is displayed in a real column or virtual column is based
on a user defined R-Group Decomposition threshold.
By default, this threshold is set to 10000. If the R-Group decomposition is performed on a number of rows below
the threshold, the R-groups are rendered in real columns as SMILES.
If the R-Group decomposition is performed on a number of rows above the threshold, you will be prompted to
select if you want real columns to be generated (rendered as SMILES) for the R-Group Decomposition results. If
you do not choose to generate real columns, the R-Group columns will be added as virtual columns.
Virtual columns are populated on an as needed basis and consequently they are rendered more quickly than
real columns. Although, they take considerably more time to generate, once in place, real columns can be
sorted, filtered, and used in other visualizations.
Note: If the threshold is set to zero, the columns will always be rendered as virtual columns, and you will not be
prompted to select the column type (real vs. virtual).
Note: R-Groups displayed in virtual columns are available for export using the Export to SDFile or Export to
ChemDraw for Excel features in Lead Discovery. Refer to the section Exporting.
10.1. Setting the R-Group Decomposition Threshold Preference
To set the R-Group Threshold:
1. Open the Spotfire client, and logon as a Spotfire Administrator. From the Tools menu, select the
Administration Manager sub-menu item. The Administration Manager is only enabled if you logon
connected to the Spotfire Server.
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The Administration Manager window opens.
2. Click on the Preferences tab.
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3. Select the Group Name to which the preferences should be applied.
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4. Expand the Structure filter.
5. Select the R-Group Decomposition preference.
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6. Click on the Edit button to open the Edit Preferences dialog.
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7. Enter a new value for the R-Group Decomposition Threshold. By default, this value is set to 10000.
Note: If the threshold is set to zero, the columns will always be rendered as virtual columns, and you will not be
prompted to select the column type (real vs. virtual).
8. Click OK.
Note: It is recommended that you restart the Spotfire Client in order for the new Preference settings to take
effect.
10.2. Performing an R-Group Decomposition Analysis
To perform an R-Group Decomposition of a Data Table:
1. Perform a Substructure filter on a data table.
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2. From the Structure Filter toolbar, click on the Insert R-Group Columns button.
A progress bar may be displayed indicating the analysis status. The Structure Filter panel is disabled during the
analysis.
The resultant R-Group template structure is displayed in the Structure Filter panel under the R-Group
Decomposition tab, similar to the example shown below.
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The decomposition results are displayed as columns which are added to the table visualization. A new column is
added for each of the R’s. The rows are populated with the R’s hits, similar to the example shown below. The
column type (real vs. virtual) is dependent on the R-Group Decomposition threshold and user input at the time of
generation.
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To remove R-Group columns from a data table:
An R-Group analysis can be removed from a data table. A data table can only contain one R-Group Decomposition analysis, and therefore before a new R-Group decomposition can be performed on the same table, the R-Group analysis must be removed.
1. From the Structure Filter toolbar, click on the Remove R-Group Columns button.
The R-Group columns, regardless if they are real or virtual, will be removed from the table visualization.
R-Group columns do not need to be removed before performing different structure filters. This enables filtering
to be performed on real RGD columns. Consequently, the RGD analysis may not necessarily apply to the
current filter in place on the panel.
If you open a table visualization after performing the R-Group Decomposition, and the virtual columns, if
applicable, are not automatically added to the table visualization, they will need to be added manually.
To add the virtual columns to a new table visualization:
1. Right-click on a table visualization and select Properties. You can also access the Table Properties by
clicking on the Visualization Properties button in the main toolbar, or via the Edit > Visualization
Properties menu item.
2. Select Virtual Columns and click on the Add button.
3. Select R-Group Decomposition Column.
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The virtual columns are now available to be added to the table visualization.
Note: If the ‘Add new columns automatically’ is set under Columns, the R-Group columns will have already been
added to the table, and it is not necessary to continue with the remaining steps to add the columns to the
visualization.
4. Select Columns. The virtual columns are listed under Available columns.
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5. Use Add >, to select virtual columns to add to the table visualization.
6. Use Move Up and Move Down to specify the order of columns in the table visualization.
7. Click Close.
11. Structure Alignment
Two molecules can be aligned by rotating one onto the other so they have the best possible overlap. In order for
the alignment to occur, the structures must have a common core or scaffold. The rendering of each molecule
that contains a common scaffold can be modified to align with the selected structure.
Lead Discovery allows you to modify the alignment of the structures in a table visualization so that they align
with a selected structure in the table. Any visible structures in the Structure Viewer and Details on Demand
panel are also aligned.
In addition, when performing a Structure filter operation, Lead Discovery allows you to optionally modify the
alignment of the structures in the table visualization such that they align with the drawn structure. The structures
are aligned in the column that is used in the filtering operation.
Note: Only the rendering of the structure is aligned. The structure data is not modified.
Aligning Structures from a table visualization
1. Right click on the structure on which you want to align and select Align to This Structure.
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All structures in the column are aligned with the selected structure, similar to the example shown below.
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Realigning to a Structure
If a column already has a structure alignment applied to it, you can realign the column to another structure in the
column.
1. Right click on the structure in the table visualization on which you want to realign and select Realign to
This Structure.
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Note: This menu option is only available if there is already an alignment applies to the selected column.
Clearing Column Structure Alignment
1. Select the column with an applied structure alignment.
2. Right click on the column in the table visualization and select Clear Column Structure Alignment.
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Aligning structures from the Structure Filter
1. Perform a Substructure filter on a data table.
2. From the Structure Filter panel, check the Align to this structure checkbox.
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All structures in the specified structure column are aligned with the selected substructure, similar to the example
shown below.
Clearing All Structure Alignments
1. If there are multiple structure alignments applied to a table (multiple structure columns), you can clear all
alignments simultaneously. From the Tools menu, select the Clear All Structure Alignments sub-
menu item.
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12. Settings
12.1. Supported Renderers
Lead Discovery modules provide support for several different renderers to display molecular structures. For
more information see the system requirements for Lead Discovery at:
http://www.cambridgesoft.com/services/EnterpriseSupport/KnowledgeBase/SystemRequirements/?fid=230
However, note that a few of the supported renderers can only be used to render structures in the table
visualization, the Structure Viewer and the Structure Filter; they cannot be used to edit structures in the
Structure Search tool. You can add one or more of these renderers to the list of default renderers, select any of
them as default for a content type, and change the renderer settings.
Note: The default Renderer settings for each content type are honored in all rendering contexts The settings
defined for a default renderer are extended to the custom panels (e.g. Structure Viewer, Structure Filter).
If a default Renderer is not configured for a supported content type, ChemDraw is automatically selected, by
default, as the renderer.
To add a renderer to the list of default renderers:
1. Select Tools > Options.
2. Select the Application tab.
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3. Click the Renderer Setting button.
4. Click Add. The Add Default Renderer dialog displays.
5. Specify the Content type and select the default renderer from the drop-down list in the dialog.
Comment: You can only specify one default renderer per content type. See the table below for a
description of content types.
To change the default renderer for a certain content type:
1. Select Tools > Options.
2. Select the Application tab.
3. Click the Renderer Settings button.
4. Click to select the content type of interest and click Edit. The Edit Default Renderer dialog displays.
5. Select a new default renderer from the drop-down list.
Note: The content type you enter can be an arbitrary string, but it is recommended that you use the
MIME types defined for molfiles, CHIME strings, and SMILES strings as shown in the table below.
Structure Format Content Type
MDL molfile chemical/x-mdl-molfile
MDL Chime string chemical/x-mdl-chime
Daylight SMILEs string
ChemDraw Chemical Structure Exchange
chemical/x-daylight-smiles
chemical/x-cdx
To change the renderer and/or renderer settings for the structures displayed in the table
visualization:
1. Right-click on a row in the table visualization and select Properties > Columns.
2. Select the column that contains chemical structures.
3. In the Renderer drop-down list, select the renderer to use.
4. Click the Settings button to change the renderer settings. The Renderer Settings dialog for the
currently used renderer displays.
5. Change the renderer settings and click OK.
To change the renderer used in Structure Viewer:
1. In the Structure Viewer pane of the Structure Viewer, right-click on the structure.
2. Select Renderer.
3. Select the renderer to use.
To edit the renderer settings in the Structure Viewer:
1. In the Structure Viewer pane of the Structure Viewer, right-click on the structure.
2. Select Renderer > Settings. The Renderer Settings dialog for the currently used renderer
displays.
3. Change the renderer settings and click OK.
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To change the renderer used in Structure Filter:
1. In the Structure Filter toolbar, click on the Renderer settings button in the toolbar.
2. Select the renderer to use.
To edit the renderer settings in the Structure Filter:
1. In the Structure Filter toolbar, click on the Renderer settings button in the toolbar.
2. Select Settings. The Renderer Settings dialog for the currently selected renderer displays.
3. Change the renderer settings and click OK.
Note: When the renderer settings are changed in a custom panel (e.g. Structure Viewer, Structure Filter), they
overwrite the default settings, and are saved with the .dxp file.
12.2. Renderer Settings
The renderer is the program responsible for the display of structures in Structure Viewer, Structure Search, and
Structure Filter and also when structures are shown in visualizations.
ChemDraw Renderer Settings
The ChemDraw renderer does not require you to select the format of the structure string. It auto-detects the data
format.
CDX content in tables is displayed natively in the ChemDraw renderer.
Show highlighting when filtering
When using the Structure Filter with the ChemDraw renderer, structures will be returned, by default, with the
query molecule highlighted when performing a chemical substructure search.
Specifying a Template File
You can select an existing ChemDraw Style Sheet file (.cds) for visualizing structures.
To specify a template (.cds) file:
1. From the ChemDraw Settings dialog, click on the Load Settings button.
2. From the drop down list box, select an existing cds template file to apply to a structure visualization.
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The selected .cds template file is displayed in the ChemDraw Settings dialog indicating that it was successfully
loaded.
3. Click ‘OK’.
If you select ‘Default Settings’ from the drop down list, the factory settings are used.
Selecting ‘Other’ from the drop down list will open a Load Settings file browser from which you can browse for
the .cds template.
Note: The settings for the ChemDraw Editor and Renderer are separate. The Editor settings are defined through
the ChemDraw application (File menu). The Renderer settings are defined as described here. For example, if a
template is loaded into the ChemDraw renderer, the Structure Filter panel will display an existing structure
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according to these settings. However, if the structure is edited using ChemDraw, although the structure is
displayed in the editor using the same format as the renderer, any edits are displayed using the default
ChemDraw editor template.
Other Structure Renderers
Other structure renderers auto detect the format to use for rendering, except if the data format is CHIME.
Note: Other structure renderers may display different type of settings, hence, the dialog you see may look
different from the example shown here (Symyx® Draw (MDL) Settings).
The table below describes the fields in the Structure Renderer Settings dialog.
Option Description
Structure string
The structure string is auto detected with the exception of MDL CHIME. Activate the checkbox if the data format is CHIME. This checkbox is disabled if the renderer does not support the CHIME data format.
Show Hydrogens
Changes the hydrogen display settings.
Possible options:
For Symyx® Draw (MDL) - Off, Hetero, Terminal, HeteroOrTerminal, All
For Accord - True, False
For Marvin - Off, Hetero, HeteroOrTerminal, All
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13. Glossary
Column
A vertical list of values in a data table
Column Name
The name of a column as displayed in the user interface. It is a normalized, trimmed, and unique text string. It is
initially set to a tidied form of the external name, but it may be modified through a Rename Column operation.
Data Source
A handle to an external data source, for example, files or information links. A data source produces a single
table of data.
Data Table
A data table in TIBCO Spotfire is defined as either data loaded from an external source, or new data created
within the application. It has one or more columns and zero or more rows. A visualization is based on a single
data table.
Data tables loaded from an external source can be linked or embedded. Linked data tables can be loaded
completely into the application, but if the source is an information link they can also be configured to load data
on demand only.
Data tables can be related to each other, using primary and/or foreign keys (key columns), but they can also be
unrelated.
Details-on-Demand
The concept of expanding a small set of items to reveal more data behind it
DXP File
The file type used for analysis files created with TIBCO Spotfire. DXP files can be saved to disk and to the
library. Defines what data to include and how to present it. Can include linked or embedded data based on user
settings when saving the file, and includes one or more pages. There can only be one analysis file open at a
time, but it is possible to run several instances of TIBCO Spotfire simultaneously, and one analysis file can also
contain several data tables.
Filter
Filers are used to reduce the amount of data to work on in TIBCO Spotfire and are the same as Query Devices
in TIBCO Spotfire DecisionSite. Filters can be either column filters, directly related to a column, or hierarchy
filters (tree filters) which represent a hierarchy. Filters can be grouped into folders in the Filters panel.
ID column
A column in the table that contains structure identifiers
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ID list
A list of structure identifiers
Information Link
Information links are predefined database queries, specifying the columns to be loaded, and any filters needed
to reduce the size of the data table prior to visualization.
Library
The library is a space on the server where you can publish or open shared analysis files. Information links and
the elements used to create information links are also stored in the library.
Marked Row
An item in a visualization becomes marked when you click on it, or, when it is captured using the rectangle
method (left mouse button pressed while moving pointer). Marked rows are given a definable color to distinguish
them from the rest of the data.
Marked Rows list
A dynamic list in the Structure Viewer called "Marked Rows" that contains the marked rows in the active
visualization.
Marking
A marking identifies marked rows in the data tables of an analysis. If the data tables are related, the marked
rows are propagated using the specified key relation between the data tables. Setting a marking in one data
table does not affect the marking of unrelated data tables. Each analysis can hold multiple markings and each
marking has its own marking color. One or more markings can be used to limit what data are displayed in a
visualization.
Page
A page can be thought of as a "container" for visualizations, filters, a Details-on-Demand, etc. Pages make it
possible to set up several sheets of visualizations that you can switch between in an analysis. Pages can
contain visualizations and text areas that guide you through the analysis. Visualizations can only exist inside a
page (they cannot be dragged outside even partly).
All visualizations in an analysis can be linked, both within and between pages, but they do not have to be. The
visualizations on a page use one or more filtering schemes, and the filtering schemes determine whether
visualizations are linked or not. The visualizations in a page can use one or several data tables.
Personalized Information Links
A personalized information link returns a subset of data depending on which user is logged in.
R-Group Decomposition
An R-Group decomposition analysis separates out the functional groups attached to a variable point of a
specified substructure.
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Row
A horizontal list of values in a data table
Structure Filter
The Structure Filter can be used to filter the contents of a data table based on chemical structure. The contents
can be filtered based on full structure, substructure or similarity.
Structure Viewer
The Structure Viewer can be used to display structures of the marked compounds in the visualizations. It can
also be used to manage and view lists from various structure searches.
Structure Search
A tool used to search for compounds similar to or containing a specified master structure.
Table
A visualization with information arranged in rows and columns.
Table Column
A vertical list of values in a table
Table Column Header
An area used to identify a table column.
Table Row
A horizontal list of values in a table
Table Row Header
An area used to identify a table row.
URL
Uniform Resource Locator (A World Wide Web address)
Visualization
A visualization is a representation of some data in TIBCO Spotfire. For example, a table, a bar chart, a pie chart,
etc. Visualizations display data from one data table. The data displayed can be limited by one or more filtering
schemes and by zero, one or several markings. Visualizations show and allow modification to one marking.
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14. Chemical Property Calculations
14.1. Balaban Index
The Balaban index, represented as J, is defined as:
Where:
q is the number of edges in the molecular graph.
μ= (q-n+1) is the cyclomatic number of molecular graph.
n is the number of atoms in the molecular graph.
Si is the sum of all entries in the ith row (or column) of the topological distance matrix of the molecule.
The distance matrix stores the shortest path between all pairs of atoms.
14.2. Boiling Point
The boiling point is report in Kelvin.
A solution boils at a slightly higher temperature than the pure solvent. The change in boiling point is calculated
using the formula:
Where Kb is the molal boiling point constant, m is the concentration of the solute expressed as molality, and DTb
is the change in temperature.
14.3. Cluster Count
The cluster count is the number of paths of a given length in the distance matrix.
14.4. Critical Pressure
Reported in bars, this is the least applied pressure required at the critical temperature to liquefy a gas.
14.5. Critical Temperature
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Critical Temperature Reported in Kelvin, this is the temperature above which a gas cannot be liquefied, regardless of the pressure
applied.
14.6. Critical Volume
Reported in cm3/mol, this is the volume occupied by one mole of a substance at the critical temperature and
pressure.
14.7. Elemental Analysis
This is a process in which a material is analyzed for its elemental and isotopic composition. Elemental analysis
can be qualitative (determining what elements are present) or quantitative (determining how much of each are
present).
14.8. Exact Mass
This is the sum of the masses of the isotopes in a molecule. For example, the exact mass of water containing
two hydrogen-1 (1H) and one oxygen-16 (16O) is 1.0078 + 1.0078 + 15.9994 = 18.0106. The exact mass of
heavy water,containing two hydrogen-2 (deuterium or 2H) and one oxygen-16 (16O) is 2.014 + 2.014 + 15.9994
= 20.027.
14.9. Formal Charge
The formal charge is the charge assigned to an atom in a molecule, assuming that electrons in a chemical bond
are shared equally between atoms, regardless of relative electronegativity. The formal charge of an atom in a
molecule can be calculated using the formula:
FC=V-N-B/2
Where ‘V’ is the number of valence electrons of the atom in isolation (atom in ground state); ‘N’ is the number of
nonbonding electrons on this atom in the molecule; and ‘B’ is the total number of electrons shared in covalent
bonds with other atoms in the molecule.
14.10. Gibbs Free Energy
Gibbs free energy is defined as:
Which is the same as:
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Where:
U is the internal energy (SI unit: Joule)
p is pressure (SI unit: Pascal)
V is volume (SI unit: m3)
T is the temperature (SI unit: Kelvin)
S is the entropy (SI unit: joule per Kelvin)
H is the enthalpy (SI unit: Joule)
Note: H and S are thermodynamic values found at standard temperature and pressure.
14.11. Heat of Forma tion
Reported in KJ/mole, the heat of formation is the increase in enthalpy resulting from the formation of one mole of
a substance from its constituent elements at constant pressure.
14.12. Henry’s Constant Law
A unitless value, Henry's Law Constant can be expressed as:
Where ‘p’ is the partial pressure of the solute in the gas above the solution, ‘c’ is the concentration of the solute
and ‘kH,pc’ is a constant with the dimensions of pressure divided by concentration. The constant, known as the
Henry's law constant, depends on the solute, solvent, and temperature.
14.13. Ideal Gas Thermal Capacity
The thermal capacity at constant volume of an ideal gas is:
Where:
cV is a constant dependent on temperature
U is the internal energy
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T is the absolute temperature
V is the volume
n is the amount of substance of the gas
R is the gas constant (8.314 J·K−1
mol-1
in SI units)
N is the number of gas particles
kB is the Boltzmann constant (1.381×10−23
J·K−1
in SI units)
The thermal capacity at constant pressure of an ideal gas is:
Where ‘H’ is the enthalpy of the gas, calculated as: H = U + pV.
14.14. m/z
The mass-to-charge ratio is a physical quantity used in the electrodynamics of charged particles. Two particles
with the same m/z ratio move in the same path in a vacuum when subjected to the same electric and magnetic
fields.
14.15. Mass
This is the mass of one molecule of a substance, relative to the unified atomic mass unit u (equal to 1/12 the
mass of one atom of 12C). Also called molecular mass.
14.16. Melting Point
Is the temperature at which a solid becomes a liquid at standard atmospheric pressure. At the melting point, the
solid and liquid phase exist in equilibrium. The formula to calculate melting point is:
Where ‘T’ is the temperature at the melting point, ‘∆S’ is the change in entropy of melting, and ‘∆H’ is the change
in enthalpy of melting.
14.17. Mol Formula
This is the molecular formula of the compound.
14.18. Mol Formula HTML
This is the molecular formula written in HTML format. You can copy and paste the output to an HTML file. Here
is an example of the output for a model of aniline:
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C<sub>6</sub>H<sub>7</sub>N
14.19. Mol Refractivity
Is a measure of the total polarizability of one mole of a substance. It is dependent on the temperature, index of
refraction, and pressure.
The molar refractivity, ‘A’ is expressed as:
Where ‘NA’ is the Avogadro constant and is the mean polarizability.
14.20. Molecular Topological Index
Is a graph index defined by:
Where Ei are the components of the vector:
Where, A is the adjacency matrix and D is the graph distance matrix, and d is the vector of vertex degrees of a
graph.
Note: An atom’s degree is the number of non-hydrogen atoms to which it is adjacent.
14.21. Mol Weight
This is the sum of the atomic weights of all atoms in a molecule.
14.22. Number of HBond Acceptors
The number of hydrogen bond acceptors in the model.
14.23. Number of HBond Donors
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The number of hydrogen bond donors in the model.
14.24. Number of Rotable Bonds
The number of rotatable bonds in a molecule. A rotatable bond is defined as an acyclic bond drawn as a single
bond (amide C-N bonds, O=C--N, are rotatable) where the atom on each end has at least one other non-
hydrogen substituent.
This topological parameter is a measure of molecular flexibility. Unsaturated bonds, and single bonds connected
to hydrogens or terminal atoms, single bonds of amides, sulphonamides, and those connecting two hindered
aromatic rings (having at least three ortho substituents) are considered non-rotatable.
14.25. Polar Surface Area
The Polar Surface Area (PSA) is defined as the surface sum over all polar atoms (usually oxygen and nitrogen)
including attached hydrogens.
14.26. Principal Moment
This refers to the principal moments of inertia about the principal axes of a molecule. The moments of inertia are
computed for a series of straight lines through the center of mass using the formula:
Where, ‘I’ is the moment of inertia, ‘mi’s are point masses whose distances from the rotation axis are denoted by
‘di’s.
Distances are established along each line proportional to the reciprocal of the square root of I on either side of
the center of mass. The locus of these distances forms an ellipsoidal surface. The principal moments are
associated.with the principal axes of the ellipsoid.
If all three moments are equal, the molecule is considered to be a symmetrical top. If no moments are equal,
themolecule is considered to be an unsymmetrical top.
14.27. Radius
The eccentricity of an atom is the largest value in its row (or column) of the distance matrix, and represents how
far away from the molecular center it resides.
The diameter (D) is the maximum such value for all atoms, and is held by the most outlying atom(s). Examples:
Diameter of methane = 0; ethane = 1; propane = 2; n-butane = 3.
The radius R is the minimum such value, and is held by the most central atom(s). Examples: Radius of methane
= 0; ethane = 1; propane = 1; n-butane = 2.
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14.28. Shape Attribute
The shape attribute (kappa) measures the branching of a molecule, and is scaled so as to fall between the
minimum and maximum values possible for the given order. The first-order shape attribute counts the number of
one-bond paths. The second-order attribute counts the number of two-bond paths, and so on. The first three
orders (1..3) are available.
14.29. Shape Coefficient
The shape coefficient, I is given by:
Where the diameter (D) is the maximum such value for all atoms, and is held by the most outlying atom(s). The
radius (R) is the minimum such value, and is held by the most central atom(s).
Examples values for D: methane = 0; ethane = 1; propane = 2; n-butane = 3.
Example values for R: Radius: methane = 0; ethane = 1; propane = 1; n-butane = 2.
14.30. Sum of Degrees
Is the sum of degrees of every atom. An atom’s degree is the number of nonhydrogen atoms to which it is
bonded.
14.31. Sum of Valence Degrees
Is the sum of degrees of every atom. An atom’s valence degree is equal to the sum of its adjacent bonds' orders,
including hydrogens.
14.32. Topological Diameter
Is the longest dimension of a molecule.
14.33. Total Connectivity
Is the connectivity considered over all the heteroatoms.
14.34. Total Valence Connectivity
Is the valence connectivity considered over all the heteroatoms.
14.35. Vapour Pressure
Is the pressure exerted by a vapor in equilibrium with its solid or liquid phase. Vapor pressure measures the
concentration of solvent molecules in the gas phase.
Vapor pressure can be calculated using Raoult’s law. The formula to calculate vapor pressure is:
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Where ‘p’ is vapor pressure, ‘i’ is a component index, and is a mole fraction.
14.36. Water Solubility
Is the maximum amount of a substance that can be dissolved in water at equilibrium at a given temperature and
pressure.
Water solubility is measured in mg/L.
14.37. Wiener Index
Provides measure of branching defined as:
where Dij are the off-diagonal elements of the distance matrix.