Lead Discovery 5 - CambridgeSoftmedia.cambridgesoft.com/support/spotfire/Manuals/LD/5.2...Lead Discovery 5.2 You can export data from Lead Discovery to an SDFile or to a ChemDraw for

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

Lead Discovery 5.2


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.


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


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.


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.


include in the SDFile and returns it to the list of available

columns.


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.


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:


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.


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


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.


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.


include in the ChemDraw Excel File and returns it to the

list of available columns.


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:



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.



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:



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.

Lead Discovery 5.2


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.

Lead Discovery 5.2


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.

Lead Discovery 5.2


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.

Lead Discovery 5.2


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.

Lead Discovery 5.2


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.

Lead Discovery 5.2


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.

Lead Discovery 5.2


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.

Lead Discovery 5.2


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.

Lead Discovery 5.2


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.

Lead Discovery 5.2


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.

Lead Discovery 5.2


All structures in the column are aligned with the selected structure, similar to the example shown below.

Lead Discovery 5.2


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.

Lead Discovery 5.2


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.

Lead Discovery 5.2


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.

Lead Discovery 5.2


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.

Lead Discovery 5.2


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.

http://www.cambridgesoft.com/services/EnterpriseSupport/KnowledgeBase/SystemRequirements/?fid=230

Lead Discovery 5.2


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.


Lead Discovery 5.2


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.


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.

Lead Discovery 5.2


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

Lead Discovery 5.2


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

Lead Discovery 5.2


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

Lead Discovery 5.2


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.

Lead Discovery 5.2


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.

Lead Discovery 5.2


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

Lead Discovery 5.2


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:

Lead Discovery 5.2


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

Lead Discovery 5.2


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:

Lead Discovery 5.2


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

Lead Discovery 5.2


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.

Lead Discovery 5.2


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:

Lead Discovery 5.2


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.

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