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ICon

LigandScout Extensions for the KNIME Workbench version 1.8.0 by InteLigand GmbH

The ICon node generates conformations using the Inte:Ligand conformer generator.

Options

Settings

Max. num. conformations
Maximum number of conformations to output for each molecule. Raising this value samples the conformational space better. (default: 100)
Max. pool size
Maximum size of intermediate pool of conformers. (default: 4000)
Timeout [sec]
After this time, the conformer generation for a molecule is stopped (and is considered to have failed!). If this occurs in the ligand-based pharmacophore generation, the whole process automatically fails. (default: 600 sec)
Max. fragment build time [sec]
Maximum time to build a fragment. (default: 30.0)
RMS threshold
RMS threshold used to determine duplicate conformations. (default: 0.7)
Energy window
Energy window used for conformer selection. (default: 15.0)
Enumerate rings
If checked, ring conformers are enumerated. (default: enabled)
Enumerate nitrogens
If checked, pyramidal invertible nitrogen geometries are enumerated. (default: enabled)
Torsion drive
Can be used to turn off the torsion driving part of conformer generation. By default, torsion search for molecules that have rotatable bonds is enabled. Setting torsionDrive to false will circumvent torsion driving, and output conformers will reflect the results of model building, puckered nitrogen enumeration, and ring conformer enumeration.(default: enabled)
Generate coords from CT
This boolean flag determines whether to generate an initial set of 3D coordinates using only the connection table of the input molecule. Initial model generation is always necessary for molecules lacking 3D coordinates. Bond lengths and angles taken from molecules with coordinates may be retained by setting this flag to false. (default: enabled)
Include input conf.
When this is checked the algorithm will include the input conformer in the set of output coordinates. This requires that the input molecule has valid 3D coordinates. (default: enabled)
Skip molecules with existing conformations
If this is enabled, molecules with already existing conformations are not overwritten with new conformations (default: disabled)
Apply FAST Settings
Fast Settings are the optimized default settings which will result in a fast generation of conformations but potentially of lower quality.
Apply BEST Settings
Best Quality Settings are the optimized default settings which will result in longer processing time but higher quality resulting conformations.

Advanced Settings

Structure column
Name of the column in the input table that holds the molecule structure.
(Default: First column with a supported molecule data type)
Add conformation count to column
If selected, the number of generated conformations will be written to the specified output column.
(Default: # Confs)
Add error message column
If selected, the second output table includes a column with error messages for each molecule that could not be processed.
(Default: Conf. Gen. Error)
Include failed molecules in first output table
If selected, molecules that could not be processed will still be included also in the first output table. Use this option if you want to include these molecules in downstream processing steps. In any case, these molecules will be present in the second output table.
(Default: False)
Keep Input Row IDs
If selected, the molecules in both output tables will use the same Row IDs as in the input tables. Use this option if you use the Row IDs to track molecules across your workflows.
(Default: False)
Multi-threaded execution
If selected, the node will launch multiple computation threads depending on the number of available CPU cores to speed up the execution time.
(Default: True)

Input Ports

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Table containing the molecule(s) for which to generate conformations

Output Ports

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Table containing the molecule(s) with generated conformations
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Table containing the molecule(s) for which conformer generation failed

Best Friends (Incoming)

Best Friends (Outgoing)

Installation

To use this node in KNIME, install LigandScout Extensions for the KNIME Workbench from the following update site:

KNIME 4.3

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Developers

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