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Forge Molecule Viewer

Cresset KNIME Nodes version 2.6.0.41359 by www.cresset-group.com

Launches Forge™ to view molecules.

Forge is a powerful computational chemistry suite for understanding SAR and design.

This node wraps the Forge executable, which must be installed with a valid license for this node to work. If this is installed in the default location on Windows, then it should be found automatically. Otherwise, you must either set the 'Cresset Home' preference setting or the CRESSET_HOME environment variable to the base Cresset software install directory. You may also set the 'Forge Path' preference setting or the CRESSE_FORGE_EXE environment variable to point directly at the executable itself.

For more information visit www.cresset-group.com or contact us at support@cresset-group.com.

Options

Basic

Column containing molecule structures
The column in the input datatable containing the molecules to visualize, or the Forge project to view.
Role
The input molecules will be assigned to the chosen role.
Protonation State
  • Ask - When the node is run, you will be asked to choose the protonation state
  • Use input protonation state - Imports the molecules 'as-is'
  • Let Forge choose the protonation state - Re-assigns protonation state for all molecules at pH 7 according to the Cresset built-in set of rules.
Read Mode
Sets the file read mode, i.e. how the molecules will be read into Forge as a function of the file content.
  • Ask - When the node is run, you will be asked for the read mode.
  • Autodetect - Will attempt to autodetect whether the file is a 'Multi-molecule' or 'Multi-conformer' file. This option works for most files and use cases.
  • Multi-molecule - Each entry in the table is treated as a different molecule that will require conformer generation before alignment.
  • Multi-conformer - The table is assumed to hold multiple conformers of a single molecule. No conformation hunt is needed before alignment.
  • Multi-molecule, single conformers, need aligning - Each entry is treated as a different molecule, which consists of just one conformation. The relative alignment of different molecules is ignored.
  • Multi-molecule, already pre-aligned - Each entry is treated as a different molecule, which consists of a single conformation in a predetermined alignment.

Input Ports

Icon
Molecules to view in SDF, PDB or Mol2 format.

Best Friends (Incoming)

Installation

To use this node in KNIME, install Cresset KNIME Nodes from the following update site:

KNIME 4.3

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Developers

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