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3D Coordinates Generator

This node generates 3D coordinates for molecules provided in SMILES, SDF, or Mol2 format.

Options

Input molecules column: For molecules provided in this column 3D coordinates are generated according to the settings below. If the input table contains more than one column with a compatible type, you can choose which column should be taken. The column has to be in SDF, Mol2 or SMILES format.
Target format: Here you can choose the format into which the molecules will be written. Possible output formats are SDF and Mol2.
Append all data columns of the library table: Select this if you want to append all data columns of your input table to the output table.
Replace source column: When having chosen to append input columns plus this option, the source molecule column won't be appended.
Keep debug files and show the log after the run: This setting keeps all temporary files and opens an editor to show the output of the external program. This setting is very helpful for debugging.

Input Ports

: Input Molecules: Input table with at least one column containing molecules in SDF, Mol2 or SMILES format to be processed.

Output Ports

: Converted Molecules: Output table containing the molecules with 3D coordinates.
: Errors: The molecules that couldn't be processed for any reason. This table contains a copy of the erroneous input table rows.

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Installation

To use this node in KNIME, install the extension BioSolveIT Coordinates3d for Knime from the below update site following our NodePit Product and Node Installation Guide:

v5.2

Plugin provider: BioSolveIT GmbH

Plugin version: 2.29.3.202309291626

On NodePit since: 2023-12-06

Last update: 2024-11-20

KNIME versions: From v3.6 to v5.2

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