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Generate 3D Coordinates

BioSolveIT Plugins version by BioSolveIT GmbH

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

The node is an interface to trigger an external 3D coordinate generator.
The path to the external executable has to be configured in
File -> Preferences -> KNIME -> BioSolveIT Settings -> 3D Generator
The 3D coordinate generator has to be licensed and installed separately.


Select the column containing the molecule(s) to generate coordinates for
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.
Select the target format
Here you can choose the format into which the molecules will be written. Possible output formats are SDF and Mol2.
Replace source column
Select if you want to replace the original column in your table with the new one that contains the molecules with 3D coordinates. Otherwise, the new column will be appended to your original table.
Caption of converted column
Here you can change the caption of the new column.
Use remote computing via SSH
Select if you want to start 3D Generator on a remote server. Please set up your remote computing settings in the 3D Generator global settings using
File -> Preferences -> KNIME -> BioSolveIT Settings -> 3D Generator
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 containing errors. This is basically the content of @error and thus it is only avaiable if @error is configured in options (see File -> Preferences -> KNIME -> BioSolveIT Settings -> 3D Generator).

Best Friends (Incoming)

Best Friends (Outgoing)


To use this node in KNIME, install BioSolveIT Interfaces from the following update site:

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