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3D Ensemble Conformator

BioSolveIT Conformator for Knime version by BioSolveIT GmbH

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


Input molecules column
For molecules provided in this column 3D conformations 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.
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

Conformations: Output table containing the molecules with multiple conformations.
Errors: The molecules that couldn't be processed for any reason. This table contains a copy of the erroneous input table rows.

Best Friends (Incoming)


To use this node in KNIME, install BioSolveIT Conformator for Knime from the following update site:


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