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Molecule Converter (Naomi)

DeprecatedBioSolveIT Plugins version by BioSolveIT GmbH

The Naomi Converter converts molecules from and to different file formats.


Select the column containing the molecule(s) to be converted
The molecules provided in this column are converted 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 converted. Possible formats are SDF, Mol2, SMILES, and also the graphics formats PNG and SVG with 2D figures of your molecules!
Replace source column
Select if you want to replace the original column in your table with the new one that contains the converted molecules. 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.
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 converted.

Output Ports

Converted Molecules: Output table containing the converted molecules or images according to your settings.
Errors: The rows of the incoming table where the molecule could not be converted by Naomi for any reason.

Best Friends (Incoming)

Best Friends (Outgoing)


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