To run the below scripts, you need a Groovy installation. The Groovy scripts use version 2.7.1 of the Chemistry Development Kit (see also doi:10.1186/s13321-017-0220-4). This library and its use in Groovy is further explain in the book Groovy Cheminformatics with the Chemistry Development Kit.
When generating InChIs, the InChI library may return two success states reflecting issues with the compound record in the SD file: WARNING and ERROR. This first script reports such issues:
groovy badRecords.groovy -f foo.sdfThe output may look like:
Sulfinpyrazone Omitted undefined stereo WARNING
Isosorbide mononitrate Charges were rearranged WARNING
Compound52 Proton(s) added/removed WARNING
The second script calculates InChIs for entries in the SD file, but only when the InChI generation was OKAY or with a WARNING (two InChI library success states):
groovy inchis.groovy -f foo.sdfWhen the success state is ERROR, nothing is outputted.
Similarly, InChIKeys can be generated:
groovy inchikeys.groovy -f foo.sdfThe last script calculates a SMILES for each entry in the SD file:
groovy smiles.groovy -f foo.sdf