Hello, I am using rdkit to read data from SD files. My goal is to extract both the molecules and their associated properties (which for our purposes are separate entities) from the SDF. [For 100% clarity: by 'properties' I don't mean calculated properties or atom or bond properties, but the text properties that were saved in the SDF with each molecule, i.e. those that you get when you do mol.GetPropsAsDict() ].
After several tests I found that Chem.ForwardSDMolSupplier does what I need. But there is an issue. When Chem.ForwardSDMolSupplier decides that a molecule is not OK, i.e. when it says it is None, the SDF record is lost: I cannot access its Props; I cannot save the failed SDF record for later inspection. [Or at least, I don't know how to do it, hence this question]. At most I can collect the indices of the records that fail. > Would anyone be able to suggest how to save to a text file (which an SDF > essentially already is) the SDF records for which Chem.ForwardSDMolSupplier > returns a None? > Even better, could the properties associated to the failed molecules be read > independently? In theory the properties are in a separate part of the CTAB, > so even when the atoms, bonds, etc. have a problem, the properties might > still be OK. (Note: PandasTools.LoadSDF gives the same issue, it does not even store in the DataFrame the records for which the molecule is None, and in any case it cannot be used with the kind of SDF's I am handling, as it uses an enormous amount of memory for the molecules - hence the decision to use Chem.ForwardSDMolSupplier and pickle the molecules as soon as they are read). Thanks This e-mail and its attachment(s) (if any) may contain confidential and/or proprietary information and is intended for its addressee(s) only. Any unauthorized use of the information contained herein (including, but not limited to, alteration, reproduction, communication, distribution or any other form of dissemination) is strictly prohibited. If you are not the intended addressee, please notify the originator promptly and delete this e-mail and its attachment(s) (if any) subsequently. Neither Galapagos nor any of its affiliates shall be liable for direct, special, indirect or consequential damages arising from alteration of the contents of this message (by a third party) or as a result of a virus being passed on.
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