Thanks. Yes, I too understood that it should get the connectivity from the distances.
I'm using PDB for it being the output from another program. I'll see what I can change then. Thanks, Gustavo. -- Gustavo Seabra ________________________________ From: Alan Kerstjens Medina <[email protected]> Sent: Sunday, April 5, 2020 9:15:26 AM To: Gustavo Seabra <[email protected]>; [email protected] <[email protected]> Subject: RE: [Rdkit-discuss] RDKit Chem.MolFromPDBFile ignores some files... Hi Gustavo, I haven’t looked into the RDKit source code for this but I assume this has to do with the lack of CONECT records in the PDB file you attached (i.e. you are only storing atom coordinates, not connectivity). >From what I could gather from the RDKit documentation, the default behaviour >for the MolFromPDBFile function is to “sense” bonds based on atom proximity >(proximityBonding=True), but I guess that isn’t happening. Maybe someone else >could chime in and clarify how to make that feature work as intended. Is there any particular reason you want to use PDB files for small molecules? They tend to be a bit of a headache and not particularly efficient storage-wise. If atom coordinates are important maybe it would be easier to use SDF or MOL2 files instead. Best regards, Alan From: Gustavo Seabra<mailto:[email protected]> Sent: 04 April 2020 22:08 To: [email protected]<mailto:[email protected]> Subject: [Rdkit-discuss] RDKit Chem.MolFromPDBFile ignores some files... Hi all, I'm having another problem when reading a PDB file. Some files just return "None", with no error message at all. For example, the attached file: >>> Chem.MolFromPDBFile("./a3.pdb") Does not return a Mol object. Does anyone know what is wrong with this file? I can open it regularly in other programs. Is there any way to "force" rdkit to recognize the file? Thanks, -- Gustavo Seabra
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