Dear colleagues, I'm working with coordination compounds and using .mol (v3000) files to describe the immediate coordination environment of my molecules. This is an example of a cobalt complex (just the coordination environment):
Mrv1827 08101911143D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 6 5 0 0 0 M V30 BEGIN ATOM M V30 1 Co 0.7663 2.1605 10.185 0 M V30 2 Cl 2.423 1.0205 11.4441 0 M V30 3 P 2.0121 2.3511 8.3115 0 M V30 4 P 0.1302 0.2072 9.1724 0 M V30 5 P -0.781 2.1773 11.8292 0 M V30 6 P 1.3423 4.1551 11.1519 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 2 9 3 1 M V30 3 9 4 1 M V30 4 9 5 1 M V30 5 9 6 1 M V30 END BOND M V30 END CTAB M END The problem is that RDKit is adding hydrogens to make the fragment make sense and I'd like to avoid that: [cid:83062c0b-f007-4673-b71e-1cce0aa1df56] Using Chem.RemoveHs(mol) is not working too. Any help is much appreciated -- Henrique C. S. Junior
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