Dear colleagues, I know that this is probably a dumb question, but since my searches showed no clarifying results I'm asking here anyway. I'm planning to use RDKit on my Ph.D. thesis, but my field of research is inorganic chemistry and molecular magnetism. That means that I'm dealing with organometallics (transition metals, lanthanides, actinides...). So far I was unable to import even a single structure to my RDKit test with different error messages like those (they are all the same structure, that is attached here):
m = Chem.MolFromMolFile('st1.pdb')
RDKit WARNING: [08:36:40] CTAB version string invalid at line 4
m = Chem.MolFromMolFile('st1.sdf')
RDKit ERROR: [08:51:30] Explicit valence for atom # 1 N, 4, is greater than
permitted
m = Chem.MolFromMolFile('st1.mol2')
RDKit WARNING: [08:52:15] Counts line too short: 'SMALL' on line4
Based on this, I'd like to as for hints on how to deal with molecules with
"unusual" valences like the ones we deal in inorganic chemistry.
Thanks in advance
--
Henrique C. S. Junior
st1.mol
Description: st1.mol
st1.mol2
Description: st1.mol2
st1.pdb
Description: st1.pdb
st1.sdf
Description: st1.sdf
st1.xyz
Description: st1.xyz
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