> > When running this code no errors are thrown but the molecule seems to > empty (molwt is zero). > Can anyone tell if this is a problem with OBabel or with the CIF files > that have been generated? >
This CIF file is weird. I tried loading it in CCDC Mercury, which I consider the “gold standard” being developed by CCDC… Mercury doesn’t show any atoms either. Here’s why.. the file lists atoms like this: _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.partial_charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z LIG O O O 0.000 1.194 1.718 -0.148 LIG C8 C C 0.000 1.487 2.434 0.797 LIG C9 C CH2 0.000 2.931 2.880 1.022 Normally, atom positions have fields like: _atom_site_fract_x Now, it’s possible certainly to patch the parser and read this, but it’s a very non-standard use of CIF. -Geoff
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