Interpreting the results of controllingAtoms (stereoAtoms) in StereoInfo #7411
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I have trouble interpreting the results of the controllingAtoms vector as returned by Here is an example to illustrate:
stereo_description_double_bond {6: rdkit.Chem.rdchem.StereoDescriptor.Bond_Cis} stereo_atoms_from_cip {6: [5, 19, 8, 4294967295]} bond_stereo_from_smi {6: rdkit.Chem.rdchem.BondStereo.STEREOE} stereo_atoms_from_smi {6: [19, 8]}
stereo_description_double_bond {5: rdkit.Chem.rdchem.StereoDescriptor.Bond_Trans} stereo_atoms_from_cip {5: [3, 4294967295, 7, 4294967295]} bond_stereo_from_smi {5: rdkit.Chem.rdchem.BondStereo.STEREOE} stereo_atoms_from_smi {5: [3, 7]}
stereo_description_double_bond {1: rdkit.Chem.rdchem.StereoDescriptor.Bond_Cis} stereo_atoms_from_cip {1: [0, 4294967295, 3, 4]} bond_stereo_from_smi {1: rdkit.Chem.rdchem.BondStereo.STEREOE} stereo_atoms_from_smi {1: [0, 4]} Note that each time the 'correct' (i.e. matching the smiles' identification) atom indices are identified by |
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Replies: 1 comment
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@najwalb The controlling atoms in a StereoInfo object (the objects returned by To interpret the values:
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@najwalb The controlling atoms in a StereoInfo object (the objects returned by
FindPotentialStereo()
) are in the order:[begin_atom_neighbor1, begin_atom_neighbor2, end_atom_neighbor1, end_atom_neighbor2]
If either begin_atom or end_atom have only one neighbor then their neighbor2 slot can have the placeholder value
Chem.StereoInfo.NOATOM
(which is 4294967295).I don't think there should be any cases where either begin_atom_neighbor1 or end_atom_neighbor1 are equal to
Chem.StereoInfo.NOATOM
To interpret the values:
Bond_Cis
means thatbegin_atom_neighbor1
andend_atom_neighbor1
are cis with respect to each other (on the same side of the double bond)Bond_Trans
means thatbegin_atom_neigh…