Dear all,
I construct my own rdkit.Mol objects from mmcif files. I wanted to use mol.GetNumAtoms(onlyExplicit=True) to get the number of heavy atoms for that molecule, however, I have noticed that the function returns all the time number of all atoms in the molecule including hydrogens (47 vs. expected 31). When I try to iterate over the atoms to get number of Implicit/Explicit Hs for each atom I get 0 for all the atoms in the molecule, although the element types are correct (C’s, O’s, H’s etc.) So I assume that I construct the molecule incorrectly and wonder if there’s a way to tag hydrogen atoms correctly when I construct them. Hydrogens are explicitly present in my input structures and I’d like to get GetNumAtoms(onlyExplicit=True) function to work as expected. Attached is a python pickle of ATP molecule with two conformations. Interestingly rdkit.Chem.Descriptors.HeavyAtomCount(self.mol) returns correct value as expected. My configuration: OS: MacOS: 10.14.4 Rdkit: 2019.03.01 Python: 3.7.3 Best, Lukas
ATP.pickle
Description: Binary data
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