Hi Lukas,
in the RDKit notation all atoms are explicit if they are present in the
molecule graph, including hydrogens. You mention that hydrogens are
explicitly present in your input structure, so that's the expected
behaviour.
If you wish to retrieve the number of heavy atoms you can use
mol.GetNumHeavyAtoms().
If you want to remove hydrogens from the molecule graph and make them
implicit, you may call Chem.RemoveHs().
Hope this helps, cheers
p.
On 05/01/19 15:23, Lukas Pravda wrote:
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
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