The documentation for GetNumAtoms says it takes an optional parameter: onlyHeavy: (optional) include only heavy atoms (not Hs) defaults to 1
In testing it with the attached SD file I found that it included the four
hydrogens with mass difference of 1
6.0300 -2.1729 0.0000 H 1 0 0 0 0 0 0 0 0 0 0 0
7.7794 0.0209 0.0000 H 1 0 0 0 0 0 0 0 0 0 0 0
7.2965 -3.1829 0.0000 H 1 0 0 0 0 0 0 0 0 0 0 0
9.0460 -0.9892 0.0000 H 1 0 0 0 0 0 0 0 0 0 0 0
8.8045 -2.5911 0.0000 H 1 0 0 0 0 0 0 0 0 0 0 0
It should have reported 28 heavy atoms (defined as non-hydrogens) and not 33.
This was from
> <PUBCHEM_COMPOUND_CID>
6914095
> <PUBCHEM_OPENEYE_ISO_SMILES>
[2H]C1=C(C(=C(C(=C1[2H])[2H])C2=NC(C(=O)N(C3=C2C=C(C=C3)Cl)[Si](C)(C)C)O[Si](C)(C)C)[2H])[2H]
My guess is that it treats the deuterium as explicit hydrogens but doesn't take
that into account when doing the heavy atom calculations.
I'm assuming the problem is from ROMol::getNumAtoms
int res = boost::num_vertices(d_graph);
if (!onlyHeavy) {
// if we are interested in hydrogens as well add them up from
// each heavy atom
ConstAtomIterator ai;
for (ai = beginAtoms(); ai != endAtoms(); ai++) {
res += (*ai)->getTotalNumHs();
}
}
return res;
where the if (onlyHeavy) case does not remove count of any verticies which are
hydrogens.
problem.sdf
Description: Binary data
Andrew
[email protected]
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