> I've been trying to generate molecules programatically in Python when I found
> a buggy behavior.
When you're creating molecules programmatically, you need to make sure you set
the perception flags.
In your case, OBAtom calls:
OBResidue *OBAtom::GetResidue()
{
OBMol *mol = this->GetParent();
if (!mol->HasChainsPerceived())
chainsparser.PerceiveChains(*mol);
return _residue;
}
Since you didn't set OBMol::SetChainsPerceived(true) it's going to throw away
your perception, attempt to find the backbone, etc.
It's in the documentation, but generating molecules programmatically definitely
has some touch points:
> Residue information is preserved if the original OBMol is marked as having
> its residues perceived. If this is not desired, either call
> OBMol::SetChainsPerceived(false) in advance on the original OBMol to avoid
> copying the residues (and then reset it afterwards), or else call it on the
> new OBMol so that residue information will be reperceived (when requested).
Hope that helps,
-Geoff
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