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Describe the bug
If a structure with aromatic rings is provided in protonated form the atoms will not be aromatic.
As result when an aromatic protonated complex is used (regardless of config.NOHYDRO = True being set),
all pi-pi interactions are lost.
To Reproduce
This toy model shows what is going on:
Expected behavior
Pybel when reading a protonated PDB block with repeated CONECT for bond order (flavor &8 in RDKit and with the -s flag for OpenBabel, will correctly assume the benzene ring is formed of 6x sp3 atoms (w/ a proton and a radical), this is corrected to non-aromatic sp2 atoms w/ OBMol.PerceiveBondOrders() but these are not aromatic. I am not sure what the pybel command to perceive Kekule bonds is.
I mention this because the extracted ligand has sp2 carbons, even when the parsed protcomplex has aromatic carbons.
Additional context
A simple solution is strip all hydrogens.
This sounds a bit wasteful especially as far as I know there's not a way to provide a reference SMILES or a reference Molecule to assign the bond order —right?
In my case, my ligands may be strained and was hoping the hydrogens would help PerceiveBondOrders get things mostly right.
The text was updated successfully, but these errors were encountered:
Describe the bug
If a structure with aromatic rings is provided in protonated form the atoms will not be aromatic.
As result when an aromatic protonated complex is used (regardless of
config.NOHYDRO = True
being set),all pi-pi interactions are lost.
To Reproduce
This toy model shows what is going on:
Expected behavior
Pybel when reading a protonated PDB block with repeated CONECT for bond order (flavor &8 in RDKit and with the -s flag for OpenBabel, will correctly assume the benzene ring is formed of 6x sp3 atoms (w/ a proton and a radical), this is corrected to non-aromatic sp2 atoms w/
OBMol.PerceiveBondOrders()
but these are not aromatic. I am not sure what the pybel command to perceive Kekule bonds is.I mention this because the extracted ligand has sp2 carbons, even when the parsed protcomplex has aromatic carbons.
Additional context
A simple solution is strip all hydrogens.
This sounds a bit wasteful especially as far as I know there's not a way to provide a reference SMILES or a reference Molecule to assign the bond order —right?
In my case, my ligands may be strained and was hoping the hydrogens would help
PerceiveBondOrders
get things mostly right.The text was updated successfully, but these errors were encountered: