Hi all,
I have docking poses (from AutoDockVina) in a format that does not
provide bond information, and there is no information on hydrogens atoms
unless they are important for hydrogens bonds. I was assigning the bond
orders from the original reference structure or it's smiles string using
the methods in
https://gist.github.com/ptosco/4844d3635cf14d11e5e14381993915c1 using
AllChem.AssignBondOrdersFromTemplate() and adding the original hydrogens
back on. This approach does not work well when I have -COOH groups
present. In AssignBondOrdersFromTemplate, the substructure match almost
always assigns the oxygens the opposite way so that my resulting
structure is -C(OH)=OH which can't be sanitized in the end. I would like
to keep the configuration of the docking output.
Is there a way to correct that in an automated way? I have quite a few
poses with that problem and can't do that manually.
I have uploaded a gist with an example problem here:
https://gist.github.com/c4asma/b338321238d1924cc2964612ed278e9e
Here, oxygen with atom number 46 has the hydrogen, and number 45 should
be assigned a double bond (input 7). But, after
AllChem.AssignBondOrdersFromTemplate() oxygen 46 is assigned the double
bond (input 15)
Thank you,
Mariana
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