Hi Mariana,
if you modify your Jupyter notebook as in
https://gist.github.com/ptosco/d807c64df9f277e92284bc5a7cecbc1d
then it should work also in the presence of graph isomorphisms.
Cheers,
p.
On 12/13/18 12:18, Mariana Assmann wrote:
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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