Hey everyone,
I have a question concerning the Chem.MolToMolFile() function.
When I open this file containing a N+ (here is the line corresponding in
the mol file) :
11.37003.4360 -11.8300 N 0 3 0 0 0 0 0 0 0 0 0 0
And I just save it back withotu any modification, the line
Hi Colin,
The RDkit outputs charge information to mol blocks using the CHG line:
In [3]: m = Chem.MolFromSmiles('C[NH3+]')
In [4]: print(Chem.MolToMolBlock(m))
RDKit 2D
2 1 0 0 0 0 0 0 0 0999 V2000
0.0.0. C 0 0 0 0 0 0 0 0 0 0 0 0
Well yes I have this line indeed, I did not put the whole file for
clarity purpose. The thing is tools as MOE, Pymol read it without
problem but RDock for example can't read it properly and returns a
neutral N which is not the case. And if I open it with pymol and save it
back in mol format, th
Dear Colin,
this is a specific problem I stumbled upon some time ago.[1]
I also mentioned it to the rDock mailing list.[2]
Maybe there is a better work-around, but in the meantime I wrote the
attached function.
It takes as input the Mol Block, which in my case are in a dataframe.
Hope that help
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