David,
Thank you very much for the reply, very smart hack!
Sam
On Wed, Aug 31, 2016 at 7:27 PM, David Hall wrote:
> It is a bit of a hack, but for certain applications where I know it is
> likely fine, I use networkx to do subgraph isomorphism while considering
> only the elements and not loo
It is a bit of a hack, but for certain applications where I know it is
likely fine, I use networkx to do subgraph isomorphism while considering
only the elements and not looking at the order of the bonds. I can
trivially draw a molecule where this does the wrong thing, but the majority
of the time,
Dear Sefano,
Thanks for the reply, I was suspecting the same. However I need the PDB 3D
coordinates mapped on the original SMILES, that's why I was trying reading
the PDB. I am wondering if there are any methods to map the PDB coordinates
of a molecule to its original SMILES?
Thanks,
Sam
On Wed
Sam,
I wouldn't trust the PDB for either bond order or connectivity.
In OB the order is inferred from the distances, which are dependent on the
quality of the
structure and the software used for the model refinement.
For example, I found that in structures generated a version of Refmac, the
oxy
I am trying to read a small molecule from PDB file and match its atom
numbers to the same molecule in a SDF file. I have tried both matching
SMART patterns and using OBIsomorphismMapper, both work for 70% of cases.
However there are cases for which OpenBabel can not simply get the right
SMILES from