Over the last few days I've developed a command-line tool that I call "smiview".
It's a SMILES viewer. It isn't a depiction tool where the input is in SMILES
but rather a tool to highlight different aspects of the SMILES string.
I'll put some examples at the end. If you want to try it out you
Hi Chris
yesterday I realize about this and using the following command appears to
do the job:
for cid in cids: AllChem.ConstrainedEmbed(newMol3D,coreMol,useTethers=True)
...
but then I cannot save the conformers because something is different:
for cid in cids:
Hi Felipe
You're doing something similar to the problem Paolo addressed.
ConstrainedEmbed (see
http://www.rdkit.org/Python_Docs/rdkit.Chem.AllChem-module.html#ConstrainedEmbed)
requires a mol object as the first parameter, but you are passing it an
integer cid value, not a molecule. Your code
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