Dear Joey,
you could use Chem.RenumberAtoms() to enforce Hs to always follow heavy
atoms in the atom list, e.g.:
from rdkit import Chem
from rdkit.Chem.Draw import IPythonConsole
IPythonConsole.drawOptions.addAtomIndices = True
IPythonConsole.molSize = (400, 400)
mol1 =
Dear All,
I have experienced a few consistency problems in 3D coordinate output with H's
not always at the end of the coordinate list.
RDKit mostly does this by default except in a few cases every few thousand and
even with simple organics.
How can I check/verify/enforce "H's at the end" on
Hello,
I have a baffling case where I am trying to match substructures on two
ligands for the goal of aligning them.
I have two ligands; one is a 6-chloroindole (6CI) and the other is a
para-chloro toluene (PCT).
I am attempting to use the following SMARTS (S1) to match
them:
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