When I cut the bonds in the daylight implementation, I add new single bonds to
xenon atoms – this means the ‘imidazole’ fragment would be [Xe]n1ccnc1, which
*is* a valid smiles. The following python code could then be used to convert
these Xe atoms to hydrogen,
from rdkit import Chem
Hi Pavel,
It is, unfortunately, not that easy.
The canonicalization algorithm does not use atomic aromaticity when
determining atom ordering, so as far as it is concerned there is no
difference between atoms 0 and 2 in either of your examples. What does get
used is the number of hydrogens, so you
Hello, I would like to draw molecules with rdkit, but only have inchikeys.
I compiled rdkit with inchi support but it seems that I can only output
inchikeys but not import them.
Are there any api function that I am missing ?
I believe InchiKey uses a 1 way hash (sha-256), so what you are asking for is
basically impossible. That is, to go from InchiKey to molecule requires already
having a table of molecules corresponding to the InchiKeys. There are various
services online that have such lookup tables for a large
Hi all,
canonicalization of fragment SMILES does not work properly. Below
there are two examples of identical fragments. The only difference is
the order of atoms (indices). However, it seems that RDKit
canonicalization does not take into account atom types.
Does someone have an idea
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