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
HYDROGEN = 1
XENON = 54
m = Chem.MolFromSmiles('[Xe]n1ccnc1')
for a in m.GetAtoms():
if a.GetAtomicNum() == XENON:
a.SetAtomicNum(HYDROGEN)
n = Chem.RemoveHs(m)
print Chem.MolToSmiles(n)
hopefully that is useful. Please fire away if you have any further questions
or would like help with any other aspects of this – it will be great to have an
RDKit version available for people to use ☺
Rich
From: Konrad Koehler [mailto:konrad.koeh...@icloud.com]
Sent: 01 August 2017 05:29
To: rdkit-discuss@lists.sourceforge.net
Subject: [Rdkit-discuss] kekulize AllChem.CanonSmiles error and workaround
Hi,
I am having trouble canonicalizing smiles with ambiguous heteroaromatic
tautomers such as imidazole. For example:
>>> from rdkit import Chem
>>> from rdkit.Chem import AllChem
>>> smiles = ‘n1cncc1'
>>> AllChem.CanonSmiles(smiles)
[21:42:52] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4
As a workaround, one can first canonicalize with Open Babel pybel to remove the
ambiguity and then canonicalize with RDKit:
>>> import pybel
>>> pybel.readstring("smi", "n1cncc1").write("can")
'c1ncc[nH]1\t\n'
>>> AllChem.CanonSmiles('c1ncc[nH]1\t\n')
'c1c[nH]cn1’
or in one line:
>>> AllChem.CanonSmiles(pybel.readstring("smi", "n1cncc1").write("can"))
'c1c[nH]cn1'
It would be nice if RDKit could do this without the assistance of pybel.
This problem arose when implementing the algorithm described in the following
paper:
Hall RJ, Murray CW, Verdonk ML. The Fragment Network: A Chemistry
Recommendation Engine Built Using a Graph Database. J Med Chem. 2017;
60(14):6440-50. PMID: 28712298, doi: 10.1021/acs.jmedchem.7b00809
Details of the algorithm are contained in supporting information:
http://pubs.acs.org/doi/suppl/10.1021/acs.jmedchem.7b00809/suppl_file/jm7b00809_si_001.pdf
The algorithm fragments the molecule at acyclic bonds connected to rings and it
is necessary to canonicalize both the parent and child fragments. The algorithm
is recursive and fortunately the smiles can be recursively processed by
AllChem.CanonSmiles after it has been disambiguated:
>>> AllChem.CanonSmiles('c1c[nH]cn1')
'c1c[nH]cn1’
I eventually plan to donate the RDKit Fragment Network script to the community
after testing and optimization.
Best,
Konrad
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