Dear Michal,
You can use
http://rdkit.org/docs/source/rdkit.Chem.rdmolops.html?highlight=path#rdkit.Chem.rdmolops.GetShortestPath
or
http://rdkit.org/docs/source/rdkit.Chem.rdmolops.html?highlight=distance#rdkit.Chem.rdmolops.GetDistanceMatrix
e.g.:
from rdkit import Chem
cx=Chem.MolFromSmiles('C1CCCCC1')
bonds=(cx.GetBondBetweenAtoms(1,2).GetIdx(),
cx.GetBondBetweenAtoms(3,4).GetIdx())
fragmented=Chem.FragmentOnBonds(cx,bonds)
mat = Chem.GetDistanceMatrix(cx)
mat[1,2]
1.0
Chem.GetShortestPath(cx, 1, 2)
(1, 2)
mat = Chem.GetDistanceMatrix(fragmented)
mat[1, 2]
100000000.0
Chem.GetShortestPath(fragmented, 1, 2)
()
Cheers,
p.
On 04/06/2020 16:17, Michal Krompiec wrote:
Hello,
When a molecule is fragmented with Chem.FragmentOnBonds, how can I
check if there still is a path between two given atoms?
For example, this snippet breaks C1-C2 and C3-C4 bonds in cyclohexane,
producing two fragments:
from rdkit import Chem
cx=Chem.MolFromSmiles('C1CCCCC1')
bonds=(cx.GetBondBetweenAtoms(1,2).GetIdx(),
cx.GetBondBetweenAtoms(3,4).GetIdx())
fragmented=Chem.FragmentOnBonds(cx,bonds)
Is there a way in RDKit to check if there is a path between, say, C1
and C2, without having to manually traverse the whole molecular graph?
I guess the alternative is to load everything into a graph library
like networkx...
Best wishes,
Michal Krompiec
Merck KGaA
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