We've been looking at something similar - the following code spits out a
canonical smiles string for each atom based at a radius of 1...maxradius.
def atomenvironments(mol, atno, maxradius=6):
for a in mol.GetAtoms():
idx = a.GetIdx()
print atno, idx, 0, a.GetSmarts()
for iradius in xrange(0, maxradius+1):
env = Chem.FindAtomEnvironmentOfRadiusN(mol, iradius,
idx)
amap = {}
submol=Chem.PathToSubmol(mol, env, atomMap=amap)
if amap.get(idx) is not None:
print atno, idx, iradius,
Chem.MolToSmiles(submol, rootedAtAtom=amap[idx], canonical=True)
You can then load the output into a DB for searching. You might be able to
tweak this to suit your purposes?
best wishes
Richard
-----Original Message-----
From: Chris Swain [mailto:sw...@mac.com]
Sent: 20 November 2016 18:44
To: rdkit-discuss@lists.sourceforge.net
Subject: [Rdkit-discuss] Atom Environments
Hi,
I have a project where I would like to find similar atom environments to a
specified atom in a selected molecule.
For example
Suppose I have this query molecule C1CNCC(C1)c1ccccc1, and the selected atom is
the nitrogen.
I also have a file containing SMILES strings and ID for a list of reference
molecules.
I would like to identify the molecule within the references molecules that
contains a nitrogen most similar to the selected atom in the query molecule
even if the rest of the molecule is very different.
My feeling is to start with say a 3 atom radius and if no similar atom is found
above a set similarity to repeat the search using a 2 atom radius, but to be
honest I suspect it will require a bit of trial and error to see what the
optimum radius is?
I'd then want to return the ID of the most similar molecule.
I’ve had a look through the examples but not found anything that close.
Cheers
Chris
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