Hi, Thanks for this, it gives me a start.
Cheers, Chris > On 21 Nov 2016, at 08:59, Richard Hall <richard.h...@astx.com> wrote: > > 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 > > > > ------------------------------------------------------------------------------ > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > This email and any attachments thereto may contain private, confidential, and > privileged material for the sole use of the intended recipient. Any review, > copying or distribution of this email (or any attachments thereto) by others > is strictly prohibited. If you are not the intended recipient, please delete > the original and any copies of this email and any attachments thereto and > notify the sender immediately. ------------------------------------------------------------------------------ _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss