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
>
>
>
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