Hi JP,
Do you want to do a shape align or just any sort of alignment?
There is a MolAlign in All.Chem which will give you an RMSD align. This works
well if you have reasonably similar molecules (do a GetSubstructMatch before to
get the atom list).
Don't think there is a shape alignment for whole molecules – there is however
the subshapeAligner module in rdkit.Chem but I never used this one.
Ciao
Nik
From: JP <[email protected]<mailto:[email protected]>>
Date: Tue, 22 Jan 2013 12:20:15 +0000
To:
"[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Subject: [Rdkit-discuss] Volume Overlap using RDKit
RDKitters,
Long time no type, I've been busy with that little chestnut of my PhD...
I would like to align two molecules and calculate the shape tanimoto with
ShapeTanimotoDist(...). The issue is that this method requires a pre-defined
alignment - which I do not have.
Is there a way how to do a molecular volume overlap in RDKit? I cannot seem to
find it and the only related discussion I can find is
here<http://www.mail-archive.com/[email protected]/msg00512.html>.
But the fourth slide
here<http://www.slideshare.net/baoilleach/cinfony-bring-cheminformatics-toolkits-into-tune>,
clearly states that RDKit is able to do this.
If this is not RDKit-doable anyone else has come across some publicly available
tools to do this? A quick search lead me to
Shape-it<http://silicos-it.com/software/shape-it/1.0.1/shape-it.html>, from
Hans (who I met at the user group meeting) - anyone used this before?
p.s. no one ever sent/made available the group photo we took at the 1st RDKit
meeting :(
-
Jean-Paul Ebejer
Early Stage Researcher
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