Thanks Niko, Taka for your prompt replies.
My molecules are not guaranteed to have some common substructure, so an
RMSD align is out of the question. I [think I] want a 3D alignment which
maximizes volume overlap between the two molecules.
-
Jean-Paul Ebejer
Early Stage Researcher
On 22 January 2013 14:10, Stiefl, Nikolaus <nikolaus.sti...@novartis.com>wrote:
> 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 <jeanpaul.ebe...@inhibox.com>
> Date: Tue, 22 Jan 2013 12:20:15 +0000
> To: "rdkit-discuss@lists.sourceforge.net" <
> rdkit-discuss@lists.sourceforge.net>
> 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/rdkit-discuss@lists.sourceforge.net/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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