Re: [Rdkit-discuss] comparing two or more tables of molecules

[Stephen O'h. <SO...@ma...>]

I think fingerprint based comparison will still not cope with equivalent structures – and I doubt that they’re guaranteed to be ‘collision’ free.

Cheers,
Steve.

From: Christos Kannas [mailto:chr...@gm...]
Sent: 28 November 2016 17:32
To: Stephen O'hagan <SO...@ma...>
Cc: rdk...@li...
Subject: Re: [Rdkit-discuss] comparing two or more tables of molecules

Hi Steve,

I think it would be better to use a similarity metric based on fingerprints.

Regards,

Christos

Christos Kannas

Researcher
Ph.D Student

On 28 November 2016 at 18:25, Stephen O'hagan <SO...@ma...<mailto:SO...@ma...>> wrote:
Has anyone come up with fool-proof way of matching structurally equivalent molecules?

Unique Smiles or InChI String comparisons don’t appear to work presumable because there are different but equivalent structures, e.g. explicit vs non-explicit H’s, Kekule vs Aromatic, isomeric forms vs non-isomeric form, tautomers etc.

I also expect that comparing InChI strings might need something more than just a simple string comparison, such as masking off stereo information when you don’t care about stereo isomers.

I assume there are suitable tools within RDKit that can do this?

N.B. I need to collate tables from several sources that have a mix of smiles / InChI / sdf molecular representations.

I usually use RDKit via Python and/or Knime.

Cheers,
Steve.


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