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

r.ac.uk>; > rdkit-discuss@lists.sourceforge.net; Francis Atkinson <fran...@ebi.ac.uk> > Subject: Re: [Rdkit-discuss] comparing two or more tables of molecules > > HI Stephen, > > Further to Greg's excellent reply, see this paper on how InChI strings and > keys ca

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

Well, since George mentioned a talk by me, I wish we would have implemented our tool back then using an open-source tool like RDKit (which wasn't very well know back then), and also would have been so smart to use SMARTS for the transformation rules (partially they are implemented as SMARTS but

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

rceforge.net; Francis Atkinson <fran...@ebi.ac.uk> Subject: Re: [Rdkit-discuss] comparing two or more tables of molecules HI Stephen, Further to Greg's excellent reply, see this paper on how InChI strings and keys can be used in practice to map together tautomer (ones covered by InChI a

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

HI Stephen, Further to Greg's excellent reply, see this paper on how InChI strings and keys can be used in practice to map together tautomer (ones covered by InChI at least), isotope, stereo and parent-salt variants. http://rd.springer.com/article/10.1186/s13321-014-0043-5 Francis (cc'ed) has a

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

On 11/29/2016 11:56 AM, Chris Swain wrote: > However I’ve found that the success is very much dependent on the > fact 1 described by Greg, get all the structures standardised then comparison using canonical SMILES or InChi seems to work fine. +1. Essentially you need to get standardized

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

Hi, I’ve done this sort of comparison many times I actually use a SVL script within Moe and there is an example here (http://www.cambridgemedchemconsulting.com/resources/hit_identification/fragment_collection_profiles.html

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

Wow, this is a great question and quite a fun thread. It's hard to really make much of a contribution here without writing a book/review article (something that I'm really not willing to do!), but I have a few thoughts. Most of this is repeating/rephrasing things others have already said. I'm

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

The Layered InChI (LyChi), developed by Trung Nguyen at NCATS was designed to directly address the problem you describe. I don't have any first hand experience with this method (yet), but it looks intriguing. https://github.com/ncats/lychi Pat On Mon, Nov 28, 2016 at 11:25 AM, Stephen O'hagan

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

On 11/28/2016 10:25 AM, Stephen O'hagan wrote: > Has anyone come up with fool-proof way of matching structurally equivalent > molecules? This is somewhat convoluted and there is no proof that it's fool-proof. A few years ago we had good results from running graphpowerhash() function here:

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

On Mon, Nov 28, 2016 at 11:31 AM, Christos Kannas wrote: I think it would be better to use a similarity metric based on fingerprints. > Hi Christos, Fingerprints will only work if the fingerprint method you use captures all of the salient information you're interested

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

It really boils down to how you standardize molecules such that you end up with a canonical structure. SMILES not the issue here - if you standardizer does a proper job with aromaticity, tautomers etc then you can get a canonical SMILES. You can use the InChI model as well as to generate a

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 [image: View Christos Kannas's profile on LinkedIn] On 28 November 2016 at 18:25, Stephen O'hagan

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

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