Jens,
I think what you're looking for is matched molecular pair finding. What you
have described I think is encoding a transformation that captures the local
chemical environment.
There are open source scripts for RDKit, and also proprietary methods.
There are some sublties on all pair finding code which may need adjusting, as
the configuration can make a significant difference.
If you would like to discuss more, mail me directly, we have a huge amount of
experience in the area.
http://pubs.acs.org/doi/abs/10.1021/jm200452d
http://pubs.acs.org/doi/abs/10.1021/acs.jcim.7b00335
Best regards,
Ed
Dr Ed Griffen,
Technical Director,
mobile +44 7762 121593
office +44 1625 238843
ed.grif...@medchemica.com
www.medchemica.com
skype: ed.griffen
Twitter: @MedChemica
Medchemica Ltd is a company registered in England and Wales with company number
8162245.
Confidentiality Notice: This message is private and may contain confidential,
proprietary and legally privileged information. If you have received this
message in error, please notify us and remove it from your system and note that
you must not copy, distribute or take any action in reliance on it. Any
unauthorised use or disclosure of the contents of this message is not permitted
and may be unlawful.
Disclaimer: Email messages may be subject to delays, interception, non-delivery
and unauthorised alterations. Therefore, information expressed in this message
is not given or endorsed by MedChemica Limited unless otherwise notified by an
authorised representative independent of this message. No contractual
relationship is created by this message by any person unless specifically
indicated by agreement in writing other than email.
Monitoring: MedChemica Limited retains and monitors all email traffic data and
content for the purposes of the prevention and detection of crime, ensuring the
security of our computer systems and checking compliance with our policies.
> On 3 Nov 2017, at 13:15, Jens Kristian Munk <jens.kristian.m...@regionh.dk>
> wrote:
>
> Hi list,
>
> I’ve searched far and wide for an answer to this; I apologize if the answer
> is obvious...
>
> I can use rdFMCS
> (http://www.rdkit.org/Python_Docs/rdkit.Chem.rdFMCS-module.html
> <http://www.rdkit.org/Python_Docs/rdkit.Chem.rdFMCS-module.html>) to find the
> maximum common substructure of a set of molecules... But how do I find the
> difference(s) between two (or more) molecules?
>
> I work with lipids a lot, so for example, the difference between palmitoic
> acid (C16:0) and stearic acid (C18:0) is SMILES ‘CC’. I would like RDkit to
> tell me just that, as well as tell me where on the maximum common
> substructure (which in this example is palmitoic acid) to add the ‘CC’ to get
> stearic acid – i.e. on the terminus of the fatty chain.
>
> Any ideas?
>
> The example above is just the first step. After that comes identifying and
> locating double bonds in the fatty chains... And then jump to phospholipids,
> with two fatty chains and a head group... J
>
> Med venlig hilsen
>
> Jens Kristian Munk
> Kemiker, Cand. Scient., Ph.D.
>
> Telefon: 3862 0398
> Mobil: 5142 3483
> E-mail: jens.kristian.m...@regionh.dk <mailto:jens.kristian.m...@regionh.dk>
>
> Klinisk Biokemisk afdeling
> Amager og Hvidovre hospital
> Kettegård Allé 30
> 2650 Hvidovre
>
> Web: www.regionh.dk <http://www.regionh.dk/>
>
>
>
>
> Denne e-mail indeholder fortrolig information. Hvis du ikke er den rette
> modtager af denne e-mail eller hvis du modtager den ved en fejltagelse, beder
> vi dig venligst informere afsender om fejlen ved at bruge svarfunktionen.
> Samtidig bedes du slette e-mailen med det samme uden at videresende eller
> kopiere den.
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org <http://slashdot.org/>!
> http://sdm.link/slashdot_______________________________________________
> <http://sdm.link/slashdot_______________________________________________>
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> <mailto:Rdkit-discuss@lists.sourceforge.net>
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
> <https://lists.sourceforge.net/lists/listinfo/rdkit-discuss>
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
