Hello,
There are several solutions, some free and open source.
I have used this one recently:
https://github.com/flatkinson/standardiser
Matt Swain mentions several others in his own one:
https://github.com/mcs07/MolVS
- RSC Chemistry Validation and Standardization Platform (CVSP)
- PubChem Standardization Service
- Tripod Structure standardizer
- FDA Substance Registration System Standard Operating Procedure
- ChemAxon Structure Standardizer
Regards,
Francois.
-------- Forwarded Message --------
Subject: Re: [Rdkit-discuss] Fingerprints standardization and cleaning
Date: Fri, 14 Sep 2018 10:20:22 +0200
From: Alexis Parenty <alexis.parenty.h...@gmail.com>
To: mario.lovri...@gmail.com
CC: RDKit Discuss <rdkit-discuss@lists.sourceforge.net>
Hi Mario, I use the python library MolVS (from Matt Swain, 2016)
https://molvs.readthedocs.io/en/latest/
Features<https://molvs.readthedocs.io/en/latest/#features>
* Normalization of functional groups to a consistent format.
* Recombination of separated charges.
* Breaking of bonds to metal atoms.
* Competitive reionization to ensure strongest acids ionize first in
partially ionize molecules.
* Tautomer enumeration and canonicalization.
* Neutralization of charges.
* Standardization or removal of stereochemistry information.
* Filtering of salt and solvent fragments.
* Generation of fragment, isotope, charge, tautomer or
stereochemistry
insensitive parent structures.
* Validations to identify molecules with unusual and potentially
troublesome characteristics.
Best,
Alexis
On Thu, 13 Sep 2018 at 20:47, Mario Lovrić <mario.lovri...@gmail.com
<mailto:mario.lovri...@gmail.com>> wrote:
Dear all,
What is your experience in preparing a compound set for fingerprint
generation, do you follow the same procedures as for descriptors
(remove salts, remove metals etc)?
Does anyone have a cleaning procedure to recommend?
Thank you in advance.
-- Mario Lovrić
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
<mailto:Rdkit-discuss@lists.sourceforge.net>
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
