Hi Rafael,
You might find the RDKitSearchSMARTS.py <http://www.mayachemtools.org/docs/scripts/html/RDKitSearchSMARTS.html> script helpful for filtering molecules using the SMARTS pattern Pat has provided in his response. For example: % RDKitSearchSMARTS.py -p '[!#1;!C;!O;!N;!S;!P;!F;!Cl;!Br;!I;!c;!o;!n;!s;!p;!Na;!K;!Mg;!Ca;!Li]' -i Sample.smi -o SampleOut.smi --outfileFiltered yes % RDKitSearchSMARTS.py -n yes -p '[!#1;!C;!O;!N;!S;!P;!F;!Cl;!Br;!I;!c;!o;!n;!s;!p;!Na;!K;!Mg;!Ca;!Li]' -i Sample.sdf -o SampleOutNotOrganic.sdf Manish From: Patrick Walters <[email protected]> Sent: Saturday, March 5, 2022 6:17 PM To: Rafael L <[email protected]> Cc: rdkit-discuss <[email protected]> Subject: Re: [Rdkit-discuss] Find structures with "non-organic" atoms Here's what I use. not_organic_pat = Chem.MolFromSmarts("[!#1;!C;!O;!N;!S;!P;!F;!Cl;!Br;!I;!c;!o;!n;!s;!p;!Na;!K;!Mg;!Ca;!Li]") cisplatin = Chem.MolFromSmiles("[NH3+]-[Pt-2](Cl)(Cl)[NH3+]") cisplatin.HasSubstructMatch(not_organic_pat) On Sat, Mar 5, 2022 at 8:08 PM Rafael L via Rdkit-discuss <[email protected] <mailto:[email protected]> > wrote: Dear all, I remember having used some SMARTS-based function to flag structures containing "non-organic" atoms. It seems that there is a knime node for that (https://forum.knime.com/t/rdkit-molecule-substructure-filter-incorrectly-matches-aromatic-sulfur-atoms-molecule-as-metal-containing-compounds/12935), but I wasn't able to find any Python implementations. Does anyone know where to find it? Thanks in advance -- Rafael da Fonseca Lameiro PhD Student - Medicinal and Biological Chemistry Group (NEQUIMED) São Carlos Institute of Chemistry - University of São Paulo - Brazil <https://info.orcid.org/wp-content/uploads/2020/12/orcid_16x16.gif> <https://orcid.org/0000-0003-4466-2682> https://orcid.org/0000-0003-4466-2682 _______________________________________________ Rdkit-discuss mailing list [email protected] <mailto:[email protected]> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
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