Thank you, all! Here is my Python implementation for anyone interested:
# Check for compounds with "non-organic" atoms
not_organic_pat =
Chem.MolFromSmarts("[!#5;!#6;!#7;!#8;!#16;!#15;!F;!Cl;!Br;!I;!#1]")
# not_organic_pat =
One minor refinement... Pat's answer can be made a bit more efficient by
replacing the atom types which appear in both aromatic and aliphatic forms
with the corresponding atom number queries and by moving the !#1 to the
end. This should produce the same results as Pat's SMARTS:
not_organic_pat =
alters
Sent: Saturday, March 5, 2022 6:17 PM
To: Rafael L
Cc: rdkit-discuss
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
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 <
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 (
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