Re: [Rdkit-discuss] Deuterium/Tritium labels in Molfile
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Re: [Rdkit-discuss] Deuterium/Tritium labels in Molfile
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From: Santiago F. <san...@me...> - 2023-04-11 11:25:13
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Dear Paolo
It is a requirement of some users to maintain the D,T labels in the molfiles,
but I will check if it could be skipped.
Regards
Santiago
[http://www.mestrelab.com/mestrelab/wp-content/uploads/signs/line3.jpg]
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SANTIAGO FRAGA
Software Developer
san...@me...<mailto:%20s...@me...>
MESTRELAB RESEARCH S.L.
PHONE +34881976775
FAX +34981941079
Feliciano Barrera, 9B-Bajo 15706
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________________________________
De: Paolo Tosco <pao...@gm...>
Enviado: martes, 11 de abril de 2023 12:17
Para: Santiago Fraga <san...@me...>
Cc: rdk...@li... <rdk...@li...>
Asunto: Re: [Rdkit-discuss] Deuterium/Tritium labels in Molfile
Dear Santiago,
Using D and T symbols for deuterium and tritium in MDL molfiles is outside the file format specification.
Nonetheless, RDKit correctly parses those non-standard D and T symbols when reading an MDL molfile that contains them, as you can verify yourself through a simple test and also looking at the source code:
<https://github.com/rdkit/rdkit/blob/36c4ec9e2ba4f5edba39f452cb7458230d9d99bc/Code/GraphMol/FileParsers/MolFileParser.cpp#L1506>
[rdkit.png]
rdkit/MolFileParser.cpp at 36c4ec9e2ba4f5edba39f452cb7458230d9d99bc · rdkit/rdkit<https://github.com/rdkit/rdkit/blob/36c4ec9e2ba4f5edba39f452cb7458230d9d99bc/Code/GraphMol/FileParsers/MolFileParser.cpp#L1506>
github.com<https://github.com/rdkit/rdkit/blob/36c4ec9e2ba4f5edba39f452cb7458230d9d99bc/Code/GraphMol/FileParsers/MolFileParser.cpp#L1506>
https://github.com/rdkit/rdkit/blob/36c4ec9e2ba4f5edba39f452cb7458230d9d99bc/Code/GraphMol/FileParsers/MolFileParser.cpp#L2179
However, when writing the molfile, RDKit will write it according to specifications, i.e. using the H symbol and adding a “M ISO” entry. Any MDL molfile parser should be able to correctly parse such a file. ChemDraw will even automatically label the atoms as D and T, while MarvinJS will add the “2” and “3” superscript prefixes.
To me, it seems a bit overkill to add a flag to preserve non-standard features in MDL molfile writing. Why would you be interested in doing that?
Cheers,
p.
On 11 Apr 2023, at 11:50, Santiago Fraga <san...@me...> wrote:
Many thanks for your examples, Wim.
But I was checking the option to save the labels D and T in the molfile for the hydrogen isotopes,
as other tools can do.
Regards
Santiago
[http://www.mestrelab.com/mestrelab/wp-content/uploads/signs/line3.jpg]
[http://www.mestrelab.com/mestrelab/wp-content/uploads/signs/M-red-200pxb.jpg]<http://www.mestrelab.com>
SANTIAGO FRAGA
Software Developer
san...@me...<mailto:%20s...@me...>
MESTRELAB RESEARCH S.L.
PHONE +34881976775
FAX +34981941079
Feliciano Barrera, 9B-Bajo 15706
Santiago de Compostela (SPAIN)
Follow us:
[Mestrelab Twitter]<https://twitter.com/mestrelab> [Mestrelab Linkedin] <https://www.linkedin.com/company/mestrelab-research> [Canal de YouTube Mestrelab] <https://www.youtube.com/channel/UCf3MVnd3XZflv0acvTv14ww> [MestreBlog] <http://mestrelab.com/blog/>
________________________________
De: Wim Dehaen <wim...@gm...>
Enviado: lunes, 10 de abril de 2023 18:07
Para: Santiago Fraga <san...@me...>
Cc: rdk...@li... <rdk...@li...>
Asunto: Re: [Rdkit-discuss] Deuterium/Tritium labels in Molfile
rdkit outputs a molfile with correct isotope labels for me using just:
mol=Chem.MolFromSmiles("[3H]c1ccccc1[2H]")
Chem.MolToMolFile(mol,"test.mol")
or labelling the atoms post hoc:
mol=Chem.MolFromSmiles("c1ccccc1")
mol=Chem.AddHs(mol)
mol.GetAtomWithIdx(6).SetIsotope(3)
mol.GetAtomWithIdx(7).SetIsotope(2)
mol=Chem.RemoveHs(mol)
Chem.MolToMolFile(mol,"test2.mol")
I hope this helps
best wishes
wim
On Mon, Apr 10, 2023 at 4:43 PM Santiago Fraga <san...@me...<mailto:san...@me...>> wrote:
Good afternoon!
I am a relatively new user of RDKit, and mainly the C++ API.
I am trying to save in a molfile the labels D and T for the hydrogen isotopes.
Like in the following molfile:
MJ230401
8 8 0 0 0 0 0 0 0 0999 V2000
-0.3572 0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.0716 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.0716 -0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3572 -1.2375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.3572 -0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.3572 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3572 1.2375 0.0000 T 0 0 0 0 0 0 0 0 0 0 0 0
1.0717 0.4125 0.0000 D 0 0 0 0 0 0 0 0 0 0 0 0
3 4 2 0 0 0 0
4 5 1 0 0 0 0
5 6 2 0 0 0 0
6 1 1 0 0 0 0
1 2 2 0 0 0 0
2 3 1 0 0 0 0
6 8 1 0 0 0 0
1 7 1 0 0 0 0
M END
I am trying to set directly the labels in the hydrogen atoms:
atom->setProp<string>("atomLabel", "D");
or
atom->setProp<string>("_displayLabel", "D");
But when the molfile is generated the labels are not transferred.
It seems also that when reading a mofile including the labels, they are discarded.
Many thanks in advance
Santiago Fraga
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