date:20230411

Re: [Rdkit-discuss] Deuterium/Tritium labels in Molfile

2023-04-11 Thread Santiago Fraga

Many thanks again, Wim
I was just moving in that direction, modifying directly the resulting molfile.

Regards
Santiago

[http://www.mestrelab.com/mestrelab/wp-content/uploads/signs/line3.jpg]
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SANTIAGO FRAGA
Software Developer
santi...@mestrelab.com

MESTRELAB RESEARCH S.L.
PHONE +34881976775
FAX +34981941079
Feliciano Barrera, 9B-Bajo 15706
Santiago de Compostela (SPAIN)

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De: Wim Dehaen 
Enviado: martes, 11 de abril de 2023 11:25
Para: Santiago Fraga 
Cc: rdkit-discuss@lists.sourceforge.net 
Asunto: Re: [Rdkit-discuss] Deuterium/Tritium labels in Molfile

Sorry for not reading your question properly. I am personally not aware of a 
way to export molfiles in this way in rdkit, but I might just be unaware. I 
think the easiest solution would be probably changing the molblock string post 
hoc by reading the M  ISO line.

for example like this in python:
```
mol=Chem.MolFromSmiles("c1c21[3H].[2H]2")

def MolToMolfileDT(mol,path):
mb=Chem.MolToMolBlock(mol).split("\n")
iso=[x for x in mb[-3].split(" ") if len(x)>0]
if iso[1]=="ISO": #check if theres isotope info
for i in range(int(iso[2])):
isotope=int(iso[4+2*i])
idx=int(iso[3+2*i])+3
if isotope in [2,3]: #only D and T
mb[idx]=mb[idx].replace("H",{2:"D",3:"T"}[isotope]) #replace 
only H (to not have issues like [3Li])
with open(path, "w") as molfile:
molfile.write("\n".join(mb))
return

MolToMolfileDT(mol,"mol.mol")```

this returns:

 RDKit  2D

  8  8  0  0  0  0  0  0  0  0999 V2000
1.50000.0. C   0  0  0  0  0  0  0  0  0  0  0  0
0.7500   -1.29900. C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7500   -1.29900. C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.50000.0. C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.75001.29900. C   0  0  0  0  0  0  0  0  0  0  0  0
0.75001.29900. C   0  0  0  0  0  0  0  0  0  0  0  0
1.50002.59810. T   0  0  0  0  0  0  0  0  0  0  0  0
1.5000   -2.59810. D   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  6  1  1  0
  8  2  1  0
M  ISO  2   7   3   8   2
M  END


best wishes
wim


On Tue, Apr 11, 2023 at 9:14 AM Santiago Fraga 
mailto:santi...@mestrelab.com>> 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]

SANTIAGO FRAGA
Software Developer
santi...@mestrelab.com

MESTRELAB RESEARCH S.L.
PHONE +34881976775
FAX +34981941079
Feliciano Barrera, 9B-Bajo 15706
Santiago de Compostela (SPAIN)

Follow us:
[Mestrelab Twitter]  [Mestrelab Linkedin] 
   [Canal de YouTube 
Mestrelab]    
[MestreBlog] 




De: Wim Dehaen mailto:wimdeh...@gmail.com>>
Enviado: lunes, 10 de abril de 2023 18:07
Para: Santiago Fraga mailto:santi...@mestrelab.com>>
Cc: 
rdkit-discuss@lists.sourceforge.net 
mailto:rdkit-discuss@lists.sourceforge.net>>
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]c1c1[2H]")
Chem.MolToMolFile(mol,"test.mol")

or labelling the atoms post hoc:

mol=Chem.MolFromSmiles("c1c1")
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 
mailto:santi...@mestrelab.com>> 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
   -0.35720.41250. C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.07160.0. C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0716   -0.82500. C   0  0  0  0  0  0  0  0  0  0  0  0

Re: [Rdkit-discuss] Deuterium/Tritium labels in Molfile

2023-04-11 Thread Paolo Tosco

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:rdkit/MolFileParser.cpp at 36c4ec9e2ba4f5edba39f452cb7458230d9d99bc · rdkit/rdkitgithub.comhttps://github.com/rdkit/rdkit/blob/36c4ec9e2ba4f5edba39f452cb7458230d9d99bc/Code/GraphMol/FileParsers/MolFileParser.cpp#L2179However, 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  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













SANTIAGO FRAGA
Software Developer
santi...@mestrelab.com


MESTRELAB RESEARCH S.L.
PHONE +34881976775
FAX +34981941079
Feliciano Barrera, 9B-Bajo 15706
Santiago de Compostela (SPAIN)


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De: Wim Dehaen 
Enviado: lunes, 10 de abril de 2023 18:07
Para: Santiago Fraga 
Cc: rdkit-discuss@lists.sourceforge.net 
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]c1c1[2H]")
Chem.MolToMolFile(mol,"test.mol")


or labelling the atoms post hoc:


mol=Chem.MolFromSmiles("c1c1")
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  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. C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0716    0.    0. C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0716   -0.8250    0. C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3572   -1.2375    0. C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3572   -0.8250    0. C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3572    0.    0. C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3572    1.2375    0. T   0  0  0  0  0  0  0  0  0  0  0  0
    1.0717    0.4125    0. 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("atomLabel", "D");

        or
     atom->setProp("_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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Re: [Rdkit-discuss] Problems reading XYZ file

2023-04-11 Thread Jan Halborg Jensen

Hi Gustavo

raw_mol = Chem.MolFromXYZFile('acetate.xyz')
mol = Chem.Mol(raw_mol)
rdDetermineBonds.DetermineBonds(mol,charge=-1)

Best regards, Jan

On 7 Apr 2023, at 22.57, Gustavo Seabra 
mailto:gustavo.sea...@gmail.com>> wrote:

Hi everyone,

I'm having difficulties using RDKit to read molecules from an XYZ file, and I 
would really appreciate some help.

The problem is that whenever i read a molecule from an XYZ file, I get just a 
disconnected clump of atoms, not a molecule. For example: the following code:

import rdkit
from rdkit import Chem
from rdkit.Chem import Draw, rdmolfiles
mol = Chem.MolFromSmiles('COC1=C(O)C[C@@](O)(CO)CC1=O')
mol = Chem.AddHs(mol)
mol



Chem.AllChem.EmbedMolecule(mol)
Chem.MolToXYZFile(mol, "rdkit_mol.xyz")
mol2 = Chem.MolFromXYZFile('rdkit_mol.xyz')
mol2

Is there a bug on the XYZ code, or am I missing something?

Thanks!
--
Gustavo Seabra.
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Re: [Rdkit-discuss] Deuterium/Tritium labels in Molfile

2023-04-11 Thread Santiago Fraga

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]

SANTIAGO FRAGA
Software Developer
santi...@mestrelab.com

MESTRELAB RESEARCH S.L.
PHONE +34881976775
FAX +34981941079
Feliciano Barrera, 9B-Bajo 15706
Santiago de Compostela (SPAIN)

Follow us:
[Mestrelab Twitter]  [Mestrelab Linkedin] 
   [Canal de YouTube 
Mestrelab]    
[MestreBlog] 




De: Wim Dehaen 
Enviado: lunes, 10 de abril de 2023 18:07
Para: Santiago Fraga 
Cc: rdkit-discuss@lists.sourceforge.net 
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]c1c1[2H]")
Chem.MolToMolFile(mol,"test.mol")

or labelling the atoms post hoc:

mol=Chem.MolFromSmiles("c1c1")
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 
mailto:santi...@mestrelab.com>> 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
   -0.35720.41250. C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.07160.0. C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0716   -0.82500. C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3572   -1.23750. C   0  0  0  0  0  0  0  0  0  0  0  0
0.3572   -0.82500. C   0  0  0  0  0  0  0  0  0  0  0  0
0.35720.0. C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.35721.23750. T   0  0  0  0  0  0  0  0  0  0  0  0
1.07170.41250. 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("atomLabel", "D");
or
     atom->setProp("_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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Re: [Rdkit-discuss] Deuterium/Tritium labels in Molfile

2023-04-11 Thread Wim Dehaen

Sorry for not reading your question properly. I am personally not aware of
a way to export molfiles in this way in rdkit, but I might just be unaware.
I think the easiest solution would be probably changing the molblock string
post hoc by reading the M  ISO line.

for example like this in python:
```
mol=Chem.MolFromSmiles("c1c21[3H].[2H]2")

def MolToMolfileDT(mol,path):
mb=Chem.MolToMolBlock(mol).split("\n")
iso=[x for x in mb[-3].split(" ") if len(x)>0]
if iso[1]=="ISO": #check if theres isotope info
for i in range(int(iso[2])):
isotope=int(iso[4+2*i])
idx=int(iso[3+2*i])+3
if isotope in [2,3]: #only D and T
mb[idx]=mb[idx].replace("H",{2:"D",3:"T"}[isotope])
#replace only H (to not have issues like [3Li])
with open(path, "w") as molfile:
molfile.write("\n".join(mb))
return

MolToMolfileDT(mol,"mol.mol")```

this returns:

 RDKit  2D

  8  8  0  0  0  0  0  0  0  0999 V2000
1.50000.0. C   0  0  0  0  0  0  0  0  0  0  0  0
0.7500   -1.29900. C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7500   -1.29900. C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.50000.0. C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.75001.29900. C   0  0  0  0  0  0  0  0  0  0  0  0
0.75001.29900. C   0  0  0  0  0  0  0  0  0  0  0  0
1.50002.59810. T   0  0  0  0  0  0  0  0  0  0  0  0
1.5000   -2.59810. D   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  6  1  1  0
  8  2  1  0
M  ISO  2   7   3   8   2
M  END


best wishes
wim


On Tue, Apr 11, 2023 at 9:14 AM Santiago Fraga 
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
>
> 
>
> SANTIAGO FRAGA
> *Software Developer*
> santi...@mestrelab.com <+santi...@mestrelab.com>
>
> *MESTRELAB RESEARCH S.L.*
> PHONE *+34881976775*
> FAX *+34981941079*
> Feliciano Barrera, 9B-Bajo 15706
> Santiago de Compostela (SPAIN)
>
> Follow us:
> [image: Mestrelab Twitter]   [image:
> Mestrelab Linkedin] 
>  [image: Canal de YouTube Mestrelab]
>   [image:
> MestreBlog] 
>
>
>
> --
> *De:* Wim Dehaen 
> *Enviado:* lunes, 10 de abril de 2023 18:07
> *Para:* Santiago Fraga 
> *Cc:* rdkit-discuss@lists.sourceforge.net <
> rdkit-discuss@lists.sourceforge.net>
> *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]c1c1[2H]")
> Chem.MolToMolFile(mol,"test.mol")
>
> or labelling the atoms post hoc:
>
> mol=Chem.MolFromSmiles("c1c1")
> 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 
> 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
>-0.35720.41250. C   0  0  0  0  0  0  0  0  0  0  0  0
>-1.07160.0. C   0  0  0  0  0  0  0  0  0  0  0  0
>-1.0716   -0.82500. C   0  0  0  0  0  0  0  0  0  0  0  0
>-0.3572   -1.23750. C   0  0  0  0  0  0  0  0  0  0  0  0
> 0.3572   -0.82500. C   0  0  0  0  0  0  0  0  0  0  0  0
> 0.35720.0. C   0  0  0  0  0  0  0  0  0  0  0  0
>-0.35721.23750. T   0  0  0  0  0  0  0  0  0  0  0  0
> 1.07170.41250. 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("atomLabel", "D");
> or
>   atom->setProp("_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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> Rdkit-discuss mailing list
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Re: [Rdkit-discuss] Deuterium/Tritium labels in Molfile

Re: [Rdkit-discuss] Deuterium/Tritium labels in Molfile

Re: [Rdkit-discuss] Problems reading XYZ file

Re: [Rdkit-discuss] Deuterium/Tritium labels in Molfile

Re: [Rdkit-discuss] Deuterium/Tritium labels in Molfile

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