date:20190225

Re: [Rdkit-discuss] Atom coordinates from PDB-file

2019-02-25 Thread Stéphane Téletchéa


Hi all,

Le 25/02/2019 à 12:38, Lukas Pravda a écrit :

Hi Illimar,

If you need to access coordinates without creating conformer object do you 
really need to use rdkit I the first place? PDB file is column based format, so 
extracting coordinates for atoms for example with python is very 
straightforward.

Lukas


To pick certains atoms on a PDB file, I'd go for biopython's Bio.PDB ->

https://biopython.org/wiki/The_Biopython_Structural_Bioinformatics_FAQ

HTH,

Stéphane

--
Lecturer, UFIP, UMR 6286 CNRS, Team Protein Design In Silico
UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes 
cedex 03, France
Tél : +33 251 125 636 / Fax : +33 251 125 632
http://www.ufip.univ-nantes.fr/ - http://www.steletch.org



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Re: [Rdkit-discuss] Evaluating ETKDG method with the Platinum Dataset

2019-02-25 Thread Geoffrey Hutchison

To give some context, it's not that we're trying to sample a diverse
set of conformers (and find something close to the experimental). In
this case, we're generating initial geometries - to assess Naruki's
fragment-based builder in Open Babel.

But you raise an excellent point - by picking only one random
conformer (as we're doing), we'll absolutely going to have a higher
RMSD than sampling 50 conformers per compound and picking the best.

We'll try a quick test to be safe, but thanks for the suggestion.

-Geoff

On Mon, Feb 25, 2019 at 3:55 PM Greg Landrum  wrote:
>
> Hi Naruki,
>
> You're only generating a single conformer per molecule; I wouldn't expect 
> that to do particularly well. It's generally better to call 
> EmbedMultipleConfs().
>
> As an aside: I've looked at the platinum set too, it might be worth checking 
> out this RDKit blog post: 
> http://rdkit.blogspot.com/2017/05/looking-at-platinum-dataset.html
>
> -greg
>
>
> On Mon, Feb 25, 2019 at 11:53 AM Naruki Yoshikawa 
>  wrote:
>>
>> Dear all,
>>
>> I'm evaluating ETKDG method implemented in RDKit using the Platinum
>> Dataset introduced in a benchmark paper
>> https://pubs.acs.org/doi/abs/10.1021/acs.jcim.7b00505/
>> SMILES generated from the dataset is served as input and a 3D
>> conformer is generated.
>> We evaluate RMSD between generated structure and experimental structure.
>>
>> Although the author of the benchmark paper reported the mean RMSD to
>> be below 1.0 angstrom, my evaluation code reports around 1.5 angstrom.
>> I can't figure out why such a big difference occurs.
>>
>> My evaluation code is here:
>> https://gist.github.com/n-yoshikawa/0ba04a1b0c718c4cc8d83702f3759afa
>> There is a link to data in this gist.
>>
>> Thanks,
>> Naruki
>>
>>
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Re: [Rdkit-discuss] Evaluating ETKDG method with the Platinum Dataset

2019-02-25 Thread Greg Landrum

Hi Naruki,

You're only generating a single conformer per molecule; I wouldn't expect
that to do particularly well. It's generally better to call
EmbedMultipleConfs().

As an aside: I've looked at the platinum set too, it might be worth
checking out this RDKit blog post:
http://rdkit.blogspot.com/2017/05/looking-at-platinum-dataset.html

-greg


On Mon, Feb 25, 2019 at 11:53 AM Naruki Yoshikawa <
naruki.yoshik...@gmail.com> wrote:

> Dear all,
>
> I'm evaluating ETKDG method implemented in RDKit using the Platinum
> Dataset introduced in a benchmark paper
> https://pubs.acs.org/doi/abs/10.1021/acs.jcim.7b00505/
> SMILES generated from the dataset is served as input and a 3D
> conformer is generated.
> We evaluate RMSD between generated structure and experimental structure.
>
> Although the author of the benchmark paper reported the mean RMSD to
> be below 1.0 angstrom, my evaluation code reports around 1.5 angstrom.
> I can't figure out why such a big difference occurs.
>
> My evaluation code is here:
> https://gist.github.com/n-yoshikawa/0ba04a1b0c718c4cc8d83702f3759afa
> There is a link to data in this gist.
>
> Thanks,
> Naruki
>
>
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[Rdkit-discuss] Evaluating ETKDG method with the Platinum Dataset

2019-02-25 Thread Naruki Yoshikawa

Dear all,

I'm evaluating ETKDG method implemented in RDKit using the Platinum
Dataset introduced in a benchmark paper
https://pubs.acs.org/doi/abs/10.1021/acs.jcim.7b00505/
SMILES generated from the dataset is served as input and a 3D
conformer is generated.
We evaluate RMSD between generated structure and experimental structure.

Although the author of the benchmark paper reported the mean RMSD to
be below 1.0 angstrom, my evaluation code reports around 1.5 angstrom.
I can't figure out why such a big difference occurs.

My evaluation code is here:
https://gist.github.com/n-yoshikawa/0ba04a1b0c718c4cc8d83702f3759afa
There is a link to data in this gist.

Thanks,
Naruki


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Re: [Rdkit-discuss] Chem.GetMolFrags and 3D coordinates

2019-02-25 Thread Michal Krompiec

Hi Greg,
Thank you, I can reproduce your example, and my own case works fine now...
Best,
Michal

On Mon, 25 Feb 2019 at 14:26, Greg Landrum  wrote:

> Hi Michal,
>
> Which version of the RDKit are you using? This should already be working.
> Here's an example demonstrating that:
>
> In [16]: m = Chem.AddHs(Chem.MolFromSmiles('c1c1.N'))
>
> In [17]: AllChem.EmbedMolecule(m)
> Out[17]: 0
>
> In [18]: fs = Chem.GetMolFrags(m,asMols=True)
>
> In [19]: print(Chem.MolToMolBlock(fs[0]))
>
>  RDKit  3D
>
>  12 12  0  0  0  0  0  0  0  0999 V2000
> 0.7943   -1.14900.0150 C   0  0  0  0  0  0  0  0  0  0  0  0
> 1.36070.1298   -0.0022 C   0  0  0  0  0  0  0  0  0  0  0  0
> 0.58981.2681   -0.0170 C   0  0  0  0  0  0  0  0  0  0  0  0
>-0.78661.1450   -0.0149 C   0  0  0  0  0  0  0  0  0  0  0  0
>-1.3413   -0.11240.0019 C   0  0  0  0  0  0  0  0  0  0  0  0
>-0.5806   -1.26560.0170 C   0  0  0  0  0  0  0  0  0  0  0  0
> 1.4026   -2.04280.0267 H   0  0  0  0  0  0  0  0  0  0  0  0
> 2.41830.2113   -0.0036 H   0  0  0  0  0  0  0  0  0  0  0  0
> 1.00752.2686   -0.0304 H   0  0  0  0  0  0  0  0  0  0  0  0
>-1.41822.0293   -0.0265 H   0  0  0  0  0  0  0  0  0  0  0  0
>-2.4222   -0.21720.0037 H   0  0  0  0  0  0  0  0  0  0  0  0
>-1.0241   -2.26520.0304 H   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  1  1  0
>   1  7  1  0
>   2  8  1  0
>   3  9  1  0
>   4 10  1  0
>   5 11  1  0
>   6 12  1  0
> M  END
>
>
> In [20]: print(Chem.MolToMolBlock(fs[1]))
>
>  RDKit  3D
>
>   4  3  0  0  0  0  0  0  0  0999 V2000
>-0.0066   -0.00990.2620 N   0  0  0  0  0  0  0  0  0  0  0  0
>-0.41360.8845   -0.0859 H   0  0  0  0  0  0  0  0  0  0  0  0
>-0.5574   -0.8197   -0.0901 H   0  0  0  0  0  0  0  0  0  0  0  0
> 0.9775   -0.0549   -0.0860 H   0  0  0  0  0  0  0  0  0  0  0  0
>   1  2  1  0
>   1  3  1  0
>   1  4  1  0
> M  END
>
>
> In [21]: print(Chem.MolToMolBlock(m))
>
>  RDKit  3D
>
>  16 15  0  0  0  0  0  0  0  0999 V2000
> 0.7943   -1.14900.0150 C   0  0  0  0  0  0  0  0  0  0  0  0
> 1.36070.1298   -0.0022 C   0  0  0  0  0  0  0  0  0  0  0  0
> 0.58981.2681   -0.0170 C   0  0  0  0  0  0  0  0  0  0  0  0
>-0.78661.1450   -0.0149 C   0  0  0  0  0  0  0  0  0  0  0  0
>-1.3413   -0.11240.0019 C   0  0  0  0  0  0  0  0  0  0  0  0
>-0.5806   -1.26560.0170 C   0  0  0  0  0  0  0  0  0  0  0  0
>-0.0066   -0.00990.2620 N   0  0  0  0  0  0  0  0  0  0  0  0
> 1.4026   -2.04280.0267 H   0  0  0  0  0  0  0  0  0  0  0  0
> 2.41830.2113   -0.0036 H   0  0  0  0  0  0  0  0  0  0  0  0
> 1.00752.2686   -0.0304 H   0  0  0  0  0  0  0  0  0  0  0  0
>-1.41822.0293   -0.0265 H   0  0  0  0  0  0  0  0  0  0  0  0
>-2.4222   -0.21720.0037 H   0  0  0  0  0  0  0  0  0  0  0  0
>-1.0241   -2.26520.0304 H   0  0  0  0  0  0  0  0  0  0  0  0
>-0.41360.8845   -0.0859 H   0  0  0  0  0  0  0  0  0  0  0  0
>-0.5574   -0.8197   -0.0901 H   0  0  0  0  0  0  0  0  0  0  0  0
> 0.9775   -0.0549   -0.0860 H   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  1  1  0
>   1  8  1  0
>   2  9  1  0
>   3 10  1  0
>   4 11  1  0
>   5 12  1  0
>   6 13  1  0
>   7 14  1  0
>   7 15  1  0
>   7 16  1  0
> M  END
>
>
>
> Best,
> -greg
>
>
> On Mon, Feb 25, 2019 at 5:54 AM Michal Krompiec 
> wrote:
>
>> Hello,
>> Let mol be a molecule with a conformer with 3D coordinates, consisting of
>> 2 fragments. Chem.GetMolFrags(mol, asMols=true) returns these fragments as
>> Molecule objects, but the 3D coordinates are lost. Is there any way to
>> preserve them?
>> Best,
>> Michal
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>>
>
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Re: [Rdkit-discuss] Chem.GetMolFrags and 3D coordinates

2019-02-25 Thread Greg Landrum

Hi Michal,

Which version of the RDKit are you using? This should already be working.
Here's an example demonstrating that:

In [16]: m = Chem.AddHs(Chem.MolFromSmiles('c1c1.N'))

In [17]: AllChem.EmbedMolecule(m)
Out[17]: 0

In [18]: fs = Chem.GetMolFrags(m,asMols=True)

In [19]: print(Chem.MolToMolBlock(fs[0]))

 RDKit  3D

 12 12  0  0  0  0  0  0  0  0999 V2000
0.7943   -1.14900.0150 C   0  0  0  0  0  0  0  0  0  0  0  0
1.36070.1298   -0.0022 C   0  0  0  0  0  0  0  0  0  0  0  0
0.58981.2681   -0.0170 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.78661.1450   -0.0149 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3413   -0.11240.0019 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5806   -1.26560.0170 C   0  0  0  0  0  0  0  0  0  0  0  0
1.4026   -2.04280.0267 H   0  0  0  0  0  0  0  0  0  0  0  0
2.41830.2113   -0.0036 H   0  0  0  0  0  0  0  0  0  0  0  0
1.00752.2686   -0.0304 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.41822.0293   -0.0265 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4222   -0.21720.0037 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0241   -2.26520.0304 H   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  1  1  0
  1  7  1  0
  2  8  1  0
  3  9  1  0
  4 10  1  0
  5 11  1  0
  6 12  1  0
M  END


In [20]: print(Chem.MolToMolBlock(fs[1]))

 RDKit  3D

  4  3  0  0  0  0  0  0  0  0999 V2000
   -0.0066   -0.00990.2620 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.41360.8845   -0.0859 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5574   -0.8197   -0.0901 H   0  0  0  0  0  0  0  0  0  0  0  0
0.9775   -0.0549   -0.0860 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  1  3  1  0
  1  4  1  0
M  END


In [21]: print(Chem.MolToMolBlock(m))

 RDKit  3D

 16 15  0  0  0  0  0  0  0  0999 V2000
0.7943   -1.14900.0150 C   0  0  0  0  0  0  0  0  0  0  0  0
1.36070.1298   -0.0022 C   0  0  0  0  0  0  0  0  0  0  0  0
0.58981.2681   -0.0170 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.78661.1450   -0.0149 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3413   -0.11240.0019 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5806   -1.26560.0170 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0066   -0.00990.2620 N   0  0  0  0  0  0  0  0  0  0  0  0
1.4026   -2.04280.0267 H   0  0  0  0  0  0  0  0  0  0  0  0
2.41830.2113   -0.0036 H   0  0  0  0  0  0  0  0  0  0  0  0
1.00752.2686   -0.0304 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.41822.0293   -0.0265 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4222   -0.21720.0037 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0241   -2.26520.0304 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.41360.8845   -0.0859 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5574   -0.8197   -0.0901 H   0  0  0  0  0  0  0  0  0  0  0  0
0.9775   -0.0549   -0.0860 H   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  1  1  0
  1  8  1  0
  2  9  1  0
  3 10  1  0
  4 11  1  0
  5 12  1  0
  6 13  1  0
  7 14  1  0
  7 15  1  0
  7 16  1  0
M  END



Best,
-greg


On Mon, Feb 25, 2019 at 5:54 AM Michal Krompiec 
wrote:

> Hello,
> Let mol be a molecule with a conformer with 3D coordinates, consisting of
> 2 fragments. Chem.GetMolFrags(mol, asMols=true) returns these fragments as
> Molecule objects, but the 3D coordinates are lost. Is there any way to
> preserve them?
> Best,
> Michal
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Re: [Rdkit-discuss] Atom coordinates from PDB-file

2019-02-25 Thread Lukas Pravda

Hi Illimar,

If you need to access coordinates without creating conformer object do you 
really need to use rdkit I the first place? PDB file is column based format, so 
extracting coordinates for atoms for example with python is very 
straightforward.

Lukas

--
Lukas Pravda, Ph.D.
Bioinformatician/Scientific Programmer
 
Protein Data Bank in Europe (PDBe)
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD
United Kingdom
 


On 25/02/2019, 10:11, "Illimar Hugo Rekand"  wrote:

Hello,


I am currently trying to access the xyz-coordinates for specific atoms (in 
a loop) from a .PDB-file. Is there an easy way to do this without creating a 
conformer of the molecule?


all the best,


Illimar Rekand

Ph.D. Candidate

Department of Biomedicine

University of Bergen


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[Rdkit-discuss] Chem.GetMolFrags and 3D coordinates

2019-02-25 Thread Michal Krompiec

Hello,
Let mol be a molecule with a conformer with 3D coordinates, consisting of 2
fragments. Chem.GetMolFrags(mol, asMols=true) returns these fragments as
Molecule objects, but the 3D coordinates are lost. Is there any way to
preserve them?
Best,
Michal
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[Rdkit-discuss] Atom coordinates from PDB-file

2019-02-25 Thread Illimar Hugo Rekand

Hello,


I am currently trying to access the xyz-coordinates for specific atoms (in a 
loop) from a .PDB-file. Is there an easy way to do this without creating a 
conformer of the molecule?


all the best,


Illimar Rekand

Ph.D. Candidate

Department of Biomedicine

University of Bergen


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Re: [Rdkit-discuss] Smiles to Mol file

2019-02-25 Thread Greg Landrum

Hi,

The "Getting Started" guide is a great place to look for things like this;
http://rdkit.org/docs/GettingStartedInPython.html#writing-molecules

-greg


On Mon, Feb 25, 2019 at 3:06 AM tech tech  wrote:

> Hi, all,
>
> Could Rdkit convert smiles file to mol file?
> If so, could anyone point out the code to do so?
>
> Thanks,
>
> Tom
>
>
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[Rdkit-discuss] Smiles to Mol file

2019-02-25 Thread tech tech

Hi, all,

Could Rdkit convert smiles file to mol file?
If so, could anyone point out the code to do so?

Thanks,

Tom


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Re: [Rdkit-discuss] Atom coordinates from PDB-file

Re: [Rdkit-discuss] Evaluating ETKDG method with the Platinum Dataset

Re: [Rdkit-discuss] Evaluating ETKDG method with the Platinum Dataset

[Rdkit-discuss] Evaluating ETKDG method with the Platinum Dataset

Re: [Rdkit-discuss] Chem.GetMolFrags and 3D coordinates

Re: [Rdkit-discuss] Chem.GetMolFrags and 3D coordinates

Re: [Rdkit-discuss] Atom coordinates from PDB-file

[Rdkit-discuss] Chem.GetMolFrags and 3D coordinates

[Rdkit-discuss] Atom coordinates from PDB-file

Re: [Rdkit-discuss] Smiles to Mol file

[Rdkit-discuss] Smiles to Mol file

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