Re: [Rdkit-discuss] atom mapping in reaction searches

2018-05-09 Thread Sebastian Wandernoth 

Hey guys,

 

any chance to get an answer on my issue? Even if the answer is that this feature is currently not included in RDKit, it would still be helpful :-)

 

Best regards

Sebastian

 

Gesendet: Dienstag, 24. April 2018 um 09:33 Uhr
Von: "Sebastian Wandernoth" 
An: rdkit-discuss@lists.sourceforge.net
Betreff: [Rdkit-discuss] atom mapping in reaction searches



Hey guys,

 

I'm still working on my search engine for reactions and I'm a bit puzzled as to what RDKit does with atom mapping information.

I'm still working with the PostgreSQL cartridge version 0.73.0, which should correspond to the release 2017.9.3.

 

I'm starting off with this example reaction which is fully mapped ([S:1]1[C:3]([Cl:4])=[N:5][CH:6]=[CH:2]1>>S(=O)(=O)1OCC([C:2]2[S:1][C:3]([Cl:4])=[N:5][CH:6]=2)=N1)

 

If I'm using a completely unmapped reaction as query I expect to find this one. So the following should return TRUE:

 


SELECT reaction_from_smarts('[S:1]1[C:3]([Cl:4])=[N:5][CH:6]=[CH:2]1>>S(=O)(=O)1OCC([C:2]2[S:1][C:3]([Cl:4])=[N:5][CH:6]=2)=N1') @> reaction_from_smarts('S1C(Cl)=NC=C1>>S(=O)(=O)1OCC(C2SC(Cl)=NC=2)=N1');

 

... which it does

 

 

Next step is to map one atom correctly in the query and try again. I still expect this to return TRUE:

 


SELECT reaction_from_smarts('[S:1]1[C:3]([Cl:4])=[N:5][CH:6]=[CH:2]1>>S(=O)(=O)1OCC([C:2]2[S:1][C:3]([Cl:4])=[N:5][CH:6]=2)=N1') @> reaction_from_smarts('[S:1]1C(Cl)=NC=C1>>S(=O)(=O)1OCC(C2[S:1]C(Cl)=NC=2)=N1');

 

... which it doesn't


 

 

With two atoms mapped correctly in the query, I wouldn't expect to get different results from the previous try:

 

SELECT reaction_from_smarts('[S:1]1[C:3]([Cl:4])=[N:5][CH:6]=[CH:2]1>>S(=O)(=O)1OCC([C:2]2[S:1][C:3]([Cl:4])=[N:5][CH:6]=2)=N1') @> reaction_from_smarts('[S:1]1C(Cl)=NC=[CH:2]1>>S(=O)(=O)1OCC([C:2]2[S:1]C(Cl)=NC=2)=N1');

 

... this one however returns TRUE again

 

 

Final try I did was to include a wrong mapping in the query. I definitely would expect to get back FALSE here (I'm mapping one sulfur atom to a carbon atom and a nitrogen to an oxygen):

 


SELECT reaction_from_smarts('[S:1]1[C:3]([Cl:4])=[N:5][CH:6]=[CH:2]1>>S(=O)(=O)1OCC([C:2]2[S:1][C:3]([Cl:4])=[N:5][CH:6]=2)=N1') @> reaction_from_smarts('[S:1]1C(Cl)=[N:2]C=C1>>S(=[O:2])(=O)1O[CH2:1]C(C2SC(Cl)=NC=2)=N1');

 

... however this returns TRUE yet again.

 

Playing around with it a bit more I found that whatever single atom I map in the query, I always get back FALSE and if I map more than one atom, I always get back TRUE...

Does this have something to do with the parameter 'rdkit.threshold_unmapped_reactant_atoms'? My suspicion is that RDKit only counts how many atoms are mapped and not compare them to the correct mapping. Can you confirm this?

Is there any way at all to include atom mapping in the query to filter the reactions the way I want to?

 

 

I hope you guys can help me here. Sorry for the lengthy question, but I wanted to include as much information as possible for you to pinpoint the issue.

 

Best regards

Sebastian



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Re: [Rdkit-discuss] Atom mapping

2018-05-09 Thread Dimitri Maziuk 
On 05/09/2018 10:27 AM, carlo del moro wrote:
> Dear All,
> 
> we would like to know if it is possible to map the atom's ID of a SMILES
> represented substructure to the atom sequence of a ligand contained in a
> pdb file. This in order to get the spatial coordinates related to such
> substructure.

http://alatis.nmrfam.wisc.edu/ will generate unique stable IDs from a 3D
structure, and output the old->new ID map. It'll take a PDB,  you'll
have to convert your SMILES into a 3D .mol. ALATIS atom IDs should be
the same in the two maps, *provided both inputs describe the exact same
ligand*.

(It's the *substructure* bit that I'm not entirely sure about.)
-- 
Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu



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Re: [Rdkit-discuss] RDKIT 2018.3 and MMPDB problem

2018-05-09 Thread Andrew Dalke 
And I have uploaded a source tar.gz and a binary wheel to PyPI.

That means you can do "pip install mmpdb" to install this most recent version.

Andrew
da...@dalkescientific.com



> On May 9, 2018, at 18:04, Kramer, Christian  
> wrote:
> 
> Dear all,
> 
> Andrew's fix for the wildcard atom representation in RDKit 2018.3 has just 
> been incorporated into the main mmpdb branch. If you download the latest 
> version of mmpdb, it should now work with with the current version and also 
> with previous RDKit versions.
> 
> Note that you have to rebuild your mmp database if you switch from a pre 2018 
> version of RDKit to a 2018+ version.
> 
> Bests,
> Christian
> 
> Dr. Christian Kramer
> 



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Re: [Rdkit-discuss] RDKIT 2018.3 and MMPDB problem

2018-05-09 Thread Kramer, Christian 
Dear all,

Andrew's fix for the wildcard atom representation in RDKit 2018.3 has just
been incorporated into the main mmpdb branch. If you download the latest
version of mmpdb, it should now work with with the current version and also
with previous RDKit versions.

Note that you have to rebuild your mmp database if you switch from a pre
2018 version of RDKit to a 2018+ version.

Bests,
Christian

*Dr. Christian Kramer*

Computer-Aided Drug Design (CADD) Senior Scientist


F. Hoffmann-La Roche Ltd

Pharma Research and Early Development
Bldg. 092/8.56 C

CH-4070 Basel


Phone +41 61 682 2471

mailto: christian.kra...@roche.com


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On Tue, May 8, 2018 at 4:04 PM, Andrew Dalke 
wrote:

> Dear Marco,
>
> > On May 7, 2018, at 23:59, Marco Stenta  wrote:
> > I had some time to set an environment for it and test it: it works fine,
> as far as my tests go. I will switch to this version and to the latest
> RDKIT now.
>
> Thanks for the feedback. Someone else sent me a private email also saying
> it worked. I'll put together the final changes for a 2.1 release, and see
> about making it accessible from PyPI so "pip install mmpdb" will work.
>
> > some questions:
> > Is there any plan to:
> > include MCS as a fragmentation method?
> > extend to matched series?
> > include "fuzzy" environment definitions based on pharmacophores (as BI
> people did)?
>
> I know of no plans for that.
>
> As a consultant, my answer is more along the lines of "are you willing to
> pay for it?" :)
>
> It won't be cheap.
>
> Speaking of which, many thanks to Roche because they funded this work,
> just like that previously funded me to develop the MCS code that is now in
> RDKit.
>
>
> > I am currently using the database file to explore the rules mainly via
> visual inspection through spotfire by means of a series of joins to
> generate suitable tables: would anybody be interested in this (also helping
> improving it)?
>
> I hope you find others and are able to get this out there.
>
> One of the reasons for developing what eventually became mmpdb 2.0 is to
> make this sort of viewer possible.
>
> That is, the unreleased mmpdb 1.0 didn't have canonical attachment point
> assignment, resulting in up to 6 different ways to represent a 3-cut
> fragment. This made it technically challenging to the simple sorts of
> analyses that mmpdb 2.0 does now, and impossible to visualize meaningfully.
>
> Cheers,
>
> Andrew
> da...@dalkescientific.com
>
>
>
> 
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Re: [Rdkit-discuss] Atom mapping

2018-05-09 Thread Paul Emsley 

On 09/05/2018 16:27, carlo del moro wrote:


we would like to know if it is possible to map the atom's ID of a SMILES represented substructure to the 
atom sequence of a ligand contained in a pdb file. This in order to get the spatial coordinates related to 
such substructure.




Depending on how the details of how you (or others) converted the SMILES to a PDB file this either could be 
a (mere) book keeping problem or a graph matching problem. Which do you think it is?


Paul.

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[Rdkit-discuss] Atom mapping

2018-05-09 Thread carlo del moro 
Dear All,

we would like to know if it is possible to map the atom's ID of a SMILES
represented substructure to the atom sequence of a ligand contained in a
pdb file. This in order to get the spatial coordinates related to such
substructure.

Best regards

Carlo
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