Re: [Rdkit-discuss] The fragmentMatcher (SubstructMatcher) is not as good as expected

2016-10-27 Thread 杨弘宾 



  




Thanks, it works!    I appreciate that Rdkit is so strict in representation of 
the the molecules and the substructures. I learned a lot in the mail list.


Hongbin Yang 

 From: Paolo ToscoDate: 2016-10-27 17:19To: 杨弘宾; rdkit-discussSubject: Re: 
[Rdkit-discuss] The fragmentMatcher (SubstructMatcher) is not as good as 
expected
  

  
  
Dear Hongbin,
I am afraid The SMARTS you are using is not valid, as no SSSR can
  have less than 3 terms, or it wouldn't be a ring. If you
  change[a!r0] into, for instance, [a!r3], then you'll find the
  match you are looking for.
Cheers,

  p.


On 27/10/2016 09:36, 杨弘宾 wrote:



  
  
  Hi,
      I
  tryied using rdkit to match fragments with compounds only to
  find that rdkit performed not well in SMARTS. The following is
  the notebook I worked.
  

  
  

  

  

  from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import FragmentMatcher
from rdkit.Chem.Draw import IPythonConsole


  

  


  
In [49]:

  

  p = FragmentMatcher.FragmentMatcher()
p.Init('[a!r0][NX3+](=[OX1])([O-])')


  

  


  
In [50]:

  

  mol  = Chem.MolFromSmiles('c1c1[N+](=O)[O-]')
mol


  

  
  

  
Out[50]:

  

  


  
In [51]:

  

  p.HasMatch(mol)


  

  
  

  
Out[51]:

  0

  

  


  
In [52]:

  

  print Chem.MolFromSmarts('[a!r0][NX3+](=[OX1])([O-])')


  

  
  

  

  None

  

  

  
  However, openbabel worked well in matching the substrcutre.
Even "or operator" was avaiable such as 
"[a!r0][$([NX3+](=[OX1])([O-])),$([NX3](=O)=O)]". 
  

  
  >>>
  s=pybel.Smarts('[a!r0][NX3+](=[OX1])([O-])')
  

  >>> s=pybel.Smarts('[a!r0][NX3+](=[OX1])([O-])')
  

  >>> a=pybel.readstring('smi','c1c1[N+](=O)[O-]')
  

  >>> s.findall(a)
  

  [(6, 7, 8, 9)]
  

  
  It is a pity that rdkit can calculate the topological
distance between two atoms while it cannot match the
fragments... Is there any better API which I didn't find?
  

  
  

  
  
  
  Hongbin
  Yang 杨弘宾
  

  Research: Toxicophore and Chemoinformatics

  Pharmaceutical Science, School of Pharmacy
  

  East China University of Science and Technology 



  

  
  

  
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Re: [Rdkit-discuss] SVG BUG (Re: Fwd: 2D drawing with atoms labeled by index)

2016-10-27 Thread Dimitri Maziuk 
On 2016-10-26 23:39, Peter S. Shenkin wrote:
> Hey, by the way, my agenda is trying to understand all this.

(Using python syntax instead of ML)

Recommended by TFM:

from "http://www.w3.org/2000/svg; import *

All svg names should work with or without package qualifier: point(), 
line(), etc., as well as svg.point(), svg.line(), ...

Rdkit way:

import "http://www.w3.org/2000/svg; as svg

All svg names must be prefixed: svg.point(), svg.line(). Using 
unqualified point() should throw an error. (Unless there's another 
'point' in the name resolution chain, yadda, yadda, yadda.)

Unfortunately I find the fact that a lot of software out there doesn't 
get it right entirely unsurprising. :(

Dima


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Re: [Rdkit-discuss] reading multiple conformers from file

2016-10-27 Thread Peter S. Shenkin 
It would seem that a major issue with RDKit's multiconformer file is the
inability to associate structure-level and atom-level properties with
conformations. t's not quite orthogonal to the question of how to read,
say, a multiconformer SD file into RDKit's multiconformer format, because
the conformers in said SD file could contain such properties, and
information would be lost.

-P.

On Thu, Oct 27, 2016 at 6:20 AM, Thomas Evangelidis 
wrote:

> Hello Greg,
>
> Is the canonical SMILES string always unique for every isomer and
> tautomerization state of a molecule? If yes, then I have already written a
> function to load multiple molecules and their conformers, which I can share
> it here.
>
> best
> Thomas
>
> PS: thanks to David for pointing this out.
>
>
>
> On 27 October 2016 at 05:20, Greg Landrum  wrote:
>
>> Hi Thomas,
>>
>> You're right, reading multiple conformations out of an SDF does seem like
>> one of those common operations. Unfortunately the RDKit does not currently
>> support it in an easy way.
>>
>> A python implementation of this would be a good topic for Friday's UGM
>> hackathon, we can see if anyone finds it interesting enough to work on.
>>
>> -greg
>>
>>
>> On Tue, Oct 25, 2016 at 2:16 AM, Thomas Evangelidis 
>> wrote:
>>
>>> Hello everyone,
>>>
>>> I am a new user of RDkit and I was looking in the documentation for an
>>> easy way to load multiple conformers from a structure file like .sdf. The
>>> code must 1) distinguish between different protonation states of the same
>>> molecule,  2) create a new Mol() object for each protonation state and load
>>> into it the respective conformers.
>>>
>>> Apparently I can work out a solution for 1)
>>> using mol.GetProp('_Name'), mol.GetNumAtoms, mol.GetNumBonds and other
>>> properties, but I was wondering if there is any more straight forward way
>>> to do it.
>>> For 2) I guess I must iterate over all molecules in the input file,
>>> create new Mol() objects (one for each protonation state of each ligand)
>>> and add conformers to these new Mol() objects. Again this sounds easily
>>> programmable, but sounds like a very common operation, thus I was wondering
>>> if it has been implemented in a function.
>>>
>>> thanks in advance
>>> Thomas
>>>
>>>
>>> --
>>>
>>> ==
>>>
>>> Thomas Evangelidis
>>>
>>> Research Specialist
>>> CEITEC - Central European Institute of Technology
>>> Masaryk University
>>> Kamenice 5/A35/1S081,
>>> 62500 Brno, Czech Republic
>>>
>>> email: tev...@pharm.uoa.gr
>>>
>>>   teva...@gmail.com
>>>
>>>
>>> website: https://sites.google.com/site/thomasevangelidishomepage/
>>>
>>>
>>> 
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>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
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>>>
>>
>
>
> --
>
> ==
>
> Thomas Evangelidis
>
> Research Specialist
> CEITEC - Central European Institute of Technology
> Masaryk University
> Kamenice 5/A35/1S081,
> 62500 Brno, Czech Republic
>
> email: tev...@pharm.uoa.gr
>
>   teva...@gmail.com
>
>
> website: https://sites.google.com/site/thomasevangelidishomepage/
>
>
> 
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>
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Re: [Rdkit-discuss] Categorising reactions using SMARTS

2016-10-27 Thread James Wallace 
Looking into this further, I've decided to use the Python option again, as
this seems to have more functions.

I run the current example, where rxn is the original example, and qrxn is
the 'query' for categorisation:

In [2]: import rdkit

In [3]: from rdkit import Chem

In [4]: from rdkit.Chem import rdChemReactions

In [5]: rxn =
rdChemReactions.ReactionFromSmarts('Nc1nc(Cl)c2[nH]cnc2n1.OCC1CCC
   ...: CC1>>Nc1nc(OCC2C2)c2[nH]cnc2n1')

In [6]: qrxn =
rdChemReactions.ReactionFromSmarts('[cH1:1]1:[c:2](-[CH2:7]-[CH2
   ...:
:8]-[NH2:9]):[c:3]:[c:4]:[c:5]:[c:6]:1.[#6:11]-[CH1;R0:10]=[OD1]>>[c:1]
   ...:
12:[c:2](-[CH2:7]-[CH2:8]-[NH1:9]-[C:10]-2(-[#6:11])):[c:3]:[c:4]:[c:5]
   ...: :[c:6]:1')


Pre-condition Violation
getNumImplicitHs() called without preceding call to calcImplicitValence()
Violation occurred on line 165 in file
C:\Users\riccardo\Anaconda\conda-bld\work
\Code\GraphMol\Atom.cpp
Failed Expression: d_implicitValence > -1


---
RuntimeError  Traceback (most recent call last)
 in ()
> 1 rdChemReactions.HasReactionSubstructMatch(rxn,qrxn)

RuntimeError: Pre-condition Violation
getNumImplicitHs() called without preceding call to
calcImplicitValence(
)
Violation occurred on line 165 in file Code\GraphMol\Atom.cpp
Failed Expression: d_implicitValence > -1
RDKIT: 2016.03.1
BOOST: 1_59


Is the code working as designed (ultimately I want to feed lists of these
together, but I'm trying one at a time for now)?


On 27 October 2016 at 12:02, James Wallace  wrote:

> Hi,
> I'm trying to replicate the Schneider categorisations with a local set of
> reactions that I have stored in SMILES. I currently have the categorisation
> filters as Reaction SMARTS, and I was hoping to do a standard substructure
> comparison between the SMARTS and the SMILES, but can't seem to do that.
>
> I'm using the Java wrapped version, and I can see how to import a
> ChemicalReaction as SMILES or SMARTS, I can't see how to compose such a
> query. Can anyone offer me any help or pointers?
>
> Thanks in advance,
> James
>
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[Rdkit-discuss] Categorising reactions using SMARTS

2016-10-27 Thread James Wallace 
Hi,
I'm trying to replicate the Schneider categorisations with a local set of
reactions that I have stored in SMILES. I currently have the categorisation
filters as Reaction SMARTS, and I was hoping to do a standard substructure
comparison between the SMARTS and the SMILES, but can't seem to do that.

I'm using the Java wrapped version, and I can see how to import a
ChemicalReaction as SMILES or SMARTS, I can't see how to compose such a
query. Can anyone offer me any help or pointers?

Thanks in advance,
James
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Re: [Rdkit-discuss] reading multiple conformers from file

2016-10-27 Thread Thomas Evangelidis 
Hello Greg,

Is the canonical SMILES string always unique for every isomer and
tautomerization state of a molecule? If yes, then I have already written a
function to load multiple molecules and their conformers, which I can share
it here.

best
Thomas

PS: thanks to David for pointing this out.



On 27 October 2016 at 05:20, Greg Landrum  wrote:

> Hi Thomas,
>
> You're right, reading multiple conformations out of an SDF does seem like
> one of those common operations. Unfortunately the RDKit does not currently
> support it in an easy way.
>
> A python implementation of this would be a good topic for Friday's UGM
> hackathon, we can see if anyone finds it interesting enough to work on.
>
> -greg
>
>
> On Tue, Oct 25, 2016 at 2:16 AM, Thomas Evangelidis 
> wrote:
>
>> Hello everyone,
>>
>> I am a new user of RDkit and I was looking in the documentation for an
>> easy way to load multiple conformers from a structure file like .sdf. The
>> code must 1) distinguish between different protonation states of the same
>> molecule,  2) create a new Mol() object for each protonation state and load
>> into it the respective conformers.
>>
>> Apparently I can work out a solution for 1) using mol.GetProp('_Name'), 
>> mol.GetNumAtoms, mol.GetNumBonds
>> and other properties, but I was wondering if there is any more straight
>> forward way to do it.
>> For 2) I guess I must iterate over all molecules in the input file,
>> create new Mol() objects (one for each protonation state of each ligand)
>> and add conformers to these new Mol() objects. Again this sounds easily
>> programmable, but sounds like a very common operation, thus I was wondering
>> if it has been implemented in a function.
>>
>> thanks in advance
>> Thomas
>>
>>
>> --
>>
>> ==
>>
>> Thomas Evangelidis
>>
>> Research Specialist
>> CEITEC - Central European Institute of Technology
>> Masaryk University
>> Kamenice 5/A35/1S081,
>> 62500 Brno, Czech Republic
>>
>> email: tev...@pharm.uoa.gr
>>
>>   teva...@gmail.com
>>
>>
>> website: https://sites.google.com/site/thomasevangelidishomepage/
>>
>>
>> 
>> --
>> The Command Line: Reinvented for Modern Developers
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>> Rdkit-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>>
>


-- 

==

Thomas Evangelidis

Research Specialist
CEITEC - Central European Institute of Technology
Masaryk University
Kamenice 5/A35/1S081,
62500 Brno, Czech Republic

email: tev...@pharm.uoa.gr

  teva...@gmail.com


website: https://sites.google.com/site/thomasevangelidishomepage/
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Re: [Rdkit-discuss] The fragmentMatcher (SubstructMatcher) is not as good as expected

2016-10-27 Thread Paolo Tosco 

Dear Hongbin,

I am afraid The SMARTS you are using is not valid, as no SSSR can have 
less than 3 terms, or it wouldn't be a ring. If you change[a!r0] into, 
for instance, [a!r3], then you'll find the match you are looking for.


Cheers,
p.

On 27/10/2016 09:36, 杨弘宾 wrote:

Hi,
I tryied using rdkit to match fragments with compounds only to 
find that rdkit performed not well in SMARTS. The following is the 
notebook I worked.


from  rdkit  import  Chem
from  rdkit.Chem  import  AllChem
from  rdkit.Chem  import  FragmentMatcher
from  rdkit.Chem.Draw  import  IPythonConsole
In [49]:
p  =  FragmentMatcher.FragmentMatcher()
p.Init('[a!r0][NX3+](=[OX1])([O-])')
In [50]:
mol   =  Chem.MolFromSmiles('c1c1[N+](=O)[O-]')
mol
Out[50]:
In [51]:
p.HasMatch(mol)
Out[51]:
0
In [52]:
print  Chem.MolFromSmarts('[a!r0][NX3+](=[OX1])([O-])')
None
However, openbabel worked well in matching the substrcutre. Even "or 
operator" was avaiable such as 
"[a!r0][$([NX3+](=[OX1])([O-])),$([NX3](=O)=O)]".


>>> s=pybel.Smarts('[a!r0][NX3+](=[OX1])([O-])')
>>> s=pybel.Smarts('[a!r0][NX3+](=[OX1])([O-])')
>>> a=pybel.readstring('smi','c1c1[N+](=O)[O-]')
>>> s.findall(a)
[(6, 7, 8, 9)]

It is a pity that rdkit can calculate the topological distance between 
two atoms while it cannot match the fragments... Is there any better 
API which I didn't find?




Hongbin Yang 杨弘宾
Research: Toxicophore and Chemoinformatics
Pharmaceutical Science, School of Pharmacy
East China University of Science and Technology


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[Rdkit-discuss] The fragmentMatcher (SubstructMatcher) is not as good as expected

2016-10-27 Thread 杨弘宾 






Hi,? ? I tryied using rdkit to match fragments with compounds only to find that 
rdkit performed not well in SMARTS. The following is the notebook I worked.
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import FragmentMatcher
from rdkit.Chem.Draw import IPythonConsole
In?[49]:p = FragmentMatcher.FragmentMatcher()
p.Init('[a!r0][NX3+](=[OX1])([O-])')
In?[50]:mol  = Chem.MolFromSmiles('c1c1[N+](=O)[O-]')
mol
Out[50]:In?[51]:p.HasMatch(mol)
Out[51]:0In?[52]:print Chem.MolFromSmarts('[a!r0][NX3+](=[OX1])([O-])')
None
However, openbabel worked well in matching the substrcutre. Even "or operator" 
was avaiable such as "[a!r0][$([NX3+](=[OX1])([O-])),$([NX3](=O)=O)]".?
>>> s=pybel.Smarts('[a!r0][NX3+](=[OX1])([O-])')

>>> s=pybel.Smarts('[a!r0][NX3+](=[OX1])([O-])')

>>> a=pybel.readstring('smi','c1c1[N+](=O)[O-]')

>>> s.findall(a)

[(6, 7, 8, 9)]
It is a pity that rdkit can calculate the topological distance between two 
atoms while it cannot match the fragments... Is there any better API which I 
didn't find?


Hongbin Yang 杨弘宾

Research: Toxicophore and Chemoinformatics
Pharmaceutical Science, School of Pharmacy

East China University of Science and Technology?


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Re: [Rdkit-discuss] reading multiple conformers from file

2016-10-27 Thread Greg Landrum 
The RDKit has support for the TPL format, an old BioCad/MSI/Accelrys format.
It's easy to imagine something better, but this is at least already there
and there could be other software that speaks it:
https://github.com/rdkit/rdkit/blob/master/Code/GraphMol/FileParsers/test_data/cmpd2.tpl

I'd still like to do a decent JSON format and adding multi-confs to that
would be logical

On Thu, Oct 27, 2016 at 6:58 AM, David Cosgrove 
wrote:

> I've been wondering if, now that you can get decent conformations from
> RDKit, it would be worth devising a multi-conformation file format to make
> reading multi-conf molecules faster for vs purposes. In my experience,
> pulling all the conformers out of an ascii file such as an sdf can become
> the RDS for pharmacophore searchimg. Something to think about at the
> hackathon maybe and certainly something that deserves a new email thread.
>
> Dave
>
>
> On Thursday, 27 October 2016, Greg Landrum  wrote:
>
>> Hi Thomas,
>>
>> You're right, reading multiple conformations out of an SDF does seem like
>> one of those common operations. Unfortunately the RDKit does not currently
>> support it in an easy way.
>>
>> A python implementation of this would be a good topic for Friday's UGM
>> hackathon, we can see if anyone finds it interesting enough to work on.
>>
>> -greg
>>
>>
>> On Tue, Oct 25, 2016 at 2:16 AM, Thomas Evangelidis 
>> wrote:
>>
>>> Hello everyone,
>>>
>>> I am a new user of RDkit and I was looking in the documentation for an
>>> easy way to load multiple conformers from a structure file like .sdf. The
>>> code must 1) distinguish between different protonation states of the same
>>> molecule,  2) create a new Mol() object for each protonation state and load
>>> into it the respective conformers.
>>>
>>> Apparently I can work out a solution for 1)
>>> using mol.GetProp('_Name'), mol.GetNumAtoms, mol.GetNumBonds and other
>>> properties, but I was wondering if there is any more straight forward way
>>> to do it.
>>> For 2) I guess I must iterate over all molecules in the input file,
>>> create new Mol() objects (one for each protonation state of each ligand)
>>> and add conformers to these new Mol() objects. Again this sounds easily
>>> programmable, but sounds like a very common operation, thus I was wondering
>>> if it has been implemented in a function.
>>>
>>> thanks in advance
>>> Thomas
>>>
>>>
>>> --
>>>
>>> ==
>>>
>>> Thomas Evangelidis
>>>
>>> Research Specialist
>>> CEITEC - Central European Institute of Technology
>>> Masaryk University
>>> Kamenice 5/A35/1S081,
>>> 62500 Brno, Czech Republic
>>>
>>> email: tev...@pharm.uoa.gr
>>>
>>>   teva...@gmail.com
>>>
>>>
>>> website: https://sites.google.com/site/thomasevangelidishomepage/
>>>
>>>
>>> 
>>> --
>>> The Command Line: Reinvented for Modern Developers
>>> Did the resurgence of CLI tooling catch you by surprise?
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>>> Rdkit-discuss@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>
>>>
>>
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