Re: [Rdkit-discuss] generate conformes with a restrained core
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Re: [Rdkit-discuss] generate conformes with a restrained core
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From: Felipe T. <fel...@gm...> - 2018-03-24 11:36:51
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Hi Chris
yesterday I realize about this and using the following command appears to
do the job:
for cid in cids: AllChem.ConstrainedEmbed(newMol3D,coreMol,useTethers=True)
...
<rdkit.Chem.rdchem.Mol object at 0x2ac7a04d6280>
<rdkit.Chem.rdchem.Mol object at 0x2ac7a04d6280>
<rdkit.Chem.rdchem.Mol object at 0x2ac7a04d6280>
<rdkit.Chem.rdchem.Mol object at 0x2ac7a04d6280>
<rdkit.Chem.rdchem.Mol object at 0x2ac7a04d6280>
<rdkit.Chem.rdchem.Mol object at 0x2ac7a04d6280>
but then I cannot save the conformers because something is different:
for cid in cids:
w.write(newMol3D, cid)
Traceback (most recent call last):
File "<stdin>", line 2, in <module>
ValueError: Bad Conformer Id
before constrainedEmbed:
conf.GetId() for conf in newMol3D.GetConformers()]
[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19]
after:
[conf.GetId() for conf in newMol3D.GetConformers()]
[0]
why I am getting only one conformer? the idea is to constrain only the core
of the molecule. The other part should be sampled to build a rotamer library
thanks again for all your help!
felipe
2018-03-24 6:11 GMT-03:00 Chris Earnshaw <cge...@gm...>:
> Hi Felipe
>
> You're doing something similar to the problem Paolo addressed.
>
> ConstrainedEmbed (see http://www.rdkit.org/Python_Docs/rdkit.Chem.AllChem-
> module.html#ConstrainedEmbed) requires a mol object as the first
> parameter, but you are passing it an integer cid value, not a molecule.
> Your code must retrieve the molecule associated with the cid number and
> pass that to ConstrainedEmbed instead of the cid number.
>
> Regards,
> Chris
>
> On 23 March 2018 at 21:58, Felipe Trajtenberg <fel...@gm...>
> wrote:
>
>> Hi Luan!
>> thanks!
>>
>> I was trying to use it but I am still struggling with very basic
>> problems. What you are saying is that I can delete the UFFOptimizeMolecule
>> and add a loop with ConstrainedEmbed to minimize with constraints?
>>
>> in my script, using:
>>
>> for cid in cids:
>> AllChem.ConstrainedEmbed(cid,coreMol,useTethers=True)
>>
>> I get the error:
>>
>> Traceback (most recent call last):
>> File "<stdin>", line 2, in <module>
>> File "/export/home/felipet/.conda/envs/my-rdkit-env/lib/python2.7
>> /site-packages/rdkit/Chem/AllChem.py", line 274, in ConstrainedEmbed
>> match = mol.GetSubstructMatch(core)
>> AttributeError: 'int' object has no attribute 'GetSubstructMatch'
>>
>> what I am missing?
>>
>> thanks!
>>
>> 2018-03-23 16:19 GMT-03:00 Luan Carvalho Martins <
>> lua...@gm...>:
>>
>>> When you used AllChem.UFFOptimizeMolecule(newMol3D,confId=cid) the
>>> minimization proceeded without constraints, therefore, the core embedding
>>> was lost. Read the source of ConstrainedEmbed [
>>> http://www.rdkit.org/Python_Docs/rdkit.Chem.AllChem-pysrc.h
>>> tml#ConstrainedEmbed]. This function does a restricted minimization
>>> using AddDistanceConstraint.
>>>
>>> Sincerely,
>>> Luan Carvalho.
>>>
>>> Atenciosamente, Luan Carvalho Martins
>>> lua...@gm...
>>>
>>> On Fri, Mar 23, 2018 at 3:56 PM, Felipe Trajtenberg <
>>> fel...@gm...> wrote:
>>>
>>>> Hi Paolo
>>>>
>>>> great! it was a very simple thing. Now the sdf file with the conformers
>>>> is generated but the conformers were not constraints at the core of the
>>>> ligand...as I was trying? can you tell me why?
>>>>
>>>> thanks a lot!
>>>>
>>>> felipet
>>>>
>>>> 2018-03-23 15:37 GMT-03:00 Paolo Tosco <pao...@un...>:
>>>>
>>>>> Dear Felipe,
>>>>>
>>>>> cids is a list of conformer ids, i.e. integer numbers. Therefore
>>>>>
>>>>> prbMol = cids[prbNum]
>>>>>
>>>>> sets prbMol to the integer value of the prbNum element of the cids
>>>>> list.
>>>>>
>>>>> The reason of the error message you are getting:
>>>>> Boost.Python.ArgumentError: Python argument types in
>>>>> SDWriter.write(SDWriter, int)
>>>>> did not match C++ signature:
>>>>> write(RDKit::SDWriter {lvalue} self, RDKit::ROMol {lvalue} mol,
>>>>> int confId=-1)
>>>>>
>>>>> is that you are passing only an int to SDWriter.write(), rather than a
>>>>> mol and an int as the function expects.
>>>>> What you need is:
>>>>>
>>>>> nMol = len(cids)
>>>>> w = Chem.SDWriter('conf_output.sdf')
>>>>>
>>>>> for prbNum in range(0, nMol):
>>>>> prbMol = cids[prbNum]
>>>>> w.write(newMol3D, prbMol)
>>>>> w.close()
>>>>>
>>>>> or, more simply:
>>>>>
>>>>> w = Chem.SDWriter('conf_output.sdf')
>>>>>
>>>>> for cid in cids:
>>>>> w.write(newMol3D, cid)
>>>>> w.close()
>>>>>
>>>>> Cheers,
>>>>> p.
>>>>>
>>>>> On 03/23/18 18:04, Felipe Trajtenberg wrote:
>>>>>
>>>>> Dear all,
>>>>>
>>>>> sorry but I am really new at using RDkit. By looking at the scripts
>>>>> and tutorial available I wrote the following script. The idea is to
>>>>> generate a number of conformers for a big and flexible ligand, but with
>>>>> constraints. This script generate a set of conformers but I can't write a
>>>>> SDF file with all of them. The error I get is:
>>>>>
>>>>> Traceback (most recent call last):
>>>>> File "<stdin>", line 3, in <module>
>>>>> Boost.Python.ArgumentError: Python argument types in
>>>>> SDWriter.write(SDWriter, int)
>>>>> did not match C++ signature:
>>>>> write(RDKit::SDWriter {lvalue} self, RDKit::ROMol {lvalue} mol,
>>>>> int confId=-1)
>>>>>
>>>>> Thanks in advance for any help
>>>>>
>>>>> felipet
>>>>>
>>>>> The script is:
>>>>>
>>>>> from rdkit import Chem
>>>>> from rdkit.Chem import AllChem
>>>>> import os
>>>>>
>>>>> mols = [x for x in Chem.SDMolSupplier('out.CRC.sdf',removeHs=False)
>>>>> if x is not None]
>>>>> core = Chem.MolFromSmarts('CCCCCCCCCCCCCCC(O)=O')
>>>>>
>>>>>
>>>>> em = Chem.EditableMol(mols[0])
>>>>> match = mols[0].GetSubstructMatch(core)
>>>>> for idx in range(mols[0].GetNumAtoms()-1,-1,-1):
>>>>> if idx not in match:
>>>>> em.RemoveAtom(idx)
>>>>>
>>>>> coreMol = em.GetMol()
>>>>> Chem.SanitizeMol(coreMol)
>>>>>
>>>>> newMol = Chem.MolFromSmiles('CCCCCCCCCCCCCCCCCCCCCCCCCC(O)=O')
>>>>>
>>>>> newMol=Chem.AddHs(newMol)
>>>>> newMol3D=AllChem.ConstrainedEmbed(newMol,coreMol)
>>>>>
>>>>> cids=AllChem.EmbedMultipleConfs(newMol3D,numConfs=100,pruneR
>>>>> msThresh=1.0,enforceChirality=True)
>>>>> for cid in cids: AllChem.UFFOptimizeMolecule(newMol3D,confId=cid)
>>>>>
>>>>> nMol = len(cids)
>>>>> w = Chem.SDWriter('conf_output.sdf')
>>>>>
>>>>> for prbNum in range(0, nMol):
>>>>> prbMol = cids[prbNum]
>>>>> w.write(prbMol)
>>>>> w.close()
>>>>>
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> Check out the vibrant tech community on one of the world's most
>>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Rdkit-discuss mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>>>
>>>>>
>>>>>
>>>>
>>>> ------------------------------------------------------------
>>>> ------------------
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>>>> _______________________________________________
>>>> Rdkit-discuss mailing list
>>>> Rdk...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>>
>>>>
>>>
>>
>> ------------------------------------------------------------
>> ------------------
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>> _______________________________________________
>> Rdkit-discuss mailing list
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>>
>>
>
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