Re: [Rdkit-discuss] generate conformes with a restrained core

[Luan C. M. <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.html#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,pruneRmsThresh=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()
>>
>>
>>
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>>
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>>
>>
>
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