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 <felipet...@gmail.com> 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 <
> luancarvalhomart...@gmail.com>:
>
>> 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
>> luancarvalhomart...@gmail.com
>>
>> On Fri, Mar 23, 2018 at 3:56 PM, Felipe Trajtenberg <felipet...@gmail.com
>> > 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 <paolo.to...@unito.it>:
>>>
>>>> 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()
>>>>
>>>>
>>>>
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>>>>
>>>>
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>>>>
>>>>
>>>
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>>
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