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.
> html#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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