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,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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