SetOwningMol

[woodg07]

Hello,

I have a couple of function definitions in a wider class that I'm writing in python. For one function I embed the molecules with n number of conformers, I then want to make sure that these conformers remain with the parsed molecule after the function call. I thought this was done by reference under the hood so I wouldn't have to specifically set the conformers (see code snippet 1. below). However, this doesn't see to be the case. I tried to parse back the conformers and then do a setOwningMol but I get an error saying that the conformer class has no attribute setOwningMol or SetOwningMol (see snippet 2.) Any ideas on how to proceed would be great.

snippet 1:

gen_conformers(rdkitmol,n)
rdkmol.GetNumConformers() #### returns 0 here, I thought this would be done by reference?

def gen_conformers(rdkitmol,n):
    cids = AllChem.EmbedMultipleConfs(rdkmol,numConfs=n)
    rdkmol.GetNumConformers() #### returns n here

snippet 2:

confs = gen_conformers(rdkitmol,n)
for conf in confs:
    conf.SetOwningMol(rdkitmol)  #### 'Conformer' object has no attribute 'SetOwningMol' I tried with setOwningMol also

def gen_conformers(rdkitmol,n):
    cids = AllChem.EmbedMultipleConfs(rdkmol,numConfs=n)
    return rdkmol.GetConformers() 

[bp-kelley]

The function you are looking for is AddConformer

>>> help(mol.AddConformer)
Help on method AddConformer:

AddConformer(...) method of rdkit.Chem.rdchem.Mol instance
    AddConformer( (Mol)self, (Conformer)conf [, (bool)assignId=False]) -> int :
        Add a conformer to the molecule and return the conformer ID
    
        C++ signature :
            unsigned int AddConformer(RDKit::ROMol {lvalue},RDKit::Conformer* [,bool=False])

[greglandrum]

@woodg07 I don't really understand what you're trying to do.

AllChem.EmbedMultipleConfs adds conformations to a molecule; you don't need to do any additional work to add the conformers to the molecule:

>>> from rdkit.Chem import AllChem
>>> from rdkit import Chem
>>> m = Chem.AddHs(Chem.MolFromSmiles('CCCO'))
>>> cids = AllChem.EmbedMultipleConfs(m,5)
>>> m.GetNumConformers()
5

If your concern is that adding the conformers in a function may not change the molecule in the calling scope, you don't need to be:

>>> def gen_confs(mol,n):
...     AllChem.EmbedMultipleConfs(mol,n)
... 
>>> m = Chem.AddHs(Chem.MolFromSmiles('CCCO'))
>>> gen_confs(m,7)
>>> m.GetNumConformers()
7

Does that answer the question? If not, can you please clarify what you're trying to do?

[woodg07]

Thank you for following up. I was having an issue with passing a copy of the molecule to the function so it looked like it wasn't updating. I appreciate that you wanted more details but I think we can close the problem now. Thank you