Hello
To change properties of a molecule, it is not necessary to convert to a
RWMol. This is required only if you want to modify the structure.
molsin2[0].GetProp('PUBCHEM_ATOM_DEF_STEREO_COUNT')
molsin2[0].SetProp('PUBCHEM_ATOM_DEF_STEREO_COUNT', str(5))
molsin2[0].GetProp('PUBCHEM_ATOM_DEF_STEREO_COUNT')
The statement Chem.RWMol(mol) instantiates an object that is a copy of the
original molecule.
Chem.RWMol(molsin2[0]).SetProp('PUBCHEM_ATOM_DEF_STEREO_COUNT', str(5))
The object is created and SetProp called for this new object. After that
statement, nothing references the new RWMol object and it therefore will go
to garbage collection. Therefore corresponds to the following code
xx = Chem.RWMol(molsin2[0])
xx.SetProp('PUBCHEM_ATOM_DEF_STEREO_COUNT', str(5))
del xx
I hope this clarifies your question.
Best
Peter
On Mon, 18 Jan 2016 at 4:24 AM chris dalton <[email protected]> wrote:
> Hi,
> I am changing the value of a property in a mol object in a SD supplier and
> I see the results below. I can only change the value of the property when I
> make an 'intermediate' variable. I don't understand why this is the case
> and is there a way I can directly change the value in the molecules in the
> supplier without doing this intermediate step?
>
> thanks
> Chris
>
> Chem.RWMol(molsin2[0]).GetProp('PUBCHEM_ATOM_DEF_STEREO_COUNT')
> '0'
> Chem.RWMol(molsin2[0]).SetProp('PUBCHEM_ATOM_DEF_STEREO_COUNT', str(5))
> Chem.RWMol(molsin2[0]).GetProp('PUBCHEM_ATOM_DEF_STEREO_COUNT')
> '0'
>
> xx = Chem.RWMol(molsin2[0])
> xx.GetProp('PUBCHEM_ATOM_DEF_STEREO_COUNT')
> '0'
> xx.SetProp('PUBCHEM_ATOM_DEF_STEREO_COUNT', str(5))
> xx.GetProp('PUBCHEM_ATOM_DEF_STEREO_COUNT')
> '5'
>
> Chem.RWMol(molsin2[0])
> <rdkit.Chem.rdchem.RWMol object at 0x00000000061A6818>
> >>> xx
> <rdkit.Chem.rdchem.RWMol object at 0x00000000061A6728>
>
>
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