Re: [Rdkit-discuss] How to construct a simple molecule with a Z stereo double bond using RWMol?

[Francois B. <ml...@li...>]

On 14/01/2021 18:36, Greg Landrum wrote:
> Hi Francois,
> 
> I would do this by setting the stereo to either STEREOCIS or
> STEREOTRANS and then calling Chem.AssignStereoChemistry():
> 
> In [6]: rwmol = Chem.RWMol()
>    ...: # create the atoms
>    ...: a0 = Chem.Atom(6)
>    ...: a1 = Chem.Atom(7)
>    ...: a2 = Chem.Atom(6)
>    ...: a3 = Chem.Atom(16)
>    ...: # add the atoms
>    ...: rwmol.AddAtom(a0)
>    ...: rwmol.AddAtom(a1)
>    ...: rwmol.AddAtom(a2)
>    ...: rwmol.AddAtom(a3)
>    ...: # add the bonds
>    ...: rwmol.AddBond(0, 1, rdkit.Chem.rdchem.BondType.SINGLE)
>    ...: rwmol.AddBond(1, 2, rdkit.Chem.rdchem.BondType.DOUBLE)
>    ...: rwmol.AddBond(2, 3, rdkit.Chem.rdchem.BondType.SINGLE)
> Out[6]: 3
> 
> In [7]: db = rwmol.GetBondWithIdx(1)
> 
> In [8]: db.SetStereoAtoms(0,3)
> 
> In [9]: db.SetStereo(Chem.BondStereo.STEREOCIS)
> 
> In [10]: Chem.MolToSmiles(rwmol)
> Out[10]: 'CN=CS'
> 
> In [11]: Chem.AssignStereochemistry(rwmol)
> 
> In [12]: Chem.MolToSmiles(rwmol)
> Out[12]: 'C/N=C\\S'

Here is the fun part:

Chem.SanitizeMol(rwmol)
print(Chem.MolToSmiles(rwmol)) # --> CN=CS

"Sanitization" of the rwmol got rid of the stereo info that
we just inserted.

Is this a "feature" of SanitizeMol?

I was being a good kid, I thought that someone must always sanitize
a RWMol prior to extracting the final resulting molecule (in the end
I want a SMILES).

Regards,
F.

> On Thu, Jan 14, 2021 at 9:46 AM Francois Berenger <ml...@li...>
> wrote:
> 
>> Hello,
>> 
>> Please tell me if you understand why the code below
>> is not working and if you know how to change it so that it does.
>> 
>> Thanks a lot! :)
>> F.
>> 
>> ---
>> #!/usr/bin/env python3
>> 
>> # try to construct a molecule with a Z stereo double bond using
>> RWMol
>> 
>> import rdkit
>> from rdkit import Chem
>> 
>> wanted_smi = 'C/N=C\\S'
>> 
>> rwmol = Chem.RWMol()
>> # create the atoms
>> a0 = Chem.Atom(6)
>> a1 = Chem.Atom(7)
>> a2 = Chem.Atom(6)
>> a3 = Chem.Atom(16)
>> # add the atoms
>> rwmol.AddAtom(a0)
>> rwmol.AddAtom(a1)
>> rwmol.AddAtom(a2)
>> rwmol.AddAtom(a3)
>> # add the bonds
>> rwmol.AddBond(0, 1, rdkit.Chem.rdchem.BondType.SINGLE)
>> rwmol.AddBond(1, 2, rdkit.Chem.rdchem.BondType.DOUBLE)
>> rwmol.AddBond(2, 3, rdkit.Chem.rdchem.BondType.SINGLE)
>> # let's see what we have so far
>> print(Chem.MolToSmiles(rwmol)) # --> 'CN=CS'; so far so good
>> # try to specify a Z stereo bond
>> db = rwmol.GetBondWithIdx(1)
>> assert(db.GetBondType() == rdkit.Chem.rdchem.BondType.DOUBLE) # just
>> 
>> checking
>> db.SetStereo(rdkit.Chem.rdchem.BondStereo.STEREOZ)
>> db.SetStereoAtoms(0, 3)
>> # let's see what we have now
>> print(Chem.MolToSmiles(rwmol)) # --> 'CN=CS'; not good enough
>> Chem.SanitizeMol(rwmol) # just checking
>> print(Chem.MolToSmiles(rwmol)) # --> 'CN=CS'; not getting better
>> ---
>> 
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