Dear Petro,
Try using: Chem.AddHs(mol, addCoords=True) to get hydrogen atoms with 3D
coordinates.
Regards,
Omar
On Tue, 20 Dec 2022 at 12:18 PM Khoroshyy Petro <khoros...@gmail.com> wrote:
> Hi, list.
> I use the code below to generate conformers.
> The thing is that If I generate conformers, they are without hydrogens,
> and when I add hydrogens, they are all in the center of the ring
> overlapping.
> What am I doing wrong?
> Thanks.
> Petro.
>
> from rdkit import Chem
> from rdkit import RDConfig
> from rdkit.Chem import AllChem
> from rdkit.Chem import rdMolAlign
> from rdkit.Chem import rdShapeHelpers
> from rdkit.Chem import rdMolDescriptors
> from rdkit.Chem import PyMol
> from rdkit.Chem import Draw
> params = Chem.rdDistGeom.srETKDGv3()
> params.randomSeed = 0xf00d
> params.clearConfs = True
> m = Chem.MolFromSmiles(''C1CCCCCCC1'')
> m2=Chem.AddHs(m)
> cids = AllChem.EmbedMultipleConfs(m2, numConfs=10, params=params)
> rmslist = []
> AllChem.AlignMolConformers(m2, RMSlist=rmslist)
> print(rmslist)
> res = []
> for i in range(5):
> mb = Chem.MolToMolBlock(m2, confId=i)
>
> mb_h = Chem.AddHs(Chem.MolFromMolBlock(mb))
> res.append(mb_h)
>
>
> --
> ______________________________
> Petro Khoroshyy
> _______________________________________________
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
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