Hello,
I think the place the hydrogens get lost is during the "MolFromMolBlock"
operation. Try to add the flag *removeHs=False.*
best wishes,
wim
On Tue, Dec 20, 2022 at 10:56 AM Omar H94 <omar8...@gmail.com> wrote:
> 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
>>
> _______________________________________________
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
