Dear Masgils,
you might look into using
AllChem.ConstrainedEmbed()
and supplying pre-generated 3D coordinates for your 6-membered chair (or
boat) ring conformations; see the example below where I constrain the
piperidine ring in bilastine to have a chair conformation.
You might need further filtering/constraints if you wish to remove axial
conformations.
Cheers,
p.
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem.Draw import IPythonConsole
import py3Dmol
cyclohexane_chair = """\
Untitled
RDKit 3D
6 6 0 0 0 0 0 0 0 0999 V2000
-2.3879 0.9357 0.3335 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.8567 1.6374 -0.9329 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3152 1.5949 -0.9570 C 0 0 0 0 0 0 0 0 0 0 0 0
0.1794 0.1349 -0.9091 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3566 -0.5682 0.3547 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.8980 -0.5257 0.3727 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 0
3 4 1 0
4 5 1 0
5 6 1 0
6 1 1 0
M END
"""
bilastine_smi =
"CCOCCn1c(C2CC[NH+](CCc3ccc(C(C)(C)C(=O)[O-])cc3)CC2)nc2ccccc21"
chair_core = Chem.MolFromMolBlock(cyclohexane_chair)
params = AllChem.AdjustQueryParameters()
params.makeAtomsGeneric = True
chair_core_generic = AllChem.AdjustQueryProperties(chair_core, params)
chair_core_generic
bilastine = Chem.AddHs(Chem.MolFromSmiles(bilastine_smi))
bilastine_3d = AllChem.ConstrainedEmbed(bilastine, chair_core_generic,
useTethers=True)
On 08/05/19 02:34, Masgils wrote:
Dear RDKitters,
I want all the nonplanar rings in a group of compounds to have the
same conformation.The goal is to make the rings perfectly aligned.
In RDkit, the boat and chair conformations generated by
AllChem.EmbedMolecule() will have different bond lengths and angles
depending on the atoms in the ring
Is it possible to unify all the rings in the chair conformation into
one conformations, and to do the same for the boat conformation?
Or can we qualify all the rings to be flat？
Best Regards,
M.
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