HI,
I want to edit the molecule's 3D structure(coordinates) without changing the
connectivity.
I did the following.
def get_conformers(smiles):
m = Chem.MolFromSmiles("CC")
m2=Chem.AddHs(m)
Sp = []
for at in m2.GetAtoms():
Sp.append(at.GetSymbol())
species = "".join(Sp)
# cids = AllChem.EmbedMultipleConfs(m2, numConfs=10*len(species),
randomSeed=24)
cids = AllChem.EmbedMultipleConfs(m2, numConfs=1, randomSeed=24)
res = AllChem.MMFFOptimizeMoleculeConfs(m2)
# run ETKDG 10 times
n_conf = len(cids)
rmslist = []
AllChem.AlignMolConformers(m2, RMSlist=rmslist)
return m2, n_conf, rmslist, species
mol_confs, n_conf, rmslist, species = get_conformers(sm)
I can get coordinates using mol_confs.GetConformer().GetPositions(). What I
want is to add say x = [1.0, 1.0, 1.0] to first carbon atom.
previous_coor = mol_confs.GetConformer().GetPositions()
new_coor = previous_coor[1] + x
I want to create new ethane with new_coor. how do I do it? I have species and
new_coor to create new ethane with no change in connectivity.
Regards,
Rohit Modee
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