I cannot understand this. Using distance geometry, you should get different
molecules each time you run the following program right (because of the
random distance matrix) ?
Why does this produce identical conformers on every run?
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import Descriptors
def generateconformations(m):
m = Chem.AddHs(m)
ids=AllChem.EmbedMultipleConfs(m, numConfs=10)
for id in ids:
AllChem.UFFOptimizeMolecule(m, confId=id)
return m
mol = Chem.MolFromSmiles('C1CCC1OC')
m = generateconformations(mol)
confIds = [x.GetId() for x in m.GetConformers()]
for id in confIds:
print Chem.MolToMolBlock(m, confId=id)
Is this the intended behaviour? A common use case is to generate conformers
for a molecule and save them in a database -- but if you run this code 10
times, you will get the same 10 conformers, 10 times...
Why is this?
--
Jean-Paul Ebejer
Early Stage Researcher
InhibOx Ltd
Pembroke House
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Oxford
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UK
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