On Mon, Apr 4, 2011 at 3:17 PM, JP <[email protected]> wrote:
> Does this AllChem.UFFOptimizeMolecule(mol_h) optimize all the
> conformers present in mol_h ?
It just optimizes a single conformer.
Since it might be interesting, here's how I answered that question:
[1]>>> from rdkit import Chem
[2]>>> from rdkit.Chem import AllChem
[3]>>> m = Chem.MolFromSmiles('CC')
[4]>>> mh = Chem.AddHs(m)
[5]>>> AllChem.EmbedMultipleConfs(mh,10)
Out[5] <rdkit.rdBase._vecti object at 0x102113bd0>
[6]>>> mh.GetNumConformers()
Out[6] 10
[7]>>> print Chem.MolToMolBlock(mh,confId=0)
-----> print(Chem.MolToMolBlock(mh,confId=0))
RDKit 3D
8 7 0 0 0 0 0 0 0 0999 V2000
-0.7598 -0.0046 -0.0515 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7378 -0.0348 0.0054 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.1359 -0.1848 0.9895 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.0737 1.0224 -0.3246 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.2022 -0.7902 -0.6806 H 0 0 0 0 0 0 0 0 0 0 0 0
1.0540 0.9002 0.5419 H 0 0 0 0 0 0 0 0 0 0 0 0
1.2277 0.0246 -0.9876 H 0 0 0 0 0 0 0 0 0 0 0 0
1.1520 -0.9329 0.5076 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
1 3 1 0
1 4 1 0
1 5 1 0
2 6 1 0
2 7 1 0
2 8 1 0
M END
[8]>>> print Chem.MolToMolBlock(mh,confId=1)
-----> print(Chem.MolToMolBlock(mh,confId=1))
RDKit 3D
8 7 0 0 0 0 0 0 0 0999 V2000
-0.7524 -0.0779 0.0214 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7451 0.0137 -0.0773 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.1939 -0.8209 -0.6615 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.1367 0.9473 -0.2152 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.0496 -0.3568 1.0611 H 0 0 0 0 0 0 0 0 0 0 0 0
1.0774 0.6281 -0.9534 H 0 0 0 0 0 0 0 0 0 0 0 0
1.0563 0.6193 0.8159 H 0 0 0 0 0 0 0 0 0 0 0 0
1.2538 -0.9528 0.0090 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
1 3 1 0
1 4 1 0
1 5 1 0
2 6 1 0
2 7 1 0
2 8 1 0
M END
[9]>>> AllChem.UFFOptimizeMolecule(mh)
Out[9] 0
[10]>>> print Chem.MolToMolBlock(mh,confId=0)
------> print(Chem.MolToMolBlock(mh,confId=0))
RDKit 3D
8 7 0 0 0 0 0 0 0 0999 V2000
-0.7592 0.0080 -0.0156 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7592 -0.0080 0.0156 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.1643 -0.1020 1.0158 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.1231 0.9691 -0.4441 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.1379 -0.8312 -0.6419 H 0 0 0 0 0 0 0 0 0 0 0 0
1.1379 0.8312 0.6419 H 0 0 0 0 0 0 0 0 0 0 0 0
1.1643 0.1020 -1.0158 H 0 0 0 0 0 0 0 0 0 0 0 0
1.1231 -0.9691 0.4442 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
1 3 1 0
1 4 1 0
1 5 1 0
2 6 1 0
2 7 1 0
2 8 1 0
M END
[11]>>> print Chem.MolToMolBlock(mh,confId=1)
------> print(Chem.MolToMolBlock(mh,confId=1))
RDKit 3D
8 7 0 0 0 0 0 0 0 0999 V2000
-0.7524 -0.0779 0.0214 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7451 0.0137 -0.0773 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.1939 -0.8209 -0.6615 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.1367 0.9473 -0.2152 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.0496 -0.3568 1.0611 H 0 0 0 0 0 0 0 0 0 0 0 0
1.0774 0.6281 -0.9534 H 0 0 0 0 0 0 0 0 0 0 0 0
1.0563 0.6193 0.8159 H 0 0 0 0 0 0 0 0 0 0 0 0
1.2538 -0.9528 0.0090 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
1 3 1 0
1 4 1 0
1 5 1 0
2 6 1 0
2 7 1 0
2 8 1 0
M END
Best,
-greg
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