Dear all,
I'm having a bit of trouble with the constrained embed functionality.
I have a core molecule (m2) with 3D co-ordinates and a molecule I would like to
superpose (m1).
Running constrained embed on these returns a value error because it is not
possible to embed m1 with the coord map (in the constrained embed function in
AllChem.py). It is possible to embed the molecule without the coordmap.
I include a working not-working example below.
I might be missing some fundamental reason why this function cannot be run on
this pair of molecules.
If not has anyone seen this problem before or no of a way to fix it?
Best wishes,
Anthony
from rdkit.Chem import AllChem
from rdkit import Chem
m1="""
RDKit
23 26 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 0
3 4 2 0
4 5 1 0
5 6 2 0
6 7 1 0
7 8 2 0
7 9 1 0
9 10 2 0
10 11 1 0
11 12 1 0
12 13 1 0
13 14 2 0
14 15 1 0
15 16 1 0
16 17 1 0
17 18 1 0
18 19 1 0
19 20 2 0
9 21 1 0
21 22 2 0
21 23 1 0
8 3 1 0
15 11 2 0
23 6 1 0
19 14 1 0
M END"""
m2 = """
RDKit 3D
14 15 0 0 0 0 0 0 0 0999 V2000
2.3310 27.3220 8.7020 C 0 0 0 0 0 0 0 0 0 0 0 0
3.2500 27.0650 8.0540 C 0 0 0 0 0 0 0 0 0 0 0 0
1.5120 28.4620 8.4140 C 0 0 0 0 0 0 0 0 0 0 0 0
0.3320 28.8100 9.1340 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.2250 28.1050 10.2030 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.5490 28.7880 10.7670 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.1290 28.2150 11.7490 O 0 0 0 0 0 0 0 0 0 0 0 0
-1.7430 27.1830 12.2850 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.0160 29.9510 10.1940 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.3640 30.5820 9.1080 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.1630 29.9910 8.5750 C 0 0 0 0 0 0 0 0 0 0 0 0
0.6500 30.4210 7.5360 N 0 0 0 0 0 0 0 0 0 0 0 0
1.6120 29.5320 7.4620 C 0 0 0 0 0 0 0 0 0 0 0 0
2.4850 29.6660 6.6370 O 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
1 3 2 3
3 4 1 0
3 13 1 0
4 5 2 0
4 11 1 0
5 6 1 0
6 7 1 0
6 9 2 0
7 8 1 0
9 10 1 0
10 11 2 0
11 12 1 0
12 13 1 0
13 14 2 0
M END"""
mol1= Chem.MolFromMolBlock(m1)
mol2= Chem.MolFromMolBlock(m2)
AllChem.ConstrainedEmbed(mol1,mol2)
Returns this error:
C:\RDKit_2011_03_2\rdkit\Chem\AllChem.pyc in ConstrainedEmbed(mol, core,
useTethers, coreConfId, randomseed)
295 ci = EmbedMolecule(mol,coordMap=coordMap,randomSeed=randomseed)
296 if ci<0:
--> 297 raise ValueError,'Could not embed molecule.'
298
299 algMap=[(j,i) for i,j in enumerate(match)]
ValueError: Could not embed molecule.
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