Hi Anthony,
For some reason that I still need to look into, there is something in this
case that's making the distance geometry embedding unhappy. I just pushed a
change to github that allows additional arguments to be provided for the
embedding when you call AllChem.ConstrainedEmbed.
I was able to get a reasonable embedding using the following arguments:
nm=AllChem.ConstrainedEmbed(mol1,mol2,ignoreSmoothingFailures=True,useRandomCoords=True,useTethers=True)
I will take a look into the problems with the default embedding and see if
I can figure out what's going on, but this should at least provide a
workaround.
-greg
On Mon, Mar 10, 2014 at 3:19 PM, Anthony Bradley <
anthony.brad...@worc.ox.ac.uk> wrote:
> 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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