Hi Jan,
It took me much longer than it should have to figure this one out...
The bounds matrix that is returned by GetMoleculeBoundsMatrix() needs to
have triangle bounds smoothing applied to it before it can be embedded. The
bounds smoothing process narrows the possible distance ranges between the
atoms. Here's a quick demo of that.
We start with your example:
In [19]: mol = Chem.MolFromSmiles("CCC")
...: mol = Chem.AddHs(mol)
...: bounds = AllChem.GetMoleculeBoundsMatrix(mol)
...: EmbedLib.EmbedMol(mol,bounds)
...:
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
<ipython-input-19-60befaacbe48> in <module>()
2 mol = Chem.AddHs(mol)
3 bounds = AllChem.GetMoleculeBoundsMatrix(mol)
----> 4 EmbedLib.EmbedMol(mol,bounds)
c:\Users\glandrum\RDKit_git\rdkit\Chem\Pharm3D\EmbedLib.py in EmbedMol(mol,
bm, atomMatch, weight, randomSeed, excludedVolumes)
183 for i in range(nAts):
184 weights.append((i, idx, weight))
--> 185 coords = DG.EmbedBoundsMatrix(bm, weights=weights, numZeroFail=1,
randomSeed=randomSeed)
186 # for row in coords:
187 # print(', '.join(['%.2f'%x for x in row]))
ValueError: could not embed matrix
But if we do the triangle bounds smoothing things embed without problems:
In [20]: from rdkit import DistanceGeometry
In [21]: DistanceGeometry.DoTriangleSmoothing(bounds)
Out[21]: True
In [22]: EmbedLib.EmbedMol(mol,bounds)
In [23]:
There is a good argument to be made for GetMoleculeBoundsMatrix() returning
the smoothed bounds matrix by default. I'll put that on the list for the
next release.
Best,
-greg
On Wed, Feb 28, 2018 at 10:41 AM, Jan Halborg Jensen <[email protected]>
wrote:
> The following code works fine with ethane (CC) but for propane (CCC) or
> anything else I get the following error
> ValueError: could not embed matrix
>
> Any ideas or solutions would be appreciated
>
> Best regards, Jan
>
>
> from rdkit import Chem
> from rdkit.Chem import AllChem
> from rdkit.Chem.Pharm3D import EmbedLib
>
>
> mol = Chem.MolFromSmiles("CCC")
> mol = Chem.AddHs(mol)
> bounds = AllChem.GetMoleculeBoundsMatrix(mol)
>
> EmbedLib.EmbedMol(mol,bounds)
> EmbedLib.OptimizeMol(mol, bounds)
>
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