Hello Greg and Jan,

This is a real newbie question, but what is the use case for this function?  Is 
it used to generate all possible connections (limited by some distance) between 
3 or more atoms given in a smiles string?


Brian


________________________________
From: Greg Landrum <greg.land...@gmail.com>
Sent: Wednesday, February 28, 2018 8:53:59 AM
To: Jan Halborg Jensen
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] problems with EmbedMol

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 
<jhjen...@chem.ku.dk<mailto:jhjen...@chem.ku.dk>> 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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