Hi Brian
My interest stems from this paper http://dx.doi.org/10.1039/c5cp04706d where
they alter the bounds matrix to impose constraints on the embedding.
In principle this could also be done with EmbedMolecule and coordMap but that
doesn't seem to be working
https://sourceforge.net/p/rdkit/mailman/message/36139015/
Best regards, Jan
________________________________
From: Bennion, Brian [[email protected]]
Sent: Wednesday, February 28, 2018 7:09 PM
To: Greg Landrum
Cc: [email protected]
Subject: Re: [Rdkit-discuss] problems with EmbedMol
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 <[email protected]>
Sent: Wednesday, February 28, 2018 8:53:59 AM
To: Jan Halborg Jensen
Cc: [email protected]
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
<[email protected]<mailto:[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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