Hi Greg,
thanks for your quick reply. This helped to improve the alignment.
How can I reproduce the alignment done in with the Open3DAlign Node in Python?
Is it possible at all?
Best Regards,
Thomas
From: greg.land...@gmail.com
Date: Fri, 27 Jun 2014 05:10:42 +0200
Subject: Re: [Rdkit-discuss] 3D alignment in Python: align conformers of 2
molecules
To: beginn...@hotmail.de
CC: rdkit-discuss@lists.sourceforge.net
Hi Thomas,
I think there are a couple of problems with the code here:1) you aren't storing
the confirmation of the conformer of mol that produces the best alignment
(cid in the above code)
2) you aren't keeping the best alignment since you repeatedly run the same
molecule instances through the alignment code. You could fix this by, after the
double conformer loop, adding something like:
AllChem.AlignMol(refMol, mol, prbCid=refConformerId, refCid=molConformerId,
atomMap=zip(refMatch,match))
where I have assumed that molConformerId is the variable you use to solve
problem 1.
The loop would become something like this:
minRmsd = 1000; for refCid in refCids:
for cid in cids:
rmsd = AllChem.AlignMol(refMol, mol, prbCid=refCid, refCid=cid,
atomMap=zip(refMatch,match))if rmsd minRmsd:
minRmsd = rmsdrefConformerId = refCid
molConformerId = cid
rmsd = AllChem.AlignMol(refMol, mol, prbCid=refConformerId,
refCid=molConformerId,
atomMap=zip(refMatch,match))
It's also not really right to compare the results of this, which uses the MCS
code to find a common set of atoms and then does an RMSD alignment of those,
and the Open3DAlign results, which use a fuzzier scheme to identify the
atom-atom mapping between the molecules.
-greg
On Thu, Jun 26, 2014 at 2:32 PM, Thomas Strunz beginn...@hotmail.de wrote:
I'm trying to align all conformers of 2 molecules (and keep the best ones)
using the python api by following some of the tutorials:
http://nbviewer.ipython.org/gist/greglandrum/4316435/Working%20in%203D.ipynb
http://nbviewer.ipython.org/github/greglandrum/rdkit_blog/blob/master/notebooks/Using%20ConstrainedEmbed.ipynb
However whatever I try the alignment is considerably different than the one
created using the Open 3D alignment node in Knime.
Currently the issue is that the molecules do not seem to be aligned properly.
There is some sort of small shift. See code below.
Best Regards,
Thomas
refCids = generateConformers(refMol, numConformers)
mcs = MCS.FindMCS([refMol,mol], ringMatchesRingOnly=matchesRingOnly)
if mcs.completed == 1 and mcs.numAtoms 0:
core = Chem.MolFromSmarts(mcs.smarts)
logger.info('MCS: %s', Chem.MolToSmiles(core))
refMatch = refMol.GetSubstructMatch(core)
match = mol.GetSubstructMatch(core)
# conformers for current target
cids = generateConformers(mol, numConformers, coordMap=coordMap)
minRmsd = 1000;
for refCid in refCids:
for cid in cids:
rmsd = AllChem.AlignMol(refMol, mol, prbCid=refCid,
refCid=cid, atomMap=zip(refMatch,match))
logger.debug('RMSD: %.2f', rmsd)
if rmsd minRmsd:
logger.debug('New min RMSD: %.2f', rmsd)
minRmsd = rmsd
refConformerId = refCid
def generateConformers(mol, numConformers):
AllChem.EmbedMolecule(mol)
AllChem.MMFFOptimizeMolecule(mol)
cids=AllChem.EmbedMultipleConfs(mol, numConfs=numConformers,
maxAttempts=50, pruneRmsThresh=0.5, coordMap=coordMap)
for cid in cids: AllChem.MMFFOptimizeMolecule(mol,confId=cid)
return cids
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