Hi all,
here the code for Open3DALIGN:
cids = generateConformers(mol, numConformers)
prbPyMP = AllChem.MMFFGetMoleculeProperties(mol)
maxScore = 0;
for refCid in refCids:
for cid in cids:
alignment = AllChem.GetO3A(mol, refMol, prbPyMP, refPyMP,
prbCid=cid, refCid=refCid,)
score = alignment.Score()
logger.debug('Score: %.2f', score)
if score > maxScore:
logger.info('New max. Score: %.2f', score)
maxScore = score
refConformerId = refCid
molCid = cid
alignment = AllChem.GetO3A(mol, refMol, prbPyMP, refPyMP,
prbCid=molCid, refCid=refConformerId)
alignment.Align()
# show in PyMol
One question I have is how I can align this to a specific fragment or the MCS?
I tried using constraintMap but for some reason o3a does not want to align the
2 structure on it. I suspect because then the rest of the alignment will not be
very good in that case.
The code:
constraintMap = []
constraintWeights = []
mcs = MCS.FindMCS([refMol,mol], bondCompare='bondtypes',
ringMatchesRingOnly=False)
if mcs.completed == 1 and mcs.numAtoms > 0:
core = Chem.MolFromSmarts(mcs.smarts) # or use specific smarts
pattern through argument option
logger.info('MCS: %s', Chem.MolToSmiles(core))
refMatch = refMol.GetSubstructMatch(core)
match = mol.GetSubstructMatch(core)
for idx, val in enumerate(match):
constraintMap.append((val, refMatch[idx]))
constraintWeights.append(100.0)
logger.info(constraintMap)
...
alignment = AllChem.GetO3A(mol, refMol, prbPyMP, refPyMP, prbCid=cid,
refCid=refCid, constraintMap=constraintMap,
constraintWeights=constraintWeights)
The alinment is different but it still does not want to align to my defined
fragment. even if I set constraintWeights to very high value. In my case I
especially want to align heteroatoms properly. For that I tried:
for idx, val in enumerate(match):
constraintMap.append((val, refMatch[idx]))
if mol.GetAtomWithIdx(val).GetAtomicNum() != 6:
constraintWeights.append(1000.0)
logger.info('Set weigth to 1000')
else:
constraintWeights.append(10.0)
But the single hetero atoms in this my test case are still not aligned on each
other. I also tried ConstrainedEmbed (or how it is called) but that results in
either an error or with relaxed parameters in a completely useless
conformation, namely on a ring.
What are my options?
From: greg.land...@gmail.com
Date: Fri, 27 Jun 2014 08:20:56 +0200
Subject: Re: [Rdkit-discuss] 3D alignment in Python: align conformers of 2
molecules
To: beginn...@hotmail.de
CC: rdkit-discuss@lists.sourceforge.net
On Fri, Jun 27, 2014 at 7:57 AM, Thomas Strunz <beginn...@hotmail.de> wrote:
thanks for your quick reply. This helped to improve the alignment.
I'm glad to hear it!
How can I reproduce the alignment done in with the Open3DAlign Node in Python?
Is it possible at all?
But of course. :-)There's some example code that shows how to do it on page 37
of Paolo's presentation from the last RDKit UGM:
https://github.com/rdkit/UGM_2013/raw/master/Presentations/Tosco.RDKit_UGM2013.pdf
-greg
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