Hi all,
I recently wanted to use RDKit to model the famous copper-catalyzed
cycloaddition of alkynes and azides.
I eventually got things working, kind of, but had two questions. First, I
was surprised to find that the products of RunReactants don't have update
property caches. Is this something I should have expected, or is it a
bug? If the latter, is it any easy-to-fix bug or a hard-to-fix one?
Second, how can I modify my SMARTS reaction query to avoid duplication of
each product?
Here's some example code, also available at
https://github.com/tentrillion/ipython_notebooks/blob/master/rdkit_smarts_reactions_needs_updating.ipynb
# -------BEGIN CODE------ #
# import rdkit components
from rdkit import rdBase
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import Draw
# use IPythonConsole for pretty drawings
from rdkit.Chem.Draw import IPythonConsole
# IPythonConsole.ipython_useSVG=True # leave out for github
# for flattening
from itertools import chain
# define reactants
diyne_smiles = 'C#CCC(O)C#C'
azide_smiles = 'CCCN=[N+]=[N-]'
diyne = Chem.MolFromSmiles(diyne_smiles)
azide = Chem.MolFromSmiles(azide_smiles)
# define reaction
copper_click_smarts =
'[C:1]#[C:2].[N:3]=[N+:4]=[N-:5]>>[c:1]1[c:2][n-0:3][n-0:4][n-0:5]1'
copper_click = AllChem.ReactionFromSmarts(copper_click_smarts)
# run reaction
products_tuples = copper_click.RunReactants((diyne, azide))
# flatten product tuple of tuples into list
products = list(chain(*products_tuples))
# FAILS: mol property caches are not updated
try:
Draw.MolsToGridImage(products)
except (RuntimeError, ValueError) as e:
print 'FAILED!'
my_error = e
# this works: force updating
for product in products:
product.UpdatePropertyCache()
Draw.MolsToGridImage(products)
my_error
products_tuples = copper_click.RunReactants((diyne, azide))
products = list(chain(*products_tuples))
# FAILS: mol property caches are not updated
Draw.MolsToGridImage(products)
# -------END CODE------ #
The stacktrace is:
---------------------------------------------------------------------------ValueError
Traceback (most recent call
last)<ipython-input-4-7962390107ec> in <module>() 2 products =
list(chain(*products_tuples)) 3 # FAILS: mol property caches are
not updated----> 4 Draw.MolsToGridImage(products)
/Users/curt/anaconda2/lib/python2.7/site-packages/rdkit/Chem/Draw/IPythonConsole.pyc
in ShowMols(mols, **kwargs) 198 else: 199 fn =
Draw.MolsToGridImage--> 200 res = fn(mols, **kwargs) 201 if
kwargs['useSVG']: 202 return SVG(res)
/Users/curt/anaconda2/lib/python2.7/site-packages/rdkit/Chem/Draw/__init__.pyc
in MolsToGridImage(mols, molsPerRow, subImgSize, legends,
highlightAtomLists, useSVG, **kwargs) 403 else: 404 return
_MolsToGridImage(mols, molsPerRow=molsPerRow, subImgSize=subImgSize,
legends=legends,--> 405
highlightAtomLists=highlightAtomLists, **kwargs) 406 407
/Users/curt/anaconda2/lib/python2.7/site-packages/rdkit/Chem/Draw/__init__.pyc
in _MolsToGridImage(mols, molsPerRow, subImgSize, legends,
highlightAtomLists, **kwargs) 344 highlights =
highlightAtomLists[i] 345 if mol is not None:--> 346 img
= _moltoimg(mol, subImgSize, highlights, legends[i], **kwargs) 347
res.paste(img, (col * subImgSize[0], row * subImgSize[1])) 348
return res
/Users/curt/anaconda2/lib/python2.7/site-packages/rdkit/Chem/Draw/__init__.pyc
in _moltoimg(mol, sz, highlights, legend, **kwargs) 309 from
rdkit.Chem.Draw import rdMolDraw2D 310 if not
hasattr(rdMolDraw2D, 'MolDraw2DCairo'):--> 311 img =
MolToImage(mol, sz, legend=legend, highlightAtoms=highlights,
**kwargs) 312 else: 313 nmol =
rdMolDraw2D.PrepareMolForDrawing(mol, kekulize=kwargs.get('kekulize',
True))
/Users/curt/anaconda2/lib/python2.7/site-packages/rdkit/Chem/Draw/__init__.pyc
in MolToImage(mol, size, kekulize, wedgeBonds, fitImage, options,
canvas, **kwargs) 112 from rdkit import Chem 113 mol =
Chem.Mol(mol.ToBinary())--> 114 Chem.Kekulize(mol) 115 116
if not mol.GetNumConformers():
ValueError: Sanitization error: Can't kekulize mol. Unkekulized atoms: 3
------------------------------------------------------------------------------
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