The outputs of reaction are a bit confusing.
Reactions can have multiple product templates so the output of RunReactants is
a list of list of molecules.
For products in result:
For molecule in products:
Molecule.UpdatePropertyCache()
However, it looks like your reaction is generating non sensical molecules so
you may want to draw with sanitizaton turned off so you can see the reaction
output.
----
Brian Kelley
> On Jan 11, 2017, at 9:11 PM, Curt Fischer <curt.r.fisc...@gmail.com> wrote:
>
> 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
>
> ------------------------------------------------------------------------------
> Developer Access Program for Intel Xeon Phi Processors
> Access to Intel Xeon Phi processor-based developer platforms.
> With one year of Intel Parallel Studio XE.
> Training and support from Colfax.
> Order your platform today. http://sdm.link/xeonphi
> _______________________________________________
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
------------------------------------------------------------------------------
Developer Access Program for Intel Xeon Phi Processors
Access to Intel Xeon Phi processor-based developer platforms.
With one year of Intel Parallel Studio XE.
Training and support from Colfax.
Order your platform today. http://sdm.link/xeonphi
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
