You need to sanitize the products, just run Chem.SanitizeMol on each
molecule. See
http://www.rdkit.org/docs/GettingStartedInPython.html#chemical-reactions :
"the molecules that are produced by the chemical reaction processing code
are not sanitized".
Best,
Michal
On 12 January 2017 at 17:22, Curt Fischer <curt.r.fisc...@gmail.com> wrote:
> What makes you think the molecules are nonsensical? They look OK to me.
> Converting to SMILES before doing any UpdatePropertyCache() stuff....
>
>
>
> *products_tuples = copper_click.RunReactants((diyne, azide))products =
> list(chain(*products_tuples))print [Chem.MolToSmiles(prod) for prod in
> products]*
>
> gives....
>
>
>> *['C#CC(O)Cc1cnnn1CCC', 'C#CC(O)Cc1cn(CCC)nn1', 'C#CCC(O)c1cn(CCC)nn1',
>> 'C#CCC(O)c1cnnn1CCC']*
>
>
> ...and those all look like valid SMILES strings to me.
>
> I'm not sure exactly how to turn off all sanitization, but I did
>
> *Draw.MolsToGridImage(products, kekulize = False)*
>
> and as long that is invoked before UpdatePropertyCache, there is a
> *different* error than the one I reported last time.
>
> ---------------------------------------------------------------------------RuntimeError
> Traceback (most recent call
> last)<ipython-input-22-0305dfc54e69> in <module>() 7 print
> [Chem.MolToSmiles(prod) for prod in products] 8 ----> 9
> Draw.MolsToGridImage(products, kekulize = False)
> /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) 400 if useSVG: 401 return
> _MolsToGridSVG(mols, molsPerRow=molsPerRow, subImgSize=subImgSize,
> legends=legends,--> 402
> highlightAtomLists=highlightAtomLists, **kwargs) 403 else: 404
> return _MolsToGridImage(mols, molsPerRow=molsPerRow, subImgSize=subImgSize,
> legends=legends,
> /Users/curt/anaconda2/lib/python2.7/site-packages/rdkit/Chem/Draw/__init__.pyc
> in _MolsToGridSVG(mols, molsPerRow, subImgSize, legends, highlightAtomLists,
> stripSVGNamespace, **kwargs) 374 nmol =
> rdMolDraw2D.PrepareMolForDrawing(mol, kekulize=kwargs.get('kekulize', True))
> 375 d2d = rdMolDraw2D.MolDraw2DSVG(subImgSize[0], subImgSize[1])-->
> 376 d2d.DrawMolecule(nmol, legend=legends[i],
> highlightAtoms=highlights) 377 d2d.FinishDrawing() 378 txt
> = d2d.GetDrawingText()
> RuntimeError: Pre-condition Violation
> getNumImplicitHs() called without preceding call to
> calcImplicitValence()
> Violation occurred on line 153 in file Code/GraphMol/Atom.cpp
> Failed Expression: d_implicitValence > -1
> RDKIT: 2016.09.2
> BOOST: 1_56
>
>
>
> On Thu, Jan 12, 2017 at 4:41 AM, Brian Kelley <fustiga...@gmail.com>
> wrote:
>
>> 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/tentrill
>> ion/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
>
>
------------------------------------------------------------------------------
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
