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/
> 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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