Re: [Rdkit-discuss] UpdatePropertyCache() after RunReactants

[Curt F. <cur...@gm...>]

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 <fus...@gm...> 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 <cur...@gm...>
> 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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