Hi Sabrina,
The molecules that come back from an RDKit reaction have not been
sanitized (i.e. the chemistry checking and valence calculations have
not yet been done).
If you just want to check if the molecules are chemically reasonable
you can do the following:
In [1]: from rdkit import Chem
In [2]: from rdkit.Chem import AllChem
In [3]: rxn = AllChem.ReactionFromSmarts('[C:1][O:2]>>[C:1][O:2]C')
In [4]: ms = [Chem.MolFromSmiles(x) for x in ('CO','CCO','COC')]
In [5]: for m in ms:
...: ps = rxn.RunReactants((m,))
...: for p in ps:
...: try:
...: Chem.SanitizeMol(p[0])
...: except:
...: print 'failed'
...: else:
...: print Chem.MolToSmiles(p[0])
...:
COC
CCOC
[14:33:13] Explicit valence for atom # 1 O, 3, is greater than permitted
failed
[14:33:13] Explicit valence for atom # 1 O, 3, is greater than permitted
failed
-greg
On Fri, Mar 22, 2013 at 1:34 AM, Syeda Sabrina <[email protected]> wrote:
> Hi everyone,
> I was trying to check whether all the atoms of product molecules for a
> reaction have right number of valences as they supposed to be. I was not
> clear whether there GetExplicitValence() is the right function to use or not
> for this purpose. So I triet to start with it and I used it in the
> following code and ended up with Runtime Error.
>
>
> rxn=AllChem.ReactionFromSmarts('[C:1]/[C:2]=[C:3]/[C:4][C:5]>>[C;1][C:2]\[C:3]=[C:4]\[C:5]')
>
> rxn.Initialize()
>
> reactants=[]
>
> reactants.append(Chem.MolFromSmiles('C/C=C/CC'))
>
> products=rxn.RunReactants(tuple(reactants))
>
> for p in products:
> for mol in p:
> for atom in mol.GetAtoms():
> print atom.GetSymbol(), atom.GetExplicitValence()
>
> C---------------------------------------------------------------------------
> RuntimeError Traceback (most recent call last)
> <ipython-input-14-513b40c7a212> in <module>()
> 2 for mol in p:
> 3 for atom in mol.GetAtoms():
> ----> 4 print atom.GetSymbol(), atom.GetExplicitValence()
> 5
>
> RuntimeError: Pre-condition Violation
>
> However, it can calculate the implicit valence. How can this be possibly
> fixed? Or, is there any other way to check whether an atom has correct
> explicit valence that could be permitted.
>
> Thanks
> Sabrina
>
>
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