Hi Taka,
You have to call SanitizeMol() on the product(s) explicitely. The error is
caused by the reactants not being 'sanitized'.
Best wishes,
Michal
On Saturday, 6 February 2016, Taka Seri <serit...@gmail.com> wrote:
> Dear RDKitters,
>
> I have question about rdkit reaction function.
> I want to generate molecules using several reaction steps.
> I referred rdkit blog post, and wrote following code.
> But second step of reaction caused error.
> I could not difference about mol and mol2 object.
> I wonder if anyone could help me.
> Best regards,
>
> Takayuki
>
>
> In [1]: from rdkit import Chem
>
> In [2]: from rdkit.Chem import AllChem
>
> In [3]: mol = Chem.MolFromSmiles("c1ccc(F)cc1")
>
> In [6]: rxn = AllChem.ReactionFromSmarts('[cH&$(c(c)c):2]>>[c:2][F]')
>
> #first step works fine.
>
> In [7]: ps = rxn.RunReactants((mol,))
>
> #Bud second step did not work...
>
> In [9]: mol2 = ps[0][0]
>
> In [11]: ps = rxn.RunReactants((mol2,))
>
> [22:23:10]
>
>
> ****
>
> Pre-condition Violation
>
> getNumImplicitHs() called without preceding call to calcImplicitValence()
>
> Violation occurred on line 166 in file
> /Users/landrgr1/anaconda3/anaconda/conda-bld/work/Code/GraphMol/Atom.cpp
>
> Failed Expression: d_implicitValence>-1
>
> ****
>
>
> ---------------------------------------------------------------------------
>
> RuntimeError Traceback (most recent call
> last)
>
> <ipython-input-11-9e3b0e79dbd7> in <module>()
>
> ----> 1 ps = rxn.RunReactants((mol2,))
>
>
> RuntimeError: Pre-condition Violation
>
>
>
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