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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