Hi Taka,
Yes, you need to sanitize every product molecule, after each step.
Best wishes,
Michal
On 7 February 2016 at 01:58, Taka Seri <serit...@gmail.com> wrote:
> Hi Michal,
>
> Thank you for your quick and kind response.
> I tried to sanitize mol according to your advice.
> And my code worked fine !
> Thanks you. ;-)
> By the way, If I want to run several reaction steps. Do I need to
> sanitize each molecules?
>
>
> # reactiontest.py
> from rdkit import Chem
> from rdkit.Chem import AllChem
>
> from rdkit import Chem
> from rdkit.Chem import AllChem
> mol = Chem.MolFromSmiles("c1ccccc1")
> rxn = AllChem.ReactionFromSmarts( "[cH&$(c(c)c):2]>>[c:2][F]" )
> ps1= rxn.RunReactants( (mol,) )
> ps1
> mol2 = ps1[0][0]
> Chem.SanitizeMol( mol2 )
> ps2= rxn.RunReactants( (mol2,) )
> uniq = set( [ Chem.MolToSmiles(x[0], isomericSmiles=True ) for x in ps2 ]
> )
> print( uniq )
> ---------------
> from shell
>
> $ python reactiontest.py
>
> {'Fc1ccc(F)cc1', 'Fc1cccc(F)c1', 'Fc1ccccc1F'}
>
> ---------------------------------------------------------
> Best regards,
> Takayuki
>
> 2016年2月6日(土) 23:01 Michal Krompiec <michal.kromp...@gmail.com>:
>
>> 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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