Re: [Rdkit-discuss] Categorising reactions using SMARTS

[Greg L. <gre...@gm...>]

Hi James,

Sorry for the slow reply, this one got lost in the rush around the UGM.
I'm not able to reproduce the error you show below with the commands you
sent. Did you do something else in between or is that the error really
coming after input [6]?

As for the larger question: are you looking to do a substructure query
between each reactant/product of rxn and each reactant/product of qrxn?

-greg

On Thu, Oct 27, 2016 at 2:17 PM, James Wallace <jea...@gm...> wrote:

> Looking into this further, I've decided to use the Python option again, as
> this seems to have more functions.
>
> I run the current example, where rxn is the original example, and qrxn is
> the 'query' for categorisation:
>
> In [2]: import rdkit
>
> In [3]: from rdkit import Chem
>
> In [4]: from rdkit.Chem import rdChemReactions
>
> In [5]: rxn = rdChemReactions.ReactionFromSmarts('Nc1nc(Cl)
> c2[nH]cnc2n1.OCC1CCC
>    ...: CC1>>Nc1nc(OCC2CCCCC2)c2[nH]cnc2n1')
>
> In [6]: qrxn = rdChemReactions.ReactionFromSmarts('[cH1:1]1:[
> c:2](-[CH2:7]-[CH2
>    ...: :8]-[NH2:9]):[c:3]:[c:4]:[c:5]:[c:6]:1.[#6:11]-[CH1;R0:10]=[
> OD1]>>[c:1]
>    ...: 12:[c:2](-[CH2:7]-[CH2:8]-[NH1:9]-[C:10]-2(-[#6:11])):[c:
> 3]:[c:4]:[c:5]
>    ...: :[c:6]:1')
>
> ****
> Pre-condition Violation
> getNumImplicitHs() called without preceding call to calcImplicitValence()
> Violation occurred on line 165 in file C:\Users\riccardo\Anaconda\
> conda-bld\work
> \Code\GraphMol\Atom.cpp
> Failed Expression: d_implicitValence > -1
> ****
>
> ------------------------------------------------------------
> ---------------
> RuntimeError                              Traceback (most recent call last)
> <ipython-input-8-98ff5fdf90be> in <module>()
> ----> 1 rdChemReactions.HasReactionSubstructMatch(rxn,qrxn)
>
> RuntimeError: Pre-condition Violation
>         getNumImplicitHs() called without preceding call to
> calcImplicitValence(
> )
>         Violation occurred on line 165 in file Code\GraphMol\Atom.cpp
>         Failed Expression: d_implicitValence > -1
>         RDKIT: 2016.03.1
>         BOOST: 1_59
>
>
> Is the code working as designed (ultimately I want to feed lists of these
> together, but I'm trying one at a time for now)?
>
>
> On 27 October 2016 at 12:02, James Wallace <jea...@gm...> wrote:
>
>> Hi,
>> I'm trying to replicate the Schneider categorisations with a local set of
>> reactions that I have stored in SMILES. I currently have the categorisation
>> filters as Reaction SMARTS, and I was hoping to do a standard substructure
>> comparison between the SMARTS and the SMILES, but can't seem to do that.
>>
>> I'm using the Java wrapped version, and I can see how to import a
>> ChemicalReaction as SMILES or SMARTS, I can't see how to compose such a
>> query. Can anyone offer me any help or pointers?
>>
>> Thanks in advance,
>> James
>>
>
>
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