Re: [Rdkit-discuss] Categorising reactions using SMARTS

[James W. <jea...@gm...>]

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
>