The new indigo 1.1 beta11 version is available for downloading:
http://ggasoftware.com/download/indigo_next
The new version contains the new RGroup Decomposition API which allows
user to iterate over all scaffold matches. More detailed description can
be found here:
https://groups.google.com/group/indigo-general/browse_thread/thread/75281df2f70ec1a
If you have any question, please let us know.
With best regards,
Alexander
> Hi everybody,
>
> We have also found this problem of non-iteration of all possible
> scaffold matching.
> So, we are interested by a new release which will fix it.
>
> For example, this will be very interesting to select the Scaffold
> Rgroup Decomposition which has the most number of Rsite (to have the
> most detailed decomposition).
>
> So let me now when this will be added to the next INDIGO release.
>
> With best regards.
>
> M�d�rich
>>>>>> structures (don�t cares in usual substructure search)
>>>>>> -Allow user to define R-Groups on core structures. R-Groups match any
>>>>>> atom, Hydrogen included.
>>>>> Here I do not fully understand the issue. Can you specify some
>>>>> examples for a core structure and expected results?
>>>> thx for your reply. I will try to explain myself.
>>>> Please keep in mind that all substructure definition are in MDL-Mol
>>>> format, although written as SMILES in this text (and my bad English
>>>> also :-) ).
>>>> In R-Group decomposition you have to perform a substructure search as
>>>> first step.
>>>> I think that substructure search should behave different for plain
>>>> substructure search and substructure search for decomposition.
>>>> If a chemist uses c1ccccc1 in substructure search he wants to select
>>>> all structures which contain phenyl. Any atom outside the ring has no
>>>> effect on the result. ( c1c[Cl]cccc1, c12ccccc1cccc2 are ok).
>>>> But in contrast if a chemist defines c[R1]1cc[R2]ccc1 as core
>>>> structure for R-Group decomposition, I think he would expect a more
>>>> rigid behaviour. I think that he expect an exact match of the
>>>> substructure on target structure. So
>>>> c1ccccc1 (benzene), c1cc[Cl]ccc1 (Chlorobenzene), c[Cl]1cc[N]ccc1 (3-
>>>> Chlorbenzene)
>>>> are valid results. But any ring, equipped with more than two heavy
>>>> atoms (e.g. c[Cl]1cc[N]ccc[C]1 �) should not considered as core