On May 8, 2014, at 5:47 PM, Craig James wrote:
> Yes. As far as I know, it's the only way to get the correct answer. Your
> original question essentially asked, "Is there a way to get OpenBabel to
> change the semantics of SMARTS?" One could write such a substructure matcher,
> but then it would
On Thu, May 8, 2014 at 8:27 AM, Andrew Dalke wrote:
> On May 8, 2014, at 5:02 PM, Craig James wrote:
> >> Is there any way I can ask Open Babel to generate a query which only
> considers the atom element number, and not the aromaticity? Better yet, if
> it considers the atom element number, and if
On Thu, May 8, 2014 at 5:34 AM, Andrew Dalke wrote:
> I want to evaluate the effectiveness of Open Babel's substructure screen
> fingerprint.
>
[...]
> I want to use the molecule as a query, and find all matches, then generate
> the fingerprint for the query and the targets and do a substructure
On May 8, 2014, at 5:02 PM, Craig James wrote:
>> Is there any way I can ask Open Babel to generate a query which only
>> considers the atom element number, and not the aromaticity? Better yet, if
>> it considers the atom element number, and if the query charge != 0 then also
>> considers the ch
I want to evaluate the effectiveness of Open Babel's substructure screen
fingerprint.
More specifically, I have a query benchmark where the queries are SMILES
strings for molecules (not SMARTS patterns - they come from, for example,
Marvin or another structure editor), and for the target I have
