Re: [Cdk-user] framework for storing and searching chemical structures

[Joos K. <jo...@su...>]

Hi Egon,

About substructure search:

Basic principle is simple. First screens based on Fingerprint, then uses 
UIT for Subgraph matching. The user can configure any implementation of 
IFingerprinter.

"Optimizations:"
- You can specify the number of search threads (eg. threads running UIT) 
so one could make use of modern CPUs.
- You can configure to keep the molecules in memory (in the format used 
in OrChem = as Strings).
- limit maximum number of hits
- Results are immediately available so the first search hits can already 
be displayed while search continues in background
- Search can be limited to a list of IDs (id = primary key column). The 
idea behind this is, if you search for substructure + property you limit 
the substructure search to structures matching the property value.

Best Regards,

Joos


Am 06.02.2012 14:17, schrieb Egon Willighagen:
> Hi Joos,
>
> On Sun, Feb 5, 2012 at 6:34 PM, Joos Kiener<jo...@su...>  wrote:
>> for my Master Thesis in computer science (Master of Advanced Studies) I have
>> created a simple framework based on the CDK for storing and searching
>> chemical structures in a relational database.
> How does it optimize substructure searching?
>
>> Note that newest
>> CDK versions won't work as IMolecule interface is used in the framework.
>> Will need to change that for next release.
> CDK 1.4.x will be the stable release for at least the next 6 months...
> Also, the 'master' branch is far from being frozen and we expect more
> API changes... just keep that in mind :)
>
> Egon
>