Re: [Scaffoldhunter-users] Introduction

[<nl...@us...>]

Hi Prateek,

thanks for your interest in Scaffold Hunter and the project idea "Substructure 
Search". Scaffold Hunter supports to filter data sets and the idea here is to 
allow the user to edit a molecular fragment with a structure editor and filter 
out all molecules that do not contain the fragment.

In a previous version of Scaffold Hunter this functionality was included by 
means of the editor JChemPaint. You may want to give version 1.7.1 a try to 
get an idea on how substructure search works. The source code of the old 
version can be found in the SVN repository located at tags/release-1.7.1.
The package subsearch contains the code implementing all basic functionality. 
The subpackages subsearch.graph, subsearch.index and subsearch.match are 
already ported to the code base of the current version version 2.1.3. You will 
find them in the package 
edu.udo.scaffoldhunter.model.filtering.subsearch.fingerprint in trunk.

Reintegrating the functionality in Scaffold Hunter requires to integrate a 
structure editor in the new filtering framework. JChemPaint [1] should be a 
good choice since it is based on the Chemitry Development Kit (CDK) [2] which 
is already used by Scaffold Hunter.
Filtering for substructure search is based on bit operations applied to 
fingerprints. As part of the project this should be implemented by database 
queries or on the client-side. Doing this by database queries is preferable 
for performance reasons. Therefore some experience with SQL databases and 
Hibernate [3] is an advantage.

Reading the paper "CT-Index" will give you some background knowledge on 
subgraph search techniques. However, it is not required to go into all 
details, since these parts are already implemented.


Regards,
Nils

[1] http://jchempaint.github.com/
[2] http://cdk.sourceforge.net/
[3] http://www.hibernate.org/

On Tuesday 09 April 2013 21:32:32 Prateek Gupta wrote:
> hello,
> I am Prateek Gupta,IInd year student pursuing Bachelors in engineering with
> majors in computer science from BITS Pilani Goa,India.
> I am interested to participate in gsoc 2013 and interested in Scaffold
> Hunter organization.
> My skill set includes C,Java,python,mysql and android application
> development.
> I am interested in the idea substructure search in the ideas list.
> If anyone could help me provide with the relative links for the further
> understanding of the idea and direct me with the requirements of the
> project?
> Thank you.