Re: [Scaffoldhunter-users] Fwd: Re: Introduction

[Till S. <til...@tu...>]

Dear Prateek,
first i would like to ask you to write your questions using the mailing list sca...@li...
for further questions. This allows us to answer questions only once and do not repeat ourself for other students.

Am 24.04.2013 15:39, schrieb Prateek Gupta:
> hi,
> I used the scaffold hunter project with the dataset after creating the database in the mysql server.
> uptil now , I am able to understand that the idea that I want to work on ,"substructure search" ,involves the filtering
> framework.
> I am briefing you my understanding and if any discrepancy please help me understand that.
> 1)After selecting the "overview over the scaffold property" , which basically targets the atom about which the filter
> framework has to work ,
> 2) proceeds to the "definition of the filter rules" ,which seeks user input as to the number of subsets that it should
> create of the compound >,=,< ,
> 3) then proceeds to substructure part , where substructure can be edited and when the option search scaffold is selected
> it analyses the compound and displays the result.
> 
> Does this project idea supposedly aims to seek user input in terms of the number of subsets that the compound needs to
> be segregated into and also about the integration of JChemPaint editor in the project!
> Can you help me in more understanding about the different filter rules applied.About the ">" , " =" , " <" options usage
> and target!

I do not know if i understood you right, but i will try to give you an answer based on what i understood. Please note
that the 1.7 Version which contains an implementation of the substructure filtering is very different from the current
version (2.x) regarding the handling of filtering in general. In general filtering is not meant to distribute a number
of molecules into different subsets but to reduce a subset by keeping only the molecules which match a set of filter
rules. For the general understanding of sets/subsets and filtering please refer to section 6.2 of the Scaffold Hunters
manual, which is part of the distributed zip-file.



Regards
Till


> And about the current editor being used in the project
> 
> Also the overall requirements of the project idea as I am starting to build my proposal and need to understand it.
> 
> Regards,
> Prateek.
> 
> 
> On Tue, Apr 16, 2013 at 2:18 AM, Nils Kriege <nil...@tu... <mailto:nil...@tu...>> wrote:
> 
>     Hi Prateek,
> 
>     did you receive my reply regarding your questions via the mailing list? In
>     case you subscribed to the list later, you can find my reply here:
> 
>     https://sourceforge.net/mailarchive/message.php?msg_id=30711483
> 
>     The project is not about implementing or improving the CT-Index approach, the
>     goal is a user-friendly integration of the existing CT-Index implementation in
>     Scaffold Hunter. Unfortunately, the term "filtering" is ambiguous: There is a
>     filtering framework in Scaffold Hunter which basically allows to create
>     subsets of compound sets by specifying rules like "all molecules with property
>     x < 7". We would like to support rules like "all molecules that contain
>     fragment z". These queries can be answered by means of CT-Index, which uses
>     fingerprint-based filtering for efficiency.
> 
> 
>     Regards
>     Nils
> 
>     On Tuesday 16 April 2013 05:26:16 Karsten Klein wrote:
>     > -------- Original-Nachricht --------
>     > Betreff:      Re: [Scaffoldhunter-users] Introduction
>     > Datum:        Mon, 15 Apr 2013 21:37:49 +0530
>     > Von:  Prateek Gupta <pra...@gm... <mailto:pra...@gm...>>
>     > An:   Karsten Klein <kar...@ud... <mailto:kar...@ud...>>
>     >
>     >
>     >
>     > hi Karsten,
>     > i have subscribed to the user and developer mailing list but there seems
>     > no activity and response.
>     > II went through the paper
>     > CT-Index: Fingerprint-based Graph Indexing Combining Cycles and Trees
>     > <http://dx.doi.org/10.1109/ICDE.2011.5767909>
>     > and tried to understand the implementation algorithm and preparing to
>     > use the software jchempaint.
>     > As for the lack in integration of the filtering technique,does the
>     > project idea aims to implement a new
>     > algorithm or is it to make the current algorithm more efficient?
>     >
>     >
>     > On Thu, Apr 11, 2013 at 5:02 PM, Karsten Klein <kar...@ud... <mailto:kar...@ud...>
>     > <mailto:kar...@ud... <mailto:kar...@ud...>>> wrote:
>     >
>     >     Hi Prateek,
>     >
>     >     as the discussion might help others too to understand a bit more what
>     >     the project is about, or some potential mentor might want to
>     >     comment, yes.
>     >
>     >         Karsten
> 
> 

-- 
Dipl.-Inf. Till Schäfer
Technische Universität Dortmund
Chair 11 - Algorithm Engineering
Otto-Hahn-Str. 14
44227 Dortmund, Germany

e-mail: til...@cs...
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