scaffoldhunter-users — General discussion list for Scaffold Hunter users

[Scaffoldhunter-users] Test Mail

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

test if the mailinglist still works

-- 
Dipl.-Inf. Till Schäfer
Technische Universität Dortmund
Chair 11 - Algorithm Engineering
Otto-Hahn-Str. 14 / Raum 237
44227 Dortmund, Germany

e-mail: til...@cs...
phone: +49(231)755-7706
fax: +49(231)755-7740
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[Scaffoldhunter-users] Google Summer of Code

[Karsten K. <kar...@ud...>]

Thanks to all students and mentors who participate in GSoC and want to
contribute to our project.

We received 19 proposals and will now go through them and rank them to
see which ones are
the most promising for us. Then we will have to see how many slots we
get from Google. Let's
hope for the best!
Acceptance will be announced on May 27 by Google.

Best,
    Karsten (on behalf of the Scaffold Hunter team)

Re: [Scaffoldhunter-users] GSoC-2013

[shruti g. <shr...@gm...>]

Dear Sir,

On Thu, May 2, 2013 at 12:05 PM, Karsten Klein
<ka...@us...>wrote:

> Sure, that needs a bit of discussion.
> Regarding the node overlap, the layout (or the method applied) has to
> guarantee that the visualization is overlap free
> for the scaffold tree view. For a similarity map etc non-overlap might
> not be such a strict requirement, but for this view
> it is.
>

I have uploaded the draft proposal on the melange site, it would be great
if you could have a look and provide some feedback regarding the same. I
would be glad to incorporate the same. I have tried to base my proposal
upon your suggestions.

Hope to hear from you soon,

Shruti.

On 2/05/2013 4:05 PM, shruti gupta wrote:
> Dear Sir,
>

> > Thank you for your reply. I will go through the paper, and  mention it
> > in the proposal. Given finite size of the nodes, reducing area of the
> > graph might also lead to overlaps, which also will have to be taken
> > care of, right? Further discussion for the Layout algorithm to be
> > used, can be left off to the Community Bonding Period if I am lucky
> > enough to be selected! Is it okay with you ?
> >
> >
> > On Thu, May 2, 2013 at 11:30 AM, Karsten Klein
> > <ka...@us... <mailto:ka...@us...>> wrote:
> >
> >     The problem is to extend a layout algorithm to adhere to the
> >     requirements we have in Scaffold Hunter.
> >     The graph here is not just an abstract mathematical structure, but
> the
> >     nodes have prescribed sizes (due to
> >     the scaffold images) that need to be respected, there is a layering
> >     given by the depth level of scaffolds within
> >     the scaffold tree inclusion hierarchy, and the user can sort the
> >     scaffolds according to some criteria, which has
> >     to be clearly reflected in the layout.
> >
> >     As long as the layout method scales to several thousand objects,  and
> >     supports those constraints, the type does
> >     not matter much, it could e.g. be a distance based method. There
> >     is for
> >     example a paper by Brandes and Pich (More
> >     flexible radial layout) that describes how the radial layout style
> can
> >     be resembled using Stress Majorization, but
> >     it is not trivial to model the system correctly in order to
> >     respect the
> >     above constraints in addition.
> >
> >     So there is a couple of options, but no preselection of a method for
> >     this project.
> >
> >         Karsten
> >
> >     On 2/05/2013 3:38 PM, shruti gupta wrote:
> >     > Dear Sir,
> >     >
> >     > Thank you for your reply. As far as I have understood, here we are
> >     > trying to reduce the area covered by the graph without affecting
> the
> >     > information conveyed by it. Are you intending to look at some
> >     > Force-directed algorithms to reduce this?
> >     > Or you have something else in mind? Or this question forms a part
> of
> >     > the Literature Survey for the project?
> >     >
> >     > Hope to hear from you soon,
> >     >
> >     > Shruti
> >     >
> >     >
> >     > On Thu, May 2, 2013 at 10:55 AM, Karsten Klein
> >     > <ka...@us... <mailto:ka...@us...>
> >     <mailto:ka...@us...
> >     <mailto:ka...@us...>>> wrote:
> >     >
> >     >     Hi Shruti,
> >     >
> >     >     thanks for your interest. It is not too late until the
> >     deadline is
> >     >     over ;-).
> >     >     You can apply any time till then. If you have any further
> >     >     questions, feel
> >     >     free to send them to this list.
> >     >
> >     >     Looking forward to your proposal,
> >     >     kind regards,
> >     >         Karsten
> >     >
> >     >     On 2/05/2013 3:13 PM, shruti gupta wrote:
> >     >     > Hello everyone,
> >     >     >
> >     >     > I am a third year undergraduate student pursuing a degree in
> >     >     > Information Systems. I am interested to work with Scaffold
> >     for GSoC
> >     >     > 2013. I am aware that it is too late to apply for a
> >     project now,
> >     >     but I
> >     >     > had been busy with my exams, and so, could not get here
> >     earlier.
> >     >     >
> >     >     >
> >     >     > I have worked on Probabilistic Graphical Models with
> >     RooStats(CERN),
> >     >     > for Google Summer of Code - 2012. The project consisted of
> >     >     > construction and sampling of Bayesian Belief Networks. The
> >     code is
> >     >     > written in C++.
> >     >     >
> >     >     > As a semester course, I have studied basic propositional
> >     logic, data
> >     >     > structures and algorithms (including graph algorithms). I
> >     have also
> >     >     > done a course in Object Oriented Programming and Design
> >     focused on
> >     >     > Java. I have also completed a basic in Graphs and Networks.
> >     >     >
> >     >     > I am interested in the following projects:
> >     >     >
> >     >     >   * Scaffold Tree Layout
> >     >     >
> >     >     >
> >     >     > I am already working on my proposal. It would be great if
> >     a mentor
> >     >     > could tell me if applying now is encouraged. And, if it is
> >     okay to
> >     >     > apply now.
> >     >     >
> >     >     > Looking forward to working with you,
> >     >     >
> >     >     > Thank you
> >     >     >
> >     >     > Shruti Gupta.
> >     >     >
> >     >     >
> >     >     >
> >     >     >
> >     >
> >
> ------------------------------------------------------------------------------
> >     >     > Introducing AppDynamics Lite, a free troubleshooting tool for
> >     >     Java/.NET
> >     >     > Get 100% visibility into your production application - at
> >     no cost.
> >     >     > Code-level diagnostics for performance bottlenecks with
> >     <2% overhead
> >     >     > Download for free and get started troubleshooting in minutes.
> >     >     > http://p.sf.net/sfu/appdyn_d2d_ap1
> >     >     >
> >     >     >
> >     >     > _______________________________________________
> >     >     > Scaffoldhunter-users mailing list
> >     >     > Sca...@li...
> >     <mailto:Sca...@li...>
> >     >     <mailto:Sca...@li...
> >     <mailto:Sca...@li...>>
> >     >     >
> >     https://lists.sourceforge.net/lists/listinfo/scaffoldhunter-users
> >     >
> >     >
> >
> >
>
>

Re: [Scaffoldhunter-users] GSoC-2013

[shruti g. <shr...@gm...>]

Dear Sir,

Thank you for your reply. I will go through the paper, and  mention it in
the proposal. Given finite size of the nodes, reducing area of the graph
might also lead to overlaps, which also will have to be taken care of,
right? Further discussion for the Layout algorithm to be used, can be left
off to the Community Bonding Period if I am lucky enough to be selected! Is
it okay with you ?


On Thu, May 2, 2013 at 11:30 AM, Karsten Klein
<ka...@us...>wrote:

> The problem is to extend a layout algorithm to adhere to the
> requirements we have in Scaffold Hunter.
> The graph here is not just an abstract mathematical structure, but the
> nodes have prescribed sizes (due to
> the scaffold images) that need to be respected, there is a layering
> given by the depth level of scaffolds within
> the scaffold tree inclusion hierarchy, and the user can sort the
> scaffolds according to some criteria, which has
> to be clearly reflected in the layout.
>
> As long as the layout method scales to several thousand objects,  and
> supports those constraints, the type does
> not matter much, it could e.g. be a distance based method. There is for
> example a paper by Brandes and Pich (More
> flexible radial layout) that describes how the radial layout style can
> be resembled using Stress Majorization, but
> it is not trivial to model the system correctly in order to respect the
> above constraints in addition.
>
> So there is a couple of options, but no preselection of a method for
> this project.
>
>     Karsten
>
> On 2/05/2013 3:38 PM, shruti gupta wrote:
> > Dear Sir,
> >
> > Thank you for your reply. As far as I have understood, here we are
> > trying to reduce the area covered by the graph without affecting the
> > information conveyed by it. Are you intending to look at some
> > Force-directed algorithms to reduce this?
> > Or you have something else in mind? Or this question forms a part of
> > the Literature Survey for the project?
> >
> > Hope to hear from you soon,
> >
> > Shruti
> >
> >
> > On Thu, May 2, 2013 at 10:55 AM, Karsten Klein
> > <ka...@us... <mailto:ka...@us...>> wrote:
> >
> >     Hi Shruti,
> >
> >     thanks for your interest. It is not too late until the deadline is
> >     over ;-).
> >     You can apply any time till then. If you have any further
> >     questions, feel
> >     free to send them to this list.
> >
> >     Looking forward to your proposal,
> >     kind regards,
> >         Karsten
> >
> >     On 2/05/2013 3:13 PM, shruti gupta wrote:
> >     > Hello everyone,
> >     >
> >     > I am a third year undergraduate student pursuing a degree in
> >     > Information Systems. I am interested to work with Scaffold for GSoC
> >     > 2013. I am aware that it is too late to apply for a project now,
> >     but I
> >     > had been busy with my exams, and so, could not get here earlier.
> >     >
> >     >
> >     > I have worked on Probabilistic Graphical Models with
> RooStats(CERN),
> >     > for Google Summer of Code - 2012. The project consisted of
> >     > construction and sampling of Bayesian Belief Networks. The code is
> >     > written in C++.
> >     >
> >     > As a semester course, I have studied basic propositional logic,
> data
> >     > structures and algorithms (including graph algorithms). I have also
> >     > done a course in Object Oriented Programming and Design focused on
> >     > Java. I have also completed a basic in Graphs and Networks.
> >     >
> >     > I am interested in the following projects:
> >     >
> >     >   * Scaffold Tree Layout
> >     >
> >     >
> >     > I am already working on my proposal. It would be great if a mentor
> >     > could tell me if applying now is encouraged. And, if it is okay to
> >     > apply now.
> >     >
> >     > Looking forward to working with you,
> >     >
> >     > Thank you
> >     >
> >     > Shruti Gupta.
> >     >
> >     >
> >     >
> >     >
> >
> ------------------------------------------------------------------------------
> >     > Introducing AppDynamics Lite, a free troubleshooting tool for
> >     Java/.NET
> >     > Get 100% visibility into your production application - at no cost.
> >     > Code-level diagnostics for performance bottlenecks with <2%
> overhead
> >     > Download for free and get started troubleshooting in minutes.
> >     > http://p.sf.net/sfu/appdyn_d2d_ap1
> >     >
> >     >
> >     > _______________________________________________
> >     > Scaffoldhunter-users mailing list
> >     > Sca...@li...
> >     <mailto:Sca...@li...>
> >     > https://lists.sourceforge.net/lists/listinfo/scaffoldhunter-users
> >
> >
>
>

Re: [Scaffoldhunter-users] GSoC-2013

[Karsten K. <ka...@us...>]

The problem is to extend a layout algorithm to adhere to the
requirements we have in Scaffold Hunter.
The graph here is not just an abstract mathematical structure, but the
nodes have prescribed sizes (due to
the scaffold images) that need to be respected, there is a layering
given by the depth level of scaffolds within
the scaffold tree inclusion hierarchy, and the user can sort the
scaffolds according to some criteria, which has
to be clearly reflected in the layout.

As long as the layout method scales to several thousand objects,  and
supports those constraints, the type does
not matter much, it could e.g. be a distance based method. There is for
example a paper by Brandes and Pich (More
flexible radial layout) that describes how the radial layout style can
be resembled using Stress Majorization, but
it is not trivial to model the system correctly in order to respect the
above constraints in addition.

So there is a couple of options, but no preselection of a method for
this project.

    Karsten

On 2/05/2013 3:38 PM, shruti gupta wrote:
> Dear Sir,
>
> Thank you for your reply. As far as I have understood, here we are
> trying to reduce the area covered by the graph without affecting the
> information conveyed by it. Are you intending to look at some
> Force-directed algorithms to reduce this?
> Or you have something else in mind? Or this question forms a part of
> the Literature Survey for the project?
>
> Hope to hear from you soon,
>
> Shruti
>
>
> On Thu, May 2, 2013 at 10:55 AM, Karsten Klein
> <ka...@us... <mailto:ka...@us...>> wrote:
>
>     Hi Shruti,
>
>     thanks for your interest. It is not too late until the deadline is
>     over ;-).
>     You can apply any time till then. If you have any further
>     questions, feel
>     free to send them to this list.
>
>     Looking forward to your proposal,
>     kind regards,
>         Karsten
>
>     On 2/05/2013 3:13 PM, shruti gupta wrote:
>     > Hello everyone,
>     >
>     > I am a third year undergraduate student pursuing a degree in
>     > Information Systems. I am interested to work with Scaffold for GSoC
>     > 2013. I am aware that it is too late to apply for a project now,
>     but I
>     > had been busy with my exams, and so, could not get here earlier.
>     >
>     >
>     > I have worked on Probabilistic Graphical Models with RooStats(CERN),
>     > for Google Summer of Code - 2012. The project consisted of
>     > construction and sampling of Bayesian Belief Networks. The code is
>     > written in C++.
>     >
>     > As a semester course, I have studied basic propositional logic, data
>     > structures and algorithms (including graph algorithms). I have also
>     > done a course in Object Oriented Programming and Design focused on
>     > Java. I have also completed a basic in Graphs and Networks.
>     >
>     > I am interested in the following projects:
>     >
>     >   * Scaffold Tree Layout
>     >
>     >
>     > I am already working on my proposal. It would be great if a mentor
>     > could tell me if applying now is encouraged. And, if it is okay to
>     > apply now.
>     >
>     > Looking forward to working with you,
>     >
>     > Thank you
>     >
>     > Shruti Gupta.
>     >
>     >
>     >
>     >
>     ------------------------------------------------------------------------------
>     > Introducing AppDynamics Lite, a free troubleshooting tool for
>     Java/.NET
>     > Get 100% visibility into your production application - at no cost.
>     > Code-level diagnostics for performance bottlenecks with <2% overhead
>     > Download for free and get started troubleshooting in minutes.
>     > http://p.sf.net/sfu/appdyn_d2d_ap1
>     >
>     >
>     > _______________________________________________
>     > Scaffoldhunter-users mailing list
>     > Sca...@li...
>     <mailto:Sca...@li...>
>     > https://lists.sourceforge.net/lists/listinfo/scaffoldhunter-users
>
>

Re: [Scaffoldhunter-users] GSoC-2013

[shruti g. <shr...@gm...>]

Dear Sir,

Thank you for your reply. As far as I have understood, here we are trying
to reduce the area covered by the graph without affecting the information
conveyed by it. Are you intending to look at some Force-directed algorithms
to reduce this?
Or you have something else in mind? Or this question forms a part of the
Literature Survey for the project?

Hope to hear from you soon,

Shruti


On Thu, May 2, 2013 at 10:55 AM, Karsten Klein
<ka...@us...>wrote:

> Hi Shruti,
>
> thanks for your interest. It is not too late until the deadline is over
> ;-).
> You can apply any time till then. If you have any further questions, feel
> free to send them to this list.
>
> Looking forward to your proposal,
> kind regards,
>     Karsten
>
> On 2/05/2013 3:13 PM, shruti gupta wrote:
> > Hello everyone,
> >
> > I am a third year undergraduate student pursuing a degree in
> > Information Systems. I am interested to work with Scaffold for GSoC
> > 2013. I am aware that it is too late to apply for a project now, but I
> > had been busy with my exams, and so, could not get here earlier.
> >
> >
> > I have worked on Probabilistic Graphical Models with RooStats(CERN),
> > for Google Summer of Code - 2012. The project consisted of
> > construction and sampling of Bayesian Belief Networks. The code is
> > written in C++.
> >
> > As a semester course, I have studied basic propositional logic, data
> > structures and algorithms (including graph algorithms). I have also
> > done a course in Object Oriented Programming and Design focused on
> > Java. I have also completed a basic in Graphs and Networks.
> >
> > I am interested in the following projects:
> >
> >   * Scaffold Tree Layout
> >
> >
> > I am already working on my proposal. It would be great if a mentor
> > could tell me if applying now is encouraged. And, if it is okay to
> > apply now.
> >
> > Looking forward to working with you,
> >
> > Thank you
> >
> > Shruti Gupta.
> >
> >
> >
> >
> ------------------------------------------------------------------------------
> > Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET
> > Get 100% visibility into your production application - at no cost.
> > Code-level diagnostics for performance bottlenecks with <2% overhead
> > Download for free and get started troubleshooting in minutes.
> > http://p.sf.net/sfu/appdyn_d2d_ap1
> >
> >
> > _______________________________________________
> > Scaffoldhunter-users mailing list
> > Sca...@li...
> > https://lists.sourceforge.net/lists/listinfo/scaffoldhunter-users
>
>

Re: [Scaffoldhunter-users] GSoC-2013

[Karsten K. <ka...@us...>]

Hi Shruti,

thanks for your interest. It is not too late until the deadline is over ;-).
You can apply any time till then. If you have any further questions, feel
free to send them to this list.

Looking forward to your proposal,
kind regards,
    Karsten

On 2/05/2013 3:13 PM, shruti gupta wrote:
> Hello everyone, 
>
> I am a third year undergraduate student pursuing a degree in
> Information Systems. I am interested to work with Scaffold for GSoC
> 2013. I am aware that it is too late to apply for a project now, but I
> had been busy with my exams, and so, could not get here earlier.
>
>
> I have worked on Probabilistic Graphical Models with RooStats(CERN),
> for Google Summer of Code - 2012. The project consisted of
> construction and sampling of Bayesian Belief Networks. The code is
> written in C++.
>  
> As a semester course, I have studied basic propositional logic, data
> structures and algorithms (including graph algorithms). I have also
> done a course in Object Oriented Programming and Design focused on
> Java. I have also completed a basic in Graphs and Networks.
>
> I am interested in the following projects:
>
>   * Scaffold Tree Layout
>
>
> I am already working on my proposal. It would be great if a mentor
> could tell me if applying now is encouraged. And, if it is okay to
> apply now.
>
> Looking forward to working with you,
>
> Thank you
>
> Shruti Gupta.
>
>
>
> ------------------------------------------------------------------------------
> Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET
> Get 100% visibility into your production application - at no cost.
> Code-level diagnostics for performance bottlenecks with <2% overhead
> Download for free and get started troubleshooting in minutes.
> http://p.sf.net/sfu/appdyn_d2d_ap1
>
>
> _______________________________________________
> Scaffoldhunter-users mailing list
> Sca...@li...
> https://lists.sourceforge.net/lists/listinfo/scaffoldhunter-users

[Scaffoldhunter-users] GSoC-2013

[shruti g. <shr...@gm...>]

Hello everyone,

I am a third year undergraduate student pursuing a degree in Information
Systems. I am interested to work with Scaffold for GSoC 2013. I am aware
that it is too late to apply for a project now, but I had been busy with my
exams, and so, could not get here earlier.


I have worked on Probabilistic Graphical Models with RooStats(CERN), for
Google Summer of Code - 2012. The project consisted of construction and
sampling of Bayesian Belief Networks. The code is written in C++.

As a semester course, I have studied basic propositional logic, data
structures and algorithms (including graph algorithms). I have also done a
course in Object Oriented Programming and Design focused on Java. I have
also completed a basic in Graphs and Networks.

I am interested in the following projects:

   - Scaffold Tree Layout


I am already working on my proposal. It would be great if a mentor could
tell me if applying now is encouraged. And, if it is okay to apply now.

Looking forward to working with you,
Thank you

Shruti Gupta.

Re: [Scaffoldhunter-users] query

[Prateek G. <pra...@gm...>]

hi,
I have posted my proposal on the gsoc melange. The link is
http://www.google-melange.com/gsoc/proposal/review/google/gsoc2013/guptaprateek/5001

If you can please review and suggest any discrepancies.

regards,
Prateek


On Mon, Apr 29, 2013 at 11:59 AM, Prateek Gupta <pra...@gm...
> wrote:

> hi,
> Is the project plan strong enough in the hibernate part modifications and
> implementations?
> I am going to distribute it in the timeline and posting the proposal by
> tonight or tomorrow.
>
> Regards,
> Prateek
>
>
> On Mon, Apr 29, 2013 at 11:48 AM, <nl...@us...> wrote:
>
>> Hi Prateek,
>>
>> thank you for the detailed implementation ideas regarding the project.
>>
>>
>> Regards,
>>   Nils
>>
>>
>> On Monday 29 April 2013 03:38:00 Prateek Gupta wrote:
>> > hi,
>> > This is the project details I have figured out with the tentative
>> necessary
>> > classes and fucntion needed to be built. If you could review them and
>> > suggest me the changes.
>> >
>> > Project plan details
>> > The project would include the development of some java classes and
>> > functions the detail info of which has been provided as below:
>> > Phase I
>> > A)Download of the JChemPaint and its dependencies
>> > 1)The project seeks to initially embedd the JChemPaint application into
>> the
>> > ScaffoldHunter project making it the structure editor and satisfy the
>> > dependencies.Firstly to download and store the JChemPaint.jar file in a
>> > separate folder named "JChemPaint" in the library of ScaffoldHunter.Then
>> > the major dependency being the Chemistry Development Kit(CDK).This
>> needs to
>> > be taken care of.
>> >
>> > 2)The CDK is already loaded in the ScaffoldHunter project in the lib/cdk
>> > folder.Hence the next target is to alter the configuration of the build
>> of
>> > the JChemPaint so as to configure the path to the CDK.For this, the
>> target
>> > file is the build.xml file.This can be altered by altering the
>> > (approximately) lines 43 - 153 and lines 306 - 353 in the build.xml file
>> > and setting the proper ids and names.
>> >
>> > 3)Apart from this, Apache maven-which is a build automation tool
>> similar to
>> > ant, needs to be imported as it facilitates the XML files to describe
>> the
>> > build. It is written in java and is required for proper build of
>> JChemPaint.
>> >
>> > B)changes in the filter module
>> > Development of a class JCP
>> > This class would handle the overall activities and functions related to
>> the
>> > JChemPaint editor code and different files.They have been described as
>> > under.
>> > 1)constructor JCP()
>> > The variables required would be declared and would be initialized with
>> the
>> > default value in this part.Their scope would be decided and worked
>> > accordingly.
>> >
>> > 2)function calljcp()
>> > *)Addition of a button for providing as a link to the JChemPaint editor
>> in
>> > the filter panel in the edu/udo/scaffoldhunter/model/db.This would call
>> the
>> > JCP class and its different functions .This would require Java GUI
>> coding.
>> > The jchempaint.jar can directly be called in the running program by
>> > building the class path properly and importing them in the program.
>> >
>> > *)After this the editor would start and the user will be able to edit
>> the
>> > molecular structure as per requirement.The file containing the structure
>> > would be created. The MDL mol format structure so created can be
>> directly
>> > imported as an object instance to the filtering framework and used.This
>> > structure would be converted to the feature and rules format by the use
>> of
>> > scaffoldhunter/model/datacalculation/DBMoleculeToCDKMoleculeTransform.
>> >
>> > 4)finally all these functions would be called in the main before the
>> > filtering procedure begins and the user entered query will be considered
>> > with the subset value that is in the current framework.The normal
>> procedure
>> > would be resumed from hereon.
>> >
>> > Phase II
>> > Modifications in the Hibernate
>> > There is no direct support for bitwise operations in the hibernate
>> > associated to the problem but there is a workaround that cannot be
>> > standardised for any database present but can be standardised for the
>> > databases being used by specific softwares. I propose the plan to modify
>> > the mysql and hsql dialect files in the embedded hibernate library.The
>> > classes will be created in both the dialects i.e.MySQLDialect and
>> > HSQLDialect.
>> >
>> > 1)The project requires development of SQLFunctionTemplates on the
>> > respective dialect subclasses.This requires analysing and maintaining
>> > record of the various queries that are facing the problem and
>> categorising
>> > them in terms of the bitwise operator requirement and to develop that
>> many
>> > SQLFunctionTemplate as the number of categories and register them as
>> > functions.
>> >
>> > 2)Development of a class SQLFunctionTemplate which would import
>> > dialect.function.VARARGSQLFunction and implement SQLFunction class. The
>> > import of the  dialect.function is for registering the template
>> functions
>> > and implementing SQLFunction is because SQLFunction class is contained
>> in
>> > it.
>> > This class would comprise of the functions that would provide for the
>> > different bitwise operation that would be required by the fingerprinting
>> > mechanism.The tentative variables and functions that would be developed
>> are:
>> > *)initialization of the required variables like template1, template2,
>> etc.
>> >
>> > *)default constructor SQLFunctionTemplate()
>> > This would consist of the registeration of the custom functions that
>> would
>> > be built as per the needs. Sample code would be like:
>> >     registerFunction("bit_",new SQLFunctionTemplate(Hibernate.Integer,
>> > template))
>> >
>> > *)function task_*()
>> > These functions would perform the task that would be associated with the
>> > corresponding bit functions which the dialect is written for. There
>> would
>> > be multiple task functions depending on the bit function that are
>> required
>> > by the fingerprinting. After doing the computation, would be returning
>> > corresponding correct value.
>> >
>> > These following functions are a part of the implementedSQLFunction and
>> will
>> > be implemented as a requirement.
>> > *)function getSQLFunctionTemplate()
>> > This would return the template of the sql function.
>> > *)function getReturntype()
>> > This would the return the return type of the template.
>> > *)function render()
>> > This would render the function call as SQL fragment.
>> >
>> > Regards,
>> > Prateek
>>
>
>

Re: [Scaffoldhunter-users] query

[Prateek G. <pra...@gm...>]

hi,
Is the project plan strong enough in the hibernate part modifications and
implementations?
I am going to distribute it in the timeline and posting the proposal by
tonight or tomorrow.

Regards,
Prateek


On Mon, Apr 29, 2013 at 11:48 AM, <nl...@us...> wrote:

> Hi Prateek,
>
> thank you for the detailed implementation ideas regarding the project.
>
>
> Regards,
>   Nils
>
>
> On Monday 29 April 2013 03:38:00 Prateek Gupta wrote:
> > hi,
> > This is the project details I have figured out with the tentative
> necessary
> > classes and fucntion needed to be built. If you could review them and
> > suggest me the changes.
> >
> > Project plan details
> > The project would include the development of some java classes and
> > functions the detail info of which has been provided as below:
> > Phase I
> > A)Download of the JChemPaint and its dependencies
> > 1)The project seeks to initially embedd the JChemPaint application into
> the
> > ScaffoldHunter project making it the structure editor and satisfy the
> > dependencies.Firstly to download and store the JChemPaint.jar file in a
> > separate folder named "JChemPaint" in the library of ScaffoldHunter.Then
> > the major dependency being the Chemistry Development Kit(CDK).This needs
> to
> > be taken care of.
> >
> > 2)The CDK is already loaded in the ScaffoldHunter project in the lib/cdk
> > folder.Hence the next target is to alter the configuration of the build
> of
> > the JChemPaint so as to configure the path to the CDK.For this, the
> target
> > file is the build.xml file.This can be altered by altering the
> > (approximately) lines 43 - 153 and lines 306 - 353 in the build.xml file
> > and setting the proper ids and names.
> >
> > 3)Apart from this, Apache maven-which is a build automation tool similar
> to
> > ant, needs to be imported as it facilitates the XML files to describe the
> > build. It is written in java and is required for proper build of
> JChemPaint.
> >
> > B)changes in the filter module
> > Development of a class JCP
> > This class would handle the overall activities and functions related to
> the
> > JChemPaint editor code and different files.They have been described as
> > under.
> > 1)constructor JCP()
> > The variables required would be declared and would be initialized with
> the
> > default value in this part.Their scope would be decided and worked
> > accordingly.
> >
> > 2)function calljcp()
> > *)Addition of a button for providing as a link to the JChemPaint editor
> in
> > the filter panel in the edu/udo/scaffoldhunter/model/db.This would call
> the
> > JCP class and its different functions .This would require Java GUI
> coding.
> > The jchempaint.jar can directly be called in the running program by
> > building the class path properly and importing them in the program.
> >
> > *)After this the editor would start and the user will be able to edit the
> > molecular structure as per requirement.The file containing the structure
> > would be created. The MDL mol format structure so created can be directly
> > imported as an object instance to the filtering framework and used.This
> > structure would be converted to the feature and rules format by the use
> of
> > scaffoldhunter/model/datacalculation/DBMoleculeToCDKMoleculeTransform.
> >
> > 4)finally all these functions would be called in the main before the
> > filtering procedure begins and the user entered query will be considered
> > with the subset value that is in the current framework.The normal
> procedure
> > would be resumed from hereon.
> >
> > Phase II
> > Modifications in the Hibernate
> > There is no direct support for bitwise operations in the hibernate
> > associated to the problem but there is a workaround that cannot be
> > standardised for any database present but can be standardised for the
> > databases being used by specific softwares. I propose the plan to modify
> > the mysql and hsql dialect files in the embedded hibernate library.The
> > classes will be created in both the dialects i.e.MySQLDialect and
> > HSQLDialect.
> >
> > 1)The project requires development of SQLFunctionTemplates on the
> > respective dialect subclasses.This requires analysing and maintaining
> > record of the various queries that are facing the problem and
> categorising
> > them in terms of the bitwise operator requirement and to develop that
> many
> > SQLFunctionTemplate as the number of categories and register them as
> > functions.
> >
> > 2)Development of a class SQLFunctionTemplate which would import
> > dialect.function.VARARGSQLFunction and implement SQLFunction class. The
> > import of the  dialect.function is for registering the template functions
> > and implementing SQLFunction is because SQLFunction class is contained in
> > it.
> > This class would comprise of the functions that would provide for the
> > different bitwise operation that would be required by the fingerprinting
> > mechanism.The tentative variables and functions that would be developed
> are:
> > *)initialization of the required variables like template1, template2,
> etc.
> >
> > *)default constructor SQLFunctionTemplate()
> > This would consist of the registeration of the custom functions that
> would
> > be built as per the needs. Sample code would be like:
> >     registerFunction("bit_",new SQLFunctionTemplate(Hibernate.Integer,
> > template))
> >
> > *)function task_*()
> > These functions would perform the task that would be associated with the
> > corresponding bit functions which the dialect is written for. There would
> > be multiple task functions depending on the bit function that are
> required
> > by the fingerprinting. After doing the computation, would be returning
> > corresponding correct value.
> >
> > These following functions are a part of the implementedSQLFunction and
> will
> > be implemented as a requirement.
> > *)function getSQLFunctionTemplate()
> > This would return the template of the sql function.
> > *)function getReturntype()
> > This would the return the return type of the template.
> > *)function render()
> > This would render the function call as SQL fragment.
> >
> > Regards,
> > Prateek
>

Re: [Scaffoldhunter-users] query

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

Hi Prateek,

thank you for the detailed implementation ideas regarding the project.


Regards,
  Nils


On Monday 29 April 2013 03:38:00 Prateek Gupta wrote:
> hi,
> This is the project details I have figured out with the tentative necessary
> classes and fucntion needed to be built. If you could review them and
> suggest me the changes.
> 
> Project plan details
> The project would include the development of some java classes and
> functions the detail info of which has been provided as below:
> Phase I
> A)Download of the JChemPaint and its dependencies
> 1)The project seeks to initially embedd the JChemPaint application into the
> ScaffoldHunter project making it the structure editor and satisfy the
> dependencies.Firstly to download and store the JChemPaint.jar file in a
> separate folder named "JChemPaint" in the library of ScaffoldHunter.Then
> the major dependency being the Chemistry Development Kit(CDK).This needs to
> be taken care of.
> 
> 2)The CDK is already loaded in the ScaffoldHunter project in the lib/cdk
> folder.Hence the next target is to alter the configuration of the build of
> the JChemPaint so as to configure the path to the CDK.For this, the target
> file is the build.xml file.This can be altered by altering the
> (approximately) lines 43 - 153 and lines 306 - 353 in the build.xml file
> and setting the proper ids and names.
> 
> 3)Apart from this, Apache maven-which is a build automation tool similar to
> ant, needs to be imported as it facilitates the XML files to describe the
> build. It is written in java and is required for proper build of JChemPaint.
> 
> B)changes in the filter module
> Development of a class JCP
> This class would handle the overall activities and functions related to the
> JChemPaint editor code and different files.They have been described as
> under.
> 1)constructor JCP()
> The variables required would be declared and would be initialized with the
> default value in this part.Their scope would be decided and worked
> accordingly.
> 
> 2)function calljcp()
> *)Addition of a button for providing as a link to the JChemPaint editor in
> the filter panel in the edu/udo/scaffoldhunter/model/db.This would call the
> JCP class and its different functions .This would require Java GUI coding.
> The jchempaint.jar can directly be called in the running program by
> building the class path properly and importing them in the program.
> 
> *)After this the editor would start and the user will be able to edit the
> molecular structure as per requirement.The file containing the structure
> would be created. The MDL mol format structure so created can be directly
> imported as an object instance to the filtering framework and used.This
> structure would be converted to the feature and rules format by the use of
> scaffoldhunter/model/datacalculation/DBMoleculeToCDKMoleculeTransform.
> 
> 4)finally all these functions would be called in the main before the
> filtering procedure begins and the user entered query will be considered
> with the subset value that is in the current framework.The normal procedure
> would be resumed from hereon.
> 
> Phase II
> Modifications in the Hibernate
> There is no direct support for bitwise operations in the hibernate
> associated to the problem but there is a workaround that cannot be
> standardised for any database present but can be standardised for the
> databases being used by specific softwares. I propose the plan to modify
> the mysql and hsql dialect files in the embedded hibernate library.The
> classes will be created in both the dialects i.e.MySQLDialect and
> HSQLDialect.
> 
> 1)The project requires development of SQLFunctionTemplates on the
> respective dialect subclasses.This requires analysing and maintaining
> record of the various queries that are facing the problem and categorising
> them in terms of the bitwise operator requirement and to develop that many
> SQLFunctionTemplate as the number of categories and register them as
> functions.
> 
> 2)Development of a class SQLFunctionTemplate which would import
> dialect.function.VARARGSQLFunction and implement SQLFunction class. The
> import of the  dialect.function is for registering the template functions
> and implementing SQLFunction is because SQLFunction class is contained in
> it.
> This class would comprise of the functions that would provide for the
> different bitwise operation that would be required by the fingerprinting
> mechanism.The tentative variables and functions that would be developed are:
> *)initialization of the required variables like template1, template2, etc.
> 
> *)default constructor SQLFunctionTemplate()
> This would consist of the registeration of the custom functions that would
> be built as per the needs. Sample code would be like:
>     registerFunction("bit_",new SQLFunctionTemplate(Hibernate.Integer,
> template))
> 
> *)function task_*()
> These functions would perform the task that would be associated with the
> corresponding bit functions which the dialect is written for. There would
> be multiple task functions depending on the bit function that are required
> by the fingerprinting. After doing the computation, would be returning
> corresponding correct value.
> 
> These following functions are a part of the implementedSQLFunction and will
> be implemented as a requirement.
> *)function getSQLFunctionTemplate()
> This would return the template of the sql function.
> *)function getReturntype()
> This would the return the return type of the template.
> *)function render()
> This would render the function call as SQL fragment.
> 
> Regards,
> Prateek

Re: [Scaffoldhunter-users] query

[Prateek G. <pra...@gm...>]

hi,
This is the project details I have figured out with the tentative necessary
classes and fucntion needed to be built. If you could review them and
suggest me the changes.

Project plan details
The project would include the development of some java classes and
functions the detail info of which has been provided as below:
Phase I
A)Download of the JChemPaint and its dependencies
1)The project seeks to initially embedd the JChemPaint application into the
ScaffoldHunter project making it the structure editor and satisfy the
dependencies.Firstly to download and store the JChemPaint.jar file in a
separate folder named "JChemPaint" in the library of ScaffoldHunter.Then
the major dependency being the Chemistry Development Kit(CDK).This needs to
be taken care of.

2)The CDK is already loaded in the ScaffoldHunter project in the lib/cdk
folder.Hence the next target is to alter the configuration of the build of
the JChemPaint so as to configure the path to the CDK.For this, the target
file is the build.xml file.This can be altered by altering the
(approximately) lines 43 - 153 and lines 306 - 353 in the build.xml file
and setting the proper ids and names.

3)Apart from this, Apache maven-which is a build automation tool similar to
ant, needs to be imported as it facilitates the XML files to describe the
build. It is written in java and is required for proper build of JChemPaint.

B)changes in the filter module
Development of a class JCP
This class would handle the overall activities and functions related to the
JChemPaint editor code and different files.They have been described as
under.
1)constructor JCP()
The variables required would be declared and would be initialized with the
default value in this part.Their scope would be decided and worked
accordingly.

2)function calljcp()
*)Addition of a button for providing as a link to the JChemPaint editor in
the filter panel in the edu/udo/scaffoldhunter/model/db.This would call the
JCP class and its different functions .This would require Java GUI coding.
The jchempaint.jar can directly be called in the running program by
building the class path properly and importing them in the program.

*)After this the editor would start and the user will be able to edit the
molecular structure as per requirement.The file containing the structure
would be created. The MDL mol format structure so created can be directly
imported as an object instance to the filtering framework and used.This
structure would be converted to the feature and rules format by the use of
scaffoldhunter/model/datacalculation/DBMoleculeToCDKMoleculeTransform.

4)finally all these functions would be called in the main before the
filtering procedure begins and the user entered query will be considered
with the subset value that is in the current framework.The normal procedure
would be resumed from hereon.

Phase II
Modifications in the Hibernate
There is no direct support for bitwise operations in the hibernate
associated to the problem but there is a workaround that cannot be
standardised for any database present but can be standardised for the
databases being used by specific softwares. I propose the plan to modify
the mysql and hsql dialect files in the embedded hibernate library.The
classes will be created in both the dialects i.e.MySQLDialect and
HSQLDialect.

1)The project requires development of SQLFunctionTemplates on the
respective dialect subclasses.This requires analysing and maintaining
record of the various queries that are facing the problem and categorising
them in terms of the bitwise operator requirement and to develop that many
SQLFunctionTemplate as the number of categories and register them as
functions.

2)Development of a class SQLFunctionTemplate which would import
dialect.function.VARARGSQLFunction and implement SQLFunction class. The
import of the  dialect.function is for registering the template functions
and implementing SQLFunction is because SQLFunction class is contained in
it.
This class would comprise of the functions that would provide for the
different bitwise operation that would be required by the fingerprinting
mechanism.The tentative variables and functions that would be developed are:
*)initialization of the required variables like template1, template2, etc.

*)default constructor SQLFunctionTemplate()
This would consist of the registeration of the custom functions that would
be built as per the needs. Sample code would be like:
    registerFunction("bit_",new SQLFunctionTemplate(Hibernate.Integer,
template))

*)function task_*()
These functions would perform the task that would be associated with the
corresponding bit functions which the dialect is written for. There would
be multiple task functions depending on the bit function that are required
by the fingerprinting. After doing the computation, would be returning
corresponding correct value.

These following functions are a part of the implementedSQLFunction and will
be implemented as a requirement.
*)function getSQLFunctionTemplate()
This would return the template of the sql function.
*)function getReturntype()
This would the return the return type of the template.
*)function render()
This would render the function call as SQL fragment.

Regards,
Prateek



On Sun, Apr 28, 2013 at 5:46 PM, Prateek Gupta
<pra...@gm...>wrote:

> hi,
> regarding to the problems in bit operations, I did not intend to solve the
> impedance mismatch problem.This is already solved by hibernate. What I
> intend to say is that out of the current databases that are used in the
> software (hsqldb , mysql).
> There is a problem in the *dialect.java files in the
> hibernate-core/src/main/java/org/hibernate/dialect.
>  I found that "bit" suffers problem in mysql but with hsql it functions
> proper if "bit" is mapped to boolean.
> Hence one method of solving such problem for mysql or any database would
> be creation of either native sql procedures or changing the queries in the
> hibernate/jpa folder and implementing bit datatype in the dialect of that
> database in hibernate
>
> Could you help me figure out?
> regards,
> Prateek
>
>
> On Sun, Apr 28, 2013 at 5:18 PM, Prateek Gupta <
> pra...@gm...> wrote:
>
>> I was thinking to open jchempaint as a separate process rather than just
>> like an editor!!
>>
>>
>> On Sun, Apr 28, 2013 at 5:17 PM, Prateek Gupta <
>> pra...@gm...> wrote:
>>
>>> Sorry I forgot of such a method and going for higher approaches. This
>>> would be fine.
>>> And is the function of receiving the structure object correct?
>>>
>>>
>>> On Sun, Apr 28, 2013 at 5:05 PM, <nl...@us...> wrote:
>>>
>>>> Hi,
>>>>
>>>> On Sunday 28 April 2013 16:55:18 Prateek Gupta wrote:
>>>> > regarding to the changes in the jchempaint algo
>>>> > 1)instead of using the shell calls , I can implement process builder
>>>> and
>>>> > provide the class path within the directory of this process builder
>>>> and
>>>> > initiate it. This would run the jchempaint.
>>>>
>>>> JChemPaint can be added to Scaffold Hunter just as the other libraries.
>>>> It
>>>> should be possible to open a window containing the editor without
>>>> starting
>>>> JChemPaint as a separate process.
>>>>
>>>>
>>>> Regards,
>>>>   Nils
>>>>
>>>
>>>
>>
>

Re: [Scaffoldhunter-users] query

[Prateek G. <pra...@gm...>]

hi,
regarding to the problems in bit operations, I did not intend to solve the
impedance mismatch problem.This is already solved by hibernate. What I
intend to say is that out of the current databases that are used in the
software (hsqldb , mysql).
There is a problem in the *dialect.java files in the
hibernate-core/src/main/java/org/hibernate/dialect.
 I found that "bit" suffers problem in mysql but with hsql it functions
proper if "bit" is mapped to boolean.
Hence one method of solving such problem for mysql or any database would be
creation of either native sql procedures or changing the queries in the
hibernate/jpa folder and implementing bit datatype in the dialect of that
database in hibernate

Could you help me figure out?
regards,
Prateek


On Sun, Apr 28, 2013 at 5:18 PM, Prateek Gupta
<pra...@gm...>wrote:

> I was thinking to open jchempaint as a separate process rather than just
> like an editor!!
>
>
> On Sun, Apr 28, 2013 at 5:17 PM, Prateek Gupta <
> pra...@gm...> wrote:
>
>> Sorry I forgot of such a method and going for higher approaches. This
>> would be fine.
>> And is the function of receiving the structure object correct?
>>
>>
>> On Sun, Apr 28, 2013 at 5:05 PM, <nl...@us...> wrote:
>>
>>> Hi,
>>>
>>> On Sunday 28 April 2013 16:55:18 Prateek Gupta wrote:
>>> > regarding to the changes in the jchempaint algo
>>> > 1)instead of using the shell calls , I can implement process builder
>>> and
>>> > provide the class path within the directory of this process builder and
>>> > initiate it. This would run the jchempaint.
>>>
>>> JChemPaint can be added to Scaffold Hunter just as the other libraries.
>>> It
>>> should be possible to open a window containing the editor without
>>> starting
>>> JChemPaint as a separate process.
>>>
>>>
>>> Regards,
>>>   Nils
>>>
>>
>>
>

Re: [Scaffoldhunter-users] query

[Prateek G. <pra...@gm...>]

I was thinking to open jchempaint as a separate process rather than just
like an editor!!


On Sun, Apr 28, 2013 at 5:17 PM, Prateek Gupta
<pra...@gm...>wrote:

> Sorry I forgot of such a method and going for higher approaches. This
> would be fine.
> And is the function of receiving the structure object correct?
>
>
> On Sun, Apr 28, 2013 at 5:05 PM, <nl...@us...> wrote:
>
>> Hi,
>>
>> On Sunday 28 April 2013 16:55:18 Prateek Gupta wrote:
>> > regarding to the changes in the jchempaint algo
>> > 1)instead of using the shell calls , I can implement process builder and
>> > provide the class path within the directory of this process builder and
>> > initiate it. This would run the jchempaint.
>>
>> JChemPaint can be added to Scaffold Hunter just as the other libraries. It
>> should be possible to open a window containing the editor without starting
>> JChemPaint as a separate process.
>>
>>
>> Regards,
>>   Nils
>>
>
>

Re: [Scaffoldhunter-users] query

[Prateek G. <pra...@gm...>]

Sorry I forgot of such a method and going for higher approaches. This would
be fine.
And is the function of receiving the structure object correct?


On Sun, Apr 28, 2013 at 5:05 PM, <nl...@us...> wrote:

> Hi,
>
> On Sunday 28 April 2013 16:55:18 Prateek Gupta wrote:
> > regarding to the changes in the jchempaint algo
> > 1)instead of using the shell calls , I can implement process builder and
> > provide the class path within the directory of this process builder and
> > initiate it. This would run the jchempaint.
>
> JChemPaint can be added to Scaffold Hunter just as the other libraries. It
> should be possible to open a window containing the editor without starting
> JChemPaint as a separate process.
>
>
> Regards,
>   Nils
>

Re: [Scaffoldhunter-users] query

[Prateek G. <pra...@gm...>]

hi,
regarding to the problems in bit operations, I did not intend to solve the
impedance mismatch problem.This is already solved by hibernate. What I
intend to say is that out of the current databases that are used in the
software (hsqldb , mysql).
There is a problem in the *dialect.java files in the
hibernate-core/src/main/java/org/hibernate/dialect.
 I found that "bit" suffers problem in mysql but with hsql it functions
proper if "bit" is mapped to boolean.
Hence one method of solving such problem for mysql or any database would be
creation of either native sql procedures or changing the queries in the
hibernate/jpa folder and implementing bit datatype in the dialect of that
database in hibernate

Could you help me figure out?
regards,
Prateek


On Sun, Apr 28, 2013 at 4:55 PM, Prateek Gupta
<pra...@gm...>wrote:

> hi,
> regarding to the changes in the jchempaint algo
> 1)instead of using the shell calls , I can implement process builder and
> provide the class path within the directory of this process builder and
> initiate it. This would run the jchempaint.
> 2)Regarding the saving the file issue. I can call the getMolFile()
> function in the jchempaint and receive an object of the current query
> structure in the editor. The filter rules as you said can be stored in the
> user profile as you said.
>
> Is this fine enough?
> Regards,
> Prateek
>
>
> On Sun, Apr 28, 2013 at 4:41 PM, <nl...@us...> wrote:
>
>> Hi Prateek,
>>
>> please see my reply to your previous mail regarding the filtering based on
>> bit-operations. Native MySQL queries should work, but we would like not
>> to be
>> restricted to a MySQL database if possible.
>>
>>
>> Regards,
>>   Nils
>>
>> On Sunday 28 April 2013 02:47:40 Prateek Gupta wrote:
>> > Hi,
>> > I have figured out another method to debug the mysql specific query
>> problem
>> > in hibernate.
>> > This method intends to identify the bit related operators and
>> operations.
>> > Then add sql functions in the mysql5dialect
>> >  java code in hibenate module that would map to these operators or
>> > operations. This would be able to solve the queries.
>> > But still if there arises some exceptional problems then working around
>> > with the development of native mysql queries
>> > in hibernate would also be a backup option. These queries can also be
>> named
>> > separately if required.
>> > So if you could help me review the methods and direct me to the right
>> path.
>> > Regards,
>> > Prateek
>>
>>
>

Re: [Scaffoldhunter-users] query

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

Hi,

On Sunday 28 April 2013 16:55:18 Prateek Gupta wrote:
> regarding to the changes in the jchempaint algo
> 1)instead of using the shell calls , I can implement process builder and
> provide the class path within the directory of this process builder and
> initiate it. This would run the jchempaint.

JChemPaint can be added to Scaffold Hunter just as the other libraries. It 
should be possible to open a window containing the editor without starting 
JChemPaint as a separate process.


Regards,
  Nils

Re: [Scaffoldhunter-users] query

[Prateek G. <pra...@gm...>]

hi,
regarding to the changes in the jchempaint algo
1)instead of using the shell calls , I can implement process builder and
provide the class path within the directory of this process builder and
initiate it. This would run the jchempaint.
2)Regarding the saving the file issue. I can call the getMolFile() function
in the jchempaint and receive an object of the current query structure in
the editor. The filter rules as you said can be stored in the user profile
as you said.

Is this fine enough?
Regards,
Prateek


On Sun, Apr 28, 2013 at 4:41 PM, <nl...@us...> wrote:

> Hi Prateek,
>
> please see my reply to your previous mail regarding the filtering based on
> bit-operations. Native MySQL queries should work, but we would like not to
> be
> restricted to a MySQL database if possible.
>
>
> Regards,
>   Nils
>
> On Sunday 28 April 2013 02:47:40 Prateek Gupta wrote:
> > Hi,
> > I have figured out another method to debug the mysql specific query
> problem
> > in hibernate.
> > This method intends to identify the bit related operators and operations.
> > Then add sql functions in the mysql5dialect
> >  java code in hibenate module that would map to these operators or
> > operations. This would be able to solve the queries.
> > But still if there arises some exceptional problems then working around
> > with the development of native mysql queries
> > in hibernate would also be a backup option. These queries can also be
> named
> > separately if required.
> > So if you could help me review the methods and direct me to the right
> path.
> > Regards,
> > Prateek
>
>

Re: [Scaffoldhunter-users] query

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

Hi Prateek,

please see my reply to your previous mail regarding the filtering based on 
bit-operations. Native MySQL queries should work, but we would like not to be 
restricted to a MySQL database if possible.


Regards,
  Nils

On Sunday 28 April 2013 02:47:40 Prateek Gupta wrote:
> Hi,
> I have figured out another method to debug the mysql specific query problem
> in hibernate.
> This method intends to identify the bit related operators and operations.
> Then add sql functions in the mysql5dialect
>  java code in hibenate module that would map to these operators or
> operations. This would be able to solve the queries.
> But still if there arises some exceptional problems then working around
> with the development of native mysql queries
> in hibernate would also be a backup option. These queries can also be named
> separately if required.
> So if you could help me review the methods and direct me to the right path.
> Regards,
> Prateek

Re: [Scaffoldhunter-users] query

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

Hi Prateek,

thanks for your detailed ideas regarding the project.

On Saturday 27 April 2013 15:02:13 you wrote:
> 2)function calljcp()
> *)Addition of a button for providing as a link to the JChemPaint editor in
> the filter panel in the edu/udo/scaffoldhunter/model/db.This would call the
> JCP class and its different functions .This would require  Java GUI coding
> for button and an important part of using shell functions or OS functions
> for initiation of the JChemPaint.jar files in the lib folder.This will be
> basically importing the I/O java library, maintaining the buffers and using
> Runtime module to start the process of JChemPaint during the running of the
> SH application.

The integration of JChemPaint should be as seamless as possible. There should 
be no need to use shell or OS functions since Scaffold Hunter and JChemPaint 
are both written in Java.

> *)After this the editor would start and the user will be able to edit the
> molecular structure as per requirement.The file containing the structure
> would be created and would be saved in the format MDL mol.This would be the
> file that would be read as a query for the filtering mechanism.

It would be more desirable not to save the file, but to directly get the query 
structure as an object from JChemPaint. However, filter rules can be stored 
with the user profile and this should also work for substructure filtering. 
For this reason the query structure should be saved in MDL mol file format 
with the profile in database.


Regards,
  Nils

Re: [Scaffoldhunter-users] query

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

Hi Prateek,

On Saturday 27 April 2013 02:18:27 Prateek Gupta wrote:
> I would like to address the ORM impedance mismatch problem. Can you give
> some review on this idea and also the volume of the queries of this type!!

implementing the filtering technique based on bit-operations does not require 
to solve the object-relational impedance mismatch problem. You may want to 
have a look at the SQL queries used in version 1.7 and at the Hibernate 
documentation to find out how to implement something similar using Hibernate. 
You may also use Google to search for "bit functions" and "Hibernate". The 
Hibernate forum contains several related questions and possible solutions. The 
volume of these queries should not be a problem. However, please note, that 
there may be tens of thousands of molecules stored in the database that must 
be searched.


Regards,
  Nils

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

[Prateek G. <pra...@gm...>]

Hi,
I have posted some queries on the mailing list. If you could please review
them so I can clear some
doubts about my project plan in my proposal
.
Regards,
Prateek


On Wed, Apr 24, 2013 at 9:28 PM, Till Schäfer <til...@tu...
> wrote:

> 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...
> phone: +49(231)755-7706
> fax: +49(231)755-7740
> web: http://ls11-www.cs.uni-dortmund.de/staff/schaefer
> pgp:
> https://keyserver2.pgp.com/vkd/SubmitSearch.event?&&SearchCriteria=0xD84DED79
>
>

Re: [Scaffoldhunter-users] query

[Prateek G. <pra...@gm...>]

Hi,
I have figured out another method to debug the mysql specific query problem
in hibernate.
This method intends to identify the bit related operators and operations.
Then add sql functions in the mysql5dialect
 java code in hibenate module that would map to these operators or
operations. This would be able to solve the queries.
But still if there arises some exceptional problems then working around
with the development of native mysql queries
in hibernate would also be a backup option. These queries can also be named
separately if required.
So if you could help me review the methods and direct me to the right path.
Regards,
Prateek


On Sat, Apr 27, 2013 at 3:02 PM, Prateek Gupta
<pra...@gm...>wrote:

> This is the algorithm to embed the JChemPaint editor in the SH software.If
> you can review and suggest some changes..
> Also if you could review my solution to the ORM problem that I mailed just
> before this.
>
> B)changes in the filter module
> Development of a class JCP
> This class would handle the overall activities and functions related to
> the JChemPaint editor code and different files.They have been described as
> under.
> 1)constructor JCP()
> The variables required would be declared and would be initialized with the
> default value in this part.Their scope would be decided and worked
> accordingly.
> 2)function calljcp()
> *)Addition of a button for providing as a link to the JChemPaint editor in
> the filter panel in the edu/udo/scaffoldhunter/model/db.This would call the
> JCP class and its different functions .This would require  Java GUI coding
> for button and an important part of using shell functions or OS functions
> for initiation of the JChemPaint.jar files in the lib folder.This will be
> basically importing the I/O java library, maintaining the buffers and using
> Runtime module to start the process of JChemPaint during the running of the
> SH application.
> *)After this the editor would start and the user will be able to edit the
> molecular structure as per requirement.The file containing the structure
> would be created and would be saved in the format MDL mol.This would be the
> file that would be read as a query for the filtering mechanism.
> 3)function resume()
> This function would
> 3)function loadquery()
> *)This function would call the CML file with the stored structure and
> would be read using the
> edu/udo/scaffoldhunter/model/datacalculation/DBMoleculeToCDKMoleculeTransform.This
> structure would be converted into the tree and cycle, and features which
> would be matched from the dataset features via CT-index mechanism.
> 4)finally all these functions would be called in the main before the
> filtering procedure begins and the user entered query will be considered
> with the subset value that is in the current framework.The normal procedure
> would be resumed from hereon.
>
> Hoping to get a reply soon.
> Regards,
> Prateek
>
>
>
> On Sat, Apr 27, 2013 at 2:18 AM, Prateek Gupta <
> pra...@gm...> wrote:
>
>> hi,
>> I have tried to understand the some brainstorming of object-relation
>> impedance mismatch problem in the ORM in hibernate.
>> Regarding the solution, I came across the compensation of query
>> technique. This method seeks to implement native sql procedure in hibernate
>> or by using Spring JdbcTemplate for those queries that are facing the
>> problem in execution and calling these procedures when these queries are
>> searched for.
>> But an important criterion is to use database in "enable debug mode" when
>> using the native sql procedure.
>>
>> I would like to address the ORM impedance mismatch problem. Can you give
>> some review on this idea and also the volume of the queries of this type!!
>>
>> Regards,
>> Prateek
>>
>>
>> On Thu, Apr 25, 2013 at 3:55 PM, Prateek Gupta <
>> pra...@gm...> wrote:
>>
>>> hi,
>>> thanks for clarifying the doubt .I am going through the hibernate part
>>> and now i can proceed with my proposal.
>>> regards,
>>> Prateek
>>>
>>>
>>> On Thu, Apr 25, 2013 at 3:42 PM, <nl...@us...> wrote:
>>>
>>>> Hi Prateek,
>>>>
>>>> On Thursday 25 April 2013 14:09:05 Prateek Gupta wrote:
>>>> > well currently I have prepared an algorithm for embedding JChemPaint
>>>> as
>>>> > structure editor for the query.
>>>> > but I need to ask that JChemPaint saves and loads the editor
>>>> structure in
>>>> > CML and MDL mol format but only loads sdf format.
>>>> > So I am employing a converter agent "obabel" so as to convert from
>>>> CML to
>>>> > sdf format.This sdf file can be used as dataset for the query.
>>>> > Is there any discrepancy with this logic?
>>>>
>>>> OpenBabel is written in C++ and using it for a cross-platform Java
>>>> application
>>>> like Scaffold Hunter has several disadvantages. Moreover, there should
>>>> be no
>>>> need to introduce additional dependencies. JChemPaint is based on CDK
>>>> and it
>>>> is straightforward to load MDL mol files with CDK using the class
>>>> MDLReader
>>>> (see
>>>>
>>>> edu.udo.scaffoldhunter.model.datacalculation.DBMoleculeToCDKMoleculeTransform
>>>> for example code). Basically SDF is a container format for MDL mol
>>>> files.
>>>>
>>>>
>>>> Regards,
>>>>   Nils
>>>>
>>>
>>>
>>
>

Re: [Scaffoldhunter-users] query

[Prateek G. <pra...@gm...>]

This is the algorithm to embed the JChemPaint editor in the SH software.If
you can review and suggest some changes..
Also if you could review my solution to the ORM problem that I mailed just
before this.

B)changes in the filter module
Development of a class JCP
This class would handle the overall activities and functions related to the
JChemPaint editor code and different files.They have been described as
under.
1)constructor JCP()
The variables required would be declared and would be initialized with the
default value in this part.Their scope would be decided and worked
accordingly.
2)function calljcp()
*)Addition of a button for providing as a link to the JChemPaint editor in
the filter panel in the edu/udo/scaffoldhunter/model/db.This would call the
JCP class and its different functions .This would require  Java GUI coding
for button and an important part of using shell functions or OS functions
for initiation of the JChemPaint.jar files in the lib folder.This will be
basically importing the I/O java library, maintaining the buffers and using
Runtime module to start the process of JChemPaint during the running of the
SH application.
*)After this the editor would start and the user will be able to edit the
molecular structure as per requirement.The file containing the structure
would be created and would be saved in the format MDL mol.This would be the
file that would be read as a query for the filtering mechanism.
3)function resume()
This function would
3)function loadquery()
*)This function would call the CML file with the stored structure and would
be read using the
edu/udo/scaffoldhunter/model/datacalculation/DBMoleculeToCDKMoleculeTransform.This
structure would be converted into the tree and cycle, and features which
would be matched from the dataset features via CT-index mechanism.
4)finally all these functions would be called in the main before the
filtering procedure begins and the user entered query will be considered
with the subset value that is in the current framework.The normal procedure
would be resumed from hereon.

Hoping to get a reply soon.
Regards,
Prateek



On Sat, Apr 27, 2013 at 2:18 AM, Prateek Gupta
<pra...@gm...>wrote:

> hi,
> I have tried to understand the some brainstorming of object-relation
> impedance mismatch problem in the ORM in hibernate.
> Regarding the solution, I came across the compensation of query technique.
> This method seeks to implement native sql procedure in hibernate or by
> using Spring JdbcTemplate for those queries that are facing the problem in
> execution and calling these procedures when these queries are searched for.
> But an important criterion is to use database in "enable debug mode" when
> using the native sql procedure.
>
> I would like to address the ORM impedance mismatch problem. Can you give
> some review on this idea and also the volume of the queries of this type!!
>
> Regards,
> Prateek
>
>
> On Thu, Apr 25, 2013 at 3:55 PM, Prateek Gupta <
> pra...@gm...> wrote:
>
>> hi,
>> thanks for clarifying the doubt .I am going through the hibernate part
>> and now i can proceed with my proposal.
>> regards,
>> Prateek
>>
>>
>> On Thu, Apr 25, 2013 at 3:42 PM, <nl...@us...> wrote:
>>
>>> Hi Prateek,
>>>
>>> On Thursday 25 April 2013 14:09:05 Prateek Gupta wrote:
>>> > well currently I have prepared an algorithm for embedding JChemPaint as
>>> > structure editor for the query.
>>> > but I need to ask that JChemPaint saves and loads the editor structure
>>> in
>>> > CML and MDL mol format but only loads sdf format.
>>> > So I am employing a converter agent "obabel" so as to convert from CML
>>> to
>>> > sdf format.This sdf file can be used as dataset for the query.
>>> > Is there any discrepancy with this logic?
>>>
>>> OpenBabel is written in C++ and using it for a cross-platform Java
>>> application
>>> like Scaffold Hunter has several disadvantages. Moreover, there should
>>> be no
>>> need to introduce additional dependencies. JChemPaint is based on CDK
>>> and it
>>> is straightforward to load MDL mol files with CDK using the class
>>> MDLReader
>>> (see
>>>
>>> edu.udo.scaffoldhunter.model.datacalculation.DBMoleculeToCDKMoleculeTransform
>>> for example code). Basically SDF is a container format for MDL mol files.
>>>
>>>
>>> Regards,
>>>   Nils
>>>
>>
>>
>

Re: [Scaffoldhunter-users] query

[Prateek G. <pra...@gm...>]

hi,
I have tried to understand the some brainstorming of object-relation
impedance mismatch problem in the ORM in hibernate.
Regarding the solution, I came across the compensation of query technique.
This method seeks to implement native sql procedure in hibernate or by
using Spring JdbcTemplate for those queries that are facing the problem in
execution and calling these procedures when these queries are searched for.
But an important criterion is to use database in "enable debug mode" when
using the native sql procedure.

I would like to address the ORM impedance mismatch problem. Can you give
some review on this idea and also the volume of the queries of this type!!

Regards,
Prateek


On Thu, Apr 25, 2013 at 3:55 PM, Prateek Gupta
<pra...@gm...>wrote:

> hi,
> thanks for clarifying the doubt .I am going through the hibernate part and
> now i can proceed with my proposal.
> regards,
> Prateek
>
>
> On Thu, Apr 25, 2013 at 3:42 PM, <nl...@us...> wrote:
>
>> Hi Prateek,
>>
>> On Thursday 25 April 2013 14:09:05 Prateek Gupta wrote:
>> > well currently I have prepared an algorithm for embedding JChemPaint as
>> > structure editor for the query.
>> > but I need to ask that JChemPaint saves and loads the editor structure
>> in
>> > CML and MDL mol format but only loads sdf format.
>> > So I am employing a converter agent "obabel" so as to convert from CML
>> to
>> > sdf format.This sdf file can be used as dataset for the query.
>> > Is there any discrepancy with this logic?
>>
>> OpenBabel is written in C++ and using it for a cross-platform Java
>> application
>> like Scaffold Hunter has several disadvantages. Moreover, there should be
>> no
>> need to introduce additional dependencies. JChemPaint is based on CDK and
>> it
>> is straightforward to load MDL mol files with CDK using the class
>> MDLReader
>> (see
>>
>> edu.udo.scaffoldhunter.model.datacalculation.DBMoleculeToCDKMoleculeTransform
>> for example code). Basically SDF is a container format for MDL mol files.
>>
>>
>> Regards,
>>   Nils
>>
>
>