[Kalzium] GSoC project.

Apekshit Sharma apeksharma at gmail.com
Mon Mar 30 20:12:13 CEST 2009

On Mon, Mar 30, 2009 at 7:06 PM, Alexandr Goncearenco <neksa at neksa.net>wrote:

> On Sun, 2009-03-29 at 13:13 +0200, Egon Willighagen wrote:
> > On Sun, Mar 29, 2009 at 1:07 PM, Carsten Niehaus <cniehaus at gmx.de>
> wrote:
> > > Am Sunday 29 March 2009 00:19:20 schrieb Apekshit Sharma:
> > >> 3)*(major)*I would also like to add a feature which i'd like to call
> > >> “compound finder”, and will do the fllowing:
> > >>
> > >> once clicking on this feature ,the user when clicks on an element ,it
> will
> > >> show all the compounds of that element .
> > >
> > > All compounds? That would mean clicking on Carbon will show you a
> billion
> > > carbonic compounds (ethanol, methane, butane, dodecane, dedecanol,
> ...)? That
> > > is impossible. You will need a database for that. But hey, that
> database
> > > exists :-)
> >
> > Alternatively, I can imagine that it finds all compounds which only
> > contain that single element... so, for carbon it would find graphite,
> > buckyball, diamond.
> This sounds ok for carbon, but I can't imagine such a query for
> non-carbon single element compounds.
> Compound filter sounds like a more vial feature than element filter,
> though I would love to be able to get a list of metal-containing
> proteins (PDB format) on my local disk by metal element, for example.

this gives me a good idea.
when i meet my current proposal goal, i will be able to help you uptill -

> "I would love to be able to get a list of metal-containing
proteins (PDB format) on my local disk"(only till here)

as when you'll select a metal , it will give you all compounds containing
that metal from the database.and i plan to show the results grouped by
families(which will obviously contain protein family) or something(not yet
decided other grouping criteria).

>  "by metal element"

has given  me  idea of incorporating a feature which might do something like
save the result.(which a currently plan to do)
take a part of result
and then regroup it on some other basis like by metal (obviously it will
lead to same compound being in multiple groups),non-metal,etc
in your case, it turns out to be be metal.
although i won't take it as a part of my mainstream project(sorry), as i
would be concentrating mainly on my first 3 proposal. but if i get time ,
i'll be glad to incorporate this feature. :-)

> > >> On subsquint selection of
> > >> elements,it will keep on filtering compounds common to all selected
> > >> elements before and the new one.
> >
> > That's quite impossible indeed... and I suggest linking to compound
> > databases on the internet for this, and open the search results in
> > Konqueror instead.
> >
> > Jerome's database will only do organic compounds...
> >
> > >> Also i will provide additional filters like
> > >> , setting min or/and max no. of atoms of each element.in the
> > >> compound,giving max or/and min molecular mass, or like comp. should
> belong
> > >> to a certain family (like alcohols,aldehydes,proteins,etc) .etc
> > >>
> > >> It will be a lot useful as it will provide functionality of finding
> > >> compounds by filters.
> > >
> > > Yes, I very much agree with this. This could even mean improving the
> > > Strigi-Chemical project from 2007!
> > >
> > >
> http://api.kde.org/playground-api/utils-apidocs/strigi-chemical/html/index.html
> > >
> > > For comments on Strigi chemical I am CC'ing Egon Willighagen. He knows
> a lot
> > > about Strigi and chemistry :-)
> >
> > Strigi comes into play, particularly, when looking for compounds on
> > the local hard disk, that match the search criteria.
> This is a great possibility to integrate Strigi with Kalzium. Although
> strigi-chemical demands a separate search/query frontend ideally, having
> a simple client embedded in Kalzium might be the best start.
> Apekshit, are you planning to submit all three proposals? You have
> marked them all as "(major)", so it's quite hard to see which one you'd
> prefer most.
> I've been a GSoC 2007 student working on strigi-chemical metadata
> extraction. Current status is that you can perform searches based on
> these chemical metadata, but we lack a frontend. Whether or not this
> should be part of Kalzium is up to Carsten, but I assure that making a
> GUI to search for chemical compounds on you harddrive (which have
> already been indexed and are there in the strigi database) is an
> exciting and rewarding project. This will also revive strigi-chemical,
> as it is hardly used by anyone by this time, mainly due to the missing
> GUI.
> Apekshit, check my blog-report: http://neksa.blogspot.com/  and the
> source: http://websvn.kde.org/trunk/playground/utils/strigi-chemical/
> Should you have any questions, don't hesitate to ask.

thanks a lot alex,
i have given a look at your blog, but i won't be getting much time before
1st april owing to my approaching lab exam :-(
It does serve my purpose of what i intend to do.
So i plan to have a better look at the same on 1st and i'll be surely giving
you pain by asking questions :-)
thank you once again for helping me out.

> Best wishes,
> Alex.

to all
it's really a great experience discussing the things on mail and exchanging
ideas with people whom i didn't even know, not even two days before.
this open source stuff is turning out to be a lot interesting.
i didn't know that there was so much help available and that there were
people always ready to help and give suggestions.
it's like, i have got a lot things needed ,but i know , there more waiting
for me.
thanks a lot to all.

apekshit sharma
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