<br><br><div class="gmail_quote">On Mon, Mar 30, 2009 at 7:06 PM, Alexandr Goncearenco <span dir="ltr"><<a href="mailto:neksa@neksa.net">neksa@neksa.net</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im"><br>
On Sun, 2009-03-29 at 13:13 +0200, Egon Willighagen wrote:<br>
> On Sun, Mar 29, 2009 at 1:07 PM, Carsten Niehaus <<a href="mailto:cniehaus@gmx.de">cniehaus@gmx.de</a>> wrote:<br>
> > Am Sunday 29 March 2009 00:19:20 schrieb Apekshit Sharma:<br>
> >> 3)*(major)*I would also like to add a feature which i'd like to call<br>
> >> “compound finder”, and will do the fllowing:<br>
> >><br>
> >> once clicking on this feature ,the user when clicks on an element ,it will<br>
> >> show all the compounds of that element .<br>
> ><br>
> > All compounds? That would mean clicking on Carbon will show you a billion<br>
> > carbonic compounds (ethanol, methane, butane, dodecane, dedecanol, ...)? That<br>
> > is impossible. You will need a database for that. But hey, that database<br>
> > exists :-)<br>
><br>
> Alternatively, I can imagine that it finds all compounds which only<br>
> contain that single element... so, for carbon it would find graphite,<br>
> buckyball, diamond.<br>
<br>
</div>This sounds ok for carbon, but I can't imagine such a query for<br>
non-carbon single element compounds.<br>
Compound filter sounds like a more vial feature than element filter,<br>
though I would love to be able to get a list of metal-containing<br>
proteins (PDB format) on my local disk by metal element, for example.</blockquote><div><br>this gives me a good idea.<br>when i meet my current proposal goal, i will be able to help you uptill - <br><blockquote style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;" class="gmail_quote">
"I would love to be able to get a list of metal-containing<br></blockquote><blockquote style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;" class="gmail_quote">
proteins (PDB format) on my local disk"(only till here)<br></blockquote></div><div><br>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). <br>
But<br><blockquote style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;" class="gmail_quote"> "by metal element"</blockquote><div><br>has given me idea of incorporating a feature which might do something like this:<br>
save the result.(which a currently plan to do)<br>take a part of result <br>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<br>in your case, it turns out to be be metal.<br>
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. :-)<br></div></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
<div class="im"><br>
> >> On subsquint selection of<br>
> >> elements,it will keep on filtering compounds common to all selected<br>
> >> elements before and the new one.<br>
><br>
> That's quite impossible indeed... and I suggest linking to compound<br>
> databases on the internet for this, and open the search results in<br>
> Konqueror instead.<br>
><br>
> Jerome's database will only do organic compounds...<br>
><br>
> >> Also i will provide additional filters like<br>
> >> , setting min or/and max no. of atoms of each <a href="http://element.in" target="_blank">element.in</a> the<br>
> >> compound,giving max or/and min molecular mass, or like comp. should belong<br>
> >> to a certain family (like alcohols,aldehydes,proteins,etc) .etc<br>
> >><br>
> >> It will be a lot useful as it will provide functionality of finding<br>
> >> compounds by filters.<br>
> ><br>
> > Yes, I very much agree with this. This could even mean improving the<br>
> > Strigi-Chemical project from 2007!<br>
> ><br>
> > <a href="http://api.kde.org/playground-api/utils-apidocs/strigi-chemical/html/index.html" target="_blank">http://api.kde.org/playground-api/utils-apidocs/strigi-chemical/html/index.html</a><br>
> ><br>
> > For comments on Strigi chemical I am CC'ing Egon Willighagen. He knows a lot<br>
> > about Strigi and chemistry :-)<br>
><br>
> Strigi comes into play, particularly, when looking for compounds on<br>
> the local hard disk, that match the search criteria.<br>
<br>
</div>This is a great possibility to integrate Strigi with Kalzium. Although<br>
strigi-chemical demands a separate search/query frontend ideally, having<br>
a simple client embedded in Kalzium might be the best start.<br>
<br>
Apekshit, are you planning to submit all three proposals? You have<br>
marked them all as "(major)", so it's quite hard to see which one you'd<br>
prefer most.<br>
<br>
I've been a GSoC 2007 student working on strigi-chemical metadata<br>
extraction. Current status is that you can perform searches based on<br>
these chemical metadata, but we lack a frontend. Whether or not this<br>
should be part of Kalzium is up to Carsten, but I assure that making a<br>
GUI to search for chemical compounds on you harddrive (which have<br>
already been indexed and are there in the strigi database) is an<br>
exciting and rewarding project. This will also revive strigi-chemical,<br>
as it is hardly used by anyone by this time, mainly due to the missing<br>
GUI.<br>
<br>
Apekshit, check my blog-report: <a href="http://neksa.blogspot.com/" target="_blank">http://neksa.blogspot.com/</a> and the<br>
source: <a href="http://websvn.kde.org/trunk/playground/utils/strigi-chemical/" target="_blank">http://websvn.kde.org/trunk/playground/utils/strigi-chemical/</a><br>
Should you have any questions, don't hesitate to ask.</blockquote><div><br>thanks a lot alex,<br>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 :-( <br>
It does serve my purpose of what i intend to do.<br>So i plan to have a better look at the same on 1st and i'll be surely giving you pain by asking questions :-)<br>thank you once again for helping me out.<br><br></div>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><br>
<br>
Best wishes,<br>
Alex.<br>
</blockquote><div><br><br><br>to all<br>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.<br>this open source stuff is turning out to be a lot interesting. <br>
i didn't know that there was so much help available and that there were people always ready to help and give suggestions.<br>it's like, i have got a lot things needed ,but i know , there more waiting for me. <br>thanks a lot to all.<br>
<br>apekshit sharma<br></div></div><br>