From owner-chemistry@ccl.net Tue Apr  3 16:40:00 2012
From: "Rajarshi Guha rajarshi.guha(~)gmail.com" <owner-chemistry+/-server.ccl.net>
To: CCL
Subject: CCL: free software for plotting with small molecule tooltips (structures)?
Message-Id: <-46627-120403152301-23854-nUxkbFmo0qo53BW4pJ/AZw+/-server.ccl.net>
X-Original-From: Rajarshi Guha <rajarshi.guha(0)gmail.com>
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Date: Tue, 3 Apr 2012 15:22:51 -0400
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Sent to CCL by: Rajarshi Guha [rajarshi.guha^^^gmail.com]
I'm not aware of a pre-packaged tool, but should be quite
straightforward using a variety if platforms. For example, using
JFreeChart to display a chart with tooltips could be combined with the
CDK or JChem to get an application that does this.

It could also be done quite easily on the Javascript side with tools
like Raphael, D3.js etc would let you do the charting easily, though
you would likely need a server side function to generate the image for
the tooltip

On Mon, Apr 2, 2012 at 12:33 PM, James Thomas Metz
James.Metz::Abbott.com <owner-chemistry++ccl.net> wrote:
>
> Sent to CCL by: "James Thomas Metz" [James.Metz()Abbott.com]
> CCL,
>
> Is anyone aware of free software that is capable of reading either an SD file with 2D small molecule structures and (x,y) coordinates, or a CSV file with structures (SMILES) and (x,y) coordinates and generating a 2D scatter plot with tooltips that pop up a decent looking 2D representation of the small molecule corresponding to that particular coordinate?
>
> Please note that I am already aware of commercial packages that can accomplish this goal.
>
> Thank you.
>
> Regards,
> Jim Metz
>
> Abbott Laboratories>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt>
>



-- 
Rajarshi Guha | http://blog.rguha.net
NIH Center for Advancing Translational Science


From owner-chemistry@ccl.net Tue Apr  3 17:57:00 2012
From: "Brian Bennion bennion1=-=llnl.gov" <owner-chemistry{:}server.ccl.net>
To: CCL
Subject: CCL: extract chemical information from PDF tables
Message-Id: <-46628-120403175557-25384-1m0VnVRg+K5Fzxaup6t5iw{:}server.ccl.net>
X-Original-From: "Brian  Bennion" <bennion1##llnl.gov>
Date: Tue, 3 Apr 2012 17:55:54 -0400


Sent to CCL by: "Brian  Bennion" [bennion1=llnl.gov]
Hello,

Does anyone have/know of code to parse pdf tables for chemical structure and activity data?

Searching the web did not result in much so I may not be searching with the correct terms.  One interesting hit was the clide code from simbiosis.

Has anyone used this for pulling structures out of pdf files?

I want to populate a repository with chemical structures and annotate the entries with the activity data given in an associated table located in the same pdf document.

Thanks
Brian