From owner-chemistry@ccl.net Wed Apr 4 18:11:00 2012 From: "TJ O Donnell tjo*o*acm.org" To: CCL Subject: CCL: extract chemical information from PDF tables Message-Id: <-46635-120404171521-25068-GFR7IfsmgSo561jOhS5xdg%server.ccl.net> X-Original-From: "TJ O'Donnell" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 4 Apr 2012 14:09:36 -0700 MIME-Version: 1.0 Sent to CCL by: "TJ O'Donnell" [tjo-*-acm.org] You might also try openbabel. The babel program can convert pdb to other formats that might be more helpful. You can also write python scripts using openbabel to read a pdb file. TJ O'Donnell On Wed, Apr 4, 2012 at 8:08 AM, Vale Cofer-Shabica dylan_cofer-shabica,,brown.edu wrote: > > Sent to CCL by: Vale Cofer-Shabica [dylan_cofer-shabica|brown.edu] > You might start with the pdftotext program. It will extract text from > pdf files, which you could then parse with another utility. The > program is included with many GNU/Linux distributions in the poppler > or poppler-utils package. The source code can also be obtained from: > http://poppler.freedesktop.org/. > > I hope that helps, > vale > > --------------------------------- > Vale Cofer-Shabica > Department of Chemistry, Brown University > Dylan_Cofer-Shabica[*]brown.edu > > > On Tue, Apr 3, 2012 at 17:55, Brian Bennion bennion1=-=llnl.gov > wrote: >> >> 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>      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>      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> >