From owner-chemistry@ccl.net Thu Apr 5 02:15:00 2012 From: "Muhammad Khaled Tumbi khaledtumbi[A]gmail.com" To: CCL Subject: CCL: extract chemical information from PDF tables Message-Id: <-46636-120405012555-31955-jfV6tO3fFToEnzxvQTowRw#server.ccl.net> X-Original-From: Muhammad Khaled Tumbi Content-Type: multipart/alternative; boundary=20cf30207984a4883c04bce7c5e1 Date: Thu, 5 Apr 2012 10:55:25 +0530 MIME-Version: 1.0 Sent to CCL by: Muhammad Khaled Tumbi [khaledtumbi : gmail.com] --20cf30207984a4883c04bce7c5e1 Content-Type: text/plain; charset=ISO-8859-1 Goto this link >>> http://swift.cmbi.ru.nl/bitmapb/access/runit.html**** 1. Click on *Runit on top left side corner***** 2. Browse your PDF file (Remember No spaces in file name)**** 3. It will asks for something like "pseudonys", write anything there, which will use to locate your Files (Identification)**** 4. submit**** 5. Go back to *runit* page,**** 6. click browse your structures**** Enjoy........**** ** ** Algorithm used: Full text paper **** http://pubs.acs.org/doi/abs/10.1021/ci2004303 =-=-=-= Tumbi Muhammed Khaled Abdul Waheed, Institute Scholar, Department Of Pharmacoinformatics, NIPER, S.A.S. Nagar, Mohali, Punjab, India. Mob. +91 78145 24855 www.niper.ac.in www.pharmacoinformatics.info On Thu, Apr 5, 2012 at 2:39 AM, TJ O Donnell tjo*o*acm.org < owner-chemistry---ccl.net> wrote: > > 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> > > --20cf30207984a4883c04bce7c5e1 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

Goto this link >>>=A0http://swift.cmbi.ru.nl/bitmapb/access/runit.html<= /span>

  1. Click on=A0Runit o= n top left side corner
  2. Browse your PDF file (Remember= No spaces in file name)
  3. It w= ill asks for something like "pseudonys", write anything there, wh= ich will use to locate your Files (Identification)
  4. submit
  5. G= o back to=A0runit=A0page,
  6. click browse your structures
    7. =

Enjoy........

<= u>=A0

Algorithm=A0used: Full text paper=A0

<= a href=3D"http://pubs.acs.org/doi/abs/10.1021/ci2004303" target=3D"_blank" = style=3D"color:rgb(17,85,204)">http://pubs.acs.org/doi/abs/10.1021/ci200430= 3

=3D-=3D-=3D-=3D
Tumbi Muhammed Khaled Abdul Waheed,
Institute = Scholar,
Department Of Pharmacoinformatics,
NIPER, S.A.S. Nagar, Moha= li,
Punjab, India.
Mob. +91 78145 24855
www.niper.ac.in



On Thu, Apr 5, 2012 at 2:39 AM, TJ O Don= nell tjo*o*acm.org <owner-chemistry---ccl.net> wrote:

Sent to CCL by: "TJ O'Donnell" [tjo-*-acm.org]
You might also try openbabel. =A0The babel program can convert pdb to other=
formats that might be more helpful. =A0You 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.e= du <o= wner-chemistry_-_ccl.net> 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<= br> > 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://p= oppler.freedesktop.org/.
>
> I hope that helps,
> vale
>
> ---------------------------------
> Vale Cofer-Shabica
> Department of Chemistry, Brown University
> Dylan_Cofer-Shabica[*]b= rown.edu
>
>
> On Tue, Apr 3, 2012 at 17:55, Brian Bennion bennion1=3D-=3Dllnl.gov
> <owner-chemistry[*]ccl= .net> wrote:
>>
>> Sent to CCL by: "Brian =A0Bennion" [bennion1=3Dllnl.gov]
>> Hello,
>>
>> Does anyone have/know of code to parse pdf tables for chemical str= ucture and activity data?
>>
>> Searching the web did not result in much so I may not be searching= with the correct terms. =A0One interesting hit was the clide code from sim= biosis.
>>
>> Has anyone used this for pulling structures out of pdf files?
>>
>> I want to populate a repository with chemical structures and annot= ate the entries with the activity data given in an associated table located= in the same pdf document.
>>
>> Thanks
>> Brian> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_= ccl_message> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_m= essage> =A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml&= gt; =A0 =A0 =A0http://www.ccl.net/spammers.txt> =A0 =A0 =A0http://www.ccl.net/= cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/cgi-b= in/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/chemistry/sub= _unsub.shtml> =A0 =A0 =A0http://www.ccl.net/spammers.txt>
>



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--20cf30207984a4883c04bce7c5e1-- From owner-chemistry@ccl.net Thu Apr 5 07:54:01 2012 From: "Rajeev Gangal rajeev.gangal() gmail.com" To: CCL Subject: CCL: extract chemical information from PDF tables Message-Id: <-46637-120405072221-23890-Ptl2tobLuBvaufR1Y79Dhw(~)server.ccl.net> X-Original-From: Rajeev Gangal Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 5 Apr 2012 16:52:11 +0530 MIME-Version: 1.0 Sent to CCL by: Rajeev Gangal [rajeev.gangal^-^gmail.com] Try http://sourceforge.net/projects/osra/?source=directory regards Rajeev Gangal India On Thu, Apr 5, 2012 at 2:39 AM, TJ O Donnell tjo*o*acm.org wrote: > > 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>      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> > From owner-chemistry@ccl.net Thu Apr 5 08:28:01 2012 From: "Alex Allardyce aa+/-chemaxon.com" To: CCL Subject: CCL: Call for papers - ChemAxon's US UGM, September 25-26, 2012 Message-Id: <-46638-120405072351-27053-2Hv3/C18EXt/SK4uSNeBIQ(0)server.ccl.net> X-Original-From: Alex Allardyce Content-Type: multipart/alternative; boundary="------------080000050001040607020605" Date: Thu, 05 Apr 2012 13:23:43 +0200 MIME-Version: 1.0 Sent to CCL by: Alex Allardyce [aa]![chemaxon.com] This is a multi-part message in MIME format. --------------080000050001040607020605 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit Excuse cross postings We are calling for papers for ChemAxon's 2012 US User Group Meeting, to be held on Tuesday and Wednesday, September 25-26 at the Babson Executive Conference Center , Wellesley, MA. The meeting will feature presentations from ChemAxon users, lightning presentations/exhibition from ChemAxon Partners and the latest updates on product developments, as well as discussion shaping future product development. Oral abstract submission deadline is *May 1st*, 2012 and for poster abstracts, September 1st. To find out more visit the meeting page and to submit an abstract please register . Guidance for presentations is here. To review the archives of previous meetings, including original presentations (slides and video) and meeting reports from Wendy Warr and Yvonne Martin visit the archive . We look forward to seeing you there. Alex *UGM Satellite meetings:* /(Sept 24th afternoon and 27th)/ /*Markush Forum* - Monday September 24th, afternoon/ Preceding the UGM we have the third US meeting of the Markush Forum, an afternoon for interested organizations to participate in the development of ChemAxon's tools for Markush structure enumeration and search. This meeting is open to users, content developers should contact us to confirm their participation. Find out more here: http://www.chemaxon.com/events/ugm-boston-2012/#markush */1-2-1 Sessions/* - /Monday September 24th, afternoon/ Following the Markush Forum we have a 1-2-1 session where our users can meet with ChemAxon staff to discuss scientific, technical or business issues. Each major product group will have a discussion area where ChemAxon experts will be on call. /*Developer and End user training* - Thursday September 27th, all day/ Following the UGM will be a 2 track developer and end user Training Day. For developers we have a tutorial/code session and for end users, for the first time, we have 2 tracks to allow focus on different products on hands-on training. The program is still under development. Find out more about the Application Focus (End user) Training here: http://www.chemaxon.com/events/ugm-boston-2012/#appfocus Find out more about the Developer Training here: http://www.chemaxon.com/events/ugm-boston-2012/#developer -- *Alex Allardyce* Marketing Dir. *ChemAxon**Ltd*. Záhony u. 7. Building HX, Budapest, 1031 Hungary http://www.chemaxon.com Tel: +361 453 0435 Fax: +361 4532659 mailto:aa!^!chemaxon.com --------------080000050001040607020605 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Excuse cross postings

We are calling for papers for ChemAxon's 2012 US User Group Meeting, to be held on Tuesday and Wednesday, September 25-26 at the Babson Executive Conference Center, Wellesley, MA.

The meeting will feature presentations from ChemAxon users, lightning presentations/exhibition from ChemAxon Partners and the latest updates on product developments, as well as discussion shaping future product development.

Oral abstract submission deadline is May 1st, 2012 and for poster abstracts, September 1st. To find out more visit the meeting page and to submit an abstract please register. Guidance for presentations is here.

To review the archives of previous meetings, including original presentations (slides and video) and meeting reports from Wendy Warr and Yvonne Martin visit the archive.

We look forward to seeing you there.

Alex

UGM Satellite meetings: (Sept 24th afternoon and 27th)

Markush Forum - Monday September 24th, afternoon
Preceding the UGM we have the third US meeting of the Markush Forum, an afternoon for interested organizations to participate in the development of ChemAxon's tools for Markush structure enumeration and search. This meeting is open to users, content developers should contact us to confirm their participation.  Find out more here: http://www.chemaxon.com/events/ugm-boston-2012/#markush

1-2-1 Sessions - Monday September 24th, afternoon
Following the Markush Forum we have a 1-2-1 session where our users can meet with ChemAxon staff to discuss scientific, technical or business issues. Each major product group will have a discussion area where ChemAxon experts will be on call.

Developer and End user training - Thursday September 27th, all day
Following the UGM will be a 2 track developer and end user Training Day. For developers we have a tutorial/code session and for end users, for the first time, we have 2 tracks to allow focus on different products on hands-on training. The program is still under development.

Find out more about the Application Focus (End user) Training here:
http://www.chemaxon.com/events/ugm-boston-2012/#appfocus

Find out more about the Developer Training here:
http://www.chemaxon.com/events/ugm-boston-2012/#developer
--
Alex Allardyce
Marketing Dir.
ChemAxon Ltd.
Záhony u. 7. Building HX, Budapest, 1031 Hungary
http://www.chemaxon.com
Tel: +361 453 0435
Fax: +361 4532659
mailto:aa!^!chemaxon.com
--------------080000050001040607020605-- From owner-chemistry@ccl.net Thu Apr 5 14:39:00 2012 From: "Wilhelm Eger eger*theochem.tu-muenchen.de" To: CCL Subject: CCL:G: Visualize NLMOs from Gaussian output/checkpoint file Message-Id: <-46639-120405103852-1647-uUTIwfHHz+mWAaeW8BGycg]![server.ccl.net> X-Original-From: Wilhelm Eger Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 05 Apr 2012 16:39:30 +0200 MIME-Version: 1.0 Sent to CCL by: Wilhelm Eger [eger*o*theochem.tu-muenchen.de] Dear all, In order to compare the shapes of a NLMO LP and its parent NBO in regard to delocalization effects, I would like to extract both as a cube file > from a Gaussian calculation. I know the actual procedure consisting of: Run the NBO calculation with the POP=(SaveNBOs) keyword. Transform the resulting checkpoint file to a formatted chechkpoint file using formchk. Look at the end of the calculation output file and get the right position of the desired NBO. Extract the NBO with cubegen 0 mo=X file.fchk MOX.cube -3 h and all other related with cubegen 0 mo=Y file.fchk MOY.cube -3 h MOX.cube to ensure the same dimensions. However, if I run the calculation with POP=(SaveNLMOs), and extract the related MO, I get exactly the same cube files as for the NBO extraction method (e.g. diff results zero). The Gaussian output tells me also of NBOs being stored in the checkpoint file instead of NLMOs. Besides of 'SaveNLMOs' I tried 'SaveMixed' and 'IOP=(6/7=3)', but still the same result. Both G03 and G09 have been used. The desired NBO and NLMO must be different due to significant delocalization of the parent NBO into antibonds. Does anybody know how to reliably extract NLMOs to cube files? Thanks in advance. Regards, Wilhelm -- Dr. Wilhelm Eger Theoretische Chemie Department Chemie Technische Universitaet Muenchen Lichtenbergstr. 4 85748 Garching Tel. 089/289-13605 From owner-chemistry@ccl.net Thu Apr 5 16:39:01 2012 From: "A. anglea a.anglea90*o*yahoo.com" To: CCL Subject: CCL: Hydrophobic interaction - precise answer Message-Id: <-46640-120405163757-13864-sio+KXhBFPkf/hV0+JZjfQ|-|server.ccl.net> X-Original-From: "A. anglea" Date: Thu, 5 Apr 2012 16:37:54 -0400 Sent to CCL by: "A. anglea" [a.anglea90 : yahoo.com] Dear colleagues In some papers, I came across "hydrophobic interactions" term. I googled and searched for this term without getting a precise answer for my question. What do they mean with that term? is that a general term for vander waals interaction or it is something else? It may be a simple question for some of you, but it is quite hard for me to understand it. Your help would be highly appreciated. Precise answer is needed, please Cheers BTW, I am a PhD student. From owner-chemistry@ccl.net Thu Apr 5 18:49:00 2012 From: "Dr. Vitaly V. Chaban vvchaban-#-gmail.com" To: CCL Subject: CCL: Hydrophobic interaction - precise answer Message-Id: <-46641-120405183958-3532-LyfSOwUtV2vChj9+FXN97g_._server.ccl.net> X-Original-From: "Dr. Vitaly V. Chaban" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 5 Apr 2012 18:39:10 -0400 MIME-Version: 1.0 Sent to CCL by: "Dr. Vitaly V. Chaban" [vvchaban[-]gmail.com] On Thu, Apr 5, 2012 at 4:37 PM, A. anglea a.anglea90*o*yahoo.com wrote: > > Sent to CCL by: "A.  anglea" [a.anglea90 : yahoo.com] > Dear colleagues > In some papers, I came across "hydrophobic interactions" term. I googled and > searched for this term without getting a precise answer for my question. > What do they mean with that term? is that a general term for vander waals interaction or it is something else? > It may be a simple question for some of you, but it is quite hard for me to > understand it. > Your help would be highly appreciated. > Precise answer is needed, please > Cheers > BTW, I am a PhD student. It is said that the substance is hydrophobic if it interacts WEAKLY with water. Or one can say it dissolves bad in water. In reality, the molecules of such substances have small electrical moments and you are right that VDW forces play a relatively big role (as compared to water) in their interactions with other particles. Correspondingly, when the people write about hydrophobic interactions, they mean such interactions, which would make the substance repel from a mass of water. Herewith, water can be absent in the considered system. Hope this is helpful. Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA