From owner-chemistry@ccl.net Fri Apr 6 01:44:00 2012 From: "Alex Allardyce aa|a|chemaxon.com" To: CCL Subject: CCL: extract chemical information from PDF tables Message-Id: <-46642-120405124245-27882-1uPJ2Vd5O2A4mhgKxk7buw_+_server.ccl.net> X-Original-From: Alex Allardyce Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 05 Apr 2012 18:42:39 +0200 MIME-Version: 1.0 Sent to CCL by: Alex Allardyce [aa : chemaxon.com] ChemAxon supports text and scanned pdf (and doc, ppt, pptx etc). It is integrated throughout our technology but probably easiest to try out in MarvinView, (free for the desktop), just 'open' the pdf (or doc or ppt etc) and all extracted structures are shown. You also access all of the functionality through the API/command line as well as KNIME and Pipeline Pilot nodes. Cheers Alex > 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> > From owner-chemistry@ccl.net Fri Apr 6 02:18:00 2012 From: "Andreas Klamt klamt.{:}.cosmologic.de" To: CCL Subject: CCL: Hydrophobic interaction - precise answer Message-Id: <-46643-120406021025-21457-Uj266oTDbnzVBMa5T1DEyw{:}server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Fri, 06 Apr 2012 08:10:15 +0200 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt**cosmologic.de] You are absolutely right being surprised by the expression "hydrophobic interaction": Although this is widely used, we first should clearly state, that from a physics point of view such an interaction does not exist. What people mean by this is the repulsion of non- or slightly polar surface area (e.g. CH2, CH3, little bit less benzen rings, alkenes, chloro, bromo, jodo groups) by water. Thermodynamically such molecular surface is much better solvated by any other solvent than water. Therefore people call this repulsion hydrophobicity. From a physicochemical point of view this comes from the fact, that in a liquid all polar surfaces pieces like to have polar surface pieces of the other sign (i.e. positive likes negative) as direct contact partners. As can be very nicely visualized within my COSMO-RS theory, water has a uniquely good balance of very positive and very negative surface, and only a small amount of non-polar surface area. Therefore in pure water we have very good and strong contacts between the polar surfaces, even forming hydrogen bonds with each other. If you now try to brig a non-polar piece of surface into this ensemble, it either has to break the strong polar contacts (which is rather impossible at room temperature), or it has to pick the very few non-polar surface segments (green in my sigma surfaces). It can rather do only the latter at room temperature. But pickig the few non-polar ones means a large loss of entropy, compared to the situation of the the non-polar surface in another solvent. And this loss of entropy causes a large positive free energy of the non-polar pieces in water. That is the hydrophobic effect: It is an entropic effect! Experimentally this can be demonstrated based on the fact that the solubility of alkanes in water has a minimum at room temperature, meaning that the enthalpy of transfer is zero, and the whole free energy of transfer of alkane into water is of entropic nature. Hope this helps. Perhaps see sigma profiles and surfaces on our web page www.COSMOlogic.de Best regards Andreas Am 05.04.2012 22:37, schrieb A. anglea a.anglea90*o*yahoo.com: > 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.> > > -- Prof. Dr. Andreas Klamt CEO / Geschäftsführer COSMOlogic GmbH& Co. KG Burscheider Strasse 515 D-51381 Leverkusen, Germany phone +49-2171-731681 fax +49-2171-731689 e-mail klamt*|*cosmologic.de web www.cosmologic.de [University address: Inst. of Physical and Theoretical Chemistry, University of Regensburg] Join us at the 4th-COSMO-RS-Symposium April 2013 Details at www.cosmologic.de/symposium2013 HRA 20653 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt Komplementaer: COSMOlogic Verwaltungs GmbH HRB 49501 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt From owner-chemistry@ccl.net Fri Apr 6 08:14:01 2012 From: "Jesse Gordon jesse.gordon++dotmatics.com" To: CCL Subject: CCL: Hydrophobic interaction - precise answer Message-Id: <-46644-120405183621-19129-STdvdGzwO2XglisF9/FbVA=server.ccl.net> X-Original-From: Jesse Gordon Content-Type: multipart/alternative; boundary=f46d040713dd8dc66004bcf62ac8 Date: Thu, 5 Apr 2012 18:36:08 -0400 MIME-Version: 1.0 Sent to CCL by: Jesse Gordon [jesse.gordon^_^dotmatics.com] --f46d040713dd8dc66004bcf62ac8 Content-Type: text/plain; charset=ISO-8859-1 Hydrophobic interactions do not include van der Waals interactions; they are different classes of interactions. Van der Waals interactions are between partially charged groups, or moieties which can have an induced partial charge -- a dipole interaction from dipoles like polar covalent bonds. Hydrophobic interactions are not based on dipoles and occur with (non-polar) covalent bonds such as long-chain aliphatics. Lipid bilayers exist because the long-chain aliphatics interact hydrophobically -- in preference to group together excluding water. Same for hydrophobic regions in protein folding -- where there are all hydrocarbons, they group together. That should get you started -- -- Jesse Gordon, Dotmatics Application Scientist On 5 April 2012 16:37, A. anglea a.anglea90*o*yahoo.com < owner-chemistry _ ccl.net> 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.> > > -- ===================================== Jesse Gordon Application Scientist Dotmatics Limited 400 West Cummings Park #5450, Woburn MA 01801 T: +1 781-305-3114 M: +1-617-320-6989 Email: jesse.gordon _ dotmatics.com Skype: jessegordon ====================================== See the latest in Dotmatics Suite of Solutions at: Booth # 11 CHI Drug Discovery Chemistry, April 17-19, 2012, Hilton San Diego Resort & Spa, San Diego, CA, www.drugdiscoverychemistry.com Booth # 323 Bio-IT World Conference, April 24-26, 2012, World Trade center, Boston, MA, www.bio-itworldexpo.com -- Disclaimer: This electronic mail and its attachments are intended solely for the person(s) to whom they are addressed and contain information which is confidential or otherwise protected from disclosure, except for the purpose for which they are intended. Dissemination, distribution, or reproduction by anyone other than the intended recipients is prohibited and may be illegal. If you are not an intended recipient, please immediately inform the sender and return the electronic mail and its attachments and destroy any copies which may be in your possession. Dotmatics Limited screens electronic mails for viruses but does not warrant that this electronic mail is free of any viruses. Dotmatics Limited accepts no liability for any damage caused by any virus transmitted by this electronic mail. Dotmatics Limited is registered in England & Wales No. 5614524 with offices at The Old Monastery, Windhill, Bishops Stortford, Herts, CM23 2ND, UK. --f46d040713dd8dc66004bcf62ac8 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hydrophobic interactions do not include van der Waals interactions; th= ey are different=A0classes of interactions.=A0=A0Van der Waals interactions= are between partially charged groups, or moieties which can have an induce= d partial charge -- a dipole interaction from dipoles like polar covalent b= onds. Hydrophobic interactions are not based on dipoles and occur with (non= -polar) covalent bonds such as long-chain aliphatics. Lipid bilayers exist = because the long-chain aliphatics interact hydrophobically -- in preference= to group=A0together excluding water. Same for hydrophobic regions in prote= in folding -- where there are all hydrocarbons, they group together.
=A0
That should get you started --
-- Jesse Gordon= , Dotmatics Application Scientist
On 5 = April 2012 16:37, A. anglea a.anglea90*o*yahoo= .com <o= wner-chemistry _ ccl.net> wrote:

Sent to CCL by: "A. =A0anglea" [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 i= nteraction 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.



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From owner-chemistry@ccl.net Fri Apr  6 08:49:00 2012
From: "suneyna bansal suneyna.bansal^gmail.com" 
To: CCL
Subject: CCL: Hydrophobic interaction - precise answer
Message-Id: <-46645-120406010450-9300-9LrsaKkR/7ra6e8WzJrX5A|*|server.ccl.net>
X-Original-From: suneyna bansal 
Content-Type: multipart/alternative; boundary=20cf301af41d40fa0904bcfb9851
Date: Fri, 6 Apr 2012 10:34:43 +0530
MIME-Version: 1.0


Sent to CCL by: suneyna bansal [suneyna.bansal{}gmail.com]
--20cf301af41d40fa0904bcfb9851
Content-Type: text/plain; charset=ISO-8859-1

Hi Dear,

I understood this term as the interactions felt by hydrophobic or
amphiphathic molecules by the exclusion of water.

Regards
Suneyna
IIT delhi
Doctoral student




On Fri, Apr 6, 2012 at 2:07 AM, A. anglea a.anglea90*o*yahoo.com <
owner-chemistry[a]ccl.net> 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.>
>
>

--20cf301af41d40fa0904bcfb9851
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable


Hi Dear,


=A0


I understood this term as the interactions felt by hydrophobic or amph=
iphathic molecules by the exclusion of water.


=A0


Regards


Suneyna


IIT delhi 


Doctoral student


=A0




=A0


On Fri, Apr 6, 2012 at 2:07 AM, A. anglea a.angl=
ea90*o*yahoo.com <owner-chemistry[a]ccl.net> wrote:




Sent to CCL by: "A. =A0angle=
a" [a.anglea90 : yahoo=
.com]

Dear colleagues
In some papers, I came across "hydrophobic interact=
ions" term. I googled and
searched for this term without getting a =
precise answer for my question.
What do they mean with that term? is tha=
t 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 ans=
wer is needed, please
Cheers
BTW, I am a PhD student.




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From owner-chemistry@ccl.net Fri Apr  6 09:24:00 2012
From: "eger::theochem.tu-muenchen.de" 
To: CCL
Subject: CCL:G: Visualize NLMOs from Gaussian output/checkpoint file
Message-Id: <-46646-120406050605-17274-yC5aiGwXsv5aHEvyCxykkQ]*[server.ccl.net>
X-Original-From: eger _ theochem.tu-muenchen.de
Content-Transfer-Encoding: 8bit
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Date: Fri, 6 Apr 2012 11:05:54 +0200
MIME-Version: 1.0


Sent to CCL by: eger**theochem.tu-muenchen.de
Well, I repeated the calculations with

IOP=(6/73=1) POP=NBO for NBO output

and

IOP=(6/73=2) POP=NBO for NLMO output.

Now I get two different cube files, which can be subtracted via cubman and
the resulting difference cube file can be visualized e.g. in Gaussview.

Thanks!

>
> 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 Fri Apr  6 09:59:00 2012
From: "Jose A. Gamez jgamez#%#mpi-muelheim.mpg.de" 
To: CCL
Subject: CCL:G: Visualize NLMOs from Gaussian output/checkpoint file
Message-Id: <-46647-120406071508-32630-R0KHU4pzMwOlgk/OYlGfDA!=!server.ccl.net>
X-Original-From: "Jose A. Gamez" 
Content-Transfer-Encoding: 8bit
Content-Type: Text/Plain;
  charset="iso-8859-1"
Date: Fri, 6 Apr 2012 13:14:55 +0200
MIME-Version: 1.0


Sent to CCL by: "Jose A. Gamez" [jgamez%%mpi-muelheim.mpg.de]
Dear Wilhelm,

Here is a small tutorial to visualise NBO related orbitals with molekel4.3 (it 
doesn't work with the last version).

You can get molekel4.3 from:

ftp://ftp.cscs.ch/out/molekel/molekel_4.3/

in the input file add: 

gfoldprint pop=(full,nboread)

and before the last blank line of the gaussian input, add:

$NBO PLOT FILE=filename $END

at the end of your calculation, in addition to the output, you will also have 
eleven filename.[31-41] files. The NLMOs are stored in the filename.39 (you 
can see it in the header of the file), NBOs in filename.38 and so on.

Now we have to convert the Gaussian09 output (output.log) in something 
understandable for molekel 4.3 (molekel.log), so just run:

sed "s/Gaussian 09/Gaussian 98/" output.log | sed 
"s/Eigenvalues/EIGENVALUES/g" > molekel.log

Open molekel, right-button click (keep pressing the button), load -> gaussian 
log and select molekel.log. Once you have your molecule, right-button click, 
load -> nbo orb (remove the filter .orb) and select filename.39. Finally, 
right-button click, compute -> orbital and select the orbital you want to 
visualise.

I hope this helps. In case you have further questions, feel free to ask me.

Cheers,

Jose

On Thursday 05 April 2012 16:39:30 you wrote:
> 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. Jose A. Gamez
Max-Planck-Institut für Kohlenforschung
Kaiser-Wilhelm-Platz 1
45470 Mülheim an der Ruhr/Germany
  Tel.: +49 208 306 2171


From owner-chemistry@ccl.net Fri Apr  6 10:35:00 2012
From: "Jesse Gordon jesse.gordon{:}dotmatics.com" 
To: CCL
Subject: CCL: extract chemical information from PDF tables
Message-Id: <-46648-120406080059-30811-IUvi+NwhUtjJ9X94q3glPw++server.ccl.net>
X-Original-From: Jesse Gordon 
Content-Type: multipart/alternative; boundary=f46d040713dd14b52504bd01682a
Date: Fri, 6 Apr 2012 08:00:45 -0400
MIME-Version: 1.0


Sent to CCL by: Jesse Gordon [jesse.gordon*|*dotmatics.com]
--f46d040713dd14b52504bd01682a
Content-Type: text/plain; charset=ISO-8859-1

Yes, I've used CLiDE to pull structures out of PDF files. There are three
versions:
- CLiDE standard is one-at-a-time; you draw a box around the structure and
CLiDE interprets it.
- CLiDE pro version recognizes all the structures in a multi-page PDF and
produces a list;
- CLiDE batch version takes a whole stack of documents.

The quality is comparable to OCR - optical character recognition - and I've
always called this method "Chemical OCR." If you're familiar with OCR, it
makes a LOT of mistakes. For example, CLiDE almost always fails to
recognize iodine, which it interprets as a methyl group with implicit
carbon and hydrogen. Or vice versa -- if your methyl group happens to be
vertical, it often gets misinterpreted as an iodine atom. Rings sometimes
end up "broken", i.e. CLiDE interprets a 6-membered ring as a chain with 6
atoms arranged in a hexagon. So it's not perfect. As with text OCR, you
have to read the result and correct it manually.

I found that using CLiDE, whether in one-at-a-time form or batch form,
requires manually comparing the original with the chemical-OCR-interpreted
result (with text OCR you can usually skip referring back to the original
since you know all the words in your head. But with chemical OCR, the two
examples I gave above are obvious upon inspection, but many other errors
are not). The best method to inspect is to assign names to the resulting
structures using some automatic structure-to-name converter. That exposes
any subtle issues like an atom being "close" to a methyl group when it
should be an atom connected by a bond. Compare the automatically generated
name to your visual inspecction of the original, and the process is pretty
quick.



On 5 April 2012 12:42, Alex Allardyce aa|a|chemaxon.com <
owner-chemistry-,-ccl.net> wrote:

>
> Sent to CCL by: Alex Allardyce [aa : chemaxon.com]
> ChemAxon supports text and scanned pdf (and doc, ppt, pptx etc). It is
> integrated throughout our technology but probably easiest to try out in
> MarvinView, (free for the desktop), just 'open' the pdf (or doc or ppt etc)
> and all extracted structures are shown. You also access all of the
> functionality through the API/command line as well as KNIME and Pipeline
> Pilot nodes.
>
> Cheers
> Alex
>
>  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 chemistry/announcements/**conferences/
>
> Search Messages: http://www.ccl.net/chemistry/**searchccl/index.shtml     http://www.ccl.net/spammers.**txt 
>
> RTFI: http://www.ccl.net/chemistry/**aboutccl/instructions/
>
>
>


-- 
=====================================
Jesse Gordon
Application Scientist
Dotmatics Limited
400 West Cummings Park #5450, Woburn MA 01801
T: +1 781-305-3114
M: +1-617-320-6989
Email: jesse.gordon-,-dotmatics.com
Skype: jessegordon
======================================

See the latest in Dotmatics Suite of Solutions at:
Booth # 11 CHI Drug Discovery Chemistry, April 17-19, 2012, Hilton San
Diego Resort & Spa, San Diego, CA, www.drugdiscoverychemistry.com
Booth # 323 Bio-IT World Conference, April 24-26, 2012, World Trade
center,  Boston,  MA, www.bio-itworldexpo.com

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registered in England & Wales No. 5614524 with offices at The Old Monastery, 
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Yes, I've used CLiDE to pull structures out of PDF files. There ar=
e three versions:
- CLiDE standard is one-at-a-time; you draw a b=
ox around the structure and CLiDE interprets it. 
- CLiDE pro ver=
sion recognizes all the structures in a multi-page PDF and produces a list;=
 


- CLiDE batch version takes a whole stack of documents. 
=A0=

The quality is comparable to OCR - optical character recognition=
 - and I've always called this method "Chemical OCR." If you&=
#39;re familiar with OCR, it makes a LOT of mistakes. For example, CLiDE al=
most always fails to recognize iodine,=A0which it interprets as a methyl gr=
oup with implicit carbon and hydrogen. Or vice versa -- if your methyl grou=
p=A0happens to be vertical, it often gets misinterpreted as an iodine atom.=
 Rings sometimes end up "broken", i.e. CLiDE interprets a 6-membe=
red ring as a chain with 6 atoms arranged in a hexagon. So it's not per=
fect. As with text OCR, you have to read the result and correct it manually=
. 


=A0
I found that using CLiDE, whether in one-at-a-time form =
or batch form, requires manually comparing the original with the chemical-O=
CR-interpreted result (with text OCR you can usually skip referring back to=
 the original since you know all the words in your head. But with chemical =
OCR, the two examples I gave above are obvious upon inspection, but many ot=
her errors are not). The best method to inspect is to assign names to the r=
esulting structures using some automatic structure-to-name converter. That =
exposes any subtle issues like an atom being "close" to a methyl =
group when it should be an atom connected by a bond. Compare the automatica=
lly generated name to your visual inspecction of the original, and the proc=
ess is pretty quick. 


=A0
=A0
=A0
On 5 A=
pril 2012 12:42, Alex Allardyce aa|a|chemax=
on.com <owner-chemistry-,-ccl.net> wrote:




Sent to CCL by: Alex Allardyce [aa : chemaxon.com]

ChemAxon supports text and scanned pdf (and doc, ppt, pptx etc). It is inte=
grated throughout our technology but probably easiest to try out in MarvinV=
iew, (free for the desktop), just 'open' the pdf (or doc or ppt etc=
) and all extracted structures are shown. You also access all of the functi=
onality through the API/command line as well as KNIME and Pipeline Pilot no=
des.




Cheers

Alex





On Tue, Apr 3, 2012 at 17:55, Brian Bennion bennion1=3D-=3Dllnl.gov

<owner-chemistry[*]ccl.net<=
/a>> =A0wrote:



Sent to CCL by: "Brian =A0Bennion" [bennion1=3Dllnl.gov]

Hello,



Does anyone have/know of code to parse pdf tables for chemical structure an=
d 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 simbiosis.


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



I want to populate a repository with chemical structures and annotate the e=
ntries with the activity data given in an associated table located in the s=
ame pdf document.



Thanks

Brian>













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-- 
=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D
Jesse Gordon
Application Scientist
Dotmatics Limited
400 West Cummings Park #5450, Woburn MA 01801=



T: +1 781-305-3114
M: +1-617-320-6989
Skype: jessegordon
=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D


=A0
See the latest in Dotmatics Suite of Solutions at:
=

Booth # 11 CHI Drug Discovery Chemistry, April 17-19, 2012, Hilton San=
 Diego Resort & Spa, San Diego, CA, www.drugdiscoverychemistry.com


Booth # 323 Bio-IT World Conference, April 24-26, 2012, World Trade ce=
nter,=A0 Boston,=A0 MA, www.bio-itworldexpo.com




-- =

Disclaimer: This electronic mail and its attachments are intended solely =
for
the person(s) to whom they are addressed and contain information which is=
 =

confidential or otherwise protected from disclosure, except for the purpo=
se
for which they are intended. Dissemination, distribution, or reproduction=
 by
anyone other than the intended recipients is prohibited and may be illega=
l.
If you are not an intended recipient, please immediately inform the sende=
r
and return the electronic mail and its attachments and destroy any copies=

which may be in your possession. Dotmatics Limited screens electronic mai=
ls
for viruses but does not warrant that this electronic mail is free of any=

viruses. Dotmatics Limited accepts no liability for any damage caused by
any virus transmitted by this electronic mail. Dotmatics Limited is =

registered in England & Wales No. 5614524 with offices at The Old Monaste=
ry, =

Windhill, Bishops Stortford, Herts, CM23 2ND, UK.
=0D
--f46d040713dd14b52504bd01682a--


From owner-chemistry@ccl.net Fri Apr  6 11:09:01 2012
From: "Karol M. Langner karol.langner::gmail.com" 
To: CCL
Subject: CCL: MDMM 2012 early bird extension
Message-Id: <-46649-120406085029-9216-xiFyMKCToXs3CUpOIXFcjg : server.ccl.net>
X-Original-From: "Karol M. Langner" 
Date: Fri, 6 Apr 2012 08:50:26 -0400


Sent to CCL by: "Karol M. Langner" [karol.langner(a)gmail.com]
Dear Collegues,

Due to popular request, we are extending the early bird registration
deadline for MDMM 2012 to April 15th. 

Also, note that the number of participants is limited by the capacity
of our lecture rooms, and applications will be accepted on
a "first paid" basis.

For more information, including registration and an updated list
of speakers, please visit www.mdmm.pl/2012

Sincerely yours,
MDMM2012 organizing committee


From owner-chemistry@ccl.net Fri Apr  6 13:10:01 2012
From: "Jim Kress ccl_nospam---kressworks.com" 
To: CCL
Subject: CCL: Hydrophobic interaction - precise answer
Message-Id: <-46650-120406130833-27457-FODmIU5Hak10QmcKSfHBig(0)server.ccl.net>
X-Original-From: "Jim Kress" 
Content-Language: en-us
Content-Transfer-Encoding: 8bit
Content-Type: text/plain;
	charset="iso-8859-1"
Date: Fri, 6 Apr 2012 13:08:12 -0400
MIME-Version: 1.0


Sent to CCL by: "Jim Kress" [ccl_nospam#,#kressworks.com]
Good answer, as usual from Andreas.

Jim

> -----Original Message-----
> From: owner-chemistry+ccl_nospam==kressworks.com]_[ccl.net
> [mailto:owner-chemistry+ccl_nospam==kressworks.com]_[ccl.net] On Behalf
> Of Andreas Klamt klamt.]_[.cosmologic.de
> Sent: Friday, April 06, 2012 2:10 AM
> To: Kress, Jim 
> Subject: CCL: Hydrophobic interaction - precise answer
> 
> 
> Sent to CCL by: Andreas Klamt [klamt**cosmologic.de] You are absolutely
> right being surprised by the expression "hydrophobic
> interaction": Although this is widely used, we first should clearly state,
that
> from a physics point of view such an interaction does not exist.
> 
> What people mean by this is the repulsion of non- or slightly polar
surface
> area (e.g. CH2, CH3, little bit less benzen rings, alkenes, chloro, bromo,
jodo
> groups) by water. Thermodynamically such molecular surface is much better
> solvated by any other solvent than water.
> Therefore people call this repulsion hydrophobicity.
>  From a physicochemical point of view this comes from the fact, that in a
> liquid all polar surfaces pieces like to have polar surface pieces of the
other
> sign (i.e. positive likes negative) as direct contact partners.  As can be
very
> nicely visualized within my COSMO-RS theory, water has a uniquely good
> balance of very positive and very negative surface, and only a small
amount
> of non-polar surface area. Therefore in pure water we have very good and
> strong  contacts between the polar surfaces, even forming hydrogen bonds
> with each other.  If you now try to brig a non-polar piece of surface into
this
> ensemble, it either has to break the strong polar contacts (which is
rather
> impossible at room temperature), or it has to pick the very few non-polar
> surface segments (green in my sigma surfaces). It can rather do only the
> latter at room temperature. But pickig the few non-polar ones means a
large
> loss of entropy, compared to the situation of the the non-polar surface in
> another solvent. And this loss of entropy causes a large positive free
energy
> of the non-polar pieces in water.
> 
> That is the hydrophobic effect: It is an entropic effect! Experimentally
this
> can be demonstrated based on the fact that the solubility of alkanes in
water
> has a minimum at room temperature, meaning that the enthalpy of transfer
> is zero, and the whole free energy of transfer of alkane into water is of
> entropic nature.
> 
> Hope this helps. Perhaps see sigma profiles and surfaces on our web page
> www.COSMOlogic.de
> 
> Best regards
> 
> Andreas
> 
> 
> 
> Am 05.04.2012 22:37, schrieb A. anglea a.anglea90*o*yahoo.com:
> > 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.>
> >
> >
> 
> 
> --
> Prof. Dr. Andreas Klamt
> CEO / Geschäftsführer
> COSMOlogic GmbH&  Co. KG
> Burscheider Strasse 515
> D-51381 Leverkusen, Germany
> 
> phone  	+49-2171-731681
> fax    	+49-2171-731689
> e-mail 	klamt#,#cosmologic.de
> web    	www.cosmologic.de
> 
> [University address:      Inst. of Physical and
> Theoretical Chemistry, University of Regensburg]
> 
> Join us at the 4th-COSMO-RS-Symposium April 2013 Details at
> www.cosmologic.de/symposium2013
> 
> HRA 20653 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt
> Komplementaer: COSMOlogic Verwaltungs GmbH HRB 49501 Amtsgericht
> Koeln, GF: Prof. Dr. Andreas KlamtTo
> recover the email address of the author of the message, please change the
> strange characters on the top line to the ]_[ sign. You can also look up the
X-
> Original-From: line in the mail header.>


From owner-chemistry@ccl.net Fri Apr  6 16:14:00 2012
From: "John Gunn jgunn]*[mailaps.org" 
To: CCL
Subject: CCL: Hydrophobic interaction - precise answer
Message-Id: <-46651-120406092839-12180-KaY3O9JjCUb0BClTSpjHFw^^server.ccl.net>
X-Original-From: John Gunn 
Content-Disposition: inline
Content-Type: text/plain; charset=us-ascii
Date: Fri, 6 Apr 2012 09:28:53 -0400
Mime-Version: 1.0


Sent to CCL by: John Gunn [jgunn+/-mailaps.org]
> You are absolutely right being surprised by the expression "hydrophobic 
> interaction": Although this is widely used, we first should clearly 
> state, that from a physics point of view such an interaction does not exist.

I wouldn't go that far.  Of course you are right in the description of the
entropic effect, but it can still be a useful concept.
 
> What people mean by this is the repulsion of non- or slightly polar 
> surface area (e.g. CH2, CH3, little bit less benzen rings, alkenes, 
> chloro, bromo, jodo groups) by water.

Actually, people often use this to refer to an effective attraction between
non-polar solutes due to the water entropy.  You can define a potential
of mean force like this:

phi(r_1,r_2) = -kTln[ (1/Z(R))int(dR) exp(-beta*E(r_1,r_2,R)) ] - U(r_1,r_2)

where r_i is the position of solute i and R is the configuration of all water
molecules and E is the energy of the entire system, in other words a pair
correlation function for the solute.  Note that phi=0 if E=U(r_1,r_2)+U(R).
Of course this implies an implicit-solvent model, but it can be used as an
empirical correction for MM forcefields, often based on surface area for the
reasons you described.

-John.


From owner-chemistry@ccl.net Fri Apr  6 17:47:00 2012
From: "Mezei, Mihaly mihaly.mezei###mssm.edu" 
To: CCL
Subject: CCL: Hydrophobic interaction - precise answer
Message-Id: <-46652-120406174512-12896-tZcOuntb3vVg6RwthIMQog,server.ccl.net>
X-Original-From: "Mezei, Mihaly" 
Content-Language: en-US
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset="us-ascii"
Date: Fri, 6 Apr 2012 21:45:03 +0000
MIME-Version: 1.0


Sent to CCL by: "Mezei, Mihaly" [mihaly.mezei,+,mssm.edu]
I was about to make this point as well. Especially since potential of men force between two methanes obtained from explicit water simulations show definite minima as well.

Mihaly Mezei

Department of Structural and Chemical Biology, Mount Sinai School of Medicine
Voice:  (212) 659-5475   Fax: (212) 849-2456
WWW (MSSM home): http://www.mountsinai.org/Find%20A%20Faculty/profile.do?id=0000072500001497192632
WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei
WWW (Department): http://atlas.physbio.mssm.edu
____________________________________
> From: owner-chemistry+mihaly.mezei==mssm.edu()ccl.net [owner-chemistry+mihaly.mezei==mssm.edu()ccl.net] on behalf of John Gunn jgunn]*[mailaps.org [owner-chemistry()ccl.net]
Sent: Friday, April 06, 2012 9:28 AM
To: Mezei, Mihaly
Subject: CCL: Hydrophobic interaction - precise answer

Actually, people often use this to refer to an effective attraction between
non-polar solutes due to the water entropy.  You can define a potential
of mean force like this:

phi(r_1,r_2) = -kTln[ (1/Z(R))int(dR) exp(-beta*E(r_1,r_2,R)) ] - U(r_1,r_2)

where r_i is the position of solute i and R is the configuration of all water
molecules and E is the energy of the entire system, in other words a pair
correlation function for the solute.  Note that phi=0 if E=U(r_1,r_2)+U(R).
Of course this implies an implicit-solvent model, but it can be used as an
empirical correction for MM forcefields, often based on surface area for the
reasons you described.

-John.


From owner-chemistry@ccl.net Fri Apr  6 18:38:01 2012
From: "Troy Wymore wymore%x%psc.edu" 
To: CCL
Subject: CCL: Workshop: Computer Simulation of Biomolecular Dynamics and Reactions
Message-Id: <-46653-120406180530-24866-zMILTpvmv9mlYVcLy9F7tA::server.ccl.net>
X-Original-From: "Troy  Wymore" 
Date: Fri, 6 Apr 2012 18:05:26 -0400


Sent to CCL by: "Troy  Wymore" [wymore/./psc.edu]
The National Resource for Biomedical Supercomputing at the Pittsburgh Supercomputing Center will host a workshop entitled:

Computer Simulation of Biomolecular Dynamics and Reactions

Workshop Dates:  Tuesday, June 5 - Friday, June 8, 2012

Location: Pittsburgh Supercomputing Center

Registration Deadline:  May 8th, 2012

Registration site: 
http://www.nrbsc.org/education/workshops/biomolecular_simulations_2012/

A PDF file that contains further information and a tentative agenda is also available at the registration site.

The workshop will present computational approaches for the simulation of biomolecular dynamics and reactions. Lectures will be held on the relevant theoretical background including the prediction and analysis of protein dynamics using normal mode analyses (NMA) and elastic network models (ENM), molecular mechanics (MM) force field parameterization of small molecules, the applicability of different Quantum Chemical (QC) methods for large molecules, re-parameterization strategies for improving Semiempirical Molecular Orbital (SMO) methods for specific reactions, and hybrid QC/MM potential energy functions and simulation techniques on high performance computers.  In-depth tutorials will be presented on applying and interpreting the results from ENM-based NMA using ProDy (www.csb.pitt.edu/prody) developed in Prof. Ivet Bahars lab, MM force field parameterization of small molecules within the CHARMM/CGenFF protocol using a newly developed toolkit ParamIT, developing corrections to SMO methods for use in quantitatively-accurate QC/MM free energy simulations, constructing a QC/MM model including pDynamos interface to ORCA, and the various methods for generating energy profiles of bio-molecular reactions to determine mechanisms and structure-function relationships employing the freely available pDynamo package (www.pdynamo.org) developed in the lab of Dr. Martin J. Field. Graphical user interfaces in Pymol and VMD for QC/MM model construction will also be demonstrated. Experience with pDynamo is helpful but not a prerequisite for attendance.  

The workshop is designed for graduate students, post-doctoral researchers and faculty in computational biophysics and physical organic chemistry who have experience with computational chemistry methods and seek to enhance their capabilities to include the modeling of enzymatic reactions. Participants are encouraged to discuss and work on bio-molecular systems from their own research during the workshop.   

Space is limited. 

This workshop is supported by the NIH-National Center for Research Resources. 

Instructors include:

Martin J. Field (Institute of Structural Biology, Grenoble, France)
Timothy Lezon (University of Pittsburgh Medical School)
Ahmet Bakan (University of Pittsburgh Medical School)
Nikolay Simakov (Pittsburgh Supercomputing Center/NRBSC)
Jose Fernando Bachega (University of Sao Paulo)
Troy Wymore (Pittsburgh Supercomputing Center/NRBSC)

Registration will be free of charge for attendees from non-profit academic institutions. Participants are expected to cover their own travel and housing expenses.

If you have any questions, please contact Troy Wymore (wymore^psc.edu)