From owner-chemistry@ccl.net Mon Mar 19 07:19:01 2007
From: "Alex Allardyce aa() chemaxon.com" <owner-chemistry]![server.ccl.net>
To: CCL
Subject: CCL: Second call for papers: ChemAxon's 2007 User Group Meeting and Training Day, June 13-14 and June 12, Budapest, Hungary
Message-Id: <-33830-070319071411-24329-NTUNpc5PjXoJlHlL7cdmaA]![server.ccl.net>
X-Original-From: Alex Allardyce <aa[-]chemaxon.com>
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Sent to CCL by: Alex Allardyce [aa##chemaxon.com]
Hi,

Please excuse multiple postings

ChemAxon's 2007 User Group Meeting will be held on Wednesday and 
Thursday, June 13-14 at the Gellert Hotel Spa in Budapest, Hungary. The 
meeting will preceded by a training day on June 12.

The User Group Meeting will feature oral and poster presentations from 
ChemAxon users, scientists and developers as well as several social 
events to mix and speak with staff and peers.

We are inviting those interested in presenting at the meeting to submit 
abstracts for review. The deadline for receipt of oral abstracts is 
March 26th and June 1st for poster abstracts. To find out more and 
submit your abstract please visit: 
http://www.chemaxon.com/UGM/07/index.html

The training day will give hands on experience with ChemAxon end user 
applications to take attendees through common tasks in the discovery and 
optimization process. Closing the training day we will have an open 
session "Live FAQ" for all meeting attendees.

We hope you can participate in what has proven to be a most interesting 
and enjoyable cheminformatics event.

See you there.

Alex

-- 
Alex Allardyce
Dir. Marketing, ChemAxon
Cell-US: 1-857-544-0541
skype: alex_allardyce


From owner-chemistry@ccl.net Mon Mar 19 08:40:01 2007
From: "Cross, Simon scross{=}tripos.com" <owner-chemistry * server.ccl.net>
To: CCL
Subject: CCL: Babel problem (?)
Message-Id: <-33831-070319055404-18010-W6JwP/u5Itz7S7Bx7y0iGQ * server.ccl.net>
X-Original-From: "Cross, Simon" <scross::tripos.com>
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Sent to CCL by: "Cross, Simon" [scross_-_tripos.com]
Martin, I'm not sure what the Babel problem is, but a simple alternative
would be to import the SDF directly into the SYBYL spreadsheet. Even
simpler would be to select SDF as the ligand input file format from the
docking interface.

If it is command-line translation you are after, SYBYL's dbtranslate
utility should also be available to you.

Regards,

Simon

------------------------------------
Dr Simon Cross                                      
Product Manager                
Tripos UK Ltd                                 
scross-#-tripos.com
Tel +44 1908 650021
Mob +44 7980 572278
Fax +44 1908 650001
------------------------------------
SYBYL, UNITY, and other products are exclusive property of Tripos & are
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-----Original Message-----
> From: owner-chemistry-#-ccl.net [mailto:owner-chemistry-#-ccl.net] 
Sent: Friday, March 16, 2007 5:16 PM
To: Cross, Simon
Subject: CCL: Babel problem (?)


Sent to CCL by: "Martin  Lindh" [martinlindh-$-yahoo.se]
Hi

I prepare ligands using LigPrep (Maestro). Since I want to dock these
ligands
in FlexX (Sybyl), I export the ligands from Maestro as a .sdf file. I
then
use Babel to convert the .sdf file to a multi .mol2 file. The .mol2 file
is
then imported into Sybyl. 

During this process some(!) of the ligands get strange mol2 formating.

Part of a molecule that is translated correctly into the mol2-file:
[A]<TRIPOS>ATOM
1 P1    -7.7746    0.3497    0.1484 P.3   	1  <1>         0.1085
2 O1    -7.2207    1.7666   -0.1209 O.2     	1  <1>        -0.4607
3 O2    -7.9571   -0.5515   -1.0931 O.co2   	1  <1>        -0.3575

Part of a molecule that is NOT translated correctly in mol2-file:

28 C         14.2736    6.1106   -1.8492 C.ar    0  UNK0        0.1493
29 N         14.3973    5.3090   -0.7250 N.ar    0  UNK0       -0.2079
30 N         13.7198    8.3248   -1.0353 N.pl3   0  UNK0       -0.3413
31 C1*       15.1231    2.8403   -3.4280 C.3     1  UNK1        0.1683
32 O4*       15.0326    3.1353   -4.7858 O.3     1  UNK1       -0.3456
33 C4*       13.7316    2.8114   -5.2536 C.3     1  UNK1        0.1126

Anyone seen this problem and have suggestions of what to do?

Thank you in advance
Martinhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt

From owner-chemistry@ccl.net Mon Mar 19 09:15:02 2007
From: "Igor Novak inovak[]csu.edu.au" <owner-chemistry^server.ccl.net>
To: CCL
Subject: CCL:G: Gaussian 03 under SuSE linux 10.1
Message-Id: <-33832-070319023722-2665-5cY3l86rit5A2Rgsg74OWQ^server.ccl.net>
X-Original-From: "Igor  Novak" <inovak*csu.edu.au>
Date: Mon, 19 Mar 2007 02:37:18 -0400


Sent to CCL by: "Igor  Novak" [inovak##csu.edu.au]
Dear netters,
I am running Gaussian 03 under SuSE 64-bit linux 10.1. My new system has 4GB RAM, AMD64 Athlon CPU, 300GB HD. When running G3B3 job containing 7 heavy atoms (diazide) it goes through OK. When I add two more azide groups (tetraazide) the job starts to access HD continuously (light is on all the time) or aborts without any error message in the output. The same tetraazide input on an older PC with identical specifications 300GB HD, 4GB RAM, SuSE linux 10.1, goes through OK.  
Has anyone else experienced similar hardware problems?
I would be grateful for any suggestions.

Regards
I.Novak
Charles Sturt University
Orange NSW, Australia


From owner-chemistry@ccl.net Mon Mar 19 10:36:01 2007
From: "Geoffrey Hutchison grh25]*[cornell.edu" <owner-chemistry---server.ccl.net>
To: CCL
Subject: CCL: Babel problem (?)
Message-Id: <-33833-070319102843-9394-n7GvuWHlafkbL+ZVFjvEpw---server.ccl.net>
X-Original-From: Geoffrey Hutchison <grh25..cornell.edu>
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Sent to CCL by: Geoffrey Hutchison [grh25:_:cornell.edu]

> I prepare ligands using LigPrep (Maestro). Since I want to dock  
> these ligands
> in FlexX (Sybyl), I export the ligands from Maestro as a .sdf file.  
> I then
> use Babel to convert the .sdf file to a multi .mol2 file. The .mol2  
> file is
> then imported into Sybyl.
>
> During this process some(!) of the ligands get strange mol2 formating.

You don't mention what version of Babel you're using, but I'll take a  
guess that it's some version of Open Babel. (Old versions of babel  
don't even attempt to assign chain/residue information.)

There are several ways to report problems with Open Babel. We have  
our own mailing lists, and you can easily post questions here:
http://openbabel.sourceforge.net/wiki/Mailing_lists

In this case, it looks like a bug, so I strongly suggest you report  
it to the bug tracker (ideally with a test file):
http://sourceforge.net/tracker/?atid=428740&group_id=40728&func=browse

My guess is that this is related to a bug I fixed last week, but it  
would be very helpful to have a file to test.

Thanks,
-Geoff

--
-Dr. Geoffrey Hutchison        <grh25^-^cornell.edu>
Cornell University, Department of Chemistry and Chemical Biology
Abruņa Group                http://abruna.chem.cornell.edu/


From owner-chemistry@ccl.net Mon Mar 19 11:15:01 2007
From: "Kalaiselvan Anbarasan kalaianbaccl ~ gmail.com" <owner-chemistry__server.ccl.net>
To: CCL
Subject: CCL: ADF - error
Message-Id: <-33834-070319111211-26972-xbItW1+VDHdwJx0tg2R2Lg__server.ccl.net>
X-Original-From: "Kalaiselvan  Anbarasan" <kalaianbaccl a gmail.com>
Date: Mon, 19 Mar 2007 11:12:07 -0400


Sent to CCL by: "Kalaiselvan  Anbarasan" [kalaianbaccl---gmail.com]
Hello,
In ADF, during the numerical frequency calculation after few geometry updates i got the error as MakeAOIndex.
Can anyone suggest me, the type of error and how to overcome it.

Thank you in advance,

Kalaiselvan


From owner-chemistry@ccl.net Mon Mar 19 12:17:01 2007
From: "Dan Maftei dan.maftei/a\chem.uaic.ro" <owner-chemistry[]server.ccl.net>
To: CCL
Subject: CCL:G: Gaussian 03 under SuSE linux 10.1
Message-Id: <-33835-070319105642-19190-d/2jGWKT4UoMSAmG4rFWjw[]server.ccl.net>
X-Original-From: Dan Maftei <dan.maftei[#]chem.uaic.ro>
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Date: Mon, 19 Mar 2007 16:54:26 +0200
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Sent to CCL by: Dan Maftei [dan.maftei{}chem.uaic.ro]
This is a multi-part message in MIME format.
--------------040902080705030404050303
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Content-Transfer-Encoding: 7bit

On the 64bit machine (the one generating the problem) try "dmesg". If 
may be a G03/l1.exe problem (check for segfaults, invalid instructions 
etc.) If g03 was compiled with the AMD64 switch on
(i. e. pgf77 -tp k8-64) you may encounter this kind of problems.


Igor Novak inovak[]csu.edu.au wrote:
> Sent to CCL by: "Igor  Novak" [inovak##csu.edu.au]
> Dear netters,
> I am running Gaussian 03 under SuSE 64-bit linux 10.1. My new system has 4GB RAM, AMD64 Athlon CPU, 300GB HD. When running G3B3 job containing 7 heavy atoms (diazide) it goes through OK. When I add two more azide groups (tetraazide) the job starts to access HD continuously (light is on all the time) or aborts without any error message in the output. The same tetraazide input on an older PC with identical specifications 300GB HD, 4GB RAM, SuSE linux 10.1, goes through OK.  
> Has anyone else experienced similar hardware problems?
> I would be grateful for any suggestions.
> 
> Regards
> I.Novak
> Charles Sturt University
> Orange NSW, Australia> 
> 
> 
> 


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fn:Dan Maftei
n:Maftei;Dan
org:"Alexandru Ioan Cuza" University;Physical, Theoretical and Materials Chemistry
adr:Nr. 11;;Bd. Carol 1, ;Iasi;;700506;Romania
email;internet:dan.maftei=chem.uaic.ro
title:Faculty of Chemistry
tel;work:+40232-201307
tel;cell:+40740-262227
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url:http://www.chem.uaic.ro/~danmaftei
version:2.1
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--------------040902080705030404050303--


From owner-chemistry@ccl.net Mon Mar 19 14:40:00 2007
From: "Jozsef Csontos jozsefcsontos * creighton.edu" <owner-chemistry-#-server.ccl.net>
To: CCL
Subject: CCL:G: Gaussian 03 under SuSE linux 10.1
Message-Id: <-33836-070319105240-17163-jG+2aJsEGotFu9VG/hR7PA-#-server.ccl.net>
X-Original-From: Jozsef Csontos <jozsefcsontos(-)creighton.edu>
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Date: Mon, 19 Mar 2007 09:52:21 -0500
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Sent to CCL by: Jozsef Csontos [jozsefcsontos=creighton.edu]
Hi,

if your older configuration is a 32bit system then the difference is
that the 64bit one needs two times of memory for the same job because of
the 64bit memory addressing. This could be the source of the intensive
harddisk I/O access.

This would be my guess, I hope it helps,
Jozsef
On Mon, 2007-03-19 at 02:37 -0400, Igor Novak inovak[]csu.edu.au wrote:
> Sent to CCL by: "Igor  Novak" [inovak##csu.edu.au]
> Dear netters,
> I am running Gaussian 03 under SuSE 64-bit linux 10.1. My new system has 4GB RAM, AMD64 Athlon CPU, 300GB HD. When running G3B3 job containing 7 heavy atoms (diazide) it goes through OK. When I add two more azide groups (tetraazide) the job starts to access HD continuously (light is on all the time) or aborts without any error message in the output. The same tetraazide input on an older PC with identical specifications 300GB HD, 4GB RAM, SuSE linux 10.1, goes through OK.  
> Has anyone else experienced similar hardware problems?
> I would be grateful for any suggestions.
> 
> Regards
> I.Novak
> Charles Sturt University
> Orange NSW, Australia> 
> 
> 
-- 
Jozsef Csontos, Ph.D.

(jozsefcsontos_at_creighton.edu)
Department of Biomedical Sciences
Creighton University,
Omaha, NE


From owner-chemistry@ccl.net Mon Mar 19 15:55:02 2007
From: "Stan van Gisbergen vangisbergen(~)scm.com" <owner-chemistry+*+server.ccl.net>
To: CCL
Subject: CCL: ADF - error
Message-Id: <-33837-070319131622-25168-8jiVtsqljuZtRc5Gs2Jbrw+*+server.ccl.net>
X-Original-From: Stan van Gisbergen <vangisbergen^scm.com>
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Sent to CCL by: Stan van Gisbergen [vangisbergen-$-scm.com]

--Apple-Mail-135-592645138
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Dear Kalaiselvan,

Please send any ADF-related questions to our support E-mail address  
support++scm.com
or post it on our ADF user forum on our website www.scm.com. You will  
then quickly get an answer.

Thank you.

Best regards,
Stan van Gisbergen

On Mar 19, 2007, at 4:12 PM, Kalaiselvan Anbarasan kalaianbaccl ~  
gmail.com wrote:

>
> Sent to CCL by: "Kalaiselvan  Anbarasan" [kalaianbaccl---gmail.com]
> Hello,
> In ADF, during the numerical frequency calculation after few  
> geometry updates i got the error as MakeAOIndex.
> Can anyone suggest me, the type of error and how to overcome it.
>
> Thank you in advance,
>
> Kalaiselvan
>
>
>
> -= This is automatically added to each message by the mailing  
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Dr. S.J.A. van Gisbergen
Scientific Computing & Modelling NV
Theoretical Chemistry, Vrije Universiteit
De Boelelaan 1083
1081 HV Amsterdam
The Netherlands
vangisbergen++scm.com
http://www.scm.com
T: +31-20-5987626
F: +31-20-5987629


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<HTML><BODY style=3D"word-wrap: break-word; -khtml-nbsp-mode: space; =
-khtml-line-break: after-white-space; ">Dear Kalaiselvan,=A0<DIV><BR =
class=3D"khtml-block-placeholder"></DIV><DIV>Please send any ADF-related =
questions to our support E-mail address <A =
href=3D"mailto:support++scm.com">support++scm.com</A></DIV><DIV>or post it =
on our ADF user forum on our website <A =
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19, 2007, at 4:12 PM, Kalaiselvan Anbarasan kalaianbaccl ~ gmail.com =
wrote:</DIV><BR class=3D"Apple-interchange-newline"><BLOCKQUOTE =
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[kalaianbaccl---gmail.com]</DIV><DIV style=3D"margin-top: 0px; =
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">Hello,</DIV><DIV style=3D"margin-top: 0px; margin-right: 0px; =
margin-bottom: 0px; margin-left: 0px; ">In ADF, during the numerical =
frequency calculation after few geometry updates i got the error as =
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--Apple-Mail-135-592645138--


From owner-chemistry@ccl.net Mon Mar 19 16:30:01 2007
From: "aa aa**chemaxon.hu" <owner-chemistry,server.ccl.net>
To: CCL
Subject: CCL: program to split sdf file
Message-Id: <-33838-070319112907-8026-QTFxv2D0Qumo+vtFwUoKQQ,server.ccl.net>
X-Original-From: aa <aa**chemaxon.hu>
Content-Type: multipart/alternative;
 boundary="------------010709000102070601030800"
Date: Mon, 19 Mar 2007 10:36:18 -0400
MIME-Version: 1.0


Sent to CCL by: aa [aa : chemaxon.hu]
This is a multi-part message in MIME format.
--------------010709000102070601030800
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Content-Transfer-Encoding: 7bit

HI,

Unix has loads of ways of doing this, some of which have already been 
suggested.
But, if you want a more graphical way of doing things then you might 
want to look a ChemAxon's Instant JChem 
(http://www.chemaxon.com/product/ijc.html) which lets you easily view 
and query chemical data imported from an SD file.

The data can be queried (in your case, just for IDs 1-3,000 etc, but 
much more complex queries are possible) and then the results exported to 
a SD file.

And yes, it is free!
Alex

Fan,Huajun hjfan^^^pvamu.edu wrote:
>
> Hi, Does anyone know any programs (preferably free) that can split a 
> big sdf file into smaller files? I got a sdf file containing 30,000 
> molecules and want to do a DOCK5. It is too big even to read it 
> through. I want to split it into 10 samller files that contains 3,000 
> each. Is it possible? The newest version of Babel seems not available 
> of this split function for SDF format.
>
>  
>
> Thanks in advance.
>
>  
>
> **Hua-Jun **
>
>  
>

--------------010709000102070601030800
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: 7bit

<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
  <meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type">
</head>
<body bgcolor="#ffffff" text="#000000">
HI,<br>
<br>
Unix has loads of ways of doing this, some of which have already been
suggested.
<br>
But, if you want a more graphical way of doing things then you might
want to look a ChemAxon's Instant JChem (<a
 class="moz-txt-link-freetext"
 href="http://www.chemaxon.com/product/ijc.html">http://www.chemaxon.com/product/ijc.html</a>)
which lets you easily view and query chemical data imported from an SD
file.
<br>
<br>
The data can be queried (in your case, just for IDs 1-3,000 etc, but
much more complex queries are possible) and then the results exported
to a SD file.
<br>
<br>
And yes, it is free!
<br>
Alex<br>
<br>
Fan,Huajun hjfan^^^pvamu.edu wrote:
<blockquote
 cite="mid-id%233d2-33812-070316013849-17333-Opfp0RYGtTO3gCZ2VNCYdg||server.ccl.net"
 type="cite">
  <meta http-equiv="Content-Type" content="text/html; ">
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  <div class="Section1">
  <p class="MsoNormal"><font face="Arial" size="2"><span
 style="font-size: 10pt; font-family: Arial;">Hi, Does anyone know any
programs (preferably free) that can
split a big sdf file into smaller files? I got a sdf file containing
30,000
molecules and want to do a DOCK5. It is too big even to read it
through. I want
to split it into 10 samller files that contains 3,000 each. Is it
possible<font color="navy"><span style="color: navy;">? The newest
version of <st1:City w:st="on"><st1:place w:st="on">Babel</st1:place></st1:City>
seems not available of this split function
for SDF format.</span></font><o:p></o:p></span></font></p>
  <p class="MsoNormal"><font face="Arial" size="2"><span
 style="font-size: 10pt; font-family: Arial;"><o:p>&nbsp;</o:p></span></font></p>
  <p class="MsoNormal"><font face="Arial" size="2"><span
 style="font-size: 10pt; font-family: Arial;">Thanks in advance.<o:p></o:p></span></font></p>
  <p class="MsoNormal"><font face="Arial" size="2"><span
 style="font-size: 10pt; font-family: Arial;"><o:p>&nbsp;</o:p></span></font></p>
  <div id="idSignature87372">
  <div>
  <div>
  <p class="MsoNormal"><strong><b><font color="navy" face="Arial"
 size="2"><span
 style="font-size: 10pt; font-family: Arial; color: navy;">Hua-Jun </span></font></b></strong><font
 color="black" face="Arial" size="2"><span
 style="font-size: 10pt; font-family: Arial; color: black;"><o:p></o:p></span></font></p>
  </div>
  </div>
  </div>
  <p class="MsoNormal"><font face="Times New Roman" size="3"><span
 style="font-size: 12pt;"><o:p>&nbsp;</o:p></span></font></p>
  </div>
</blockquote>
</body>
</html>

--------------010709000102070601030800--


From owner-chemistry@ccl.net Mon Mar 19 20:31:00 2007
From: "Iain MacDougall iain.macdougall##studentmail.newcastle.edu.au" <owner-chemistry:+:server.ccl.net>
To: CCL
Subject: CCL: comparing database results
Message-Id: <-33839-070319202054-27459-0TPh7aCun2NxYKmI5//6Yg:+:server.ccl.net>
X-Original-From: "Iain  MacDougall" <iain.macdougall*o*studentmail.newcastle.edu.au>
Date: Mon, 19 Mar 2007 20:20:50 -0400


Sent to CCL by: "Iain  MacDougall" [iain.macdougall\a/studentmail.newcastle.edu.au]
I have two sets of compounds from in silico database searching. I have compared the compounds and have found that none are identical, however I wish to find similar hits as well. I can do this by eye for small numbers of hits but this will be impossible for some of my larger hitlists. Does anyone know of freeware that will do some kind of structural comparison/similarity searching for me?
Thanks for your help!


From owner-chemistry@ccl.net Mon Mar 19 22:13:01 2007
From: "Wolf-D. Ihlenfeldt wdi{:}xemistry.com" <owner-chemistry*server.ccl.net>
To: CCL
Subject: CCL: comparing database results
Message-Id: <-33840-070319220912-26233-Zl0gDvQ6g/4cmzGe+c/ohg*server.ccl.net>
X-Original-From: "Wolf-D. Ihlenfeldt" <wdi##xemistry.com>
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Sent to CCL by: "Wolf-D. Ihlenfeldt" [wdi~~xemistry.com]

Hi Iain,

that can easily be done with a small CACTVS script (CACTVS is free for
academic use). In what format do you have your data, and what kind of
similarity criterion do you want to use?


> -----Original Message-----
> From: owner-chemistry_-_ccl.net [mailto:owner-chemistry_-_ccl.net] 
> Sent: Monday, March 19, 2007 8:21 PM
> To: Ihlenfeldt, W.d. 
> Subject: CCL: comparing database results
> 
> 
> Sent to CCL by: "Iain  MacDougall" 
> [iain.macdougall\a/studentmail.newcastle.edu.au]
> I have two sets of compounds from in silico database 
> searching. I have compared the compounds and have found that 
> none are identical, however I wish to find similar hits as 
> well. I can do this by eye for small numbers of hits but this 
> will be impossible for some of my larger hitlists. Does 
> anyone know of freeware that will do some kind of structural 
> comparison/similarity searching for me?
> Thanks for your help!
> 
> 
> 
> -= This is automatically added to each message by the mailing 
> script =- To recover the email address of the author of the 
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>


From owner-chemistry@ccl.net Mon Mar 19 22:47:01 2007
From: "Brunsteiner, Michael micb+*+uic.edu" <owner-chemistry**server.ccl.net>
To: CCL
Subject: CCL: comparing database results
Message-Id: <-33841-070319212448-20660-FHsR0kEfpNMolHKgY9NF9g**server.ccl.net>
X-Original-From: "Brunsteiner, Michael" <micb__uic.edu>
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Date: Mon, 19 Mar 2007 20:24:28 -0500 (CDT)
MIME-Version: 1.0


Sent to CCL by: "Brunsteiner, Michael" [micb^_^uic.edu]
On Mon, March 19, 2007 19:20, Iain MacDougall
iain.macdougall##studentmail.newcastle.edu.au wrote:
>
> Sent to CCL by: "Iain  MacDougall"
> [iain.macdougall\a/studentmail.newcastle.edu.au]
> I have two sets of compounds from in silico database searching. I have
> compared the compounds and have found that none are identical, however I
> wish to find similar hits as well. I can do this by eye for small numbers
> of hits but this will be impossible for some of my larger hitlists. Does
> anyone know of freeware that will do some kind of structural
> comparison/similarity searching for me?
> Thanks for your help!

you might want to have a look at ROCS
(http://www.eyesopen.com/docs/html/rocs/)
> from openeye, its free for academia.
mic


From owner-chemistry@ccl.net Mon Mar 19 23:42:01 2007
From: "Wolf-D. Ihlenfeldt wdi=xemistry.com" <owner-chemistry/./server.ccl.net>
To: CCL
Subject: CCL: program to split sdf file
Message-Id: <-33842-070319234024-13232-soHYqi9usu+Ci4/M6g4sHA/./server.ccl.net>
X-Original-From: "Wolf-D. Ihlenfeldt" <wdi---xemistry.com>
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Sent to CCL by: "Wolf-D. Ihlenfeldt" [wdi|a|xemistry.com]
This message is in MIME format. Since your mail reader does not understand
this format, some or all of this message may not be legible.

------=_NextPart_000_0AF8_01C76A7F.E91421B0
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There have now been quite a number of helpful suggestions on how to perform
the split - but none of them are really robust, which is essential if files
become too big for visual inspection of the results. Remember: Murphy lives!
 
Take the following completely legal SD file record:
 
----

  -ISIS-  03190722292D
$$$$
  1  0  0  0  0  0  0  0  0  0999 V2000
   -2.3167   -0.2167    0.0000 Au  0  0  0  1  0  0  1  0  0  0  0  0
M  END
> <PRICE>
$$$$
 
$$$$
------
 
This is a single record,  with multiple "$$$$" in places where they are
*not* record terminators. All simple string search methods with awk or
similar tools which simply look for the $$$$ line will fail on this. Never
assume that such records do not exist. I *have* seen $$$$ in SD data lines
before.
 
A record splitter thus needs more chemical intelligence to process such
files. 
 
OpenBabel has been suggested for problem. There are several problems with
that proposal:
a) It does not scale to really big files, because Babel has no method to
output multiple files. Every batch is a separate command and needs to skip
to the first copy position. Not a problem with a few thousand cpds, but
ultimately this approaches n**2 performance law and if you need to split
your full PubChem 10 mil cpds download, you have a problem.
b) While Babel is smart enough to read and output the first records from an
SD input file with repeated records as above (almost) correctly, its skip
function seems to have less brainpower and gets confused. It simply silently
quits without any message. It is not possible to output records starting
after first record from above repeated multi-record test file or after
encountering such as record anywhere in the skipped part. A bad thing if
something like this happens in the middle of your 500Mb file where you
cannot edit.
c) While on superficial inspection the Babel output looks correct when run
on the first records, a closer look shows that critical information has been
lost. Babel needs to read records into its internal datastructure before
output via conversion.However, its Molfile parser is rather simple and
supports few of the more advanced Molfile encoding conventions. In this
case, Babel silently drops the critical H0 designator flag (plus a second
flag) which lets a Molfile reader distinguish between metal Au and AuH3 with
implicit H. So after the pass through Babel, the compound has changed,
without any notification, from metal Au to AuH3. That can be a problem.
 
OK, enough criticism, here is constructive help:
 
-----snip---store as script.tcl---
set fname [lindex $argv 0]
set fhin [molfile open $fname]
set setsize [lindex $argv 1]
set startrec 1
while 1 {
        set fhout [open [file rootname $fname]_${startrec}_[expr
$startrec+$setsize-1][file extension $fname] w]
        if {[catch {molfile copy $fhin $fhout $setsize}]} {
                close $fhout
                exit
        }
        close $fhout
        incr startrec $setsize
}
-------
 
Above is a really simple (and not user-proofed, no parameter checking)
script for the CACTVS toolkit (www.xemistry.com/academic). Run it with the
generic script interpreter from the packages as
 
csts -f script.tcl filename.sdf setsize
 
The script will output a set of files like "myfile_1_99.sdf",
"myfile_100_199.sdf", etc. in the same directory as the source file. 
 
This script:
a) Processes above sample file (or any other input file) without a single
change of bytes in the split records, similar to line-copying awk scripts
etc.. The record copy function does not decode and re-encode the data; it
just keeps an eye on the passing data to detect proper record boundaries.
b) Does not need to know anything about the input file format. It will
autodetect the format (independent of the suffix) and work with any
supported multi-record format.
 
 

W. D. Ihlenfeldt
Xemistry GmbH
wdi-x-xemistry.com
  

 


  _____  

> From: owner-chemistry-x-ccl.net [mailto:owner-chemistry-x-ccl.net] 
Sent: Monday, March 19, 2007 10:36 AM
To: Ihlenfeldt, W.d. 
Subject: CCL: program to split sdf file


HI,

Unix has loads of ways of doing this, some of which have already been
suggested. 
But, if you want a more graphical way of doing things then you might want to
look a ChemAxon's Instant JChem (http://www.chemaxon.com/product/ijc.html)
which lets you easily view and query chemical data imported from an SD file.


The data can be queried (in your case, just for IDs 1-3,000 etc, but much
more complex queries are possible) and then the results exported to a SD
file. 

And yes, it is free! 
Alex

Fan,Huajun hjfan^^^pvamu.edu wrote: 

Hi, Does anyone know any programs (preferably free) that can split a big sdf
file into smaller files? I got a sdf file containing 30,000 molecules and
want to do a DOCK5. It is too big even to read it through. I want to split
it into 10 samller files that contains 3,000 each. Is it possible? The
newest version of Babel seems not available of this split function for SDF
format.



Thanks in advance.



Hua-Jun 




------=_NextPart_000_0AF8_01C76A7F.E91421B0
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<BODY text=3D#000000 bgColor=3D#ffffff>
<DIV dir=3Dltr align=3Dleft><FONT face=3DArial color=3D#0000ff=20
size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial color=3D#0000ff size=3D2></FONT>&nbsp;</DIV>
<DIV><SPAN class=3D622164102-20032007><FONT face=3DArial color=3D#0000ff =
size=3D2>There=20
have now been quite a number of helpful suggestions on how to perform =
the split=20
- but none of them are&nbsp;really robust, which is essential if files =
become=20
too big for visual inspection of the results. Remember: Murphy=20
lives!</FONT></SPAN></DIV>
<DIV><SPAN class=3D622164102-20032007><FONT face=3DArial color=3D#0000ff =

size=3D2></FONT></SPAN>&nbsp;</DIV>
<DIV><SPAN class=3D622164102-20032007><FONT face=3DArial color=3D#0000ff =
size=3D2>Take=20
the following completely legal SD file record:</FONT></SPAN></DIV>
<DIV><SPAN class=3D622164102-20032007><FONT face=3DArial color=3D#0000ff =

size=3D2></FONT></SPAN>&nbsp;</DIV>
<DIV><SPAN class=3D622164102-20032007><FONT face=3DArial color=3D#0000ff =

size=3D2>----</FONT></SPAN></DIV><SPAN class=3D622164102-20032007>
<DIV><FONT face=3DArial color=3D#0000ff size=3D2></FONT><BR><FONT =
face=3DArial=20
color=3D#0000ff size=3D2>&nbsp; -ISIS-&nbsp; =
03190722292D<BR>$$$$<BR>&nbsp; 1&nbsp;=20
0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0999=20
V2000<BR>&nbsp;&nbsp; -2.3167&nbsp;&nbsp; -0.2167&nbsp;&nbsp;&nbsp; =
0.0000=20
Au&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 1&nbsp; 0&nbsp; 0&nbsp; 1&nbsp; 0&nbsp; =
0&nbsp;=20
0&nbsp; 0&nbsp; 0<BR>M&nbsp; END<BR>&gt; =
&lt;PRICE&gt;<BR>$$$$</FONT></DIV>
<DIV><FONT face=3DArial color=3D#0000ff size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial color=3D#0000ff size=3D2>$$$$</FONT></DIV>
<DIV></SPAN><SPAN class=3D622164102-20032007><FONT face=3DArial =
color=3D#0000ff=20
size=3D2>------</FONT></SPAN></DIV>
<DIV><SPAN class=3D622164102-20032007><FONT face=3DArial color=3D#0000ff =

size=3D2></FONT></SPAN>&nbsp;</DIV>
<DIV><SPAN class=3D622164102-20032007><FONT face=3DArial color=3D#0000ff =
size=3D2>This=20
is a single record,&nbsp; with multiple "$$$$" in places where they are =
*not*=20
record terminators. All simple string search methods with awk or similar =
tools=20
which simply look&nbsp;for the $$$$ line&nbsp;will fail on this. Never =
assume=20
that such records do not exist. I *have* seen $$$$ in SD&nbsp;data lines =

before.</FONT></SPAN></DIV>
<DIV><SPAN class=3D622164102-20032007><FONT face=3DArial color=3D#0000ff =

size=3D2></FONT></SPAN>&nbsp;</DIV>
<DIV><SPAN class=3D622164102-20032007><FONT face=3DArial color=3D#0000ff =
size=3D2>A=20
record splitter thus needs more chemical intelligence to process such =
files.=20
</FONT></SPAN></DIV>
<DIV><SPAN class=3D622164102-20032007><FONT face=3DArial color=3D#0000ff =

size=3D2></FONT></SPAN>&nbsp;</DIV>
<DIV><SPAN class=3D622164102-20032007><FONT face=3DArial color=3D#0000ff =

size=3D2>OpenBabel has been suggested for problem. There are several =
problems with=20
that proposal:</FONT></SPAN></DIV>
<DIV><SPAN class=3D622164102-20032007><FONT face=3DArial color=3D#0000ff =
size=3D2>a) It=20
does not&nbsp;scale to really big files, because Babel has no method to =
output=20
multiple files. Every batch is a separate command and needs to skip to =
the first=20
copy position. Not a problem with a few thousand cpds, but ultimately =
this=20
approaches n**2 performance law and if you need to split your full =
PubChem 10=20
mil cpds download, you have a problem.</FONT></SPAN></DIV>
<DIV><SPAN class=3D622164102-20032007><FONT face=3DArial color=3D#0000ff =
size=3D2>b)=20
While Babel is smart enough to read and output the first records from an =
SD=20
input&nbsp;file with repeated records as above (almost) correctly, its =
skip=20
function seems to have less brainpower and gets confused. It simply =
silently=20
quits without any message. It is not possible to output records starting =
after=20
first record from above repeated multi-record test file&nbsp;or after=20
encountering such as record anywhere in the skipped part. A bad thing if =

something like this happens in the middle of your 500Mb file where you =
cannot=20
edit.</FONT></SPAN></DIV>
<DIV><FONT face=3DArial><FONT color=3D#0000ff><FONT size=3D2><SPAN=20
class=3D622164102-20032007>c) While on superficial inspection the Babel =
output=20
looks correct when run on the first records, a closer look shows that =
critical=20
information has been lost. Babel needs to read records into its internal =

datastructure before output via conversion.However, its Molfile parser =
is rather=20
simple and supports few of the more advanced Molfile encoding =
conventions. In=20
this case, Babel silently drops the critical H0 designator flag (plus a =
second=20
flag) which lets a Molfile reader distinguish between metal Au and AuH3 =
with=20
implicit H.</SPAN>&nbsp;<SPAN class=3D622164102-20032007>So after the =
pass through=20
Babel, the compound has changed, without any notification,&nbsp;from =
metal Au to=20
AuH3. That can be a problem.</SPAN></FONT></FONT></FONT></DIV>
<DIV><FONT face=3DArial><FONT color=3D#0000ff><FONT size=3D2><SPAN=20
class=3D622164102-20032007></SPAN></FONT></FONT></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial><FONT color=3D#0000ff><FONT size=3D2><SPAN=20
class=3D622164102-20032007>OK, enough criticism, here is constructive=20
help:</SPAN></FONT></FONT></FONT></DIV>
<DIV><FONT face=3DArial><FONT color=3D#0000ff><FONT size=3D2><SPAN=20
class=3D622164102-20032007></SPAN></FONT></FONT></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial><FONT color=3D#0000ff><FONT size=3D2><SPAN=20
class=3D622164102-20032007>-----snip---store as=20
script.tcl---</SPAN></FONT></FONT></FONT></DIV>
<DIV><FONT face=3DArial><FONT color=3D#0000ff><FONT size=3D2><SPAN=20
class=3D622164102-20032007>set fname [lindex $argv 0]<BR>set fhin =
[molfile open=20
$fname]<BR>set setsize [lindex $argv 1]<BR>set startrec 1<BR>while 1=20
{<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; set fhout [open [file =
rootname=20
$fname]_${startrec}_[expr $startrec+$setsize-1][file extension $fname]=20
w]<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; if {[catch {molfile =
copy $fhin=20
$fhout $setsize}]}=20
{<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&n=
bsp;&nbsp;&nbsp;&nbsp;=20
close=20
$fhout<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nb=
sp;&nbsp;&nbsp;&nbsp;&nbsp;=20
exit<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=20
}<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; close=20
$fhout<BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; incr startrec=20
$setsize<BR>}</SPAN></FONT></FONT></FONT></DIV>
<DIV><FONT face=3DArial><FONT color=3D#0000ff><FONT size=3D2><SPAN=20
class=3D622164102-20032007>-------</SPAN></FONT></FONT></FONT></DIV>
<DIV><FONT face=3DArial><FONT color=3D#0000ff><FONT size=3D2><SPAN=20
class=3D622164102-20032007></SPAN></FONT></FONT></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial><FONT color=3D#0000ff><FONT size=3D2><SPAN=20
class=3D622164102-20032007>Above is a really simple (and not =
user-proofed, no=20
parameter checking) script for the CACTVS toolkit (<A=20
href=3D"http://www.xemistry.com/academic">www.xemistry.com/academic</A>).=
 Run=20
it&nbsp;with the generic script interpreter from the packages=20
as</SPAN></FONT></FONT></FONT></DIV>
<DIV><FONT face=3DArial><FONT color=3D#0000ff><FONT size=3D2><SPAN=20
class=3D622164102-20032007></SPAN></FONT></FONT></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial><FONT color=3D#0000ff><FONT size=3D2><SPAN=20
class=3D622164102-20032007>csts -f script.tcl filename.sdf=20
setsize</SPAN></FONT></FONT></FONT></DIV>
<DIV><FONT face=3DArial><FONT color=3D#0000ff><FONT size=3D2><SPAN=20
class=3D622164102-20032007></SPAN></FONT></FONT></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial><FONT color=3D#0000ff><FONT size=3D2><SPAN=20
class=3D622164102-20032007>The script&nbsp;will output a set of files =
like=20
"myfile_1_99.sdf", "myfile_100_199.sdf", etc. in the same directory as =
the=20
source file. </SPAN></FONT></FONT></FONT></DIV>
<DIV><FONT face=3DArial><FONT color=3D#0000ff><FONT size=3D2><SPAN=20
class=3D622164102-20032007></SPAN></FONT></FONT></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial><FONT color=3D#0000ff><FONT size=3D2><SPAN=20
class=3D622164102-20032007>This =
script:</SPAN></FONT></FONT></FONT></DIV>
<DIV><FONT face=3DArial><FONT color=3D#0000ff><FONT size=3D2><SPAN=20
class=3D622164102-20032007>a) Processes above sample file (or any other =
input=20
file) without a single change of bytes in the split records, similar to=20
line-copying awk scripts etc.. The record copy function does not decode =
and=20
re-encode the data; it just keeps an eye on the passing data to detect =
proper=20
record boundaries.</SPAN></FONT></FONT></FONT></DIV>
<DIV><FONT face=3DArial><FONT color=3D#0000ff><FONT size=3D2><SPAN=20
class=3D622164102-20032007>b)&nbsp;Does not need to know anything about =
the input=20
file format. It will autodetect the format (independent of the suffix) =
and work=20
with any supported multi-record =
format.</SPAN></FONT></FONT></FONT></DIV>
<DIV><FONT face=3DArial><FONT color=3D#0000ff><FONT size=3D2><SPAN=20
class=3D622164102-20032007></SPAN></FONT></FONT></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial><FONT color=3D#0000ff><FONT size=3D2><SPAN=20
class=3D622164102-20032007></SPAN></FONT></FONT></FONT>&nbsp;</DIV><!-- =
Converted from text/plain format -->
<P><FONT size=3D2>W. D. Ihlenfeldt<BR>Xemistry=20
GmbH<BR>wdi-x-xemistry.com<BR>&nbsp;</FONT> </P>
<DIV><FONT face=3DArial color=3D#0000ff size=3D2></FONT>&nbsp;</DIV><BR>
<BLOCKQUOTE dir=3Dltr=20
style=3D"PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #0000ff 2px =
solid; MARGIN-RIGHT: 0px">
  <DIV class=3DOutlookMessageHeader lang=3Den-us dir=3Dltr align=3Dleft>
  <HR tabIndex=3D-1>
  <FONT face=3DTahoma size=3D2><B>From:</B> owner-chemistry-x-ccl.net=20
  [mailto:owner-chemistry-x-ccl.net] <BR><B>Sent:</B> Monday, March 19, =
2007 10:36=20
  AM<BR><B>To:</B> Ihlenfeldt, W.d. <BR><B>Subject:</B> CCL: =
program to=20
  split sdf file<BR></FONT><BR></DIV>
  <DIV></DIV>HI,<BR><BR>Unix has loads of ways of doing this, some of =
which have=20
  already been suggested. <BR>But, if you want a more graphical way of =
doing=20
  things then you might want to look a ChemAxon's Instant JChem (<A=20
  class=3Dmoz-txt-link-freetext=20
  =
href=3D"http://www.chemaxon.com/product/ijc.html">http://www.chemaxon.com=
/product/ijc.html</A>)=20
  which lets you easily view and query chemical data imported from an SD =
file.=20
  <BR><BR>The data can be queried (in your case, just for IDs 1-3,000 =
etc, but=20
  much more complex queries are possible) and then the results exported =
to a SD=20
  file. <BR><BR>And yes, it is free! <BR>Alex<BR><BR>Fan,Huajun=20
  hjfan^^^pvamu.edu wrote:=20
  <BLOCKQUOTE=20
  =
cite=3Dmid-id%233d2-33812-070316013849-17333-Opfp0RYGtTO3gCZ2VNCYdg(a)ser=
ver.ccl.net=20
  type=3D"cite">
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    <DIV class=3DSection1>
    <P class=3DMsoNormal><FONT face=3DArial size=3D2><SPAN=20
    style=3D"FONT-SIZE: 10pt; FONT-FAMILY: Arial">Hi, Does anyone know =
any=20
    programs (preferably free) that can split a big sdf file into =
smaller files?=20
    I got a sdf file containing 30,000 molecules and want to do a DOCK5. =
It is=20
    too big even to read it through. I want to split it into 10 samller =
files=20
    that contains 3,000 each. Is it possible<FONT color=3Dnavy><SPAN=20
    style=3D"COLOR: navy">? The newest version of <ST1:CITY =
w:st=3D"on"><ST1:PLACE=20
    w:st=3D"on">Babel</ST1:PLACE></ST1:CITY> seems not available of this =
split=20
    function for SDF format.</SPAN></FONT><O:P></O:P></SPAN></FONT></P>
    <P class=3DMsoNormal><FONT face=3DArial size=3D2><SPAN=20
    style=3D"FONT-SIZE: 10pt; FONT-FAMILY: =
Arial"><O:P></O:P></SPAN></FONT></P>
    <P class=3DMsoNormal><FONT face=3DArial size=3D2><SPAN=20
    style=3D"FONT-SIZE: 10pt; FONT-FAMILY: Arial">Thanks in=20
    advance.<O:P></O:P></SPAN></FONT></P>
    <P class=3DMsoNormal><FONT face=3DArial size=3D2><SPAN=20
    style=3D"FONT-SIZE: 10pt; FONT-FAMILY: =
Arial"><O:P></O:P></SPAN></FONT></P>
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    <DIV>
    <DIV>
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size=3D2><SPAN=20
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    </SPAN></FONT></B></STRONG><FONT face=3DArial color=3Dblack =
size=3D2><SPAN=20
    style=3D"FONT-SIZE: 10pt; COLOR: black; FONT-FAMILY: =
Arial"><O:P></O:P></SPAN></FONT></P></DIV></DIV></DIV>
    <P class=3DMsoNormal><FONT face=3D"Times New Roman" size=3D3><SPAN=20
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