From toukie@zui.unizh.ch Mon Jul 21 03:12:28 1997 Received: from zzmkgtw.zzmk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.8.3/950822.1) id DAA05211; Mon, 21 Jul 1997 03:00:08 -0400 (EDT) Received: by zzmkgtw.zzmk.unizh.ch; (5.65v3.2/1.3/10May95) id AA01873; Mon, 21 Jul 1997 09:00:07 +0200 Message-Id: <1.5.4.32.19970721070230.00664960@highdent.zzmk.unizh.ch> X-Sender: toukie@highdent.zzmk.unizh.ch (Unverified) X-Mailer: Windows Eudora Light Version 1.5.4 (32) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 21 Jul 1997 09:02:30 +0200 To: chemistry@www.ccl.net From: "Hr. Dr. S. Shapiro" Subject: MOPAC50ESP Dear Colleagues; I am seeking a programme called "MOPAC50ESP". An Altavista search turned up thirteen relevent web sites, but I was not able access MOPAC50ESP from any of these thirteen sites. If anyone knows of a website or FTP site from which I can _really_ obtain information about MOPAC50ESP, or would be willing to share with me other information about this programme, please contact me directly at toukie@zui.unizh.ch Thanks in advance to all responders, S. Shapiro toukie@zui.unizh.ch From mzapalow@mitr.p.lodz.pl Mon Jul 21 05:12:28 1997 Received: from mitr.p.lodz.pl for mzapalow@mitr.p.lodz.pl by www.ccl.net (8.8.3/950822.1) id EAA05498; Mon, 21 Jul 1997 04:51:52 -0400 (EDT) Received: from mitr-mz.p.lodz.pl by mitr.p.lodz.pl with SMTP (5.65/25-eef) id AA09283; Mon, 21 Jul 97 10:33:53 +0200 Message-Id: <9707210833.AA09283@mitr.p.lodz.pl> Comments: Authenticated sender is From: "Michal Zapalowski" Organization: MITR To: "Gustavo A. Mercier Jr" Date: Mon, 21 Jul 1997 10:54:44 +0000 Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7BIT Subject: Re: CCL:babel 1.6 & Windows NT Dos Cc: chemistry@www.ccl.net Return-Receipt-To: "Michal Zapalowski" Priority: normal In-Reply-To: <199707181545.LAA06782@mail.med.upenn.edu> X-Mailer: Pegasus Mail for Win32 (v2.52) Gustavo A. Mercier Jr wrote: > I am trying to use the Babelwin interface, but upon opening the > DOS shell and calling babel, babel fails to open the input file. > It appears to be a problem with babel, rather than Babelwin. You're not right, I'm afraid. BabelWin generates batch file named babelwin.bat which looks like this: c:\ cd C:\tools\babel babel -ig94 D:\T9_pm3g.out -omopint D:\output.zmt pause The first command contains excess backslash, you should remove it with your favourite text editor: c: cd C:\tools\babel ... etc and run babelwin.bat manually. Regards, Michal Zapalowski -------------------------- Michal Zapalowski, MSc email: mzapalow@mitr.p.lodz.pl phone: (+48 42) 313-177 fax: (+48 42) 360-246 IARC, Technical University of Lodz ul. Wroblewskiego 15 93 - 590 Lodz, Poland From rgab@proteus.co.uk Mon Jul 21 07:12:29 1997 Received: from petersgate.proteus.co.uk for rgab@proteus.co.uk by www.ccl.net (8.8.3/950822.1) id HAA05907; Mon, 21 Jul 1997 07:08:29 -0400 (EDT) Received: from Icthus.proteus.co.uk (Icthus [193.115.24.114]) by petersgate.proteus.co.uk (8.6.12/8.6.6) with ESMTP id MAA11059 for ; Mon, 21 Jul 1997 12:09:09 GMT Message-Id: <199707211209.MAA11059@petersgate.proteus.co.uk> From: Richard Bone Date: Mon, 21 Jul 1997 12:08:30 +0100 To: CHEMISTRY@www.ccl.net Subject: SMILES databases - summary Following up on my enquiry about SMILES databases last week, here is a brief summary of the responses. They fell into 3 different categories (besides the inevitable "please send us the answers ... "): 1) Why not just use a format-interchange program to convert a database in some other format to SMILES? (Or, just dump a selection of an existing database out specifying SMILES as the output option; or create some combinatorial library and do the same) DOUGH@mdli.com twells@mdli.com (Terry Wells) stevew@mdli.com (Steve Welford) 2) Try to find a way of automating their generation. jsb@camsoft.com (Jonathan Brecher, CambridgeSoft Corporation ) 3) Examples of SMILES databases already 'out there'. a) 8,000 small organics. Contact J. Eric Slone (eslone@patriot.net). b) Database of organic compounds (Possibly in SMILES, and probably used for QSAR). Contact Lowell Hall (hall@enc.edu); communicated by Tod Story, (story@ksu.edu). c) First 4,000 (non metal-containing) entries of the NCI database. Supplied by Wolfgang Utz (utz@pharmazie.uni-erlangen.de). Available by FTP: (ftp://schiele.organik.uni-erlangen.de/pub/nci/nci4000.smi.gz) d) 400 example small molecules available for free. (http://esc.syrres.com/~ESC/examples.htm) A commercially available database with 100,000 SMILES and CAS-numbers available from Syracuse Research Corp. Contact meylan@syrres.com In addition, I came across a web-site at Pomona College which contained a number of files of compounds organised by molecular empirical formula, and containing their SMILES strings. http://clogp.pomona.edu/medchem/chem/master/mf/ghindex.html It does not appear to be possible to download these 'in batch', but it is a most \\formidable\\ source of data. Thanks to everyone for their input. Richard Bone ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | Richard G. A. Bone, Ph.D. | | | Senior Computational Chemist | | | Proteus Molecular Design Ltd. | Tel: +44 (0)1625 500555 | | Lyme Green Business Park | Fax: +44 (0)1625 500666 | | Macclesfield, Cheshire | Email: rgab@proteus.co.uk | | United Kingdom SK11 0JL | Web: http://www.proteus.co.uk | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From jenninaj@mh.uk.sbphrd.com Mon Jul 21 10:12:29 1997 Received: from ns01.sbphrd.com for jenninaj@mh.uk.sbphrd.com by www.ccl.net (8.8.3/950822.1) id KAA06579; Mon, 21 Jul 1997 10:07:35 -0400 (EDT) Received: by ns01.sbphrd.com; id KAA29944; Mon, 21 Jul 1997 10:07:36 -0400 Received: from phinet.sbphrd.com(139.136.64.5) by ns01.sbphrd.com via smap (3.2) id xma029876; Mon, 21 Jul 97 10:07:29 -0400 Received: from hbu037.ha.uk.sbphrd.com by phinet.sbphrd.com; (5.65v3.0/1.1.8.2/06Mar95-1250PM) id AA18596; Mon, 21 Jul 1997 10:07:29 -0400 Received: from hgu118.ha.uk.sbphrd.com (hgu118.ha.uk.sbphrd.com [139.136.157.118]) by hbu037.ha.uk.sbphrd.com (8.8.5/pe/sbphrd/mh/970220) with ESMTP id PAA30406 for ; Mon, 21 Jul 1997 15:07:26 +0100 (BST) Received: from localhost (jenninaj@localhost) by hgu118.ha.uk.sbphrd.com (8.8.5/pe/sbphrd/clnt/970220) with SMTP id PAA02119 for ; Mon, 21 Jul 1997 15:07:27 +0100 (BST) X-Authentication-Warning: hgu118.ha.uk.sbphrd.com: jenninaj owned process doing -bs Date: Mon, 21 Jul 1997 15:07:26 +0100 (BST) From: Andy Jennings To: Comp-Chem-List Subject: Retrosynthesis Programs Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII All, After the discussion of programs to plan retrosynthetic pathways to desired targets I wonder which companies out there do actually use them. The comments that they are difficult to use or that the databases are too limited were valid some time ago but I wonder what the current state-of-play actually is. I would be grateful if any of you could let me know what the situation is within your own companies, particularly if they are involved in pharmaceutical research. I would ideally like to know what programs you have, what the general impression is and whether the programs are actually used! Any replies gratefully received...perhaps directly to me to save clogging up the newsgroup with non-scientific matters? Thanks in advance, Andy ============================================================ Andy Jennings - SmithKline Beecham Pharmaceuticals Phone: +44 (0) 1279 627682 Fax: +44 (0) 1279 627685 From dalke@ks.uiuc.edu Mon Jul 21 20:12:35 1997 Received: from london.ks.uiuc.edu for dalke@ks.uiuc.edu by www.ccl.net (8.8.3/950822.1) id UAA10109; Mon, 21 Jul 1997 20:12:32 -0400 (EDT) Received: from bilbao.ks.uiuc.edu by london.ks.uiuc.edu with ESMTP (1.37.109.20/16.2 [TBG Mods]) id AA031490352; Mon, 21 Jul 1997 19:12:32 -0500 Received: (from dalke@localhost) by bilbao.ks.uiuc.edu (940816.SGI.8.6.9/8.6.9)id TAA11576 for chemistry@www.ccl.net; Mon, 21 Jul 1997 19:12:32 -0500 Date: Mon, 21 Jul 1997 19:12:32 -0500 From: Andrew Dalke Message-Id: <199707220012.TAA11576@bilbao.ks.uiuc.edu> To: chemistry@www.ccl.net Subject: Re: CCL:Object-oriented means for computational chemistry programming Konrad Hinsen commented: > Just a crazy idea: create an institution > devoted to "scientific computing" for the academic community. Staff it > with application scientists and computer scientists, and let it work > on a high-level language for scientific applications ... That's somewhat like what the Numerical Algor. Group does (www.nag.com). From http://www.nag.com/0h/AboutNAG.html : > NAG produces and distributes numerical, symbolic, statistical and > visualisation software for the solution of problems in a wide range of > applications in such areas as science, engineering, financial analysis > and research. > > For users who write programs and build packages, NAG produces > sub-program libraries in a wide range of computer languages (Ada, > C, Fortran, Pascal, Turbo Pascal). [...] NAG provides several > powerful mathematical and statistical packages for interactive use. In a non-commercial sense I think most application domains have their own set of tools, and it will be very hard to convince mathematicians to give up MatLab/Mathematics and astronomers to give up AIPS/AIPS++ and statisticians give up S-Plus and ... Granted, scripting languages like Python can incorporate all of these interfaces, but it takes time, money and expertise. Konrad went on to say: > I'd like to propose an alternative > model for developing scientific code: define a "lifetime" of between > five and ten years for each package (depending on the speed of method > development) and throw it away after that time, replacing it with > new code containing the useful part of the functionality and written > according to the state of the art of programming. If the code is implemented "correctly" there is no reason to do this. When was the last time you needed to upgrade ftp, or telnet, or bc, or yacc? I use libpdb from the CGL to read PDB files and the library hasn't changed in years (though the PDB format has :). Yet it still works very well. The C and Fortran APIs for PVM haven't changed very much over the last 5 years, and there isn't much call for a change. I think the problem isn't that code naturally decays over time but that it wasn't well designed in the first place. Flaws in the architecture are glossed over as the project grows until it becomes a morass of hacked fixes, until finally the thing is chucked. Done well (modular code, consistant design, well thought out APIs, etc.) there's no reason you shouldn't use a 15-year library. However, it is hard to do. Andrew Dalke dalke@ks.uiuc.edu P.S. Oh yeah, and another reason for code to change -- creaping featurism!