From adler@pulsar.cs.wku.edu Thu Jul 24 04:13:08 1997 Received: from axp1.wku.edu for adler@pulsar.cs.wku.edu by www.ccl.net (8.8.3/950822.1) id EAA24590; Thu, 24 Jul 1997 04:06:44 -0400 (EDT) Received: from pulsar.cs.wku.edu (161.6.17.52) by axp1.wku.edu (MX F5.0) with SMTP; Thu, 24 Jul 1997 03:06:42 -0500 Received: by pulsar.cs.wku.edu (SMI-8.6/SMI-SVR4) id DAA20882; Thu, 24 Jul 1997 03:03:03 -0500 From: adler@pulsar.cs.wku.edu (Allen Adler) Message-ID: <199707240803.DAA20882@pulsar.cs.wku.edu> Subject: water on the sun To: chemistry@www.ccl.net Date: Thu, 24 Jul 1997 03:03:03 -0500 (CDT) X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Apparently it is known that sun spots contain water vapor. This was confirmed by observations of the solar spectrum and by theoretical calculations of the spectrum of very hot water. I haven't seen the Science article yet (and might not understand it if I did), but I'm told that one can't compute such spectra using perturbations and instead one has to compute the energy levels by some more direct method. Does anyone on this group know what they did to compute the spectra and whether any of the various programs that one commonly sees talked about on this group could duplicate the results? Allan Adler adler@pulsar.cs.wku.edu From mbdtsrh@afs.mcc.ac.uk Thu Jul 24 05:13:06 1997 Received: from curlew.cs.man.ac.uk for mbdtsrh@afs.mcc.ac.uk by www.ccl.net (8.8.3/950822.1) id EAA24798; Thu, 24 Jul 1997 04:54:07 -0400 (EDT) Received: from mchhpb02.ch.man.ac.uk by curlew.cs.man.ac.uk with SMTP (PP); Thu, 24 Jul 1997 09:52:34 +0100 From: mbdtsrh Message-Id: <760.9707240852@mchhpb02.ch.man.ac.uk> Subject: Is there a tin force field available? To: chemistry@www.ccl.net Date: Thu, 24 Jul 1997 09:52:51 +0100 (BST) Reply-To: r.hall@man.ac.uk X-Mailer: ELM [version 2.4 PL24alpha3] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear all, I am interested in using AMBER to model a molecule containing a tin atom, but am having trouble finding the relevant parameters. Any pointers to work performed in this area would be gratefully received. thanks in advance, Richard. -- ------------------------------------------------------------------------ Richard Hall Department of Chemistry email: Richard.Hall@man.ac.uk University of Manchester tel: (0161) 275 4686 Manchester, UK, M13 9PL ------------------------------------------------------------------------ From Gerald.Loeffler@univie.ac.at Thu Jul 24 08:13:08 1997 Received: from sandwich.mdy.univie.ac.at for Gerald.Loeffler@univie.ac.at by www.ccl.net (8.8.3/950822.1) id HAA25345; Thu, 24 Jul 1997 07:58:11 -0400 (EDT) Received: from sandwich.mdy.univie.ac.at by sandwich.mdy.univie.ac.at via SMTP (940816.SGI.8.6.9/930416.SGI.AUTO) id NAA02500; Thu, 24 Jul 1997 13:49:10 +0200 Sender: gl@univie.ac.at Message-ID: <33D74135.167E@univie.ac.at> Date: Thu, 24 Jul 1997 13:49:09 +0200 From: Gerald Loeffler Organization: I.M.P. X-Mailer: Mozilla 3.01Gold (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: Andrew Dalke CC: chall003@maroon.tc.umn.edu, chemistry@www.ccl.net Subject: Re: CCL:Optimization hinders evolution References: <199707231919.OAA14690@bilbao.ks.uiuc.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi there! Andrew Dalke wrote: > > Hello, > > I agree with your statement that emphasis on optimization of > current methods without exploration of alternate approaches > can cause "very well engineered dinosaurs." What I like about > current advances in C++ (templates) is you get the ability > to organize your data in more complicated ways (with classes > and better data hiding) without the effort it would take to > achieve the same in Fortran and without appreciable performance > loss. Just a short remark to emphasize that all our programming problems are not yet solved by the above mentioned "advances in C++ templates": I like C++ templates, they are elegant, potentially efficient, simply great, BUT someone wrote in a column about the proposed C++ Standard Library (!) in the "C++ Report" earlier this year (quoted from the top of my head): "The caveat of this approach is that it uses partial template spezialisation. No compiler we know of supports this language feature." I know this is an unfair, mean remark, but nevertheless it's true ... Cheers, gerald -- Gerald Loeffler PostDoc in Theoretical Biophysics EMail: Gerald.Loeffler@univie.ac.at Phone: +43 1 79730 554 Fax: +43 1 7987153 SMail: I.M.P. - Research Institute of Molecular Pathology Dr. Bohr-Gasse 7 A-1030 Vienna AUSTRIA From msj@fskru5.hre.hydro.com Thu Jul 24 10:13:09 1997 Received: from fskru5.hre.hydro.com for msj@fskru5.hre.hydro.com by www.ccl.net (8.8.3/950822.1) id JAA25687; Thu, 24 Jul 1997 09:26:08 -0400 (EDT) Received: by fskru5.hre.hydro.com (950413.SGI.8.6.12/930416.SGI.AUTO) for chemistry@www.ccl.net id PAA19436; Thu, 24 Jul 1997 15:55:38 +0200 From: "Merethe Sjovoll" Message-Id: <9707241555.ZM19434@fskru5.hre.hydro.com> Date: Thu, 24 Jul 1997 15:55:37 -0600 Reply-To: Merethe.Sjovoll@hre.hydro.com X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: chemistry@www.ccl.net Subject: Intermolecular distance in benzene stacks Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hello everyone, benzene has a tendency to form stacks by interaction between the pi systems of the benzene rings. Does anybody know the equilibrium distance between two benzene molecules in such an arrangement? regards, Merethe -- ******************************************************** Merethe Sjovoll, Ph.D. * * Research Scientist * * Norsk Hydro a.s Research Center * * * * P.O.Box 2560 * HYDRO * N-3901 Porsgrunn, * RESEARCH * Norway * * * ((( * email: Merethe.Sjovoll@hre.hydro.com * (=====) * Phone:+47 35 56 48 97 * * Fax :+47 35 56 36 86 * * ******************************************************** From i1s@email.psu.edu Thu Jul 24 11:13:10 1997 Received: from f01n05.cac.psu.edu for i1s@email.psu.edu by www.ccl.net (8.8.3/950822.1) id KAA25955; Thu, 24 Jul 1997 10:17:18 -0400 (EDT) Received: from [146.186.73.41] (I1S.OZ.PSU.EDU [146.186.73.41]) by f01n05.cac.psu.edu (8.7.6/8.6.12) with SMTP id KAA33652 for ; Thu, 24 Jul 1997 10:17:23 -0400 Message-Id: <199707241417.KAA33652@f01n05.cac.psu.edu> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 24 Jul 1997 11:12:03 -0400 To: chemistry@www.ccl.net From: i1s@psu.edu (Inge Schuster) Subject: mac program for solving chemical equilibria Hi! Does anyone know of any program for the Mac which can do calculations associated with simultaneous chemical equilibria, titrations, etc. in non-aqueous media ( where pH is not a factor)? Inge Schuster I1S@Psu.edu From SMITHJA@ucarb.com Thu Jul 24 11:19:09 1997 Received: from hscmg02.hou.ucarb.com for SMITHJA@ucarb.com by www.ccl.net (8.8.3/950822.1) id KAA26225; Thu, 24 Jul 1997 10:53:23 -0400 (EDT) Received: by hscmg02.hou.ucarb.com with Internet Mail Service (5.0.1457.3) id ; Thu, 24 Jul 1997 09:54:17 -0500 Message-ID: From: "Smith JA (Jack)" To: "'Ping Du'" Cc: "'CHEMISTRY@www.ccl.net'" Subject: RE: CCL:Object-oriented means for computational chemist Date: Thu, 24 Jul 1997 09:52:29 -0500 X-Priority: 3 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.0.1457.3) Content-Type: text/plain -- Ping Du said: > I found the discussions on OO programming very useful! However, > there is a point that I would like to bring up. That is, is it > possible to implement an OO design using a non-OO language? The main > design features of OOD are abstraction, encapsulation, and > inheritance. One may achieve abstraction and encapsulation in a > non-OO language by forcing discipline. For example, use struct in C > as if there were classes and access data members through "interface" > functions. However, implementing inheritance is impossible without > an OO language. Inheritance is pobably the most important feature of > OO design if you would like your program to be extensible and > reusable. -- I'm finally glad to see someone make this point. I've been wanting to make the very same point, but I hesitated to get into the OO programming/design/language debate when I've got so many other things to do - like putting a C/C++ frontend to some really old FORTRAN (ANSI 66) code! ;-) > - Jack > > -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- > Jack A. Smith || > Union Carbide || Phone: (304) 747-5797 > Catalyst Skill Center || FAX: (304) 747-5571 > P.O. Box 8361 || > S. Charleston, WV 25303 || smithja@ucarb.com > -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- > From zfeng@blac.bim.anl.gov Thu Jul 24 11:23:02 1997 Received: from blac.bim.anl.gov for zfeng@blac.bim.anl.gov by www.ccl.net (8.8.3/950822.1) id KAA26119; Thu, 24 Jul 1997 10:40:07 -0400 (EDT) Received: from blac.bim.anl.gov (localhost [127.0.0.1]) by blac.bim.anl.gov (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id JAA12492; Thu, 24 Jul 1997 09:36:25 -0500 Sender: zfeng@blac.bim.anl.gov Message-ID: <33D76868.41C6@blac.bim.anl.gov> Date: Thu, 24 Jul 1997 09:36:24 -0500 From: Zhou Feng X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX 6.3 IP32) MIME-Version: 1.0 To: Ping Du CC: chemistry@www.ccl.net Subject: Re: CCL: CCL:Object-oriented means for computational chemist References: <19970722083948.138bb7cb.in@S2> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Ping Du wrote: > > Hi, > > I found the discussions on OO programming very useful! However, > there is a point that I would like to bring up. That is, is it > possible to implement an OO design using a non-OO language? The main > design features of OOD are abstraction, encapsulation, and > inheritance. One may achieve abstraction and encapsulation in a > non-OO language by forcing discipline. A perfect example of enforcing OO-like methodology in non-OO language would be Visual Basic, in fact it not only gave the appearance of OO but also has a GUI tightly coupled to the commonly used objects. However there seems to be a couple of important thing missing for this type of language, one important feature would be the data encapsulation capability, i.e., you can still manipulate variables of other classes in a different class. In C++ for example, you can declare those variables as private and avoid such mess in data manipulation. It is certainly an important feature for bussiness type development to avoid security loopholes and undesired programming tricks, I don't know whether it is that important for computational scientist (maybe for the compute objects and the type of programming Andrew Dalke mentioned). However, it would be quite a pain to do thing in the object oriented way without the help of the language itself and the compiler, just imagine the book keeping and debugging. Feng Zhou Argonne National Lab. From sanjoy@sg17.chem.upenn.edu Thu Jul 24 12:13:10 1997 Received: from sg17.chem.upenn.edu for sanjoy@sg17.chem.upenn.edu by www.ccl.net (8.8.3/950822.1) id LAA26453; Thu, 24 Jul 1997 11:19:55 -0400 (EDT) Received: (from sanjoy@localhost) by sg17.chem.upenn.edu (950413.SGI.8.6.12/SAS 8.03) id LAA18812 for CHEMISTRY@www.ccl.net; Thu, 24 Jul 1997 11:19:57 -0400 Date: Thu, 24 Jul 1997 11:19:57 -0400 From: sanjoy@sg17.chem.upenn.edu (Sanjoy Bandyopadhyay) Posted-Date: Thu, 24 Jul 1997 11:19:57 -0400 Message-Id: <199707241519.LAA18812@sg17.chem.upenn.edu> To: CHEMISTRY@www.ccl.net Subject: Crystal structure data of Glycerol Hi, Can anyone tell me where can I get crystal structure data of glycerol? Thanks in advance, Sanjoy Bandyopadhyay. Center for Molecular Modelling, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323. Tel no. 215-898-1582 Fax: 215-573-6233 From heelisp@newi.ac.uk Thu Jul 24 12:17:52 1997 Received: from mail.u-net.net for heelisp@newi.ac.uk by www.ccl.net (8.8.3/950822.1) id MAA26839; Thu, 24 Jul 1997 12:06:44 -0400 (EDT) Received: from netsci.u-net.com ([194.119.133.204]) by mail.u-net.net with SMTP id <30320-21733>; Thu, 24 Jul 1997 16:59:44 +0100 Message-Id: <3.0.32.19970724170540.006e57d8@cygnus.newi.ac.uk> X-Sender: heelisp@cygnus.newi.ac.uk X-Mailer: Windows Eudora Pro Version 3.0 (32) Date: Thu, 24 Jul 1997 17:05:46 +0100 To: CHEMISTRY@www.ccl.net From: Paul Heelis Subject: software and courses database Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear All, I am compiling a list of pointers for chemists (http://www.infochem.co.uk) . I am including a number of headings but I would be particularly interested in hearing about software and online courses of interest to chemists. Thanks in advance for any information. Paul Heelis Dr Paul Heelis Reader in Chemistry North East Wales Institute of Higher Education Mold Rd Wrexham LL11 2AW UK e-mail editor@netsci.u-net.com or heelisp@newi.ac.uk fax +44 1978 290008 tel +44 1978 293372 Internet Journal of Science - Biological Chemistry First Internet Conference on Photochemistry and Photobiology http://www.netsci-journal.com/97v3/ Infochem, chemist's database http://www.infochem.co.uk From shenkin@still3.chem.columbia.edu Thu Jul 24 13:13:12 1997 Received: from mailrelay1.cc.columbia.edu for shenkin@still3.chem.columbia.edu by www.ccl.net (8.8.3/950822.1) id MAA26912; Thu, 24 Jul 1997 12:16:30 -0400 (EDT) Received: from still3.chem.columbia.edu (still3.chem.columbia.edu [128.59.112.36]) by mailrelay1.cc.columbia.edu (8.8.5/8.8.5) with SMTP id MAA03260 for <@smtp.columbia.edu:CHEMISTRY@www.ccl.net>; Thu, 24 Jul 1997 12:16:29 -0400 (EDT) Received: by still3.chem.columbia.edu (950413.SGI.8.6.12/930416.SGI.AUTO) for CHEMISTRY@www.ccl.net id MAA13273; Thu, 24 Jul 1997 12:16:29 -0400 From: "Peter Shenkin" Message-Id: <9707241216.ZM13271@still3.chem.columbia.edu> Date: Thu, 24 Jul 1997 12:16:28 -0400 In-Reply-To: "Smith JA (Jack)" "CCL:Object-oriented means for computational chemist" (Jul 24, 9:52am) References: X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: "'CHEMISTRY@www.ccl.net'" Subject: Re: CCL:Object-oriented means for computational chemist Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii On Jul 24, 9:52am, Smith JA (Jack) wrote: > Subject: CCL:Object-oriented means for computational chemist > -- Ping Du said: > > ... One may achieve abstraction and encapsulation in a > > non-OO language by forcing discipline.... > > However, implementing inheritance is impossible without > > an OO language. Inheritance is pobably the most important feature of > > OO design if you would like your program to be extensible and > > reusable. > I'm finally glad to see someone make this point. I've been wanting to > make the very same point, but I hesitated to get into the OO > programming/design/language debate when I've got so many other things to > do - like putting a C/C++ frontend to some really old FORTRAN (ANSI 66) > code! ;-) All this is true. However, there's another side to the coin. Using non-OO languages, like C and Fortran, one can assemble abstracted and encapsulated libraries that can be called from a wide variety of languages: C, C++, F77, F90, .... It's true that you don't get inheritance if you do this. On the other hand, using C++, it's not possible to write a general-purpose library callable from other languages, even if one writes a set of interface routines that are type-specific, so that they avoid name-mangling, etc. Or so I'm told by those more conversant in C++ than I. This is regrettable. It means that once you start with C++, you're stuck in a C++ world. This is fine for many, but not all. -P. -- **** "Deep Blue can't triumph in the game of life." (NY Times, 5/13/97) *** * Peter S. Shenkin; Chemistry, Columbia U.; 3000 Broadway, Mail Code 3153 * ** NY, NY 10027; shenkin@columbia.edu; (212)854-5143; FAX: 678-9039 *** *MacroModel WWW page: http://www.columbia.edu/cu/chemistry/mmod/mmod.html * From duanx@Picard.ml.wpafb.af.mil Thu Jul 24 16:13:14 1997 Received: from nsrhost.ml.wpafb.af.mil for duanx@Picard.ml.wpafb.af.mil by www.ccl.net (8.8.3/950822.1) id PAA27861; Thu, 24 Jul 1997 15:17:20 -0400 (EDT) Received: from Picard.ml.wpafb.af.mil by nsrhost.ml.wpafb.af.mil with SMTP (1.39.111.2/16.2) id AA219101684; Thu, 24 Jul 1997 15:14:44 -0400 Received: by Picard.ml.wpafb.af.mil (4.1/version) id AA10598; Thu, 24 Jul 97 15:17:20 EDT Date: Thu, 24 Jul 1997 15:17:20 -0400 (EDT) From: Xiaofeng Duan To: chemistry@www.ccl.net Subject: compiling Gamess on SGI O2 Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Does anyone has experience in compiling Gamess on SGI O2 (R10000) machine? We tried to do so (Gamess version 31 Oct. 96) recently on the machine (IRIX 6.3, Fortran 7.1), and it seemed like everything went smoothly, no error messages during compiling and linking. However, the binary file was not excutable. When we run it, we get a message like "Exec format error". We tried to set ARCH='-r10000' and ARCH=' '; the result was the same. It would be appreciated if someone can help in pointing out what the problem could be? **************************************** Xiaofeng Duan WL/MLBP, Bldg. 654 2941 P St. Ste. 1 Wright-Patterson AFB, OH 45433 (937)255-9164 duanx@Picard.ml.wpafb.af.mil **************************************** From shenkin@still3.chem.columbia.edu Thu Jul 24 16:19:48 1997 Received: from mailrelay1.cc.columbia.edu for shenkin@still3.chem.columbia.edu by www.ccl.net (8.8.3/950822.1) id PAA28011; Thu, 24 Jul 1997 15:48:51 -0400 (EDT) Received: from still3.chem.columbia.edu (still3.chem.columbia.edu [128.59.112.36]) by mailrelay1.cc.columbia.edu (8.8.5/8.8.5) with SMTP id PAA14024 for <@smtp.columbia.edu:CHEMISTRY@www.ccl.net>; Thu, 24 Jul 1997 15:48:50 -0400 (EDT) Received: by still3.chem.columbia.edu (950413.SGI.8.6.12/930416.SGI.AUTO) for CHEMISTRY@www.ccl.net id PAA14630; Thu, 24 Jul 1997 15:48:49 -0400 From: "Peter Shenkin" Message-Id: <9707241548.ZM14628@still3.chem.columbia.edu> Date: Thu, 24 Jul 1997 15:48:49 -0400 In-Reply-To: "Smith JA (Jack)" "RE: Object-oriented means for computational chemist" (Jul 24, 2:27pm) References: X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: "'CHEMISTRY@www.ccl.net'" Subject: Re: Object-oriented means for computational chemist Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii On Jul 24, 2:27pm, Smith JA (Jack) wrote: > Peter Shenkin[SMTP:shenkin@still3.chem.columbia.edu] wrote: > >All this is true. However, there's another side to the coin. Using > >non-OO languages, like C and Fortran, one can assemble abstracted and > >encapsulated libraries that can be called from a wide variety of > >languages: C, C++, F77, F90, .... It's true that you don't get > >inheritance if you do this. > > > >On the other hand, using C++, it's not possible to write a > >general-purpose library callable from other languages... > >Or so I'm told by those more conversant in C++ than I. > And now we're back to the mixed language debate > I find little problem with > maintaining the overall system architecture and handling the user > interface with a good application C++ class library, writing reusable > non-computational 'modules' in plain C, and making use of (and even > extending) existing FORTRAN libraries and program segments for the bulk > of the computational work. Your point is well taken, and I don't disagree. On the other hand, that's not quite the issue I was trying to raise. The issue I was trying to raise is that regardless of whether one wants to write the front end in C, C++ or Fortran, or anything else, the language definition of C++ *precludes* writing a linkable code libraries in C++ if one ever wants to access the library routines >from another language. This is really too bad, because, whether it's optimal right now or not, OO techniques, including inheritance, are not inherently ill-suited for efficient computational methods and even offer some advantages. I'd love to be able to write some of these underlying libraries in C++, but right now I cannot, because I don't feel that I can tie the *users* of the libraries -- who may not be limited to me -- to C++ exclusively. -P. -- **** "Deep Blue can't triumph in the game of life." (NY Times, 5/13/97) *** * Peter S. Shenkin; Chemistry, Columbia U.; 3000 Broadway, Mail Code 3153 * ** NY, NY 10027; shenkin@columbia.edu; (212)854-5143; FAX: 678-9039 *** *MacroModel WWW page: http://www.columbia.edu/cu/chemistry/mmod/mmod.html * From SMITHJA@ucarb.com Thu Jul 24 16:23:21 1997 Received: from hscmg02.hou.ucarb.com for SMITHJA@ucarb.com by www.ccl.net (8.8.3/950822.1) id PAA27890; Thu, 24 Jul 1997 15:27:22 -0400 (EDT) Received: by hscmg02.hou.ucarb.com with Internet Mail Service (5.0.1457.3) id ; Thu, 24 Jul 1997 14:28:13 -0500 Message-ID: From: "Smith JA (Jack)" To: "'Peter Shenkin'" Cc: "'CHEMISTRY@www.ccl.net'" Subject: RE: Object-oriented means for computational chemist Date: Thu, 24 Jul 1997 14:27:08 -0500 X-Priority: 3 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.0.1457.3) Content-Type: text/plain Peter Shenkin[SMTP:shenkin@still3.chem.columbia.edu] wrote: >On Jul 24, 9:52am, Smith JA (Jack) wrote: >> Subject: CCL:Object-oriented means for computational chemist >> -- Ping Du said: >> > ... One may achieve abstraction and encapsulation in a >> > non-OO language by forcing discipline.... >> > However, implementing inheritance is impossible without >> > an OO language. Inheritance is pobably the most important feature of >> > OO design if you would like your program to be extensible and >> > reusable. > >> I'm finally glad to see someone make this point. I've been wanting to >> make the very same point, but I hesitated to get into the OO >> programming/design/language debate when I've got so many other things to >> do - like putting a C/C++ frontend to some really old FORTRAN (ANSI 66) >> code! ;-) > >All this is true. However, there's another side to the coin. Using >non-OO languages, like C and Fortran, one can assemble abstracted and >encapsulated libraries that can be called from a wide variety of >languages: C, C++, F77, F90, .... It's true that you don't get >inheritance if you do this. > >On the other hand, using C++, it's not possible to write a general-purpose >library callable from other languages, even if one writes a set >of interface routines that are type-specific, so that they avoid >name-mangling, etc. Or so I'm told by those more conversant in C++ >than I. This is regrettable. It means that once you start with C++, >you're stuck in a C++ world. This is fine for many, but not all. And now we're back to the mixed language debate (I knew I shouldn't have jumped into this!). I find little problem with maintaining the overall system architecture and handling the user interface with a good application C++ class library, writing reusable non-computational 'modules' in plain C, and making use of (and even extending) existing FORTRAN libraries and program segments for the bulk of the computational work. However, if I could start all over, I'm really not sure how much of the FORTRAN I'd rewrite in C/C++, or how much of the C I'd promote to C++. Since I (and most of us) don't have the luxury of time to start over, I don't worry about it too much, and I find the 'application class library'/C++/C/FORTRAN/'numerical subroutine library' approach to be an acceptable compromise. And I know I have a lot company. - Jack From govindan@chet.medc.umn.edu Thu Jul 24 17:13:13 1997 Received: from chet.medc.umn.edu for govindan@chet.medc.umn.edu by www.ccl.net (8.8.3/950822.1) id QAA28350; Thu, 24 Jul 1997 16:30:06 -0400 (EDT) Received: (from govindan@localhost) by chet.medc.umn.edu (8.8.5/8.8.5) id PAA18030 for CHEMISTRY@www.ccl.net; Thu, 24 Jul 1997 15:30:04 -0500 (CDT) From: Govindan Subramanian Message-Id: <199707242030.PAA18030@chet.medc.umn.edu> Subject: AMBER parameters To: CHEMISTRY@www.ccl.net Date: Thu, 24 Jul 1997 15:30:01 -0500 (CDT) X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Hai, I am interested in getting AMBER force-field parameters for the sp2 oxygen (in say furan) and the sulfur atoms (in say thiophene). Will post the summary, if I receive sufficent details. Thanks. -subramanian.g From support@mathtrek.com Thu Jul 24 17:21:18 1997 Received: from granite.sentex.net for support@mathtrek.com by www.ccl.net (8.8.3/950822.1) id RAA28487; Thu, 24 Jul 1997 17:08:12 -0400 (EDT) Received: from p3a.silicon.sentex.ca (p3a.silicon.sentex.ca [207.245.212.36]) by granite.sentex.net (8.8.6/8.6.9) with SMTP id RAA09732; Thu, 24 Jul 1997 17:17:21 -0400 (EDT) Message-Id: <3.0.16.19970724170557.291f8052@mathtrek.com> X-Sender: mathtrek@mathtrek.com X-Mailer: Windows Eudora Pro Version 3.0 (16) Date: Thu, 24 Jul 1997 17:05:59 -0400 To: i1s@psu.edu (Inge Schuster), chemistry@www.ccl.net From: "W. R. Smith" Subject: Re: CCL:mac program for solving chemical equilibria Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Hello, If you have SoftWindows emulation, our EQS4WIN fit your requirements. A free downloadable Lite Version is available from our web site (UEL below). It can do small-problem calculations, and has a number of built-in example problems from many areas, including those you mention. At 11:12 AM 7/24/97 -0400, Inge Schuster wrote: >Hi! Does anyone know of any program for the Mac which can do calculations >associated with simultaneous chemical equilibria, titrations, etc. in >non-aqueous media ( where pH is not a factor)? > > Inge Schuster >I1S@Psu.edu > > > >-------This is added Automatically by the Software-------- >-- Original Sender Envelope Address: i1s@email.psu.edu >-- Original Sender From: Address: i1s@psu.edu >CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator >MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 >Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > > > -- W. R. Smith, PhD, P. Eng., Senior Scientist, Mathtrek Systems -- 3-304 Stone Road West, Suite 165, Guelph, Ontario CANADA N1G 4W4 EMail: support@mathtrek.com Tel:519-763-1356,FAX:519-763-4525 --------------------- http://www.mathtrek.com --------------------- -Mathtrek Systems - Home of EQS4WIN Chemical Equilibrium Software - From omar@arkham.boston.sgi.com Thu Jul 24 18:13:15 1997 Received: from sgi.sgi.com for omar@arkham.boston.sgi.com by www.ccl.net (8.8.3/950822.1) id RAA28668; Thu, 24 Jul 1997 17:49:08 -0400 (EDT) Received: from sgibos.boston.sgi.com ([169.238.34.4]) by sgi.sgi.com (950413.SGI.8.6.12/970507) via ESMTP id OAA01586; Thu, 24 Jul 1997 14:49:07 -0700 env-from (omar@arkham.boston.sgi.com) Received: from arkham.boston.sgi.com by sgibos.boston.sgi.com via ESMTP (951211.SGI.8.6.12.PATCH1042/940406.SGI) id RAA14062; Thu, 24 Jul 1997 17:49:03 -0400 Received: (from omar@localhost) by arkham.boston.sgi.com (950413.SGI.8.6.12/950213.SGI.AUTOCF) id RAA28643; Thu, 24 Jul 1997 17:49:01 -0400 From: "Omar G. Stradella" Message-Id: <9707241749.ZM28641@arkham.boston.sgi.com> Date: Thu, 24 Jul 1997 17:49:01 -0400 In-Reply-To: Xiaofeng Duan "CCL:compiling Gamess on SGI O2" (Jul 24, 3:17pm) References: Organization: Silicon Graphics, Inc. Reply-to: omar@boston.sgi.com X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: chemistry@www.ccl.net, duanx@Picard.ml.wpafb.af.mil Subject: Re: CCL:compiling Gamess on SGI O2 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii On Jul 24, 3:17pm, Xiaofeng Duan wrote: > Subject: CCL:compiling Gamess on SGI O2 > Does anyone has experience in compiling Gamess on SGI O2 (R10000) machine? > We tried to do so (Gamess version 31 Oct. 96) recently on the machine (IRIX > 6.3, Fortran 7.1), and it seemed like everything went smoothly, no > error messages during compiling and linking. However, the binary file was > not excutable. When we run it, we get a message like "Exec format error". We > tried to set ARCH='-r10000' and ARCH=' '; the result was the same. > It would be appreciated if someone can help in pointing out what the problem > could be? > Hi Xiaofeng, You have to compile and link with 32bits because the IRIX 6.3 kernel that runs on O2 machines doesn't support execution of 64bit executables. Change in comp, compall and lked all -64 (related to SGI) into -n32. Omar. -- +---------------------------------------------------------------------+ Omar G. Stradella, Ph.D. Supercomputing Applications Silicon Graphics, Inc. Computational Chemistry One Cabot Road, Hudson, MA 01749, USA N 42 22'41" W 71 33'45" E-mail: omar@boston.sgi.com Phone: +1-508-567-2258 FAX: +1-508-562-4755 http://www.sgi.com/ChemBio http://reality.sgi.com/omar +-------- Ph-nglui mglw'nafh Cthulhu R'lyeh wgah'nagl fhtagn -------+ From SMITHJA@ucarb.com Thu Jul 24 18:18:12 1997 Received: from hscmg02.hou.ucarb.com for SMITHJA@ucarb.com by www.ccl.net (8.8.3/950822.1) id RAA28681; Thu, 24 Jul 1997 17:52:20 -0400 (EDT) Received: by hscmg02.hou.ucarb.com with Internet Mail Service (5.0.1457.3) id ; Thu, 24 Jul 1997 16:53:13 -0500 Message-ID: From: "Smith JA (Jack)" To: "'Peter Shenkin'" Cc: "'CHEMISTRY@www.ccl.net'" Subject: RE: Object-oriented means for computational chemist Date: Thu, 24 Jul 1997 16:52:25 -0500 X-Priority: 3 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.0.1457.3) Content-Type: text/plain >> >On the other hand, using C++, it's not possible to write a >> >general-purpose library callable from other languages... >> >Or so I'm told by those more conversant in C++ than I. > >> I find little problem with >> maintaining the overall system architecture and handling the user >> interface with a good application C++ class library, writing reusable >> non-computational 'modules' in plain C, and making use of (and even >> extending) existing FORTRAN libraries and program segments for the bulk >> of the computational work. > >Your point is well taken, and I don't disagree. On the other hand, >that's not quite the issue I was trying to raise. > >The issue I was trying to raise is that regardless of whether one >wants to write the front end in C, C++ or Fortran, or anything else, >the language definition of C++ *precludes* writing a linkable code >libraries in C++ if one ever wants to access the library routines >from another language. This is really too bad, because, whether >it's optimal right now or not, OO techniques, including inheritance, >are not inherently ill-suited for efficient computational methods and >even offer some advantages. I'd love to be able to write some of these >underlying libraries in C++, but right now I cannot, because I >don't feel that I can tie the *users* of the libraries -- who may >not be limited to me -- to C++ exclusively. I guess the issue comes down to 'reusable'. Traditional subroutine libraries are quite reusable in almost any programming paradigm, while C++ (or other OO language) objects are 'reusable' primarily through inheritance, which requires an appropriate OO environment (and which unfortunately may be OO language dependent). I suppose this is a good argument for using an OO development environment even if you don't intend to fully exploit it. What we need is the ability to mix OO languages/classes like we can non-OO languages. I predict that that day will come relatively soon. There was a time when mixing Object Pascal and MPW C++ within the MacApp framework was workable on the Mac. Perhaps now its time for Object FORTRAN! ;-) I'd suggest that OO development environments and class libraries/frameworks are today what linkage editors and object libraries were in the late 60's and early 70's (for those who remember the simple "compile, load & go" days where the only thing you 'inherited' was someone's job control cards and a place in line at the keypuch or the card reader). I wish the OO paradigm was more mature when X came into vogue. The choice of going with an X toolkit (and a starter set of widgets) or using just the intrinsic library was an analogous issue. I went the library route and later regretted it. - Jack (This is my last public post on this issue - I promise!) From fgonzale@lauca.usach.cl Thu Jul 24 19:13:14 1997 Received: from ralun.usach.cl for fgonzale@lauca.usach.cl by www.ccl.net (8.8.3/950822.1) id SAA28983; Thu, 24 Jul 1997 18:52:55 -0400 (EDT) Received: from lauca.usach.cl (lauca.usach.cl [158.170.64.28]) by ralun.usach.cl (8.6.11/8.6.9) with ESMTP id TAA21888 for ; Thu, 24 Jul 1997 19:01:52 -0500 Received: (from fgonzale@localhost) by lauca.usach.cl (8.6.12/8.6.12) id SAA25258; Thu, 24 Jul 1997 18:56:18 -0400 Date: Thu, 24 Jul 1997 18:56:17 -0400 (CST) From: Fdo Danilo Gonzalez Nilo To: chemistry@www.ccl.net Subject: g94w debugging Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, folks: If anything goes wrong when running a gaussian g94w job and the link dies,a short message like "severe error message # 2070" doesn't help much. Is there any way of knowing where exactly the problem was ? Thanks a lot for any help. ************************************************************************* Fernando Danilo Gonzalez N. University of Santiago de Chile Faculty of Chemistry and Biology Casilla 40, Correo 33, Santiago, Chile fono: 681 2575 E-mail : fgonzale@lauca.usach.cl fax : (562) 681 2108 danilo@quimbio.usach.cl URL : http://quimbio.usach.cl/~danilo/ *************************************************************************x From Willie@microsimulations.com Thu Jul 24 20:13:15 1997 Received: from maple.nis.net for Willie@microsimulations.com by www.ccl.net (8.8.3/950822.1) id TAA29157; Thu, 24 Jul 1997 19:42:50 -0400 (EDT) Received: from DELLLM by maple.nis.net with smtp (Smail3.1.29.1 #13) id m0wrXR3-0010TTC; Thu, 24 Jul 97 19:36 EDT Message-ID: <33D8055D.3731@microsimulations.com> Date: Thu, 24 Jul 1997 18:46:05 -0700 From: Willie Cui Organization: microsimulations X-Mailer: Mozilla 2.02E-KIT (Win95; U; 16bit) MIME-Version: 1.0 To: "Dr. Heinz Schiffer" CC: Computational Chemistry List Subject: Re: CCL:Fortran for C Programmers? References: <9707220138.AA23901@chasma.harvard.edu> <33D46209.794B@h1tw0036.hoechst.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Heinz, I could not found any good book on C++ for Fortran programer when I started to learn C++ a few year ago. I benefited from the following books in my learning of C++. Bjarne Stroustrup, Addison Wesley The C++ Programming Lauguage, 2nd Edition 0-201-53992-6 The Design and Evolution of C++ 0-201-54330-3 If you like to learning by writing, try Teach Yourself Visual C++ in 21 days or something similar. This type of books are normally not well written. However, it get you start fast and have fun. Oh, the tutorial sample for Visual C++, Scribble, is well designed. I started with this, I enjoyed it. This comes with the VC++ compiler CD. Hope this is useful. Enjoy C++ programming! Dr. Heinz Schiffer wrote: > > Gabriel Berriz wrote: > > > > While we're on the subject of mixed-language programming, does anyone > > know of a book (or any other reference) on Fortran for C programmers? > > In my view the very best book on FORTRAN is : > > Michael Metcalf > Effective Fortran 77 > Oxford University Press, Oxford 1987 > ISBN 0-19-853709-3 > > > would be extremely helpful. (Unfortunately, there seems to be more > > demand and supply for guides to C for Fortran programmers than the > > other way around... :/ ) > > I am really looking for a good book on C and C++ for FORTRAN > programmers. I know, that depend on the personal style. So, I > would like to have a Metcalf for C++. I never saw one, so may be > some of you can recommend something. > > Thanks a lot, > Ciao > Heinz > > -- > Dr. Heinz Schiffer Phone ++49-69-305-2330 > Hoechst CR&T Fax ++49-69-305-81162 > Scientific Computing, G864 Email schiffer@h1tw0036.hoechst.com > 65926 Frankfurt am Main Schiffer@CRT.hoechst.com > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: schiffer@h1tw0036.hoechst.com > -- Original Sender From: Address: schiffer@h1tw0036.hoechst.com > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html -- Willie Cui, Ph.D. voice 201-512-0486 MicroSimulations fax: 201-512-0489 478 Green Mountain Rd. email: willie@microsimulations.com Mahwah, NJ 07430 URL: http://www.microsimulations.com From Jeffrey.Gosper@brunel.ac.uk Wed Jul 23 05:12:59 1997 Received: from himiko.brunel.ac.uk for Jeffrey.Gosper@brunel.ac.uk by www.ccl.net (8.8.3/950822.1) id EAA17839; Wed, 23 Jul 1997 04:38:35 -0400 (EDT) Received: from castjjg.brunel.ac.uk (actually chem-pc-03.brunel.ac.uk) by himiko.brunel.ac.uk with SMTP-BRUNEL (PP); Wed, 23 Jul 1997 09:38:29 +0100 Date: Wed, 23 Jul 1997 09:35:08 PDT From: Jeffrey Gosper Subject: BABELWin on NT To: chemistry@www.ccl.net Message-ID: Priority: Normal MIME-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Dear CCL users, there has been a couple of problems using BABELWin under NT as well as the inclusion of spaces in filenames and directories names. Pat Walters has suggested and simple fix for the spaces problem by enclosing the filenames in double quotes. I am please to report that I have fixed these bugs and a new version of BABELWin (v1.03) for Win95/NT is now located on my ftp server (ftp.brunel.ac.uk in /pc/chem/babelwin.zip). I hope you all enjoy using BABELWin and please drop me a line if you download the program. Also free feel to report any bugs you find in the program. Cheers. /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\ Dr. Jeff Gosper, Dept. of Chemistry, BRUNEL University Uxbridge Middx UB8 3PH, UK voice: 01895 274000 x2187, facsim: 01895 256844 internet/email/work: Jeffrey.Gosper@brunel.ac.uk internet/WWW: http://www.brunel.ac.uk/~castjjg Re_View's home page (molecular animations or Chem-4D): http://www.brunel.ac.uk/depts/chem/ch241s/re_view/re_view.htm \/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/ From rgab@proteus.co.uk Wed Jul 23 09:12:55 1997 Received: from petersgate.proteus.co.uk for rgab@proteus.co.uk by www.ccl.net (8.8.3/950822.1) id IAA18782; Wed, 23 Jul 1997 08:54:35 -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 NAA18599; Wed, 23 Jul 1997 13:54:10 GMT Message-Id: <199707231354.NAA18599@petersgate.proteus.co.uk> From: Richard Bone Date: Wed, 23 Jul 1997 13:54:44 +0100 To: wdi@eros.ccc.uni-erlangen.de Subject: Re: CCL:SMILES databases - ERROR Cc: utz@pharmazie.uni-erlangen.de, CHEMISTRY@www.ccl.net References: <199707211209.MAA11059@petersgate.proteus.co.uk> Apologies: in sorting through my replies, I mis-attributed authorship. The message from Wolfgang Utz concerned a suggestion to use a structure- editor at http://schiele.organik.uni-erlangen.de Sorry again; there was no attempt by anyone to claim authorship for anything they hadn't done. 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 MAILER-DAEMON@www.ccl.net Wed Jul 23 09:13:01 1997 Received: from schiele for MAILER-DAEMON@www.ccl.net by www.ccl.net (8.8.3/950822.1) id IAA18754; Wed, 23 Jul 1997 08:46:14 -0400 (EDT) Received: by schiele (950911.SGI.8.6.12.PATCH825/940406.SGI.AUTO) id OAA05700; Wed, 23 Jul 1997 14:46:33 +0200 From: "Wolf-Dietrich Ihlenfeldt" Message-Id: <9707231446.ZM5698@eros.ccc.uni-erlangen.de> Date: Wed, 23 Jul 1997 14:46:29 -0600 In-Reply-To: Richard Bone "CCL:SMILES databases - summary" (Jul 21, 12:08) References: <199707211209.MAA11059@petersgate.proteus.co.uk> Reply-To: wdi@eros.ccc.uni-erlangen.de X-Phones: +49-9131-85-6579 X-Fax: +49-9131-85-6566 X-Mailer: Z-Mail (3.2.2 10apr95 MediaMail) To: Richard Bone Subject: Re: CCL:SMILES databases - ERROR Cc: utz@pharmazie.uni-erlangen.de, CHEMISTRY@www.ccl.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 8bit On Jul 21, 12:08, Richard Bone wrote: > Subject: CCL: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 ... "): > > 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). WHAT IS THIS? Wolfgang Utz DID NOT MAKE THESE COMPOUNDS AVAILABLE. He was not involved at all at any step. I (Wolf-D. Ihlenfeldt) did all the steps of the conversion myself, with my own software. Please refrain >from claiming authorship for work you do not have participated in! > Available by FTP: > (ftp://schiele.organik.uni-erlangen.de/pub/nci/nci4000.smi.gz) > This is the server I administer. Wolfgang Utz does not even have an account here. -- Dr. Wolf-D. Ihlenfeldt Computer Chemistry Center, University of Erlangen-Nuernberg Naegelsbachstrasse 25, D-91052 Erlangen (Germany) Tel (+49)-(0)9131-85-6579 Fax (+49)-(0)9131-85-6566 --- The three proven methods for ultimate success and fame: 1) Nakanu nara koroshite shimae hototogisu 2) Nakanu nara nakasete miseyou hototogisu 3) Nakanu nara naku made matou hototogisu From MAILER-DAEMON@www.ccl.net Wed Jul 23 11:28:42 1997 Received: from schiele for MAILER-DAEMON@www.ccl.net by www.ccl.net (8.8.3/950822.1) id LAA19550; Wed, 23 Jul 1997 11:02:41 -0400 (EDT) Received: by schiele (950911.SGI.8.6.12.PATCH825/940406.SGI.AUTO) id RAA06562; Wed, 23 Jul 1997 17:02:52 +0200 From: "Wolf-Dietrich Ihlenfeldt" Message-Id: <9707231702.ZM6560@eros.ccc.uni-erlangen.de> Date: Wed, 23 Jul 1997 17:02:48 -0600 In-Reply-To: Richard Bone "CCL:SMILES databases - summary" (Jul 21, 12:08) References: <199707211209.MAA11059@petersgate.proteus.co.uk> Reply-To: wdi@eros.ccc.uni-erlangen.de X-Phones: +49-9131-85-6579 X-Fax: +49-9131-85-6566 X-Mailer: Z-Mail (3.2.2 10apr95 MediaMail) To: CHEMISTRY@www.ccl.net Subject: Re: CCL:SMILES databases - summary Cc: webmaster@clogp.pomona.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 8bit On Jul 21, 12:08, Richard Bone wrote: > Subject: CCL:SMILES databases - summary > 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. Well, regularly structured websites can be easily milked: Hack, hack, hack... ---------------------------- #!tcl exec wget -r --no-parent http://clogp.pomona.edu/medchem/chem/master/mf/ set filelist [exec find clogp.pomona.edu/medchem/chem/master/mf/ \ -name *.html -print] foreach file $filelist { set fh [open $file] set data [read $fh] while {[regexp -nocase -indices "
smiles\[ \t\n\]+
(\[^\t\n\]*)\[ \t\n\]+
full name\[ \t\n\]*
(\[^\t\n\]*)\[ \t\n\]*" $data dummy sidx nidx]} { lassign $sidx sstart sstop if {$sstart>$sstop} break set smiles [string trim [crange $data $sstart $sstop]] lassign $nidx nstart nstop if {$nstart<$nstop} { set name [string trim [crange $data $nstart $nstop]] } else { set name "Unnamed" } puts "$smiles\t$name" set data [crange $data $nstart+5 end] } close $fh } exec rm -r clogp.pomona.edu ------------------------------------------------- You need tclx, wget and find on your machine to execute this. The program yields 30914 structures in an hour or so (limited by the speed of web access). Is this politically correct to execute? I don't know, the website is not very clear about this. To avoid problems, please do not ask me for the dataset. -- Dr. Wolf-D. Ihlenfeldt Computer Chemistry Center, University of Erlangen-Nuernberg Naegelsbachstrasse 25, D-91052 Erlangen (Germany) Tel (+49)-(0)9131-85-6579 Fax (+49)-(0)9131-85-6566 --- The three proven methods for ultimate success and fame: 1) Nakanu nara koroshite shimae hototogisu 2) Nakanu nara nakasete miseyou hototogisu 3) Nakanu nara naku made matou hototogisu From brian@bert.chem.wsu.edu Wed Jul 23 13:12:59 1997 Received: from cheetah.it.wsu.edu for brian@bert.chem.wsu.edu by www.ccl.net (8.8.3/950822.1) id MAA20196; Wed, 23 Jul 1997 12:59:05 -0400 (EDT) Received: from bert.chem.wsu.edu (bert.chem.wsu.edu [134.121.43.22]) by cheetah.it.wsu.edu (8.8.5/8.8.5) with SMTP id JAA05791 for ; Wed, 23 Jul 1997 09:59:04 -0700 (PDT) Received: by bert.chem.wsu.edu (AIX 3.2/UCB 5.64/4.03) id AA16388; Wed, 23 Jul 1997 09:49:19 -0700 From: brian@bert.chem.wsu.edu (Brian W. Beck) Message-Id: <9707231649.AA16388@bert.chem.wsu.edu> Subject: Software:Equation Editors (Summary) To: CHEMISTRY@www.ccl.net (Computational Chemistry List) Date: Wed, 23 Jul 1997 09:49:19 -0700 (PDT) X-Mailer: ELM [version 2.4 PL24] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Here is the summary of responses I got concerning equation editors for Mac using MS Word. Specifically, I was looking for something for equations as Endnote is for references and the most important feature I was looking for was global search and replace (i.e. replace all V(x) with U(t) through a whole document. Hope this helps, -Brian --------------------------------------------------------------------- 1) Expressionist (from Waterloo MapleSoft ) shenkin@still3.chem.columbia.edu (Peter Shenkin) Hi. I've used Expressionist for many years, and it's very good. It's lots better than the equation formatter in MS/Word/5, but I've not tried the one in MS/Word/6. Pieter Stouten I have used (don't have much need for an equation editor at the moment) Expressionist extensively. It is not as seamlessly integrated with MSWord as EndNote (which I heavily use), but it is almost there. One can double-click Expressionist equations and that opens Expressionist. Closing the equation window pastes the updated equation back into Word. Expressionist is very easy to use and gives me enough control to produce equations that are good enough for me. Your mileage may vary, but I'd suggest you give Expressionist a try. --------------------------------------------------------------------- 2) Word Formula Entry Kieran F Lim (Lim Pak Kwan)" before Microsoft signed the deal with MathType to have an object based eqn. editor, Word (version 4) had a formula-entry capability eg something like CMD-OPTION-\ then FRAC to get a fraction .\frac(top,bottom) automatically set up in the old FORMALA GLOSSARY which came FREE with the Word program back in the good ol' days! R.G.Gilbert and S.C.Smith used this formula-entry capability to write EVERY equation in their book "Theory of Unimolecular Reactions ..." so it is a very powerful tool. have a look in your library to see what the final product looks like. (free plug for my friends here) this capability still exists in word 5 and 6, but is now omitted from the manual. and you don't get the FORMALA GLOSSARY any more. I use a mixture of Word's formula entry and a program called Expressionist which is another object based eqn. editor BUT it does the capability to convert all its objects INTO WORD MARKUP FORMULA ENTRIES. Expressionist is made by Prescience fax 1-(415) 882-0530] try Prescience.com as an e-mail or WWW site I do NOT know of any program which has the ability to back-convert word formula entries into an object based eqn for easy editting. personally, I prefer Expressionist, but I recommend you should get either the FULL version of MathType, not the toy version in Word or the Expressionist program or beg, borrow or steal a manual for Word 4 which sets out Word's formula entry capability. --------------------------------------------------------------------- 3) Mathtype (which appears to be the progenitor of the Eqn Ed.) Krzysztof Radacki Try MathType by Design Sicience Inc (http://www.mathtype.com/mathtype/). Guido Germano You can try "MathType", which is an enhanced version of "Equation Editor", but which hasn't all the features you want, or resort to "Scientific Word", a program which looks like a conventional WYSIWIG word processor, but saves the documents in LaTeX format; however, I don't know whether there exist a port for the Mac (I saw it only for Windows so far). Or convert yourself altogether to LaTeX, using for instance "TeXtures", which compiles your document while you write the source. --------------------------------------------------------------------- 4) TeX Editor for Macs Juan Carlos Paniagua I don't know such an equation editor for MSWord, but the TeX editor Scientific Word is, in principle, a good alternative: it has the tools for editing text and formulas in the same window (with e pseudo-wysiwyg look), distinguishes between both types of information, and imports documents produced with other editors via the MS-RTF format. The problem is that some important features, like the translation from RTF, don't work well due to bugs of the software, and the support service of the company that produces it (TCI) is inoperative. You can have a look at http://www.thomson.com/tcisoft/products/mac25.html or http://www.matstat.unit.no/~yngvesv/swp/swp.html victoria@acdlabs.com (Victoria Barclay) There *is* a version of TeX for the Mac; it's called OzTeX. It's shareware (I think) developed by an Australian fellow. clifford@lorentzian.com (Simon Clifford) After I used Word 5's equation editor to type the equations in my thesis I swore never again. Now by choice I use LaTeX. Since you already have experience with this it might be worth using LaTeX on the Mac? There is at least one very good shareware port, called OzTeX, which should be available on any info-mac mirror. --------------------------------------------------------------------- Since it seemed like a number of people were suggesting Expressionist, I sent a query to customer support. ptarr@maplesoft.com (Patti Tarr) Thanks for your interest in Maple software. Any questions you may have can be directed to me at ptarr@maplesoft.com or by calling 1-800-267-6583 ext. 227. There are no compatiblity issues using Expressionist 3.2 with Word 5.1a for Mac. You should have no problems running Expressionist in this environment. me> me> Can I do global search and replace with me> Expressionist? For example, if I have me> a paper full of equations and I me> want to change all the V(r) to U(r) me> through the whole document, can I do me> this? A global search and replace won't work. When you paste an expression into Word, it is considered a graphic rather than text so is not included when Word searches through the document. Unfortunately, there isn't really a way around this. The only alternative to manually make each change. Please let me know if I can be of further assistance. Sincerely, Patti Tarr Waterloo Maple Inc. 1-800-267-6583 ext. 227 ptarr@maplesoft.com ---------------------------------------------------------------------------- Finally, I asked them if it were possible to keep a "library" of equations which could be "Publish/Subscribed" into a word document such that the word document would automatically update if you changed the Expressionist "library". They indicated that this was partially possible in that you could make a library of equations, but that each time you put an equation into Word, it became an independent entity and double-clicking would bring up a new Expressionist document not the original "library". -- ============================================================================= | .---------.| Brian W. Beck | E-mail Addresses: | |/\ | || Biochem/Biophysics | brian@bert.chem.wsu.edu | || \\ WSU || Washington St. Univ| brian_beck@wsu.edu | |\ - *|| 639 Fulmer | URL http://elmo.chem.wsu.edu/~brian | | | || Pullman, WA, USA | VOICE (509) 335-4083 | | \___________|| 99164-4660 | FAX (509) 335-9688 | ============================================================================= From bernhold@tarkovsky.npac.syr.edu Wed Jul 23 18:13:02 1997 Received: from postoffice.npac.syr.edu for bernhold@tarkovsky.npac.syr.edu by www.ccl.net (8.8.3/950822.1) id SAA22606; Wed, 23 Jul 1997 18:10:35 -0400 (EDT) Received: from tarkovsky.npac.syr.edu (tarkovsky-007.npac.syr.edu [128.230.7.175]) by postoffice.npac.syr.edu (8.7.5/8.7.1) with ESMTP id SAA21548; Wed, 23 Jul 1997 18:08:14 -0400 (EDT) Received: from localhost (bernhold@localhost) by tarkovsky.npac.syr.edu (8.8.5/8.7.1) with SMTP id SAA26888; Wed, 23 Jul 1997 18:08:13 -0400 (EDT) Message-Id: <199707232208.SAA26888@tarkovsky.npac.syr.edu> X-Authentication-Warning: tarkovsky.npac.syr.edu: bernhold@localhost didn't use HELO protocol To: "Ping Du" cc: chemistry@www.ccl.net Subject: Re: CCL: CCL:Object-oriented means for computational chemist In-reply-to: <19970722083948.138bb7cb.in@S2> Date: Wed, 23 Jul 1997 18:08:13 -0400 From: "David E. Bernholdt" On Tue, 22 Jul 1997 07:45:08 +0000 "Ping Du" wrote: > Inheritance is pobably the most important feature of > OO design if you would like your program to be extensible and > reusable. I don't entirely agree. Having done OO _design_ and implemented those designs in "non-OO" languages, I believe that the other principles of OO design (abstraction, encapsulation, modularity) are probably more important and more powerful. I have not encountered a case where I felt at a serious disadvantage because the languages I was using did not support inheritance. But in any case, I must stress the importance of design. Looking back, I think that a thorough design phase probably allowed us to find the right abstractions so that inheritance was really not an issue, and we could do what inheritance was required "manually". It also may be a property of the problem to some extent (in our case a broad spectrum of electronic structure methods). -- David E. Bernholdt | Email: bernhold@npac.syr.edu Northeast Parallel Architectures Center | Phone: +1 315 443 3857 111 College Place, Syracuse University | Fax: +1 315 443 1973 Syracuse, NY 13244-4100 | URL: http://www.npac.syr.edu From ccl@www.ccl.net Wed Jul 23 20:13:04 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id TAA23059; Wed, 23 Jul 1997 19:55:39 -0400 (EDT) Received: from auric.chem.csiro.au for Dave.Winkler@molsci.csiro.au by bedrock.ccl.net (8.8.6/950822.1) id TAA17524; Wed, 23 Jul 1997 19:55:34 -0400 (EDT) Received: from [138.194.46.107] (cpr-46107.chem.csiro.au) by auric.chem.csiro.au with SMTP id AA18471 (5.67b/IDA-1.5 for chemistry@ccl.net); Thu, 24 Jul 1997 09:52:18 +1000 X-Sender: win097@auric.chem.csiro.au Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 24 Jul 1997 09:54:30 +1000 To: CHMINF-L@LISTSERV.INDIANA.EDU, chemistry@ccl.net From: "Dr. Dave Winkler" Subject: Pi stacking energies Hi, Netters, Can anyone give me an estimate of the contribution to ligand binding energy which may result from an optimum pi-stacking interaction in the active site? I have a tyrosine forming the base of a site and good ligands contain aromatic rings which lie ~3.5 A above the aromatic ring of tyrosine. Cheers, Dave Dr. David A. Winkler Email: dave.winkler@molsci.csiro.au Senior Principal Research Scientist Voice: 61-3-9545-2477 CSIRO Division of Molecular Science Fax: 61-3-9545-2446 Private Bag 10,Clayton South MDC, http://www.csiro.au Clayton 3169, Australia http://www.molsci.csiro.au