From chemistry-request@server.ccl.net Tue Apr 11 15:03:22 2000 Received: from icarus.cc.uic.edu (icarus.cc.uic.edu [128.248.121.53]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA01939 for ; Tue, 11 Apr 2000 15:03:22 -0400 Received: from localhost (akulka1@localhost) by icarus.cc.uic.edu (8.8.8/8.8.8) with ESMTP id OAA00443; Tue, 11 Apr 2000 14:01:17 -0500 (CDT) X-Authentication-Warning: icarus.cc.uic.edu: akulka1 owned process doing -bs Date: Tue, 11 Apr 2000 14:01:16 -0500 (CDT) From: Amit Subhash Kulkarni X-Sender: akulka1@icarus.cc.uic.edu To: Daniel Severance cc: "CCL (E-mail)" Subject: Re: CCL:CAS Numbers In-Reply-To: <15189A4705A8D31189B700805F85410B1D821D@sdnt1> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Dan, Check out www.chemfinder.com It is very nice site where you can search for molecules with there CAS numbers. Best Luck Cheers Amit ############################## Laboratory of Drug Design University of Illinois at Chicago Department of Medicinal Chemistry akulka1@uic.edu ############################## On Mon, 10 Apr 2000, Daniel Severance wrote: > Hi, > I have a list of about 2000 CAS numbers - is there a reasonably > inexpensive way to use those numbers to retrieve the corresponding > structures? Also one that wouldn't take weeks of a human's time would be > nice :-). > Thanks! > Dan > > > ____________________________________________________ > Daniel L. Severance Ph.D. > Computational Chemistry > ACADIA Pharmaceuticals > 3911 Sorrento Valley Boulevard > San Diego CA 92121-1402 USA > > phone (858) 558 2871 > fax (858) 558 2872 > dseverance@acadia-pharm.com > www.acadia-pharm.com > > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > k From chemistry-request@server.ccl.net Tue Apr 11 18:20:20 2000 Received: from wn1.sci.kun.nl (wn1.sci.kun.nl [131.174.8.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA02909 for ; Tue, 11 Apr 2000 18:20:20 -0400 Received: from studs3.sci.kun.nl by wn1.sci.kun.nl via studs3.sci.kun.nl [131.174.124.4] with ESMTP for id AAA02974 (8.8.8/3.29); Wed, 12 Apr 2000 00:20:18 +0200 (MET DST) From: "E.L. Willighagen" Received: by studs3.sci.kun.nl via egonw@localhost for CHEMISTRY@ccl.net id AAA16767 (8.8.8/3.1); Wed, 12 Apr 2000 00:20:18 +0200 (MET DST) Date: Wed, 12 Apr 2000 00:20:18 +0200 (MET DST) Message-Id: <200004112220.AAA16767@studs3.sci.kun.nl> To: CHEMISTRY@ccl.net Subject: re: CML is dead > I realize that there is a need for (web) publishing tools, > and that the current java tools are a means to this end, however > without programs that generate CML there is nothing to publish. 1. web publishing is *very* important... note that many ecommerce is based in web technology... 2. generation is not that big a problem... several formats can be translated into CML (mopac, gaussian, pdb, xyz, mdl-mol to give a short list). Combined with the (standard desktop) tool Babel, you can transform almost any information automatically into CML... and information in *any* format can be generated by all software... So i disagree, that generation of CML data is the problem. A second thing though is the availability of CML data. And i think in the "Dutch Dictionary on Organic Chemistry" (http://www.sci.kun.nl/woc/) we do a fine job in providing "OpenSource" CML data, which consists mostly of 2D/3D coordinates, but also a growing list of animations (with energies for each frame). Moreover, without proper tools to view/use CML data, there is no use in generating CML data... But oke, this is maybe what we in the Netherlands call "het kip en het ei probleem"... (translated: what came earlier: the chicken or the egg) And i think with these new XSLT stylesheets (see H.Rzepa email) the CML community is doing a very good job in making CML usefull... All these effords are a bit inmature now, but will evolve rapidly in the next year... (i'll promise you that...) But one thing we certainly *DO* need, is a day-by-day up-to-date website where every CML tool/application is mentioned... Finally, we now have a tool to check to validity of CML tools/software which is a very good thing. Egon From chemistry-request@server.ccl.net Wed Apr 12 03:28:47 2000 Received: from judy.ic.ac.uk (judy.ic.ac.uk [155.198.5.28]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA05844 for ; Wed, 12 Apr 2000 03:28:46 -0400 Received: from juliet.ic.ac.uk ([155.198.5.4]) by judy.ic.ac.uk with esmtp (Exim 2.12 #1) id 12fHa1-0004ru-00 for CHEMISTRY@ccl.net; Wed, 12 Apr 2000 08:28:53 +0100 Received: from origin.ch.ic.ac.uk ([155.198.224.252] helo=chcmga.ch.ic.ac.uk) by juliet.ic.ac.uk with esmtp (Exim 2.12 #1) id 12fHZm-0003Tb-00 for CHEMISTRY@ccl.net; Wed, 12 Apr 2000 08:28:38 +0100 Received: from rzepa.ch.ic.ac.uk ([155.198.234.86]) by chcmga.ch.ic.ac.uk with esmtp (Exim 2.02 #1) id 12fHZu-0026D6-00; Wed, 12 Apr 2000 08:28:46 +0100 Mime-Version: 1.0 X-Sender: rzepa@argon.ch.ic.ac.uk Message-Id: In-Reply-To: References: Date: Wed, 12 Apr 2000 08:22:02 +0100 To: CHEMISTRY@ccl.net From: "Rzepa, Henry" Subject: Re: CCL:Is CML dead? Content-Type: text/plain; charset="us-ascii" >On Tue, 11 Apr 2000, Rzepa, Henry wrote: > >>We have mounted a number of XML tests using CML on >>http://www.xml-cml.org/test/ (a mirror site if the above is slow is >>http://www.ch.ic.ac.uk/chimeral/test/ ) You will need Internet >>Explorer 5.0 or 5.5 for Windows. > >I think this is close to the heart of the problem. The current efforts >are directed to *new* tools for visualisation (I work in a >Windows-Free (tm) environment) while we have plenty of old tools which >do the job, but are just not CML/XML enabled. I should note that at the above site and elsewhere, a fair number of legacy2cml converters (perl scripts and C programs) are available. I know others have written such programs, a large number by Peter Murray-Rust, but also others. This is of course a community effort, and will succeed as such. I also point our the richness of such tools originating from the bioinformatics communities; there are several pdb2cml converters, and also eg swissprot2cml etc etc >In the tests there are examples of combined structure/spectra >files. Instead of dumping the CML in a slow browser I would like to >give the CML file to rasmol to view the structure and the same file to >e.g. xmgrace to see a spectrum. Certainly as applications become DOM (Document object model) aware, this sort of behaviour will become routine. It need not be restricted to eg Browsers. Components for implementing DOMs are becoming available. We are writing an article on the chemical DOM API which will address some of these issues. Can I just add in the above example, that using two separate "legacy" programs to view separate elements of the XML document can only be an interim solution. Simple requirements such as atom <=> peak linking etc become difficult. The trend is to structured components, take for example the Chemsymphony/Chime/Cambridgesoft/Daylight etc etc Java classes. >What is needed for that is a simple >comprehensive C-library which can be called by the respective >programs. I believe a few years ago, Peter Murray-Rust developed about 400+ C classes called Euclid that does this. There are others (I believe crystallographers have developed similar solutions using CORBA). Would the list like to comment? >I realize that there is a need for (web) publishing tools, >and that the current java tools are a means to this end, however >without programs that generate CML there is nothing to publish. >I am willing to contribute to the library, as long as someone else (Henry?) >keeps the overview and coordinates things, which as Christoph Steinbeck >pointed out is crucial. We strongly encourage this. We will update our notes on legacy2cml tools and welcome people letting us know of others. -- Henry Rzepa. +44 (0)20 7594 5774 (Office) +44 (0)20 7594 5804 (Fax) Dept. Chemistry, Imperial College, London, SW7 2AY, UK. http://www.ch.ic.ac.uk/rzepa/ From chemistry-request@server.ccl.net Wed Apr 12 02:42:51 2000 Received: from scan1.fhg.de (scan1.fhg.de [153.96.1.35]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id CAA05476 for ; Wed, 12 Apr 2000 02:42:51 -0400 Received: from scan1.fhg.de (localhost [127.0.0.1]) by scan1.fhg.de (8.9.3/8.9.3) with ESMTP id IAA11275; Wed, 12 Apr 2000 08:42:34 +0200 (MET DST) Received: from iuct.iuct.fhg.de (iuct.iuct.fhg.de [153.96.228.2]) by scan1.fhg.de (8.9.3/8.9.3) with ESMTP id IAA11267; Wed, 12 Apr 2000 08:42:33 +0200 (MET DST) Received: from iuct.fhg.de (iuct190 [153.96.228.190]) by iuct.iuct.fhg.de (8.9.3/8.9.3) with ESMTP id IAA10037; Wed, 12 Apr 2000 08:42:27 +0200 (MET DST) Message-ID: <38F41BA6.28732433@iuct.fhg.de> Date: Wed, 12 Apr 2000 08:45:58 +0200 From: Martin Mueller Organization: Fh IUCT X-Mailer: Mozilla 4.7 [en] (Win98; I) X-Accept-Language: de,en MIME-Version: 1.0 To: Daniel Severance CC: "CCL (E-mail)" Subject: Re: CCL:CAS Numbers References: <15189A4705A8D31189B700805F85410B1D821D@sdnt1> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Daniel Severance wrote: > > Hi, > I have a list of about 2000 CAS numbers - is there a reasonably > inexpensive way to use those numbers to retrieve the corresponding > structures? Also one that wouldn't take weeks of a human's time would be > nice :-). SMILECAS database from Syracuse Research contains more than 103000 SMILES-Codes and CAS-numbers. In conjunction with their estimation software it takes only some minutes to search for thousands of CAS-numbers and to retrieve SMILES-Codes and names of chemicals. http://esc.syrres.com/interkow/smilecas.htm Martin -- Martin Mueller Fraunhofer-Institut fuer Umweltchemie und Oekotoxikologie http://www.iuct.fhg.de/ From chemistry-request@server.ccl.net Wed Apr 12 02:54:56 2000 Received: from dual.fqspl.com.pl (dual.fqspl.com.pl [212.244.147.6]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id CAA05594 for ; Wed, 12 Apr 2000 02:54:45 -0400 Received: from victor (victor.fqspl.com.pl [10.10.10.5]) by dual.fqspl.com.pl (8.9.3/8.9.3) with SMTP id HAA01381 for ; Wed, 12 Apr 2000 07:57:41 +0200 Message-ID: <00c201bfa44b$725886d0$050a0a0a@victor.fqspl.com.pl> From: "Victor Anisimov" To: Subject: Re: CCL:Is CML dead? Date: Wed, 12 Apr 2000 08:50:53 +0200 X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Hi, all. I have also failed finding such a library one can use for development of XML type applications. Without such a public domain or commercial available library it is difficult to expect a visible progress in CML/XML development. In my company I work with a variety of GUIs and computational engines. Thinking how to reduce an amount of my work I spend on development of new interface I realized for myself that I strongly need such a library. As a result I developed a proprietary XML type library which I call NTM which stands for Network Transparent Model and serves as a data exchange and event handling layer between GUI and computational engine either located on the same machine or separated by means of LAN or Internet. Having no XML library available I have designed NTM as an alternative standard to XML preserving only similar philosophy. Extra new standard is of course not good but as a developer I need a standard not only on a paper but as a library that should simplify my work. Another reason why I thought of development of proprietary protocol is related to XML functionality. I've heard a lot about unification of data exchange mechanism, but I've never heard about event handling features which are extremely necessary for GUI - "computational engine" communication, and which make this link alive. Therefore in addition to question of Peter Shenkin about XML library I would also add my piece of question - does somebody know about event handling features implementes in such assume somewhere existing XML library? With best regards, Victor Anisimov. -----Original Message----- From: Peter Shenkin To: chemistry@ccl.net Date: 12 апреля 2000 г. 1:25 Subject: CCL:Is CML dead? :Hear, hear. : :It was a lack of such tools several years ago that caused us to :shy away from XML/CML when designing our new Maestro interface. : :It is disappointing if, indeed, there are no such tools linkable :to C, Fortran and C++ even today. : :Henry, what sayest thou? : : -P. : :On Sat, 8 Jul 2000, David van der Spoel wrote: : :> On Tue, 11 Apr 2000, Rzepa, Henry wrote: :> :> >We have mounted a number of XML tests using CML on :> >http://www.xml-cml.org/test/ (a mirror site if the above is slow is :> >http://www.ch.ic.ac.uk/chimeral/test/ ) You will need Internet :> >Explorer 5.0 or 5.5 for Windows. :> :> I think this is close to the heart of the problem. The current efforts :> are directed to *new* tools for visualisation (I work in a :> Windows-Free (tm) environment) while we have plenty of old tools which :> do the job, but are just not CML/XML enabled. :> :> In the tests there are examples of combined structure/spectra :> files. Instead of dumping the CML in a slow browser I would like to :> give the CML file to rasmol to view the structure and the same file to :> e.g. xmgrace to see a spectrum. What is needed for that is a simple :> comprehensive C-library which can be called by the respective :> programs. I realize that there is a need for (web) publishing tools, :> and that the current java tools are a means to this end, however :> without programs that generate CML there is nothing to publish. :> I am willing to contribute to the library, as long as someone else (Henry?) :> keeps the overview and coordinates things, which as Christoph Steinbeck :> pointed out is crucial. :> :> Groeten, David. :> ________________________________________________________________________ :> Dr. David van der Spoel Biomedical center, Dept. of Biochemistry :> s-mail: Husargatan 3, Box 576, 75123 Uppsala, Sweden :> e-mail: spoel@xray.bmc.uu.se www: http://zorn.bmc.uu.se/~spoel :> phone: 46 18 471 4205 fax: 46 18 511 755 :> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ :> :> :> :> :> :> :> :> : :-- :** Whether the playing field is level depends on the coordinate system. *** :********* Peter S. Shenkin; Schrodinger, Inc.; (201)433-2014 x111 ********* :*********** shenkin@schrodinger.com; http://www.schrodinger.com *********** : : :-= This is automatically added to each message by mailing script =- :CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins :MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH :CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 :Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net : : : : From chemistry-request@server.ccl.net Wed Apr 12 03:31:36 2000 Received: from hermes.bmc.uu.se (hermes.bmc.uu.se [130.238.39.159]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA05900 for ; Wed, 12 Apr 2000 03:31:36 -0400 Received: from alpha2.bmc.uu.se ([130.238.37.65]) by hermes.bmc.uu.se (Post.Office MTA v3.5.3 release 223 ID# 0-62649U1500L1000S0V35) with SMTP id se; Wed, 12 Apr 2000 09:32:51 +0200 Received: from zorn.bmc.uu.se by alpha2.bmc.uu.se (5.65v3.2/1.1.10.5/07Jan00-1145AM) id AA08883; Wed, 12 Apr 2000 09:31:32 +0200 Date: Sun, 9 Jul 2000 09:20:34 +0200 (CEST) From: David van der Spoel X-Sender: spoel@zorn.bmc.uu.se To: "E.L. Willighagen" Cc: CHEMISTRY@ccl.net Subject: Re: CCL:CML is dead In-Reply-To: <200004112220.AAA16767@studs3.sci.kun.nl> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 12 Apr 2000, E.L. Willighagen wrote: >1. web publishing is *very* important... note that many ecommerce is > based in web technology... Yes but we're talking science here. >2. generation is not that big a problem... several formats can be > translated into CML (mopac, gaussian, pdb, xyz, mdl-mol to give > a short list). Combined with the (standard desktop) tool Babel, > you can transform almost any information automatically into > CML... and information in *any* format can be generated by all > software... I don't want babel! I want native support by *all* chemistry applications. That's right *all* applications! I realize that is a tad optimistic, especially considering that we have already lost Schrodingers support. But if that is not the aim, CML is just another file format. Users don't want to keep track of N versions of the same data, just because their N different applications need a reformatted version of this data. Even if you can convert with babel, this is still extremely messy. >Moreover, without proper tools to view/use CML data, there is no use >in generating CML data... That's why someone has to bite the bullet and write the library, and then implement it in some of the leading packages, like rasmol and xmgrace. I keep hammering on those two programs, because those are the most important ones! >All these effords are a bit inmature now, but will evolve rapidly in the >next year... (i'll promise you that...) There is no sign of evolution in the direction that I pointed out. >Finally, we now have a tool to check to validity of CML tools/software >which is a very good thing. I agree to this, and moreover I don't want to suggest that the current tools are useless. However I think what the average user wants is her/his program to generate data that she/he can load into another analysis program immediately. If one could also use the data in a web presentation that would be a big plus. What needs to be done is probably to involve organisations like ACS and others, and have them bless CML as the standard of chemical information. Looking on the ACS website I found that CML is already being accepted for electronic submission of two ACS journals, which is promising in this respect. Groeten, David. ________________________________________________________________________ Dr. David van der Spoel Biomedical center, Dept. of Biochemistry s-mail: Husargatan 3, Box 576, 75123 Uppsala, Sweden e-mail: spoel@xray.bmc.uu.se www: http://zorn.bmc.uu.se/~spoel phone: 46 18 471 4205 fax: 46 18 511 755 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From chemistry-request@server.ccl.net Wed Apr 12 05:07:43 2000 Received: from desmtp02.henkel.de (desmtp02.henkel.de [139.3.202.18]) by server.ccl.net (8.8.7/8.8.7) with SMTP id FAA06973 for ; Wed, 12 Apr 2000 05:07:42 -0400 From: Matthias.Hloucha@DENOTES.HENKEL.DE Received: by desmtp02.henkel.de(Lotus SMTP MTA v4.6.6 (890.1 7-16-1999)) id 412568BF.00374C6F ; Wed, 12 Apr 2000 11:04:00 +0100 X-Lotus-FromDomain: HENKEL KGAA To: chemistry@ccl.net Message-ID: <412568BF.00374A77.00@desmtp02.henkel.de> Date: Wed, 12 Apr 2000 11:03:16 +0100 Subject: simulation of surfactants Mime-Version: 1.0 Content-type: text/plain; charset=us-ascii Content-Disposition: inline Dear colleagues, who are the experts in the area of: -> simulation of surfactants in aqueous solution ? Best wishes Matt From chemistry-request@server.ccl.net Wed Apr 12 06:24:58 2000 Received: from wn1.sci.kun.nl (wn1.sci.kun.nl [131.174.8.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA07447 for ; Wed, 12 Apr 2000 06:24:58 -0400 Received: from studs3.sci.kun.nl by wn1.sci.kun.nl via studs3.sci.kun.nl [131.174.124.4] with ESMTP for id MAA17978 (8.8.8/3.29); Wed, 12 Apr 2000 12:24:48 +0200 (MET DST) From: "E.L. Willighagen" Received: by studs3.sci.kun.nl via egonw@localhost for CHEMISTRY@ccl.net id MAA07368 (8.8.8/3.1); Wed, 12 Apr 2000 12:24:47 +0200 (MET DST) Date: Wed, 12 Apr 2000 12:24:47 +0200 (MET DST) Message-Id: <200004121024.MAA07368@studs3.sci.kun.nl> To: CHEMISTRY@ccl.net Subject: re: CML is dead > I don't want babel! I want native support by *all* chemistry applications. > That's right *all* applications! Ah, that would be nice indeed... For Java i have developed such a toolbox one and a half year ago. I would love to see this ported to C(++) as wel... :) Oke, on native support: since CML is an XML application there are already file readers for every programming language... you can even select between different parsing styles: event based (startElement etc, SAX/SAX2) or object based (element-trees, DOM)... My Java CML Filter Library is based on SAX... and about DOM. Peter MR is working on ChemDom (in Java i think), but this is also quite easily ported to other language, since at is based on DOM which is already available in the other directory... Egon Java CML Filter Library: http://www.openscience.org/~egonw/cml/ Note that the site is a bit out of date... version 1.2.2 is out but i wanted to write an article first about the changes... From chemistry-request@server.ccl.net Wed Apr 12 06:41:38 2000 Received: from tisch.mail.mindspring.net (tisch.mail.mindspring.net [207.69.200.157]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA07583 for ; Wed, 12 Apr 2000 06:41:37 -0400 Received: from josiah (pool-207-205-146-158.dlls.grid.net [207.205.146.158]) by tisch.mail.mindspring.net (8.9.3/8.8.5) with ESMTP id GAA09913; Wed, 12 Apr 2000 06:39:26 -0400 (EDT) Message-ID: <001f01bfa46b$c80b4160$9e92cdcf@josiah.daylight.com> From: "Andrew Dalke" To: "Victor Anisimov" , Subject: Re: CCL:Is CML dead? Date: Wed, 12 Apr 2000 04:42:19 -0600 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.3155.0 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3155.0 Victor Anisimov said: >I have also failed finding such a library one can use for development >of XML type applications. Without such a public domain or commercial >available library it is difficult to expect a visible progress in CML/XML >development. The premier XML non-validating parser is a C library called "expat", >from http://www.jclark.com/xml/expat.html , which is available under the GNU GPL or the Mozilla public license. It's been around for a couple of years and is from all accounts well written and very fast. It is also used as the basis for XML parsers for languages other than C and has been throughly tested. I just searched freshmeat.net for "XML parser". It came back with 161 matches of which over 20 are XML parsing libraries (I didn't look past the first 30 results). Looking at the first few: XML Parser for Java (a validating parser in pure Java) http://www.alphaworks.ibm.com/tech/xml4j free to use but restricted XML::Parser for Perl (uses expat) http://wwwx.netheaven.com/~coopercc/xmlparser/intro.html under the Perl licenses. eXML for Eiffel (uses expat) http://exml.sourceforge.net/ under the Eiffel Forum Freeware License NanoXML for Java (non-validating, and only 5K in size!) http://nanoxml.sourceforge.net/ BSD-like license Python/XML (expat based, I think) http://www.python.org/topics/xml/ BSD-like license XML for C++ (validating) http://www.alphaworks.ibm.com/tech/xml4c free to use but restricted XML for SCRIPT (nonvalidating, and written in JavaScript) http://www.idle.org/experimental/ under the GNU LGPL libxml, or "The XML library for Gnome" (in C, incomplete validation) http://xmlsoft.org/ under the W3C IPR and the GNU LGPL One of those should fulfill your needs. > Another reason >why I thought of development of proprietary protocol is related to XML >functionality. I've heard a lot about unification of data exchange mechanism, >but I've never heard about event handling features which are extremely >necessary for GUI - "computational engine" communication, and which make >this link alive. >does somebody know about event handling >features implementes in such assume somewhere existing XML library? You may want to look into Glade, at http://glade.pn.org/history.html which stores the project and GUI description in XML. Probably more relevant is XUL, from Mozilla. I think the main page is http://www.mozilla.org/docs/xul/xulnotes/ . The page http://www.mozilla.org/xpfe/xptoolkit/xulintro.html says: ] XUL (pronounced "zuul," as if that spelling helped any, and short ] for "XML-based User Interface Language") is our name for the ] language in which these UI descriptions are built. Not that I've *used* either one. Andrew Dalke dalke@acm.org From chemistry-request@server.ccl.net Wed Apr 12 08:12:03 2000 Received: from relay1.scripps.edu (relay1.scripps.edu [137.131.200.29]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA08981 for ; Wed, 12 Apr 2000 08:12:03 -0400 Received: from redox.scripps.edu (redox.scripps.edu [137.131.240.50]) by relay1.scripps.edu (8.9.3/TSRI-3.1.0r) with ESMTP id FAA12780; Wed, 12 Apr 2000 05:09:52 -0700 (PDT) Received: from localhost (jesusmc@localhost) by redox.scripps.edu (8.9.2/TSRI-3.0.1) with SMTP id FAA09942; Wed, 12 Apr 2000 05:10:13 -0700 (PDT) Date: Wed, 12 Apr 2000 05:10:12 -0700 (PDT) From: "Jesus M. Castagnetto" Sender: jesusmc@scripps.edu To: "E.L. Willighagen" cc: CHEMISTRY@ccl.net Subject: Re: CCL:CML is dead In-Reply-To: <200004121024.MAA07368@studs3.sci.kun.nl> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII (Are there 2 separate threads of discussion, or someone transposed "Is CML" to "CML is"?) This has been a very illuminating discussion, because several libs I did not know existed have been discussed (like one that Egon mentions below) On Wed, 12 Apr 2000, E.L. Willighagen wrote: > Date: Wed, 12 Apr 2000 12:24:47 +0200 (MET DST) > From: "E.L. Willighagen" > To: CHEMISTRY@ccl.net > Subject: CCL:CML is dead [...snip...] > Ah, that would be nice indeed... > > For Java i have developed such a toolbox one and a half year ago. I > would love to see this ported to C(++) as wel... :) [...snip...] > My Java CML Filter Library is based on SAX... and about DOM. Peter MR is > working on ChemDom (in Java i think), but this is also quite easily > ported to other language, since at is based on DOM which is already > available in the other directory... > > Egon > > Java CML Filter Library: http://www.openscience.org/~egonw/cml/ Now, it would be relatively simple to either use these libs (or other ones depending on the programming language you are using), to retrofit old programs, or simply write a wapper that calls the all program and act as a layer to translate to/from whatever the old program uses and CML, for all purposes the user will see only CML as output or input, the rest can be handled by a generic or especific wrapper application. And this application does not need to be a C or Java program, it can be a web application. It can be a servlet that receives a request to convert to/from CML to the format of choice, and then does it remotely. Or it can siply be a C program, or a Python, Perl or PHP script. The existence of this distributed application servers, which would have low overhead, would allow the writing of generic shell/C wrappers that can have the URLs harcoded or can pool a directory. This can be slow for some applications, but for other ones in which is not feasible to retrofit the old program, it will be a good solution. Imagine that instead of every single person needing to install the equivalent of babel for converting from old-format to CML, your program could just pool a server that tells it where to send its data to be converted to/from that old-format. If you are connected to the net this will be completely transparent to the user, and if a new version of the conversion system is made, it will also be transparent to the user and the program. Cheers. -- Jesus M. Castagnetto - "Ken Zen Ichi-nyo" Program Project: http://www.scripps.edu/research/metallo/ Metalloprotein DB: http://metallo.scripps.edu/ Pilot Stuff: http://www.geocities.com/ResearchTriangle/Lab/1059/ From chemistry-request@server.ccl.net Wed Apr 12 08:48:17 2000 Received: from hermes.bmc.uu.se (hermes.bmc.uu.se [130.238.39.159]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA09208 for ; Wed, 12 Apr 2000 08:48:16 -0400 Received: from alpha2.bmc.uu.se ([130.238.37.65]) by hermes.bmc.uu.se (Post.Office MTA v3.5.3 release 223 ID# 0-62649U1500L1000S0V35) with SMTP id se; Wed, 12 Apr 2000 14:49:27 +0200 Received: from werkman.bmc.uu.se by alpha2.bmc.uu.se (5.65v3.2/1.1.10.5/07Jan00-1145AM) id AA03270; Wed, 12 Apr 2000 14:48:08 +0200 Date: Wed, 12 Apr 2000 13:43:02 +0200 (CEST) From: David van der Spoel X-Sender: spoel@werkman.bmc.uu.se To: "Jesus M. Castagnetto" Cc: "E.L. Willighagen" , CHEMISTRY@ccl.net Subject: Re: CCL:CML is dead In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 12 Apr 2000, Jesus M. Castagnetto wrote: >(Are there 2 separate threads of discussion, or someone transposed >"Is CML" to "CML is"?) Unintended I assume (but not quite sure...) >And this application does not need to be a C or Java program, it can >be a web application. It can be a servlet that receives a request to >convert to/from CML to the format of choice, and then does it remotely. NOOOOOOOOOOOOOOOOOOOOOOOOOO! It should also work when I sit in the garden with my laptop! >Imagine that instead of every single person needing to install the >equivalent of babel for converting from old-format to CML, your program >could just pool a server that tells it where to send its data to be >converted to/from that old-format. If you are connected to the net this >will be completely transparent to the user, and if a new version of the >conversion system is made, it will also be transparent to the user and >the program. See above. The web stuff is the icing on the cake. Native support comes first. I also need this to be able to visualize my 100000 atom system so java is out. Native support in *all* applications. Groeten, David. ________________________________________________________________________ Dr. David van der Spoel Biomedical center, Dept. of Biochemistry s-mail: Husargatan 3, Box 576, 75123 Uppsala, Sweden e-mail: spoel@xray.bmc.uu.se www: http://zorn.bmc.uu.se/~spoel phone: 46 18 471 4205 fax: 46 18 511 755 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From chemistry-request@server.ccl.net Wed Apr 12 06:14:51 2000 Received: from mailix.TELE.NET (mailix.tele.net [194.208.240.150]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA07397 for ; Wed, 12 Apr 2000 06:14:49 -0400 Received: from www.imp.univie.ac.at (www.imp.univie.ac.at [131.130.80.2]) by mailix.TELE.NET (8.9.3/8.9.3) with SMTP id MAA17008 for ; Wed, 12 Apr 2000 12:14:38 +0200 (MET DST) Message-ID: <38F44C63.8F01F4A2@vienna.at> Received: from BIOINFO2 by www.imp.univie.ac.at via smtpd (for mailix.tele.net [194.208.240.150]) with SMTP; 12 Apr 2000 10:13:57 UT Date: Wed, 12 Apr 2000 12:13:55 +0200 From: Gerald Loeffler Reply-To: Gerald.Loeffler@vienna.at X-Mailer: Mozilla 4.7 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: Re: CCL:CML is dead References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit okay - I can't resist adding my $0.02: When talking about XML there are 2 completely separate issues that are constantly being mixed up here - allow me too to try to clear the matter a bit: XML itself just defines the plain general syntax for writing _conformant_ XML-files (equivalent to saying "we are using comma-separated text-files") and also provides the means of describing what a particular _valid_ XML-document must look like (through the DTD, equivalent to saying "the first column in this comma-separated text-file is the 3-letter atom-code"). (note: "valid" is stronger than "conformant"!) So: 1) XML-enabled software must be able to parse (read!) XML-files and DTDs: parsers for this _are_ available _now_ in all languages that matter in this context (C (http://www.jclark.com/xml/expat.html, ...), C++ (http://www.alphaworks.ibm.com/tech/xml4c, ...), Java (http://www.alphaworks.ibm.com/tech/xml4j, ...), ... no FORTRAN). This enables the software to read conformant _and_ valid XML-files of any (!) kind. 2) CML-enabled software must additionally (!) be able to "understand" the CML-semantics (it must "know" what a 3-letter atom-code means) and must be willing to write CML-files. This is an additional issue and different chemistry software packages won't be any more "co-operating" than now unless all agree to "speak" CML (or any other chemistry-DTD) (in addition to XML)! cheers, gerald -- Gerald.Loeffler@vienna.at Tel.: +43 676 3289588 From chemistry-request@server.ccl.net Wed Apr 12 07:28:00 2000 Received: from mum.mans.eun.eg (mum.mans.eun.eg [193.227.50.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA08756 for ; Wed, 12 Apr 2000 07:27:58 -0400 Received: by mum.mans.eun.eg with Internet Mail Service (5.5.2650.21) id <2A2NSNJ5>; Wed, 12 Apr 2000 13:29:07 +0200 Message-ID: <4EF2E03A9B67D2119E2E0000F80534994273AD@mum.mans.eun.eg> From: Tarek Mamoun El-Gogary To: "'chemistry@ccl.net'" Date: Wed, 12 Apr 2000 13:29:05 +0200 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: text/plain Dear Netters, Could anyone tell me where can I find AM1 parameters for Na and K metals. I appreciate any responses. Tarek From chemistry-request@server.ccl.net Wed Apr 12 07:46:41 2000 Received: from relay2.scripps.edu (relay2.scripps.edu [137.131.200.30]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA08879 for ; Wed, 12 Apr 2000 07:46:40 -0400 Received: from redox.scripps.edu (redox.scripps.edu [137.131.240.50]) by relay2.scripps.edu (8.9.3/TSRI-3.1.0r) with ESMTP id EAA13889; Wed, 12 Apr 2000 04:44:24 -0700 (PDT) Received: from localhost (jesusmc@localhost) by redox.scripps.edu (8.9.2/TSRI-3.0.1) with SMTP id EAA09855; Wed, 12 Apr 2000 04:44:45 -0700 (PDT) Date: Wed, 12 Apr 2000 04:44:45 -0700 (PDT) From: "Jesus M. Castagnetto" Sender: jesusmc@scripps.edu To: Victor Anisimov cc: chemistry@ccl.net Subject: Re: CCL:Is CML dead? In-Reply-To: <00c201bfa44b$725886d0$050a0a0a@victor.fqspl.com.pl> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id HAA08880 My 2 cents about the lack of XML libraries On Wed, 12 Apr 2000, Victor Anisimov wrote: > Date: Wed, 12 Apr 2000 08:50:53 +0200 > From: Victor Anisimov > To: chemistry@ccl.net > Subject: CCL:Is CML dead? > > Hi, all. > > I have also failed finding such a library one can use for development > of XML type applications. Without such a public domain or commercial > available library it is difficult to expect a visible progress in CML/XML > development. There may not be a specific CML lib, but there are many, reliable and robust general XML libraries. James Clark's expat, xt, jade and the sgmtools come to mind. If that is not enough, ther is XML4J (for Java) from IBM, as well as the XML libaries from the Apache group (Xerces, Xalan, etc.) for C++, Java and Perl are available. I do not understand there what the problem with not existentence of very specific CML parsers. Just use XML4J (for example) and you will get a DOM tree that you can manipulate to your heart's desire. And if you want validation then XML4J will do that if you got the DTD. If you write in C, then expat will allow you to generate any random parser, and xt (if memory serves), will allow you validation. Why then the need of a monolithical CML parser, when a general one that creates the parser from the DTD is possible in Java or C++? > In my company I work with a variety of GUIs and computational engines. > Thinking how to reduce an amount of my work I spend on development > of new interface I realized for myself that I strongly need such a library. > > As a result I developed a proprietary XML type library which I call NTM > which stands for Network Transparent Model and serves as a data > exchange and event handling layer between GUI and computational engine > either located on the same machine or separated by means of LAN or Internet. For data interchange there is WDDX and XML-RPC. The later serves even as a protocol over HTTP to be able to create modular distributed web or network applications. There are WDDX libs for many languages (even javascript), see www.wddx.org for more info. Similarly there are libs for XML-RPC, see www.xml-rpc.com Other DTDs exist that are being used/worked on around, but those are the ones w/ existing support and examples of applications. > Having no XML library available I have designed NTM as an alternative > standard to XML preserving only similar philosophy. Extra new standard > is of course not good but as a developer I need a standard not only > on a paper but as a library that should simplify my work. Another reason > why I thought of development of proprietary protocol is related to XML > functionality. I've heard a lot about unification of data exchange mechanism, > but I've never heard about event handling features which are extremely > necessary for GUI - "computational engine" communication, and which make > this link alive. That is very strange as GNome uses ORB and XML packets alongside w/ CORBA for managing very complex GUIs. It seems to me that there are examples of usage of XML in applications all over the place. A visit to Sourceforge.net or to Freshmeat.net will be illuminating. > Therefore in addition to question of Peter Shenkin about XML library I would > also add my piece of question - does somebody know about event handling > features implementes in such assume somewhere existing XML library? Look at the Gnome architecture, and get in touch w/ the developers. I may be getting the model not completely correct. See www.gnome.org Also, there are java application servers that user not only RMI but also XML to pass pback and forth information. Some are very scalable, a search for application servers will turn out some. For a web application that works w/ XML and XSLT, see Cocoon, which is now part of the XML group of the Apache foundation (xml.apache.org). There are general XMl libs for Perl, Python, PHP, C, C++, Java, and even some for Javascript. Mozilla (www.mozilla.org) understands XML (the new Netscape 6 is based on Mozilla). Bottom line: - There are parser generating libraries for many languages - You can use event driven libs (expat is an example), or DOM based ones - With a DTD, you can even generate validators - You can use the parser to process anything you want: CML, WDDX, etc. I have used the XML support in PHP (which is based on expat), to very concisely parse CML files. It is even simpler in Java, as JMol, Jumbo and the pdb2cml programs demonstrate. Another nice example of a nice XML parser/validator is Xeena, the editor from IBM's Alphaworks. I step down now from my soapbox. I like discussions like this in CCL. Cheers > > With best regards, > Victor Anisimov. > > > -----Original Message----- > From: Peter Shenkin > To: chemistry@ccl.net > Date: 12 апреля 2000 г. 1:25 > Subject: CCL:Is CML dead? > > > :Hear, hear. > : > :It was a lack of such tools several years ago that caused us to > :shy away from XML/CML when designing our new Maestro interface. > : > :It is disappointing if, indeed, there are no such tools linkable > :to C, Fortran and C++ even today. > : > :Henry, what sayest thou? > : > : -P. > : > :On Sat, 8 Jul 2000, David van der Spoel wrote: > : > :> On Tue, 11 Apr 2000, Rzepa, Henry wrote: > :> > :> >We have mounted a number of XML tests using CML on > :> >http://www.xml-cml.org/test/ (a mirror site if the above is slow is > :> >http://www.ch.ic.ac.uk/chimeral/test/ ) You will need Internet > :> >Explorer 5.0 or 5.5 for Windows. > :> > :> I think this is close to the heart of the problem. The current efforts > :> are directed to *new* tools for visualisation (I work in a > :> Windows-Free (tm) environment) while we have plenty of old tools which > :> do the job, but are just not CML/XML enabled. > :> > :> In the tests there are examples of combined structure/spectra > :> files. Instead of dumping the CML in a slow browser I would like to > :> give the CML file to rasmol to view the structure and the same file to > :> e.g. xmgrace to see a spectrum. What is needed for that is a simple > :> comprehensive C-library which can be called by the respective > :> programs. I realize that there is a need for (web) publishing tools, > :> and that the current java tools are a means to this end, however > :> without programs that generate CML there is nothing to publish. > :> I am willing to contribute to the library, as long as someone else (Henry?) > :> keeps the overview and coordinates things, which as Christoph Steinbeck > :> pointed out is crucial. > :> > :> Groeten, David. > :> ________________________________________________________________________ > :> Dr. David van der Spoel Biomedical center, Dept. of Biochemistry > :> s-mail: Husargatan 3, Box 576, 75123 Uppsala, Sweden > :> e-mail: spoel@xray.bmc.uu.se www: http://zorn.bmc.uu.se/~spoel > :> phone: 46 18 471 4205 fax: 46 18 511 755 > :> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > :> > :> > :> > :> > :> > :> > :> > :> > : > :-- > :** Whether the playing field is level depends on the coordinate system. *** > :********* Peter S. Shenkin; Schrodinger, Inc.; (201)433-2014 x111 ********* > :*********** shenkin@schrodinger.com; http://www.schrodinger.com *********** > : > : > : > : > : > : > > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > -- Jesus M. Castagnetto - "Ken Zen Ichi-nyo" Program Project: http://www.scripps.edu/research/metallo/ Metalloprotein DB: http://metallo.scripps.edu/ Pilot Stuff: http://www.geocities.com/ResearchTriangle/Lab/1059/ From chemistry-request@server.ccl.net Wed Apr 12 09:04:43 2000 Received: from relay1.scripps.edu (relay1.scripps.edu [137.131.200.29]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA09478 for ; Wed, 12 Apr 2000 09:04:43 -0400 Received: from redox.scripps.edu (redox.scripps.edu [137.131.240.50]) by relay1.scripps.edu (8.9.3/TSRI-3.1.0r) with ESMTP id GAA13459; Wed, 12 Apr 2000 06:02:31 -0700 (PDT) Received: from localhost (jesusmc@localhost) by redox.scripps.edu (8.9.2/TSRI-3.0.1) with SMTP id GAA10011; Wed, 12 Apr 2000 06:02:52 -0700 (PDT) Date: Wed, 12 Apr 2000 06:02:52 -0700 (PDT) From: "Jesus M. Castagnetto" Sender: jesusmc@scripps.edu To: David van der Spoel cc: "E.L. Willighagen" , CHEMISTRY@ccl.net Subject: Re: CCL:CML is dead In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 12 Apr 2000, David van der Spoel wrote: > Date: Wed, 12 Apr 2000 13:43:02 +0200 (CEST) > From: David van der Spoel > To: "Jesus M. Castagnetto" > Cc: "E.L. Willighagen" , CHEMISTRY@ccl.net > Subject: Re: CCL:CML is dead > > On Wed, 12 Apr 2000, Jesus M. Castagnetto wrote: > > >(Are there 2 separate threads of discussion, or someone transposed > >"Is CML" to "CML is"?) > Unintended I assume (but not quite sure...) > > >And this application does not need to be a C or Java program, it can > >be a web application. It can be a servlet that receives a request to > >convert to/from CML to the format of choice, and then does it remotely. > NOOOOOOOOOOOOOOOOOOOOOOOOOO! > It should also work when I sit in the garden with my laptop! Then pick your wrapper, written in the poison^H^H^H^H^H^Hlanguage of your choice :) This will allow you to retrofit your old applications by using a Python, Perl, Tcl/Tk, or even C/C++ wrapper that handles the conversion on the fly and then passes the info to the program, this is doable for interactive and non-interactive programs. Also, ever heard of broadband wireless Internet connections? ;-) > >Imagine that instead of every single person needing to install the > >equivalent of babel for converting from old-format to CML, your program > >could just pool a server that tells it where to send its data to be > >converted to/from that old-format. If you are connected to the net this > >will be completely transparent to the user, and if a new version of the > >conversion system is made, it will also be transparent to the user and > >the program. > See above. The web stuff is the icing on the cake. Native support comes > first. I also need this to be able to visualize my 100000 atom system > so java is out. Native support in *all* applications. No java? We routinely use a Java 3D application (and rememeber that the Java3D specs and SDKs are not fully stable yet), to manipulate proteins w/ electrostatic surfaces calculated on the flyi (via JPython calls to MSMS). I do not know what Java applications you have used/seen, but something akin to AVS is doable. The construction of such tool is being done here at Scripps, and as part of several projects, one of which is related to the Metalloprotein DB, which uses a lightweight and small applet to do interactive searches too. Java is not as fast as C, but it is modular. A well written application should just load the classes it needs, and handle the rest dynamically and using threads appropriately. Also, it is not that difficult to have the heavy calculation bits written in a native language, that is the reason for JNI. And do not discount scripting languages, like Python, which has a good scientific/numeric support, and a molecular modelling package based on Python and Tcl/Tk. So, I still think that even old pieces of softaware can be retrofited, just need the appropriate interfacing/wrapping/translation layer, which could reside locally or somewhere else. > > Groeten, David. > ________________________________________________________________________ > Dr. David van der Spoel Biomedical center, Dept. of Biochemistry > s-mail: Husargatan 3, Box 576, 75123 Uppsala, Sweden > e-mail: spoel@xray.bmc.uu.se www: http://zorn.bmc.uu.se/~spoel > phone: 46 18 471 4205 fax: 46 18 511 755 > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > Regards. -- Jesus M. Castagnetto - "Ken Zen Ichi-nyo" Program Project: http://www.scripps.edu/research/metallo/ Metalloprotein DB: http://metallo.scripps.edu/ Pilot Stuff: http://www.geocities.com/ResearchTriangle/Lab/1059/ From chemistry-request@server.ccl.net Wed Apr 12 14:18:08 2000 Received: from space5.chemistry.duq.edu (space5.chemistry.duq.edu [165.190.32.243]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA12186 for ; Wed, 12 Apr 2000 14:18:07 -0400 Received: from space1.chemistry.duq.edu (localhost [127.0.0.1]) by space5.chemistry.duq.edu (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id OAA87318; Wed, 12 Apr 2000 14:17:48 -0400 (EDT) Sender: space@space1.chemistry.duq.edu Message-ID: <38F4BDCB.F8B8CD0D@space1.chemistry.duq.edu> Date: Wed, 12 Apr 2000 14:17:47 -0400 From: Brian Space X-Mailer: Mozilla 4.61C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: CHEMISTRY@ccl.net, space@space1.chemistry.duq.edu Subject: Reduced Mass Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit In Gaussian output how is the reduced mass defined? See for example the result for water below: reduced masses (AMU), force constants (mDyne/A) and normal coordinates: 1 2 3 A1 A1 B2 Frequencies -- 1659.0480 3844.3493 3951.2790 Red. masses -- 1.0828 1.0451 1.0815 Frc consts -- 1.7559 9.1001 9.9481 IR Inten -- 0.0000 0.0000 0.0000 Raman Activ -- 0.0000 0.0000 0.0000 Depolar -- 0.0000 0.0000 0.0000 Atom AN X Y Z X Y Z X Y Z 1 1 0.00 0.43 0.56 0.00 0.58 -0.40 0.00 -0.56 0.43 -- @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ Professor Brian Space Department of Chemistry and Biochemistry Duquesne University Pittsburgh, PA 15282-1530 phone:(412)396-4732 lab :(412)396-4369 fax: (412)396-5683 Home: Home: 1317 Sarah St. Pittsburgh, PA 15203-1516 Home machine: space@space1.chemistry.duq.edu Home Page: http://nexus.chemistry.duq.edu/snes/chemistry/faculty/space.html @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ From chemistry-request@server.ccl.net Wed Apr 12 15:22:29 2000 Received: from hermes.bmc.uu.se (hermes.bmc.uu.se [130.238.39.159]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA13122 for ; Wed, 12 Apr 2000 15:22:29 -0400 Received: from alpha2.bmc.uu.se ([130.238.37.65]) by hermes.bmc.uu.se (Post.Office MTA v3.5.3 release 223 ID# 0-62649U1500L1000S0V35) with SMTP id se; Wed, 12 Apr 2000 21:23:50 +0200 Received: from zorn.bmc.uu.se by alpha2.bmc.uu.se (5.65v3.2/1.1.10.5/07Jan00-1145AM) id AA18995; Wed, 12 Apr 2000 21:22:32 +0200 Date: Sun, 9 Jul 2000 21:11:37 +0200 (CEST) From: David van der Spoel X-Sender: spoel@zorn.bmc.uu.se To: "Jesus M. Castagnetto" Cc: Victor Anisimov , chemistry@ccl.net Subject: Re: CCL:Is CML dead? In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII OK, once more, but now I'll be a bit more to the point: this is the kind of functions that I would like to see: extern FILE *cml_open(char *filename); /* Open filename and return file pointer, or NULL on failure */ extern int cml_validate(char *filename); /* Validate the internal consistency of the file, return 1 on success */ extern int cml_read_coordinates(FILE *fp,int natoms,float **x); /* Read coordinates for natoms particles, return the number of * coordinates found */ extern int cml_read_atom_names(FILE *fp,int natoms,char **names); /* Read the names of natoms particles, return the number of coordinates * found */ extern int cml_read_bonds(FILE *fp,int natoms,int **connect); /* Read a connection table, return the number of bonds */ OK, I hope you get the idea, of course there are zillions of ways to define such an interface. Is something like this available? Is there anyone else who would like to have something like this? I also did have a look at the Gnome web site (www.gnome.org), since they obviously have open source XML tools. It is amazing how complicated even the simplest example there is. Happily the CML DTD is not extensible. Groeten, David. ________________________________________________________________________ Dr. David van der Spoel Biomedical center, Dept. of Biochemistry s-mail: Husargatan 3, Box 576, 75123 Uppsala, Sweden e-mail: spoel@xray.bmc.uu.se www: http://zorn.bmc.uu.se/~spoel phone: 46 18 471 4205 fax: 46 18 511 755 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From chemistry-request@server.ccl.net Wed Apr 12 17:04:50 2000 Received: from wn1.sci.kun.nl (wn1.sci.kun.nl [131.174.8.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA13824 for ; Wed, 12 Apr 2000 17:04:50 -0400 Received: from studs3.sci.kun.nl by wn1.sci.kun.nl via studs3.sci.kun.nl [131.174.124.4] with ESMTP id XAA20409 (8.8.8/3.29); Wed, 12 Apr 2000 23:01:00 +0200 (MET DST) From: "E.L. Willighagen" Received: by studs3.sci.kun.nl via egonw@localhost id XAA18006 (8.8.8/3.1); Wed, 12 Apr 2000 23:00:59 +0200 (MET DST) Date: Wed, 12 Apr 2000 23:00:59 +0200 (MET DST) Message-Id: <200004122100.XAA18006@studs3.sci.kun.nl> To: chemistry@ccl.net, spoel@xray.bmc.uu.se Subject: CML Status (was Is CML dead?) > It is amazing how complicated even the simplest example there is. do they use DOM or SAX? I know SAX can be complicated since you have to do bookkeeping... > Happily the CML DTD is not extensible. Mmmm... nice statement... while in principle true, in practice it is not... Since CML is an open framework that can do much more than coordinates alone, it can get very messy quickly... take this example: 78 -195.0 And do some cross combinations... try to match that... (now this is a bit simple example, but you probably get my point). Since CML has only little to say on what you can and cannot give (what kind of properties) and how they are supposed to be given (except for coordinates/charges and some other basic stuff), building one standard library is difficult, but certainly not impossible... > extern int cml_read_bonds(FILE *fp,int natoms,int **connect); Oke, this is such a basic 'stuff'... but where is this going to end? BTW, on ending... shall we move our discussing to this mailling list: http://ala.vsms.nottingham.ac.uk/biodom/xml-mol/ We can posed announcement and conclusion on this list when appropriate... Egon From chemistry-request@server.ccl.net Wed Apr 12 17:14:52 2000 Received: from medicor.wustl.edu (medicor.wustl.edu [128.252.223.195]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA13894 for ; Wed, 12 Apr 2000 17:14:51 -0400 From: ReichertD@mir.wustl.edu Subject: OPLS non-bonded potential To: chemistry@ccl.net X-Mailer: Lotus Notes Release 5.0.1b September 30, 1999 Message-ID: Date: Wed, 12 Apr 2000 16:14:02 -0500 X-MIMETrack: Serialize by Router on Medicor/Washington University(Release 5.0.2c |February 2, 2000) at 04/12/2000 04:14:04 PM MIME-Version: 1.0 Content-type: text/plain; charset=us-ascii Greetings, I'm hoping someone can lend some insight into a problem, that I just don't see the answer to. According to the definition of the OPLS non-bonded potential (Jorgensen, JACS 110, 2988, 1657) the intermolecular interaction energy is sum of the Coulombic term ((q1*q2*e^2)/r12) and the Lennard-Jones term. Here's my problem, what is e^2 and where does it come from ? The charges q are in electron units, r is in angstroms, and somehow the overall units need to end up in kcal/mol. I'm pretty sure I'm missing something fundamental here. thanks in advance, -david David Reichert, Ph.D. Washington University School of Medicine 510 S. Kingshighway, Campus Box 8225 St Louis, MO 63110 e-mail: reichertd@mir.wustl.edu voice: (314) 362-8461 fax: (314) 362-9940 From chemistry-request@server.ccl.net Wed Apr 12 15:58:03 2000 Received: from lrz.uni-muenchen.de (root@lsanca1-ar99-078-042.biz.dsl.gtei.net [4.3.78.42]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA13381 for ; Wed, 12 Apr 2000 15:58:02 -0400 Received: (from eugene.leitl@localhost) by lrz.uni-muenchen.de (8.8.8/8.8.8) id MAA25667; Wed, 12 Apr 2000 12:57:38 -0700 From: Eugene Leitl MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Message-ID: <14580.54577.645975.71570@lrz.uni-muenchen.de> Date: Wed, 12 Apr 2000 12:57:37 -0700 (PDT) To: Matthias.Hloucha@DENOTES.HENKEL.DE Cc: chemistry@ccl.net Subject: CCL:simulation of surfactants In-Reply-To: <412568BF.00374A77.00@desmtp02.henkel.de> References: <412568BF.00374A77.00@desmtp02.henkel.de> X-Mailer: VM 6.71 under 21.1 (patch 4) "Arches" XEmacs Lucid Matthias.Hloucha@DENOTES.HENKEL.DE writes: > who are the experts in the area of: > > -> simulation of surfactants in aqueous solution ? I personally find the following approach fascinating: B.M. Boghosian, P.V. Coveney, Mesoscale Modeling of Amphiphilic Fluid Dynamics http://physics.bu.edu/~bruceb/MolSim/ I would be grateful if you could summarize your responses, including nonmesoscale approaches (large scale MD with full atomic detail). Regards, Eugene Leitl From chemistry-request@server.ccl.net Wed Apr 12 16:35:20 2000 Received: from Kitten.mcs.net (Kitten.mcs.com [192.160.127.90]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA13617 for ; Wed, 12 Apr 2000 16:35:20 -0400 Received: from oemcomputer (P23-Chi-Dial-2.pool.mcs.net [205.253.224.87]) by Kitten.mcs.net (8.9.3/8.9.3) with SMTP id PAA70833; Wed, 12 Apr 2000 15:35:14 -0500 (CDT) (envelope-from rone@mcs.net) Message-ID: <00df01bfa4bd$b576cfe0$62e0fdcd@oemcomputer> From: "Rebecca Rone" To: "Boyd" , "OSC CCL" Subject: Re: CCL:old computational chemists don't fade away Date: Wed, 12 Apr 2000 15:28:47 -0500 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.3110.1 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Dear Dr. Boyd, I am an "old" computational chemist with 15 years experience in the field. Though not retired I am currently working as an independent consultant on software for informatics and molecular modelling. My resume is on my Web site www.mcs.net/~rone. Can I be of help? A question in passing: I have docking code that I wrote in grad school and never found the time to deposit to QCPE. It is on an old 8 track tape. Any idea who might be able to read this? Thanks. Dr. Rebecca Rone Chicago, IL. 773-646-2585 -----Original Message----- From: Boyd To: OSC CCL Date: Monday, April 10, 2000 12:24 PM Subject: CCL:old computational chemists don't fade away >Dear CCLers, > >I am curious if there are any subscribers to this list who are officially >retired but are nevertheless still interested in staying involved in the >field. >If so, please contact me. > >Thanks, Don > >Donald B. Boyd, Ph.D. >Editor, Reviews in Computational Chemistry > http://chem.iupui.edu/rcc/rcc.html >Editor, Journal of Molecular Graphics and Modelling > (publication of the ACS COMP division and MGMS) > http://chem.iupui.edu/~boyd/jmgm.html >Indiana University-Purdue University at Indianapolis >E-mail boyd@chem.iupui.edu > > >-= This is automatically added to each message by mailing script =- >CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins >MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH >CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 >Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > From chemistry-request@server.ccl.net Wed Apr 12 16:42:22 2000 Received: from Kitten.mcs.net (Kitten.mcs.com [192.160.127.90]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA13707 for ; Wed, 12 Apr 2000 16:42:21 -0400 Received: from oemcomputer (P23-Chi-Dial-2.pool.mcs.net [205.253.224.87]) by Kitten.mcs.net (8.9.3/8.9.3) with SMTP id PAA71628 for ; Wed, 12 Apr 2000 15:42:20 -0500 (CDT) (envelope-from rone@mcs.net) Message-ID: <00eb01bfa4be$b3a46460$62e0fdcd@oemcomputer> From: "Rebecca Rone" To: Subject: Report on bioinformatics at BIO2000 Date: Wed, 12 Apr 2000 15:35:51 -0500 Is it appropriate to post this on the CCL? Dear CCL'ers, In case you missed the panel on bioinformatics at the BIO200 conference I am considering posting my notes as a business report on my website www.mcs.net/~rone. Is anyone on this list interested? A previous report on information technology, as well as anitbiotics and genomics, discussed at the MBC Investor's conference last October is posted there already. Let me know of any interest. Thanks. Dr. Rebecca Rone (Becky) Rone Biotechnology Consulting Chicago, IL. 773-646-2585 From chemistry-request@server.ccl.net Wed Apr 12 16:47:22 2000 Received: from Kitten.mcs.net (Kitten.mcs.com [192.160.127.90]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA13763 for ; Wed, 12 Apr 2000 16:47:20 -0400 Received: from oemcomputer (P36-Chi-Dial-3.pool.mcs.net [205.253.224.164]) by Kitten.mcs.net (8.9.3/8.9.3) with SMTP id PAA72076; Wed, 12 Apr 2000 15:46:34 -0500 (CDT) (envelope-from rone@mcs.net) Message-ID: <00ee01bfa4bf$4b0fd1e0$62e0fdcd@oemcomputer> From: "Rebecca Rone" To: "Charlie Laughton" , Subject: Re: CCL:Comp Chem Lab Design Date: Wed, 12 Apr 2000 15:39:26 -0500 Dear Charlie, When I was at MSI we typically had posters made from color slides to show some of our and our customer's "success" stories. These were in the lobby, the conference rooms, the halls proceeding to the demo room, and in the demo room. These "successes" make interesting conversation pieces. All of the demo rooms were interior rooms. This is helpful to people who do not sit in front of the computer all day looking at graphics. They need to be able to focus their full visual attention on the screen in order to "see" the 3D representations. Otherwise, they still "see" it in 2D. If you cannot arrange an interior room for visitors please get heavy drapes to be able to shut out the majority of light. Vertical blinds normally used for conference rooms are just not thick enough to do the job. This is very important in using stereo options. For every day use, I personally like to face a window with the terminal set to the left side of the window to prevent glare. That way I can still look outdoors to rest my eyes or think about a problem. This only works for those of us who do these visualizations every day. Even so, you may need a glare screen over your monitors. Normal room blinds work well enough for me in this situation when the afternoon sun starts to come in the window. Don't use the perforated (light filtering) kind. Think about where you wish to place manuals. They need to be conveniently located, but most people are daunted by an entire wall of manuals mounted over the desktop. Particularly people new to the task of using computers, i.e. junior personnel or bench chemists trying to get a handle on computational techniques. I like a little space to the right of the keyboard (past the mouse pad) for note taking on a legal pad. Actually a "return" on that side is preferable. I also prefer a space to the left big enough for a full binder manual to lie open. Once I used a printer table as a desk for my graphics monitor. That worked very well. The height was right and the cables all came up through the paper slot. Please check out ergonomic considerations for your employees particularly pull out trays under the tabletop in order to lower the keyboard. Fully adjustable chairs are preferable for employees who sit all day. If I can be of more help please call 773-646-2585 and/or check out my website www.mcs.net/~rone. -----Original Message----- From: Charlie Laughton To: CHEMISTRY@ccl.net Date: Friday, April 07, 2000 10:00 AM Subject: CCL:Comp Chem Lab Design >Dear All, > >I have the opportunity to design from scratch a new comp. chem. facility >of about 50 sq. m. Our current layout is very basic - just desking >against the walls. It would be nice to have something that created a >more inspiring environment. > >I would be interested to hear from other members of the list who have >experience of successful (and unsuccessful!) designs as to what sort of >layouts can work well. > >Regards, > >Charlie > >-- >--------------------------------------------------------------------------- >Dr Charlie Laughton | >Lecturer in Drug Design and Discovery | Phone: (+44) 115 951 3405 >School of Pharmaceutical Sciences | Fax: (+44) 115 951 3412 >University of Nottingham | Email: >Nottingham NG7 2RD | >charles.laughton@nottingham.ac.uk >UK | >---------------------------------------------------------------------------