From csron@wicc.weizmann.ac.il Tue Sep 5 04:28:15 1995 Received: from wishful.weizmann.ac.il for csron@wicc.weizmann.ac.il by www.ccl.net (8.6.10/950822.1) id EAA25942; Tue, 5 Sep 1995 04:27:22 -0400 Received: from wizard.weizmann.ac.il (wizard-gate.weizmann.ac.il [132.76.63.23]) by wishful.weizmann.ac.il (8.6.5/8.6.5) with ESMTP id KAA116045 for ; Tue, 5 Sep 1995 10:27:50 +0300 From: Ron Edgar Received: from localhost (csron@localhost) by wizard.weizmann.ac.il (8.6.5/8.6.5) id KAA53802 for chemistry@www.ccl.net; Tue, 5 Sep 1995 10:28:03 +0300 Message-Id: <199509050728.KAA53802@wizard.weizmann.ac.il> Subject: algorithms for basic molecule manipulations To: chemistry@www.ccl.net Date: Tue, 5 Sep 1995 10:28:03 +0300 (WET) X-Mailer: ELM [version 2.4 PL22] Content-Type: text Content-Length: 1029 Dear Netters, I'm writing a C++ library to deal with atoms/molecules. In the good tradition of trying to avoid re-inventing the wheel I would appreciate any references (or source) to algorithms for basic operations which can be applied to groups of atoms defined in Cartesian OR fractional coordinate systems, e.g. torsion and "bend" angles, rotations along an arbitrary vector, etc. Also I would be interested in means of finding internal molecular symmetries for a given set of coordinates. Please reply directly to me, I will summarize to the group. Thanks, Ron -------------------------------------- ---------------------------------- Ron Edgar | email: csron@wicc.weizmann.ac.il Dept. of Materials & Interfaces | Voice: 972-8-342136 (work) The Weizmann Institute of Science | 972-8-472766 (home) Rehovot 76100 Israel | Fax : 972-8-344138 -------------------------------------- ---------------------------------- From glotov@mbi.FTA-Berlin.DE Tue Sep 5 05:43:16 1995 Received: from cuboid.mbi.fta-berlin.de for glotov@mbi.FTA-Berlin.DE by www.ccl.net (8.6.10/950822.1) id FAA26578; Tue, 5 Sep 1995 05:34:51 -0400 Message-Id: <199509050934.FAA26578@www.ccl.net> Received: from a1pc06.mbi.FTA-Berlin.de by cuboid.mbi.fta-berlin.de with SMTP (1.37.109.4/16.2) id AA28360; Tue, 5 Sep 95 11:34:11 +0200 Comments: Authenticated sender is From: "Aleksei Glotov" To: chemistry@www.ccl.net Date: Tue, 5 Sep 1995 11:31:56 +0000 Subject: searching for a molecular structure viewing program Reply-To: glotov@mbi.fta-berlin.de Priority: normal X-Mailer: Pegasus Mail for Windows (v2.0-WB4) Hi. I am looking for a program for viewing a molecular structure if I have as a data input file - the file with atoms coordinates. ! Program should be HEWLETT PACKARD campatible ! An example of that kind one but non-HP - xmol. Everybody can get latter one from ftp.kfa-juelich.de (login: ftp). Thanks beforehand, Alexei Glotov ---------------------------------- Alexei Glotov Max-Born-Institut, Berlin, Germany glotov@mbi.fta-berlin.de ---------------------------------- From cyber@csb0.IPC.PKU.EDU.CN Tue Sep 5 09:28:19 1995 Received: from csb0.IPC.PKU.EDU.CN for cyber@csb0.IPC.PKU.EDU.CN by www.ccl.net (8.6.10/950822.1) id JAA28962; Tue, 5 Sep 1995 09:27:35 -0400 Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for chemistry@www.ccl.net id AA10066; Tue, 5 Sep 95 21:15:54 -0700 Date: Tue, 5 Sep 1995 21:15:53 -0700 (PDT) From: cyberspace To: CCL Mailing List Subject: Calculation of LogP Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, everyone! We have set to develope methods for the LogP calculation. Since LogP has long been used as an important parameter of QSAR, much effort has been devoted to LogP claculation. So it is really difficult to have a thorough review. So, could you tell us which works are classical, which works are interesting and which works are the newest? I will appreciate it very much if you can give a list of related articles or books. I will surely put back the summary. Thanks in advance. Please answer to my personal e-mail account. Arthur Wang arthur@ipc.pku.edu.cn Peking Univ., Beijing, China From states@rucola.wustl.edu Tue Sep 5 11:13:20 1995 Received: from wugate.wustl.edu for states@rucola.wustl.edu by www.ccl.net (8.6.10/950822.1) id LAA01812; Tue, 5 Sep 1995 11:01:29 -0400 Received: from rucola (rucola.wustl.edu [128.252.122.177]) by wugate.wustl.edu (8.6.12/8.6.11) with ESMTP id KAA20255 for <@wugate.WUStL.EDU:chemistry@www.ccl.net>; Tue, 5 Sep 1995 10:01:28 -0500 Received: by rucola (950215.SGI.8.6.10/930416.SGI) for chemistry@www.ccl.net id KAA29125; Tue, 5 Sep 1995 10:01:26 -0500 From: states@rucola.WUStL.EDU (David J. States) Message-Id: <9509051001.ZM29123@rucola.wustl.edu> Date: Tue, 5 Sep 1995 10:01:25 -0500 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chemistry@www.ccl.net Subject: Java chemistry applets? Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 Sun has been promoting a new programming language, java, as a tool for creating portable applications on internet. Instead of constantly going back to the host for additional information (a response to a mouse click, for example), the applet executes on the local client. One of their demos is a page of molecules that can be viewed and rotated in the web browser. See: http://java.sun.com/applets/applets/ChemicalModels/index.html but you need a "java capable" web browser such as hotjava, available >from http://java.sun.com. Netscape has announced support for java, but I have not seen a date for when the product will be released. I was wondering, has anyone picked up on the Sun demo? Are people designing chemistry and biochemistry specific java class libraries and applets? Seems like it could be a powerful set of tools. David -- David J. States Institute for Biomedical Computing / Washington University in St. Louis From jkl@ccl.net Tue Sep 5 12:28:21 1995 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.6.10/950822.1) id MAA03073; Tue, 5 Sep 1995 12:19:25 -0400 Received: from relay1.pipex.net for adam@cherwell.com by bedrock.ccl.net (8.6.10/950822.1) id MAA16793; Tue, 5 Sep 1995 12:19:21 -0400 Received: from cherwell.com by flow.pipex.net with SMTP (PP); Tue, 5 Sep 1995 17:16:05 +0100 Received: from wharfe ([194.128.255.53]) by cherwell.com (4.1/SMI-4.1) id AA06711; Tue, 5 Sep 95 16:52:03 BST Message-Id: <9509051552.AA06711@cherwell.com> X-Sender: adam@cherwell.com (Unverified) X-Mailer: Windows Eudora Version 1.4.4 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 05 Sep 1995 16:52:14 +0100 To: chemistry@ccl.net From: adam@cherwell.com (Adam Hodgkin) Subject: Cherwell Scientific announces MOL2MOL MOL2MOL -- an easy-to-use file conversion program for the chemist. Mol2Mol automatically converts many of the widely used file formats in chemistry. Running under Windows, Mol2Mol helps you with the conversion, manipulation and inspection of different molecular structure files. Currently over twenty different molecule file formats are supported, as well as your own free format ASCII files. Mol2Mol automatically recognizes the format of most of these files. The program also helps in capturing co-ordinates from the big output files of quantum chemistry programs. It possesses some chemical intelligence for recognizing extended atom and bond types, chemical environments, which is necessary for converting simpler formats to SYBYL, HyperChem or PCMODEL files, for example. Mol2Mol is more than just a file conversion system. It has a number of features which offer outstanding ease-of-use to a researcher who needs different tools for file conversion and molecule inspection. * Graphical window to inspect the input molecule with standard manipulations (translation, rotation, stereo modes etc.) * Quick calculation of basic geometrical data (distances, angles, planes, pyramidality, proton-proton and proton-methyl centroid distances etc) * Simple correction of atom or bond types * In the case of problems an ASCII editor for manual corrections of input or output file * Batch process for files of similar type * Text window to follow the conversion process. MOL2MOL can automatically recognize (R) and write (W) the following co-ordinate file formats: ALCHEMY I-III *RW SYBYL MOL and MOL2 *RW CPSS, ISIS mol *RW MOLIDEA *RW Desktop Molecular Modeller *RW PCMODEL *RW HyperChem *RW MOBY (Cartesian) *RW Beilstein Rosdal *R ChemDraft (Cartesian) *RW ChemWindow (mol) *RW Brookhaven PDB *RW Z matrix, free format #*RW AMPAC *RW MOPAC *RW X-ray fractional CIF *R Cambridge FDAT *R Cambridge MODEL *R user's free format #R Cartesian free format #R PLUTO W PLT W WIMP (.ftr) W Schakal W * recognized automatically # insertion of a marker is necessary when capturing co-ordinates Since many of the above programs are also capable of communicating with others or accepting different database formats (e.g. Protein Data Bank, CSSR files), the effective range of MOL2MOL is even wider. Several programs not included in the above table use common formats (ChemDraw, ChemX, MPG, Insight, etc.). MOL2MOL will continue to be developed to accept or write new file formats (MacroModel, MDL V3000, Insight, ChemDraw CT, Xmol, POV-Ray etc) System requirements: IBM PC with Windows 3.1, 4 MB RAM, maths coprocessor. We are posting a free demo version to the CCL archives. For more information contact: in USA and Canada: Cherwell Scientific 744 San Antonio Road #27A, Palo Alto, CA 94303 Tel: (415) 852 0720 Fax: (415) 852 0723 e-mail: mol2mol-usa@cherwell.com in Germany, Austria and Switzerland: Cherwell Scientific c/o CHEM Research GmbH, Hamburger Allee 26-28 D-60486 Frankfurt Tel: 069 970841-11 Fax: 069 970841-41 e-mail: mol2mol-d@cherwell.com UK and Rest of World Address: Cherwell Scientific The Magdalen Centre, Oxford Science Park Oxford, OX4 4GA Tel: +44 (0)1865 784800 Fax: +44 (0)1865 784801 e-mail: mol2mol@cherwell.com --- --- Adam Hodgkin | e-mail: adam@cherwell.com Managing Director | Phone: +44 (0)1865 784800 Cherwell Scientific Publishing | Fax: +44 (0)1865 784801 Oxford | http://www.cherwell.com/cherwell --- --- From ejfried@herzberg.ca.sandia.gov Tue Sep 5 16:28:25 1995 Received: from herzberg.ca.sandia.gov for ejfried@herzberg.ca.sandia.gov by www.ccl.net (8.6.10/950822.1) id QAA07526; Tue, 5 Sep 1995 16:21:59 -0400 Received: (from ejfried@localhost) by herzberg.ca.sandia.gov (8.6.11/8.6.10) id UAA08522 for chemistry@www.ccl.net; Tue, 5 Sep 1995 20:20:29 GMT From: "Ernest Friedman-Hill" Message-Id: <9509051320.ZM8520@herzberg.ca.sandia.gov> Date: Tue, 5 Sep 1995 13:20:29 -0700 In-Reply-To: states@rucola.WUStL.EDU (David J. States) "CCL:Java chemistry applets?" (Sep 5, 10:01am) References: <9509051001.ZM29123@rucola.wustl.edu> X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chemistry@www.ccl.net Subject: Re: CCL:Java chemistry applets? Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 I've been looking at java for chemical (and other) applications. Both the potential and the limitations are surprising in the current incarnation. We're going to need some ports of the Solaris- and NT- specific implementations to other platforms before java/HotJava starts to take off; the insanely Sparc/Solaris-specific prototype was a big turn-off for me. I got the code, and the accompanying material in effect "dares you" to port it. Another big question was - why invent a new language for this purpose; why not use (for example) Safe-Tcl? My biggest problems with HotJava as it stands are that the java applets are 1) painfully unaware of the browser they're running in (for example, they cannot (without some MAJOR hacking) access the fields of and HTML form on the page in which they're embedded, and 2) the security aspects are pretty dismal, despite Sun's claims to the contrary. But the CONCEPT - active messages on the WWW - is and will be the Next Big Thing (TM), mark my words. On Sep 5, 10:01am, David J. States wrote: > Subject: CCL:Java chemistry applets? > Sun has been promoting a new programming language, java, as a tool > for creating portable applications on internet. Instead of constantly > going back to the host for additional information (a response to a mouse > click, for example), the applet executes on the local client. > > One of their demos is a page of molecules that can be viewed and rotated > in the web browser. See: > > http://java.sun.com/applets/applets/ChemicalModels/index.html > > but you need a "java capable" web browser such as hotjava, available > from http://java.sun.com. Netscape has announced support for java, > but I have not seen a date for when the product will be released. > > I was wondering, has anyone picked up on the Sun demo? Are people > designing chemistry and biochemistry specific java class libraries > and applets? Seems like it could be a powerful set of tools. > > David > > -- > David J. States > Institute for Biomedical Computing / Washington University in St. Louis > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: states@rucola.wustl.edu > -- Original Sender From: Address: states@rucola.WUStL.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 >-- End of excerpt from David J. States -- --------------------------------------------------------- Ernest Friedman-Hill Senior Member of Technical Staff Scientific Computing Department Sandia National Laboratories Org. 8117, MS 9214 PO Box 969 Livermore, CA 94550 From h.rzepa@ic.ac.uk Tue Sep 5 17:28:26 1995 Received: from romeo.ic.ac.uk for h.rzepa@ic.ac.uk by www.ccl.net (8.6.10/950822.1) id RAA09498; Tue, 5 Sep 1995 17:23:05 -0400 Received: from cscmgb.cc.ic.ac.uk (actually host sg1.cc.ic.ac.uk) by romeo.ic.ac.uk with SMTP (PP); Tue, 5 Sep 1995 22:13:01 +0100 Received: from [155.198.63.18] by cscmgb.cc.ic.ac.uk (940816.SGI.8.6.9/4.0) id WAA25468; Tue, 5 Sep 1995 22:13:16 +0100 X-Sender: rzepa@sg1.cc.ic.ac.uk Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 5 Sep 1995 22:19:08 +0000 To: chemistry@www.ccl.net From: h.rzepa@ic.ac.uk (Rzepa, Henry) Subject: Re: CCL:Java chemistry applets? >I've been looking at java for chemical (and other) applications. Both the >potential and the limitations are surprising in the current incarnation. >We're going to need some ports of the Solaris- and NT- specific implementations >to other platforms before java/HotJava starts to take off; the insanely >Sparc/Solaris-specific prototype was a big turn-off for me. I got the code, >and the accompanying material in effect "dares you" to port it. > >Another big question was - why invent a new language for this purpose; why >not use (for example) Safe-Tcl? Another consideration will be to establish standards. What we do not need is many and perhaps competing applets for say visualising molecules, or their orbitals etc etc. Thus there must be around 20-50 molecular viewers of various sorts out there as stand alone applications, and heaven forbid we get similar proliferation of Java applets. Dr Henry Rzepa, Department Chemistry, Imperial College, London, SW7 2AY. Tel: +44 171 594 5774. Fax: +44 171 594 5804. E-mail: rzepa@ic.ac.uk URL: http://www.ch.ic.ac.uk/rzepa/ Sent using Eudora Pro 2.1.3 From jkl@ccl.net Tue Sep 5 22:13:29 1995 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.6.10/950822.1) id WAA12395; Tue, 5 Sep 1995 22:06:05 -0400 Received: from is.nyu.edu for jesus@canarylab.chem.nyu.edu by bedrock.ccl.net (8.6.10/950822.1) id WAA22029; Tue, 5 Sep 1995 22:06:02 -0400 Received: from CANARYLAB.CHEM.NYU.EDU by is.nyu.edu; (5.65/1.1.8.2/23Sep94-1121PM) id AA06160; Tue, 5 Sep 1995 22:06:03 -0400 Received: by canarylab.chem.nyu.edu (940406.SGI/931108.SGI.AUTO.ANONFTP) for @is.NYU.EDU:CHEMISTRY@ccl.net id AA06889; Tue, 5 Sep 95 22:16:31 -0400 Date: Tue, 5 Sep 95 22:16:31 -0400 From: jesus@canarylab.chem.nyu.edu (Jesus M. Castagnetto Mizuaray) Message-Id: <9509060216.AA06889@canarylab.chem.nyu.edu> To: CHEMISTRY@ccl.net Subject: CCL: Searching for analysis of GPC Hello all! We are searching for software to analyze GPC runs, be them freeware/shareware or if commecial affordable ones. Any info/hint/lead will be appreciated. Thanks in advance. Greetings. _____ Jesus M. Castagnetto Mizuaray . "Energy of activation: The useful Dep. of Chemistry - NYU . amount of energy contained in a 4 Washington Pl, Rm 514, NY 10003 . cup of coffe" (The Last Word-The cstgnttj@acfcluster.nyu.edu . Ultimate Scientific Dictionary)