From chemistry-request@server.ccl.net Sun Aug 1 23:59:15 1999 Received: from nucleus.harvard.edu (nucleus.harvard.edu [140.247.90.196]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id XAA10488 for ; Sun, 1 Aug 1999 23:59:15 -0400 Received: from localhost (daizadeh@localhost) by nucleus.harvard.edu (8.9.3/8.9.3) with ESMTP id XAA05611 for ; Sun, 1 Aug 1999 23:54:13 -0400 (EDT) Date: Sun, 1 Aug 1999 23:54:13 -0400 (EDT) From: Iraj Daizadeh To: chemistry@ccl.net Subject: Re:In sum... CCL:pythonVSperl... Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Drs. Ehrlich and Dalke are thanked for their contributions to addressing my query concerning the current use of python vs. perl in chem-bioinformatics. Dr. Hinsen is on vacation; I am sure he'll have some input on this as well...Iam anxiously awaiting his return to hear what he has to say... Thanks again...iraj, Iraj Daizadeh, Ph.D. Harvard University Department of Cellular and Molecular Biology The Biological Laboratories 16 Divinity Avenue Cambridge, MA 02138 Phone: (617) 495-0783 (617) 495-0560 Fax: (617) 496-4313 Email: daizadeh@nucleus.harvard.edu WebPage: http://mcb.harvard.edu/gilbert/daizadeh xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx Original Query: Hello. Perl seems to dominate the chem(bio)-informatical sciences these days. An example of such dominance is descibed on papers describing the BioPerl consortium http://bio.perl.org (see, e.g., an article in http://www.bitsjournal.com Bioperl:Standard perl modules for bioinformatics)... The question is why...why has python been neglected >from its role in the informatics fields.... Your responses would be appreciated...Iraj. xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx Hello Iraj, I think you'll have to note a clear separation here; in the bioinformatics (read sequence analysis as opposed to structure analysis) field, Perl had strong support from the start on. When I speak to bioinfo people here at EMBL, code reuse seems to be the dominant motive for choosing Perl. In my eyes, things are different in the structure-related comp chem field. Right now, I see a lot of projects which use Python in favor of Perl; for example look at Konrad Hinsen's excellent Molecular Modelling Toolkit (http://starship.python.net/crew/hinsen/mmtk.html). Companies like Bioreason or Exelyxis are now looking for people with Python coding experience. People here in NMR at EMBL even dream about developing a next-generation XPLOR as libraries to be used as Python modules. Given Python's excellent CORBA, number crunching and XML support, as well as the Java integration and existing class libraries relevant to the comp chem field, I think it's just a matter of time when Python catches up. Tight integration with web application servers like Zope (http://www.zope.org) could make a big difference in writing web services for the biocomputing community. After having used Perl4 and Perl5 for years, I wonder where people see advantages of Perl in the comp chem field? Comments anybody? Regards, Lutz ______________________________________________________________________ Lutz Ehrlich http://www.embl-heidelberg.de/~ehrlich mailto:lutz.ehrlich@embl-heidelberg.de European Molecular Biology Laboratory phone: +49-6221-387-140 Meyerhofstr. 1 fax : +49-6221-387-517 D-69012 Heidelberg, Germany xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx ---------- Forwarded message ---------- Date: Thu, 29 Jul 1999 17:24:27 -0600 From: Andrew Dalke To: Iraj Daizadeh Subject: Re: CCL:pythonVSperl... Here are some bioinformatics/chemical inforamtics/structural biology Python references: http://theopenlab.uml.edu/development.html http://starship.python.net/crew/hinsen/mmtk.html http://starship.python.net/crew/dalke/ http://www.scripps.edu/pub/olson-web/people/sanner/html/cv.html (search for Python) You'll notice most of these are structural based. That's probably from a combination of biases. My background is in protein structure modeling, so I'm prone to know more about those types of efforts. More relevant to your question, I've found that Perl is harder to use for developing complicated data structures (eg, describing a molecule in 3D) than Python. On the other hand, most of the traditional bioinformatics work seems heavily string based, which is Perl's bread&butter. I also know that Perl is still better in I/O performance than Python. I hear that the Perl implementation muck around with implementation differences in the FILE* for STDIO to get about a two-fold speed advantage over even generic C code. Since for many sorts of bioinformatics work, the needs are "traverse that gigabyte file and extract this information", which is I/O bound, perl makes sense. Python's advantage comes with building larger or more complicated programs, especially when several people are involved and the code needs to be more maintainable and easier to read. (The Python community calls this "programming in the large"). It is much easier to write reusable libraries -- and actually have someone else understand them enough to reuse them -- in Python than Perl. That's why we've chosen Python over Perl for our LeadFinder package for high-throughput screening analysis. Andrew Dalke dalke@bioreason.com xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx From chemistry-request@server.ccl.net Mon Aug 2 14:11:55 1999 Received: from neon.chem.ucla.edu (neon.chem.ucla.edu [128.97.35.251]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA16702 for ; Mon, 2 Aug 1999 14:11:54 -0400 Received: from localhost (kuwata@localhost) by neon.chem.ucla.edu (8.8.0/8.8.0) with SMTP id LAA01612 for ; Mon, 2 Aug 1999 11:13:07 -0700 (PDT) X-Authentication-Warning: neon.chem.ucla.edu: kuwata owned process doing -bs Date: Mon, 2 Aug 1999 11:13:06 -0700 (PDT) From: Keith Kuwata Reply-To: Keith Kuwata To: chemistry@server.ccl.net Subject: GUGA in MOLCAS 4.0--solution Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi folks, This was my problem. While attempting to run GUGA, my jobs would crash with the error NUMBER OF VERTICES EXCEEDS 299 I was wondering, what does this mean? This error message was explained by Fernando Vila: From: Fernando Vila This means you have reached the internal limit for the number of vertices in the GUGA diagram. It is an internal hardwired limit (or at least it used to be in earlier versions). One way to fix it is to reduce the number of references, for example, by eliminating the last reference you can reduce the number of active orbitals by 2 (the first and last turn into inactive and virtual). Another way is to recompile the code with a larger number of vertices allowed. I'm not sure is this is possible in the version you are working with. Thanks also to Eric V. Patterson and Mike Falcetta for their suggestions. Keith Kuwata From chemistry-request@server.ccl.net Mon Aug 2 15:53:43 1999 Received: from si.fi.ameslab.gov (si.fi.ameslab.gov [147.155.20.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA18669 for ; Mon, 2 Aug 1999 15:53:43 -0400 Received: (from pradipta@localhost) by si.fi.ameslab.gov (AIX4.2/UCB 8.7/8.7) id OAA32610 for chemistry@ccl.net; Mon, 2 Aug 1999 14:52:14 -0500 (CDT) From: Pradipta Bandyopadhyay Message-Id: <199908021952.OAA32610@si.fi.ameslab.gov> Subject: summary: center of cavity in continuum methods! To: chemistry@ccl.net (CCL) Date: Mon, 2 Aug 1999 14:52:14 -0500 (CDT) X-Mailer: ELM [version 2.4 PL25] Content-Type: text hi everybody, I posted the following message a few days back. --------------------------------------------------------------------- Dear ccl-members, I have a question about the continuum method of solvation. Does it matter where I put my molecule inside the cavity? If I put the molecule ( dipole) in the center of the cavity and then put it away from the center, the dipole moment ( with respect to the origin) changes but the dipole moment of uncharged systems are independent of the origin. So is it really independent of the postion of the dipole? I want to know the answer for both quantum mechanical and classica\ l treatment of the dipole(when the charge is zero). Can anyone tell me the answer for both quantum menchanical and classical cases? Thanks in advance. ------------------------------------------------------------------ rather than putting all the replies I write the answer. For the onsager model (or for any model, which doesn't put any charge on the surface) it doesn't matter where I put the solute inside the cavity as long as the soule is neutral. However, for more sophisticated continuum models like PCM, COSMO ( which put charges or other 'objects' on the cavity boundary) it matters where I put the solute. I thank Dr. Toomas Tamm, Dr. Antonio Luiz and Dr. Chaitanya Shridhar for their messages. Pradipta -- ***************************************** * Dr. Pradipta Bandyopadhyay * * AMES LAB * * Department of Chemistry * * Iowa State Unievrsity * * Ames, IA 50011 * * USA * * e-mail: pradipta@si.fi.ameslab.gov * * Phone : 515-294-4604 (Lab) * * : 515-232-8067 (Residence) * * Fax : 515-294-0105 * * URL: http://www.msg.ameslab.gov/ * * Group/pradipta/index.html * ***************************************** ------------------------------------------------------------------------------ ...FOR AFTERWARDS A MAN FINDS PLEASURE IN HIS PAINS, WHEN HE HAS SUFFERED LONG AND WANDERED FAR. -- HOMER ------------------------------------------------------------------------------