From chemistry-request &$at$& server.ccl.net Mon Dec 9 04:10:24 2002 Received: from mailstudenti.unimi.it ([159.149.10.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gB99ANi24610 for ; Mon, 9 Dec 2002 04:10:23 -0500 Received: from smtp.unimi.it (smtp.unimi.it [159.149.10.3]) by mailstudenti.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with ESMTP id <0H6U00DA7HH435-0at0-mailstudenti.unimi.it> for CHEMISTRY-0at0-ccl.net; Mon, 09 Dec 2002 10:10:17 +0100 (MET) Received: from Villa (villa.farma.unimi.it [159.149.79.66]) by smtp.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with SMTP id <0H6U00EHIHH5DY-: at :-smtp.unimi.it> for CHEMISTRY-: at :-ccl.net; Mon, 09 Dec 2002 10:10:17 +0100 (MET) Date: Mon, 09 Dec 2002 10:12:45 +0100 From: Giulio Vistoli Subject: Re: CCL:file formats/mol. medels; was:V3000 molfile format To: petitjean : at : itodys.jussieu.fr, CHEMISTRY : at : ccl.net Message-id: <000f01c29f63$23162df0$424f959f %! at !% Villa> Organization: =?iso-8859-1?Q?Universit=E0_di_Milano?= MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 X-Mailer: Microsoft Outlook Express 6.00.2800.1106 Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 7BIT X-Priority: 3 X-MSMail-priority: Normal References: <02120613563688 (+ at +) itodys.jussieu.fr> We are tackling the problem of file formats for several years and our software VEGA (http://www.ddl.unimi.it) is now recognized as one of the most interesting product to handle and manage the molecular files. In this product we have implemented some features that could aid the use of file formats: - PDBFat format: this format was created in order to include extra information keeping the compatibility with the Brookhaven National Library specifications. For this reason, a sequence of REMARK records (one for each atom) was added at the beginning of file. The REMARK type is the user defined REMARK 77 (see PDB specifications) followed by the EXTRA keyword. In these extra lines you can add several information that will be read by specific programs, while the other softwares will skip these remark lines without any compatibility problems. - The Interchange File Format (IFF) is a binary file with an chunk structure (like IFF-ILBM, AIFF, etc). All chunks are optional (with the exception of the first) and the structure is totally expandable. With this powerful format you can store the maximum number of information and VEGA uses this format to save several ancillary information (like, atom color, atom selected, labels, measures, rototranslations, etc) that could not be saved with other formats. - ATDL language allows to define atom types. With ATDL you can describe any atom specification and you can add new force field templates so that VEGA can recognize them assigning the atom types and atomic charges. Using ATDL you can both convert file formats and change the force field assignment. Moreover we think that a software like VEGA, cannot be a black box, but it must be a totally expandable program so that everyone can add specific functions for particular purposes. For this reason we improve VEGA with two systems to develop new VEGA features: a plug-in architecture and a script language. On this ground the user can utilize the already existent VEGA functions as a pieces of code to build new features. Finally we are very interested to know the opinions and requirements of the people that must work with the plethora of formats that invaded the molecular modelling and we think that the definition of a standard format, usable for the standard applications, is a problem that we must try to resolve as soon as possible. Giulio Vistoli -------------- Giulio Vistoli Istituto di Chimica Farmaceutica e Tossicologica Viale Abruzzi, 42 I-20131 Milano Italia Tel. +39-02-50317545 Fax +39-02-50317565 giulio.vistoli \\at// unimi.it http://www.ddl.unimi.it