Subject: Re: CCL:file formats/mol. medels; was:V3000 molfile format

From: Giulio Vistoli <[email-masked]>
Date: Mon, 09 Dec 2002 10:12:45 +0100

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
[email-masked]
http://www.ddl.unimi.it