Useful Tools Useful ToolsA (I think) complete list of the tools, programs, and databases we currently use to prepare these pages. For this page only, the color of the small dots adjacent to the anchors roughly indicate our major application for each package (it's all software, or magenta).
Three-Dimensional Molecular Models
Roger Sayle's
Rasmol
is used to view PDB files and to generate the static GIF images.
Klaus Shculten's group at the University of Illinois, Urbana-Champaign,
has produced a very powerful visualization tool for a wide variety of
molecular structure data,
VMD. We're using it increasingly
in place of RasMol.
Klotho supports the Chemical MIME type proposed by Henry Rzepa and wonderfully
illustrated in the
Hyperactive Molecules
Chemical MIME Type
page. For more information on the type and how to configure your machine so you can
interact with Klotho's structures more directly, check
here
.
CONCORD, written by Robert Pearlman and colleagues of the University of Texas, Austin, accepts a SMILES string and computes an approximately energy-minimized three-dimensional structure. The output can be obtained in the form of a PDB file, which is how we do it, but many other output file formats are supported. CONCORD is sold by
Image
Manipulation and Display
Ghostview
is used to preview the Postscript versions of the Fischer diagrams.
John Bradley's wonderful
xv is used to crop gif images by hand.
DuPont kindly makes
ImageMagick
available. It has a very nice set of image conversion and processing tools,
particularly suitable for batch mode and pipelining operations.
All of Moirai's code is written in Quintus Prolog, a semi-commercial version of the
logic programming language which seems to cleave quite closely to what may eventually
become the ISO standard for Prolog. We recommend it highly, especially for its nifty
libraries and garbage collection. It is now distributed through SICS, the Swedish Institute of Computer
Science.
We also check our code occasionally to be sure it runs on
SWI Prolog
Perl
TeX is the extraordinary typesetting system of Donald E. Knuth. It is
perhaps one of the most lovingly crafted public domain software systems in existence, and
provides an unmatched versatility. It can seem a little obscure however, which is why
beginners should start with
LaTeX
Tex can be found at
TUG
Donald E. Knuth, The TeXbook, Addison-Wesley Publishing Co., Reading MA, 1992.
Leslie Lamport's LaTeX is a set of macros built on
TeX
Leslie Lamport, LaTeX: A Document Preparation System, Addison-Wesley
Publishing Co., Reading MA, 1986.
Diller's book contains a number of useful tips, and is especially great at mathematical
formatting. Antoni Diller, LaTeX Line by Line, John Wiley and Sons, Chicester, 1993.
Pierre MacKay's ibygrk offers the full range of diacritical marks and alternate
letters in Silvio Levy's lovely Greek font. We
modified
Maple is the commercial package we use for symbolic and numerical calculations (for example, getting
the units to come out properly when computing the Keqs for a set of reactions). We have
found we can interface Maple to Prolog via some shell scripts fairly well. Maple can be
obtained from:
xv
ImageMagick
Computer LanguagesProlog
,
a public-domain Prolog which runs on several different platforms. We have been pleased
with it too; we have supplemented it with a reimplementation of a string
predicate Toni particularly likes.
Perl, Glue of the Web
is used for text manipulation, conversion, and general glue.
Text ProcessingTeX, Something that Needs No Introduction
,
a series of TeX macros devised by Leslie Lamport. But TeX itself will amply repay study.
,
as well as other anonymous ftp sites.
LaTeX, A Great Place to Start
to
simplify the
preparation of documents. One can exist quite happily with LaTeX for years without
needing to plunge into TeX proper.
Ibygrk
it to produce a 20pt
font. ibygrk proper can be found in several places, including
wuarchive
and
Duke
.
Numerical and Symbolic MathematicsMaple
Toni Kazic, August 30, 1995
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