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This document describes the Perl modules and scripts contained in this
distribution for parsing STAR compliant data files and dictionaries.
It contains the following parts:
-- General description
-- Installation instructions
-- Usage instructions
-- Copyright notice
General description
-------------------
This distribution contains a set of Perl modules for parsing STAR compliant
data files and dictionaries, for example CIF or mmCIF data files and
dictionaries. While these tools are not limited to CIF or mmCIF files, they
do not allow the presence of nested loops.
The following modules are included in this distribution:
STAR::Parser
STAR::DataBlock
STAR::Dictionary
STAR::Writer
STAR::Checker
STAR::Filter
Some simple examples of application scripts are also included.
Installation instructions
-------------------------
Unzip and untar the archive:
% gunzip STAR.tar.gz
% tar xvf STAR.tar
% cd STAR
Install the perl modules:
% perl Makefile.PL
% make
% make test
% make install
These commands should install the modules into a default location on your
system.
Alternatively, you may create a STAR directory in a location of your choice,
copy the "*.pm" files into the newly created STAR directory, and include a
"use lib" line in all of the "*.pl" scripts in the bin directory:
use lib "<path to the directory above STAR>";
The modules require Storable to be installed in your Perl distribution.
(See ftp://ftp.cpan.org/pub/perl/CPAN/modules/by-module/Storable/ )
Usage instructions
------------------
Users are expected to have a working knowledge of Perl and a basic familiarity
of CIF or some other STAR compliant data file formats.
Detailed documentation for each "*.pm" Perl module can be extracted
with pod2html:
% pod2html Parser.pm > Parser.html
or viewed with perldoc:
% perldoc Parser.pm
Each "*.pl" script has a minimum description and usage information embedded,
which can be viewed with perldoc:
% perldoc parse.pl
The included scripts are a mixture of basic utility scripts (e.g. parse.pl or
check.pl), and very simplistic examples that are meant to test certain methods
in the modules (e.g. create.pl). Most users would generally be expected to
write their own customized scripts.
The included documentation should be sufficient for all the scripts and
modules. As a general comment, please be aware of the type of files each
script operates on:
parse.pl reads a CIF text file (.cif file). It has an option of saving
the parsed data structure as a ".cob" (cif object) file. Note that the file
extentions are by convention only, and are not enforced.
write.pl reads a data structure (.cob file) and outputs a CIF text file
(.cif file).
All other scripts operate on data structures (.cob files), *NOT* on CIF text
files (.cif files).
Therefore, a user will probably want to first parse files and dictionaries,
save the data structures (as .cob files) and then apply some of the other
scripts to the saved data structures:
% perl parse.pl -s 1LEP.cif
% perl parse.pl -Ds mmcif1000.dic
% perl check.pl -l 1LEP.cob cif_mm.dic.cob
etc.
More information on mmCIF can be found at these web sites:
http://pdb.rutgers.edu/mmcif/
http://ndbserver.rutgers.edu/mmcif/
Additional questions or comments may be directed to the author of these
modules and scripts:
Wolfgang Bluhm
mail@wbluhm.com
Copyright notice
----------------
A full copyright statement is provided with the distribution
(c) 2000 University of California, San Diego
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