Free chemistry help software for linux

Chemistry::SQL is an access database functions module.

SYNOPSIS

use strict;
use Chemistry::SQL;
use Chemistry::Artificial::SQL;

my $db_name = $ARGV[0];
my $file = $ARGV[1];

my $db1 = Chemistry::SQL::new(db_host=>"127.0.0.1",db_user=>"root",db_port=>"3306",db_pwd=>"",
db_name=>$db_name,db_driver=>"mysql");
if ($db1->db_exist)
{ $db1->connect_db;
$db1->del_tables;
$db1->create_tables_mysql;
$db1->inscomp_from_file("$file");
}
else
{
$db1->create_db;
$db1->connect_db;
$db1->create_tables_mysql;
$db1->inscomp_from_file("$file");
}
# Reaction Insertion

my $qart = Chemistry::Artificial::SQL::new($db1);
my $qr =$qart->q_reaccion(C=CC=C.C=C>>C1=CCCCC1,smiles);
$db1->reactionsert($qr,"","0");

This package provides the necessary functions to interact with the database. The methods implemented in this module are oriented to give users control of the database without knowing how to use SQL queries.

Chemistry Development Kit classes are Java utitility classes for ChemoInformatics and Computational chemistry, written in Java. They are developed constantly developed parallel to other projects that make use of them.
They are a complete re-write of the CompChem classes that were the basis of JChemPaint, a Java Editor for 2D chemical structures, and of JMDraw, a Java package for the graphical layout of 2D chemical structures.
The CDK project was started in September 2000 to replace the CompChem libraries used by JChemPaint, Jmol and SENECA. It no longer is in its initial stage, but is slowly getting a solid state.
The people involved in setting up the project are Christoph Steinbeck then at the Chemoinformatics Group at the Max Planck Institute of Chemical Ecology in Jena, as well as Egon Willighagen from the University of Nijmegen, The Netherlands, who is also involved with JChemPaint and many other Java Chemoinformatics programs, and Dan Gezelter from Notre Dame University, South Bend, USA, the initiator of Jmol, a 3D viewer and analyzer for molecules .
Now, the rewrite of these CompChem/CDK library classes do somehow effect all of our projects. All of our code relies to some extend on the so-called CompChem classes for computational chemistry.
Christoph Steinbeck started this chemistry library when he started programming SENECA, a system for Computer Assisted Structure Elucidation. It turned out that some of the code had design flaws that prevented others, like the authors of (Jmol) to use it.
Enhancements:
- This release consists of mostly some bugfixes, but also solves a few Java 1.4.2 compile problems and adds more functionality to the SMARTS parser.

Chemistry::Artificial::Graphics is a graphic plot for artificial with database support.

SYNOPSIS

use strict;
use Chemistry::SQL;
use Chemistry::Artificial::Graphics;

my $dbname = $ARGV[0];
my $chaname = $ARGV[1];
my $file = $ARGV[2];
my $mode = $ARGV[3];

if (scalar(@ARGV)!=4)
{ print "Error in parameter number n";
print "perl chaplot.pl DB_NAME
CHA_NAME FILE_NAME MODE (svg | svg_static | text)n";
exit;
}
my $db1 =
Chemistry::SQL->new(db_host=>"127.0.0.1",db_user=>"root",db_port=>"3306",sb_pwd=>"",db_name=>"$dbname",db_driver=>"mysql");
$db1->connect_db;
my $pcha = Chemistry::Artificial::Graphics->new(db => $db1, width=> "800",height=>"600",radius=> "10",distanceh=>"200",file=> $file,
mode=> $mode);
$pcha->ch_plot("$chaname");

This package, along with Chemistry::SQL, includes all the necessary to generate graphics of the artificial chemistry in database.

Chemtool project is a small program for drawing chemical structures on Linux and Unix systems using the GTK toolkit under X11.
Chemtool relies on transfig by Brian Smith for postscript printing and exporting files in PicTeX and EPS formats. Its companion program, XFig, is recommended for enhancing the output of chemtool, and for creation of 2D diagrams and schematics in general.
Both are included with most distributions of Linux, and are available through a number of websites including www.xfig.org. If you want to import chemtool drawings into word processing programs other than LaTeX, you will probably want to add a preview bitmap to them, as neither StarOffice/OpenOffice nor that software from Redmond seem to be able to display postscript inserts on screen without them.
For this purpose, using either ps2epsi, which comes with ghostscript, or epstool, a part of gsview is recommended. Since chemtool-1.6, this option is supported directly (through the equivalent function offered by recent versions of transfig).
Chemtool was originally written by Thomas Volk, then a student of chemistry and biology at the university of Ulm, Germany. His version, which was described in an article in the german periodical LinuxMagazin, was using plain X11.
The bond types available in chemtool are:
- a single bond
- a double bond (with one line shorter than the other)
- a double bond (having the shorter line on the opposite side)
- a centered double bond
- a triple bond (with the flanking lines shorter than the center)
- a wedge-shaped bond
- a dashed wedge-shaped bond
- a wavy line
- a dashed wide line
- a half arrow
- an arrow
- a wide bond
- a circle
- a dotted line
- a single bond that cuts out a segment from any bond it crosses
- a triple bond (with equal line lengths)
- a quadruple bond
Enhancements:
- PNG export, kprinter support, and a few new template structures were added.
- Screen rendering of complex labels was improved.
- Several problems with text input in UTF8-enabled locales were fixed.
- Arrowhead size in EPS output and the appearance of arrowheads, superscripts, and national characters in SVG output were fixed.

Tk::Help is simple widget for creating a help system for Perl/Tk applications.

SYNOPSIS

use Tk::Help;
my $help = $main->Help(-variable => @array);

This is an answer to a personal need to be able to create help systems for my Perl/Tk applications. Originally, I just created a really big dialog and formatted all the text, which was tedious and clumsy.

I wanted to create something that looked similar to the Windows help. This is by no means as featured or fluid as the Windows help, but it should provide a (somewhat) simple means to create a help dialog where all someone should need to do is create the array with their help content.

Getopt::Mixed::Help Perl module can combine Getopt::Mixed with usage and help.

SYNOPSIS

use Getopt::Mixed::Help
(< filenames >... => filenames to be processed,
ENV => SCRIPT_OPT_,
ENV_ => SCRIPT_OPT_,
d>debug:i number => turn on debugging information (*),
e>execute => do it without asking for confirmation,
f>force => override all safety checks,
i>interactive => asks for confirmation before doing it,
n>no-execute => just print what would be done without doing it,
q>quiet => suppress all information,
s>summary => print summary information on exit,
v>verbose:i number => turn on verbose information (*),
(*) => (*) You may add a positive integer for a higher level.
);
if ($opt_...

export SCRIPT_OPT_INTERACTIVE=1
test_script -d -v 2 --summary some_file.ext other_file.ext

ABSTRACT

Getopt::Mixed::Help is a simplified interface to Getopt::Mixed adding usage (help) functionality. It automatically adds the options -?, -h and --help (the last two configurable) to print the usage text. It allows to get option values from the environment (if the operating system it runs on supports environment variables). It can also add different flavours of support for multiple options. Finally it supports debugging output of the options used.

The module uses a direct import mechanism called with a hash as parameter. The structure of the hash is as follows:

The key is a combined (SHORT > LONG [ARGUMENT SPECIFIER [VALUE IDENTIFIER]]) option description for Getopt::Mixed, except for the VALUE IDENTIFIER which is simply included into the help text. The value following the key is simply the help text for this option.

If the second character of the first key is not >, the first key is taken as descriptive identifiers for additional parameters and the help for them.
Any key starting with ( and ending with ) will be interpreted as a footnote (additional help text) to the real options. They should be used at the end of the list only.

A key equal to ENV is used to get default values for the remaining options from the environment. For any option not initialised on the command line an environment variable with the prefix of the value following ENV and a rest of the name identical to the uppercase long option name (e.g. SCRIPT_OPT_DEBUG) will be checked. If this environment variable exists, it will be used to set the option. Note that in the name of the rest of the environment variable uppercase is used and hyphens are relaced with underlines.

A key equal to ENV_ is used in the same way as the key ENV. In addition it allows for a special environment variable with the prefix of the value following ENV followed by a single underline (_) as combined initialiser (for more than one option, e.g. export SCRIPT_OPT__=debug verbose=2). Note that no whitespaces are allowed in the values of the options initialised this way as the string in the environment variable is parsed in a simple way.

The module defines the variable $optUsage containing the complete help text.
If an option debug exists and is choosen on the command line, this module will print all option values and all remaining parameters to standard error. The name of this option may be changed, see "changing the debug option" below in the "CHANGING DEFAULT BEHAVIOUR" section.

IRC::Bot::Help is a module to dispatch help for IRC::Bot.

SYNOPSIS

use IRC::Bot::Help;
my $seen = IRC::Bot::Help->new();

# later on...

# User asks for help in DCC CHAT
sub on_dcc_chat {
my ( $kernel, $id, $who, $msg ) = @_[ KERNEL, ARG0, ARG1, ARG3 ];

my $nick = ( split /!/, $who )[0];

# Do Stuff...
if ( $msg =~ m/^.help/i ) {

my $topic = $help->ask_help(all);
$kernel->post( NICK, dcc_chat, $id, $topic );

}

}

Basically holds a list of help topics and dispatches them on demand.