Free chemistry utils 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::Mol is a molecule object toolkit.

SYNOPSIS

use Chemistry::Mol;

$mol = Chemistry::Mol->new(id => "mol_id", name => "my molecule");
$c = $mol->new_atom(symbol => "C", coords => [0,0,0]);
$o = $mol->new_atom(symbol => "O", coords => [0,0,1.23]);
$mol->new_bond(atoms => [$c, $o], order => 3);

print $mol->print;

This package, along with Chemistry::Atom and Chemistry::Bond, includes basic objects and methods to describe molecules.
The core methods try not to enforce a particular convention. This means that only a minimal set of attributes is provided by default, and some attributes have very loosely defined meaning.

This is because each program and file type has different idea of what each concept (such as bond and atom type) means. Bonds are defined as a list of atoms (typically two) with an arbitrary type. Atoms are defined by a symbol and a Z, and may have 3D and internal coordinates (2D coming soon).

Gnosis Utils contains several Python modules for XML processing. Gnosis Utils has other generally useful tools:
- xml.pickle (serializes objects to/from XML
- API compatible with the standard pickle module)
- xml.objectify (turns arbitrary XML documents into Python objects)
- xml.validity (enforces XML validity constraints via DTD or Schema)
- xml.indexer (full text indexing/searching), and many more.
Enhancements:
- This release fixes a bug in XML pickling of mx.DateTime objects.

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.

CGI::Utils is a Perl module for retrieving information through the Common Gateway Interface and mod_perl.
Enhancements:
- This release adds support for mod_perl 2 in addition to mod_perl 1.
- It fixes some formatting issues with the POD documentation and adds underscore versions of more methods.

Array::Utils module contains small utils for array manipulation.

SYNOPSIS

use Array::Utils qw(:all);

my @a = qw( a b c d );
my @b = qw( c d e f );

# symmetric difference
my @diff = array_diff(@a, @b);

# intersection
my @isect = intersect(@a, @b);

# unique union
my @unique = unique(@a, @b);

# check if arrays contain same members

if ( !array_diff(@a, @b) ) {
# do something
}

FUNCTIONS

unique

Returns an array of unique items in the arguments list.

intersect

Returns an intersection of two arrays passed as arguments.

array_diff

Return symmetric difference of two arrays passed as arguments

My Own Dialup Utils is a Linux-oriented textual dialup toolkit with support for MS callback and iptables.
It is intended to be flexible enough to dialup to many ISPs without much configuration.
Enhancements:
- This release features new documentation and howtos, a fix for MS RAS callback, and support for SecureID hardware key generators.