Free history of chemistry software for linux

Gnome Chemistry Utils software provides C++ classes and Gtk+-2 widgets related to chemistry. They are used in both Gnome Crystal and GChemPaint.

To compile and use the Gnome Chemistry Utils, you need libglade-2, and GtkGLExt, and their own dependencies. Everything except GtkGLExt is available from the Gnome repository or one of its mirrors.

The GtkChem3DViewer widget also needs Gnome-vfs and OpenBabel to be built.

GChemistry Utils are distributed under the LGPL license.

Gnome Chemistry Utils are in an early development stage.

Three widgets:

- a periodic table,
- a crystal structure viewer,
- a 3D molecular structure viewer.

The last widget is also accesible as a Bonobo control.

The Gnome Chemistry Utils are the basis for the development of both GChemPaint and Gnome Crystal

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).

Kemistry is a collection of chemical applications for the K Desktop Environment (release 3.x).

Originally the applications were distributed in a single source package, but currently every application is distributed in a standalone package. The available applications are

* KMolCalc - molecular weight and elemental composition calculator
* KemBabel - a file conversion program based on Open Babel

Browser-history is a small and efficient daemon that keeps your browser history, independent of the browser you use.
Browser-history came from the will to overcome a Netscape bug: there was no global history, and if you close a window, its whole history is lost. For people browsing lots of sites, having a possibility to track back where one has been before means that you dont have to put everything in your bookmarks file. If you are not sure if a site may be worth remebering, dont add it in your bookmarks. If you need it later, just browse your history files.
Later, it came to our minds that this also could be a valuable add-on to people writing experimental browsers, so they dont have to add this functionality to their browser itself, and to users able thus to track their web history regardless of the browser they used.
Browser-history is a small and efficient daemon. Real user services could be built on top of the log files it maintains for more possibilities (graphical representation, advanced search options, collective histories). It can be seen as a quick-and-dirty hack wrt to the general solution of using a personal proxy to provide this history and housekeeping facilities. For now, it is easy to use and it works very good.
And now that Netscape has a semi-decent history, browser-history is still valuable, as it is difficult to search in the netscape history, its file format is not defined, and entries expire after some time.
Enhancements:
- bugfix: since 2.6, internal links of default generated headers were false

Rails History Plugin is a Ruby on Rails plugin that stores user actions (i.e. URLs that the user has recently visited).
It avoids storage of POST and AJAX requests, and it provides a manual way to specify which actions not to store.
Installation:
Unpack into the vendor/plugin and that should be it.
Usage:
In your app/controllers/application_controller.rb, add a history line like this:
class ApplicationController < ActionController::Base
history :default => "http://default.url.com/",
:max => 10
end
The history function accepts a hash of options
:default, the default URL to redirect
:max, the maximum locations to remember (five by defaults).
None of the parameters are required. If somebody knows of a better way to obtain the default URL, he is welcomed to tell me how.
You can use the method history_skip in your controller if you want to avoid certain location to be stored in the history. By default, action resulting from a POST, PUT, DELETE request or an Ajax request are not stored in the history.
class FooController < ApplicationController
history_skip :action_to_skip
def action_to_skip
# I will not be stored in the history
end
end
In your actions, you can then use the following methods:
last_location: returns the last visited location, can be used with one numeric argument precising how many locations to go back in the history (1 by default),
peek_last_location: like last_location but dont remove it from the history,
redirect_back: redirect the user to the last location in history, it takes the same arguments as last_location,
store_location(force = false): stores the current location in the history, set force parameter to true to store location even if it would be skipped.
Note that if you want to use the plugin to create a "back" link on a page, you must go back two times. For example, using this controller
class HistoryController < ApplicationController
def foo
end
def bar
end
def back
redirect_back(2)
end
end
Ill try to explain clearly why. Lets say that in your bar view, you create a back link wich links to the back action. Now a user visits foo then bar. What you want is your user being redirected to foo when clicking your "back" link. Now your user hits the link. The controller will call the back action. From its point of view, you are in the back action so going back one time would take you to the bar action.
Enhancements:
- This release fixes a bug where a user variable was stored in a class variable instead of a session one, so a user going back would make another one skip a page in its history.
- The plugin no longer stores PUT and DELETE requests.
- A peek_last_location method was added to look at the history without modifying it, and a "force" parameter was added to the store_location method to force storing of a location even if it would normally be skipped.

Tie::HashHistory can track history of all changes to a tied hash.

SYNOPSIS

my $hh = tie %hash => Tie::HashHistory, PACKAGE, ARGS...;

@values = $hh->history(KEY);

Tie::HashHistory interposes itself between your program and another tied hash. Fetching and storing to the hash looks completely normal, but Tie::HashHistory is keeping a record of all the changes to the each key, and can Tie::HashHistory will give you a list of all the values the key has ever had, in chronological order.

The arguments to the tie call should be Tie::HashHistory, and then the arguments that you would have given to tie to tie the hash without the history feature. For example, suppose you wanted to store your hash data in an NDBM file named database. Normally, you would say:

tie %hash => NDBM_File, database, $flags, $mode;

to get this history feature, just add Tie::HashHistory before NDBM_File:

my $hh = tie %hash => Tie::HashHistory,
NDBM_File, database, $flags, $mode;

The data will still be stored in database, and it will still be an NDBM file. All the fetching and storing will look the same, but the change history of each key will be available.
The tie call will return an object; to find out the history of a key, use the history method on this object. It takes one argument, which is a key string. It will return a list of all the values that have ever been associated with the key, in chronological order, starting with the most recent. For example:

$hash{a} = first;
$hash{b} = second;
$hash{a} = third; # Overwrites old value

# Prints "third second" as you would expect
print "$hash{a} $hash{b}n";

@values = $hh->history(a);
# @values now contains (third, first)

@values = $hh->history(b);
# @values now contains (second)

At present, if called in scalar context, the history() method will return the number of items in the history. This behavior may change in future versions.

The underlying hash can be any tied hash class at all. To use a regular in-memory hash, use Tie::StdHash (distributed with Perl) as the underlying implementation:

use Tie::Hash; # *NOT Tie::StdHash*
my $hh = tie %hash => Tie::HashHistory, Tie::StdHash;

This is not as efficient as it could be because fetches and stores on %hash still go through two layers of tieing. I may fix this in a future release.