Free levels of protein structure software for linux

XML::Structured is a simple conversion API from XML to perl structures and back.

SYNOPSIS

use XML::Structured;

$dtd = [
element =>
attribute1,
attribute2,
[],
element1,
[ element2 ],
[ element3 =>
...
],
[[ element4 =>
...
]],
];

$hashref = XMLin($dtd, $xmlstring);
$hashref = XMLinfile($dtd, $filename_or_glob);
$xmlstring = XMLout($dtd, $hashref);

The XML::Structured module provides a way to convert xml data into a predefined perl data structure and back to xml. Unlike with modules like XML::Simple it is an error if the xml data does not match the provided skeleton (the "dtd"). Another advantage is that the order of the attributes and elements is taken from the dtd when converting back to xml.

GraphViz::Data::Structure can visualise data structures.

SYNOPSIS

use GraphViz::Data::Structure;

my $gvds = GraphViz:Data::Structure->new($data_structure);
print $gvds->graph()->as_png;

This module makes it easy to visualise data structures, even recursive or circular ones.
It is provided as an alternative to GraphViz::Data::Grapher. Differences:

GraphViz::Data::Structure handles structures of arbitrary depth and complexity, automatically following links using a standard graph traversal algorithm.
GraphViz::Data::Grapher creates graphics of indiividual substructures (arrays, scalars, hashes) which keep the substructure type and data together; GraphViz::Data::Structure does this by shape alone.
GraphViz::Data::Structure encapsulates object info (if any) directly into the node being used to represent the class.
GraphViz::Data::Grapher colors its graphs; GraphViz::Data::Structure doesnt by default.
GraphViz::Data:Structure can parse out globs and CODE references (almost as well as the debugger does).

Generic Data Structures Library (GDSL) is a collection of routines for generic data structures manipulation.
Generic Data Structures Library is a portable and re-entrant library fully written from scratch in pure ANSI C. It is designed to offer for C programmers common data structures with powerful algorithms, and hidden implementation.
Available structures are lists, queues, stacks, hash tables, binary trees, binary search trees, red-black trees, 2D arrays, and permutations.
GDSL provides a modern Applications Programming Interface (API) for C programmers, while allowing wrappers to be written for very high level languages.
The library covers the following data structures:
- Low-level doubly-linked nodes
- Low-level doubly-linked low-level lists
- Low level binary trees
- Low level binary search trees
- Binary search trees
- Red-black trees
- 2D arrays
- Hash tables
- Lists
- Queues
- Stacks
- Permutations
Enhancements:
- A bug that was introduced in gdsl_hash_insert in the previous release was fixed.
- A missing include in gdsl.h was fixed.

Project Foundry provides a integrated project management tool.
Project Foundry is a tool to create and maintain information used during the development of software projects.
It is oriented towards the high level management of the projects, and aims to better integrate the usual tasks of management.
In particular, one can keep track of:
- Meetings minutes
- Stakeholders
- Requirements
- Models of GUI
- Work breakdown structure (Gantt chart scheduler)
- A glossary so that important words are defined and used correctly all around the project

BALLView is an extensible viewer for bio-molecular structures.
BALLView project provides all standard models and offers rich functionality for molecular simulation and modeling, including molecular mechanics methods (AMBER and CHARMM force fields), continuum electrostatics methods employing a Finite-Difference Poisson Boltzmann solver, and secondary structure calculation.
Since BALLView is based on BALL (the Biochemical ALgorithms Library), it is easily extensible on the level of C++ code and it has an Python interface to allow interactive rapid prototyping.
Whats New in 1.1.1 Stable Release:
- This version finally brings full support for Python, DLLs, and nmake Makefiles under Windows.
- A large number of prominent fixes were made, especialy for g++ 4.x.
- Some new functionality was added to BALLView.
Whats New in 1.2 pre 06.07 Development Release:
- Two new minimizers and support for the MMFF94 electrostatics switching function were added.
- The documentation was extended.
- Severals bugs were fixed.

Image::MetaData::JPEG::Structures is a Perl module that describes the structure of a JPEG file; it is an appendix to the main manual page of the Image::MetaData::JPEG module, which the reader should refer to for further details and the general scope.

THE STRUCTURE OF JPEG PICTURES

The JPEG (Joint Photographic Experts Group) ISO standard is a lossy image compression mechanism developed before 1990, designed for compressing colour or gray-scale photo-realistic images (it performs poorly on line-art drawings). The JPEG mechanism is designed to exploit known limitations of the human eye, in particular the fact that colour changes are perceived less accurately than changes in brightness.

Note that although the "baseline" JPEG format is patent-free, there are patents associated with some optional features, namely arithmetic coding and hierarchical storage. For this reason, these optional features are never used on the Web (good job, patent fans ...). JPEG refers only to a class of compression algorithms, not to a specific file format. In order to produce files with embedded JPEG streams, a number of file format (semi-)standards have been adapted or devised, some of which are listed in the format section. The structure of a well formed JPEG file can be described by the following pseudo production rules (for sake of simplicity, some additional constraints between tables and SOF segments are neglected).

JPEG --> (SOI)(misc)*(image)?(EOI)
(image) --> (hierarch.)|(non-hier.)
(hierarch.) --> (DHP)(frame)+
(frame) --> (misc)*(EXP)?(non-hier.)
(non-hier.) --> (SOF)(scan)+
(scan) --> (misc)*(SOS)(data)*(ECS)(DNL)?
(data) --> (ECS)(RST)
(misc) --> (DQT)|(DHT)|(DAC)|(DRI)|(COM)|(APP)

(SOI) = Start Of Image
(EOI) = End Of Image
(SOF) = Start Of Frame header (10 types)
(SOS) = Start Of Scan header
(ECS) = Entropy Coded Segment (row data, not a real segment)
(DNL) = Define Number of Lines segment
(DHP) = Define Hierarchical P??? segment
(EXP) = EXPansion segment
(RST) = ReSTart segment (8 types)
(DQT) = Define Quantisation Table
(DHT) = Define Huffman coding Table
(DAC) = Define Arithmetic coding Table
(DRI) = Define Restart Interval
(COM) = COMment segment
(APP) = APPlication segment

This package does not check that a JPEG file is really correct; it accepts a looser syntax, were segments and ECS blocks are just contiguous (basically, because it does not need to display the image!). All meta-data information is concentrated in the (COM*) and (APP) Segments, exception made for some records in the (SOF*) segment (e.g. image dimensions).

Reference: B< "Digital compression and coding of continuous-tone still
images: requirements and guidelines", CCITT recommend. T.81, 1992,
The International Telegraph and Telephone Consultative Committee,
standard ISO/IEC IS 10918-1 or ITU-T Recommendation T.81 >.
Also: B< "The JPEG still picture compression standard", G.K.Wallace,
1991, IEEE Transactions on Consumer Electronics >.

The Klorofil Collaboration Project, which initiated and sponsored by Saltanera Teknologi, is an open source initiative through which the Klorofil community and industry partners will together build a new PHP enterprise-level application development and deployment environment.
Klorofil project is an open source project initiated by Saltanera Teknologi, an e-business solution provider company.
The goal of the project is to build a new PHP enterprise-level application development and deployment environment. One of Klorofils product is an open source platform for PHP named as Klorofil Platform.
Klorofil Platform is an open source project made available by Saltanera under Common Public License version 1.0 ("CPL"). CPL is an open source license which has been approved by Open Source Initiative.
Klorofil Platform Basic Structure:
- Class Registration
- Application Launcher
- Collection Classes
- I/O Classes
- Network Classes
Socket
HTTP
Email
SMS
- Compression
- Byte Compiler
- XML
gambArt (Klorofil GUI)
Basic Structure
- Application
- Canvas
- Component
- Control
- Form
Component
- Button
- Flat Button
- Label
- Edit
- Dialog
- Radio Button
- CheckBox
- Panel
- Image
- ListBox
- DropDownBox
- PageControl
- ToolBar
- MainMenu
- Timer
Enhancements:
- Bug fixed on Windows launcher to use php.ini file from klorofils directory
- Bug fixed on Calculator samples, button 9
- Enhancement of memory allocation model for event handler, not every component handling event
- Enhancement of receive focus process of control, not every control accept focus