Free chemical structures 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.

Memory Structures Library (MemSL) is a complete data structures/collection classes library with memory tracing, memory debugging, entry/exit tracing, exception handling, definable memory handlers, built-in thread support, and much more.

The project supports single, double, and circular linked lists, AVL balanced and threaded binary trees, dynamic hashing tables, stacks, queues and dequeues (using arrays or linked lists), sets (Pascal implementation, with union, difference, intersection, etc.), bags, tables and dictionaries, priority heaps, priority search queue, and more.

kfile_chemical is a set of kfile plugins for chemistry documents. It has support for XYZ, PDB, MDL mol/sd, Mol2, CML, ShelX, SMILES and CIF files.
kfile_chemical is currently in alpha stage: 1.0 will be alpha too; it will be feature complete, i.e. proving plugins kfile plugins for all files mentioned at the official chemical mime page (and a few more).
Version 2.0 will be beta, and feature a more organized set of extracted pieces of information.
Version 3.0 will be beta too, and mime magic, which is a method to detect the mime type not from the file extension, but from the content.
Verion 4.0 will be the first stable release and is aimed to be ready with Kubuntu 6.04 and KDE 4.0.
Enhancements:
- This release adds support for chemical-mime-data, thus synchronizing with the main MIME type library for chemical data.
- It also fixes QChar / QString conversion, the FSF address, and the contact email address.

Xephyrus Data Structures Tag Library provides an easy way to create and manipulate the contents of common Java data-structures such as maps and lists.
Enhancements:
- The library was polished up.
- Several improvements were made and a few bugs were fixed.
- This version is aimed at Java 5 and JSP 2.0.

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 >.

GChemPaint is a 2D chemical structures editor for the Gnome desktop.

GChemPaint should enable embedding some chemistry in files from other programs using Bonobo.

MKDoc::Text::Structured::Inline is a Perl module to convert text to HTML without handling block-level tags.

SYNOPSIS

my $text = some_structured_text();
my $this = MKDoc::Text::Structured::Inline::process ($text);
my $that = MKDoc::Text::Structured::Inline::process_entities_only ($text);

Struct::Compare is a recursive diff for perl structures.

SYNOPSIS

use Struct::Compare;
my $is_different = compare($ref1, $ref2);

Compares two values of any type and structure and returns true if they are the same. It does a deep comparison of the structures, so a hash of a hash of a whatever will be compared correctly.

This is especially useful for writing unit tests for your modules!

PUBLIC FUNCTIONS

$bool = compare($var1, $var2)

Recursively compares $var1 to $var2, returning false if either structure is different than the other at any point. If both are undefined, it returns true as well, because that is considered equal.