Free protein structure function software for linux

Erwin Data Structures is a library that is meant to be the ultimate data structure library for mixed usage of C and C++.

Arbitrary key and value types are implemented by template files that dont use C++ templates, but are instantiated by a Perl script.

This way, mixed usage in C and C++ is possible. However, a C++ interface is generated to support the advantages of the C++ language. No templates, no void*.
Erwin contains a number of tools, too, all of them written in Perl. The following list shows the data structures and tools, together with some typical examples.

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.

Structured Document Validator project implements a generalized method for validating both the structure and content of structured documents.

Any data format that can be deterministically divided into tags and data is classed as a structured document. This definition applies to a wide array of data formats, including XML, Java properties files, and delimited value files.

The application performs validations based on user-defined Structured Document Definitions (SDDs). It provides an environment for validation, SDD development, and document editing.

Rhino in Spring is a project that intends to integrate Mozilla Rhino JavaScript interpreter, the interpreter for the best (in our opinion) dynamic language on the Java platform with Spring Framework, the also best (again, in our opinion) enterprise framework on the Java platform.
Rhino in Springs aim is to provide a system that amalgamates the rapid development benefits and flexibility of a dynamic language with the strength, scalability and versatility of the Java platform and the Spring framework.
At the moment, the project delivers a controller component for Spring MVC that allows complex control flows spanning several webpages in web applications to be expressed as a single structured algorithm in JavaScript, putting the rich set of control flow structures and function reusability of a full-blown language at your fingertips. It transparently maps the users requests to the correct points of execution in your JavaScript code, even as the user freely navigates your website using the browsers back button or even "File-New Window" functionality!
A flexible set of state persistence options (including one where all state management is shifted to the browser, for maximum server scalability) is included.
Enhancements:
- Added support for relative pathnames in include(), with backward compatible lookup of absolute pathnames
- Fixed bug when an implicitly created ScriptStorage wasnt properly initialized

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 >.

pokertimer project is just a very little script for poker-turnaments.

Just execute the file. (You may want to configure the file to fit your desired blind-structure).

Data::PropertyList is a Perl module that can convert arbitrary objects to/from strings.

SYNOPSIS

use Data::PropertyList qw(astext fromtext);

$hash_ref = { items => [ 7 .. 11 ], key => value };
$string = astext($hash_ref);
# ...
$hash_ref = fromtext($string);
print $hash_ref->{items}[0];

$array_ref = [ 1, { key => value }, Omega ];
$string = astext($array_ref);
# ...
$array_ref = fromtext($string, -array=>1 );
print $array_ref->[1]{key};

Data::Propertylist provides functions that turn data structures with nested references into NeXTs Property List text format and back again.

You may find this useful for saving and loading application information in text files, or perhaps for generating error messages while debugging.

astext( $reference ) : $propertylist_string;

Writes out a nested Perl data structure in NeXT property list format.

fromtext( $propertylist_string ) : $hash_ref

fromtext( $propertylist_string, -array=>1 ) : $array_ref

Reconstructs a Perl data structure of nested references and scalars from a NeXT property list. Use the -array flag if the string encodes an array rather than a hash.

Bio::Tools::Run::PiseApplication::charge is a Perl module.

Bio::Tools::Run::PiseApplication::charge
Bioperl class for:

CHARGE Protein charge plot (EMBOSS)


Parameters:

(see also:
http://bioweb.pasteur.fr/seqanal/interfaces/charge.html
for available values):


charge (String)

init (String)

seqall (Sequence)
seqall -- protein [sequences] (-seqall)
pipe: seqsfile

window (Integer)
Window (-window)

aadata (String)
Amino acid property data file name (-aadata)

plot (Switch)
Produce graphic (-plot)

graph (Excl)
graph (-graph)

outfile (OutFile)
outfile (-outfile)

auto (String)

psouput (String)