Free primary protein structure software for linux

Primary is an cursor theme.

Finally, a colour version of my Monochrome iconset: (http://www.kde-look.org/content/show.php?content=18317)

These icons have been sitting on my computer for long enough, so I decided to post them here, even though all icons are not yet in colour (though the most commonly used ones are, of course.

2474 icons in this release.

Dont forget to leave feedback!

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.

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 >.

Data Architects, DBAs, Analysts and Designers rely on Data Modeling tools to facilitate and simplify their data Modeling efforts, while maximizing the use of their resources. The Power*Architect allows these busy highly technical resources to perform this most intricate part of their job in a fraction of the time.
Power*Architect project is an innovative Java-based data modeling tool geared specifically for Data Warehouse and Data Mart design. It allows the designer to open multiple concurrent source Database connections, create and explore profiles of the source data, drag and drop source schemas, tables and columns into the data modeling playpen, and forward engineer the resultant target database and its associated ETL template.
Main features:
- Access any JDBC or ODBC accessible source database
- Quickly create profiles of source data, including information about the size of the data in each column, maximum and minimum values, frequency distribution of values in a column, and more.
- Profile information is saved with the project, so profile data can still be used to aid off-site design sessions when it is not possible to access the source databases.
- Design the target database Data Model (Data Warehouse)
- Compare the database structure of any two databases highlighting the structural differences and generating the required DDL to synchronize
- Compare the Data Model data structures to an existing target database
- Save a snapshot of all source systems data structures in the project file, allowing data warehouse designers to evolve their target data model remotely
- Forward engineer to Oracle, SQL Server, DB2, and PostgreSQL and more.
- Forward engineer ETL Templates containing source-to-target data mappings
- Invoke ETL Engine to load initial set of data into the target database
- Enable easy centralized installation and updates to many end users (Supports Java WebStart technology).
- The Power*Architect can open multiple source databases concurrently, even if they are from competing database vendors. Another key feature of the Power*Architect, that sets it apart from other data modeling tools, is that it remembers the origin of each column, and is capable of automatically generating the source-to-target data mappings.
- Whether youre building or maintaining your Data Warehouse data model, the Power*Architect will provide you a complete view of all required database structures and will expedite every aspect of your data warehouse design.
- Design your Data Warehouse in a fraction of the time with the Power*Architect.
- We look forward to showing you how!
- The Power*Architect is available now for download! The product is available for free to individuals for personal use. Commercial licensing and support are available at competitive prices. Please call us at 1-866-SQL-POWR to purchase.
Enhancements:
- This release fixes a bug that caused corrupt project files to be saved.
- The handling of automatic cascading primary keys in multi-level identifying relationships now works better.
- The profile manager is now even more stable.
- It is now possible to add new database connection types from within the GUI.

IRCTree is a project which shows a tree representing the structure of an IRC network in ASCII.

Introduction

IRCTree shows a tree in ascii format representing the structure of an
IRC network.

You need netcat (nc) for it to work.

Example uses

$ irctree irc.swipnet.se

Compiling

No need to compile, but you can copy it into /usr/local/bin with make install.

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.

Bio::Tools::CodonTable is a bioperl codon table object.

SYNOPSIS

# This is a read-only class for all known codon tables. The IDs are
# the ones used by nucleotide sequence databases. All common IUPAC
# ambiguity codes for DNA, RNA and animo acids are recognized.

# to use
use Bio::Tools::CodonTable;

# defaults to ID 1 "Standard"
$myCodonTable = Bio::Tools::CodonTable->new();
$myCodonTable2 = Bio::Tools::CodonTable -> new ( -id => 3 );

# change codon table
$myCodonTable->id(5);

# examine codon table
print join ( , "The name of the codon table no.", $myCodonTable->id(4),
"is:", $myCodonTable->name(), "n");

# translate a codon
$aa = $myCodonTable->translate(ACU);
$aa = $myCodonTable->translate(act);
$aa = $myCodonTable->translate(ytr);

# reverse translate an amino acid
@codons = $myCodonTable->revtranslate(A);
@codons = $myCodonTable->revtranslate(Ser);
@codons = $myCodonTable->revtranslate(Glx);
@codons = $myCodonTable->revtranslate(cYS, rna);

#boolean tests
print "Is a startn" if $myCodonTable->is_start_codon(ATG);
print "Is a termianatorn" if $myCodonTable->is_ter_codon(tar);
print "Is a unknownn" if $myCodonTable->is_unknown_codon(JTG);

Codon tables are also called translation tables or genetics codes since that is what they try to represent. A bit more complete picture of the full complexity of codon usage in various taxonomic groups presented at the NCBI Genetic Codes Home page.

CodonTable is a BioPerl class that knows all current translation tables that are used by primary nucleotide sequence databases (GenBank, EMBL and DDBJ). It provides methods to output information about tables and relationships between codons and amino acids.

This class and its methods recognized all common IUPAC ambiguity codes for DNA, RNA and animo acids. The translation method follows the conventions in EMBL and TREMBL databases.
It is a nuisance to separate RNA and cDNA representations of nucleic acid transcripts. The CodonTable object accepts codons of both type as input and allows the user to set the mode for output when reverse translating. Its default for output is DNA.

Note: This class deals primarily with individual codons and amino acids. However in the interest of speed you can translate longer sequence, too. The full complexity of protein translation is tackled by Bio::PrimarySeqI::translate.