Free list of protein structure prediction software software for linux

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.

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.

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

Bioperl class for:

CONSENSUS Identification of consensus patterns in unaligned DNA and protein sequences (Hertz, Stormo)

References:

G.Z. Hertz and G.D. Stormo. Identification of consensus patterns in unaligned DNA and protein sequences: a large-deviation statistical basis for penalizing gaps. In: Proceedings of the Third International Conference on Bioinformatics and Genome Research (H.A. Lim, and C.R. Cantor, editors). World Scientific Publishing Co., Ltd. Singapore, 1995. pages 201--216.

Parameters:

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


consensus (Excl)
Program to run

sequence (Sequence)
Sequences file (-f)
pipe: seqsfile

width (Integer)
Width of pattern (consensus only) (-L)

out (String)

consensus_matrix (String)

complement (Excl)
Complement of nucleic acid sequences (-c)

ascii_alphabet (InFile)
Alphabet and normalization information (if not DNA) (-a)

prior (Switch)
Use the designated prior probabilities of the letters to override the observed frequencies (-d)

dna (Switch)
Alphabet and normalization information for DNA

protein (Switch)
Alphabet and normalization information for protein

queue (Integer)
Maximum number of matrices to save between cycles of the program -- ie: queue size (-q)

standard_deviation (Float)
Number of standard deviations to lower the information content at each position before identifying information peaks (mandatory for wconsensus) (-s)

progeny (Excl)
Save the top progeny matrices (-pr1)

linearly (Switch)
Seed with the first sequence and proceed linearly through the list (-l)

max_cycle_nb (Integer)
Maximum repeat of the matrix building cycle (-n or -N)

max_cycle (Excl)
How many words per matrix for each sequence to contribute (-n or -N)

distance (Integer)
Minimum distance between the starting points of words within the same matrix pattern (-m)

terminate (Integer)
Terminate the program this number of cycles after the current most significant alignment is identified (-t)

terminal_gap (Excl)
Permit terminal gaps (-pg) (wconsensus only)

top_matrices (Integer)
Number of top matrices to print (-pt)

final_matrices (Integer)
Number of final matrices to print (-pf)

List::Intersperse Perl module can intersperse / unsort / disperse a list.

SYNOPSIS

use List::Intersperse qw/intersperseq/;

@ispersed = intersperseq {substr($_[0],0,1)} qw/A1 A2 B1 B2 C1 C2/;

@ispersed = List::Intersperse::intersperse qw/A A B B B B B B C/;

intersperse and intersperseq evenly distribute elements of a list. Elements that are considered equal are spaced as far apart from each other as possible.

FUNCTIONS

intersperse LIST

This function returns a list of elements interspersed so that equivalent items are evenly distributed throughout the list.

intersperseq BLOCK LIST

intersperseq works like intersperse but it applies BLOCK to the elements of LIST to determine the equivalance key.

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.

List::Util::Superpositions is a Perl module that provides any and all for lists.
Synopsis
This module extends the methods provided by List::Util to offer the any() and all() operators from Quantum::Superpositions as part of the List::Util feature set.
use List::Util::Superpositions;
my $foo = List::Util::Superpositions->new();
...
Exports & Inheritances
Quantum::Superpositions
- any
- all
List::Util
- first
- max
- maxstr
- min
- minstr
- reduce
- shuffle
- sum

List::MoreUtils is a Perl module that can provide the stuff missing in List::Util.

SYNOPSIS

use List::MoreUtils qw(any all none notall true false firstidx first_index
lastidx last_index insert_after insert_after_string
apply after after_incl before before_incl indexes
firstval first_value lastval last_value each_array
each_arrayref pairwise natatime mesh zip uniq minmax);

List::MoreUtils provides some trivial but commonly needed functionality on lists which is not going to go into List::Util.

All of the below functions are implementable in only a couple of lines of Perl code. Using the functions from this module however should give slightly better performance as everything is implemented in C. The pure-Perl implementation of these functions only serves as a fallback in case the C portions of this module couldnt be compiled on this machine.

any BLOCK LIST

Returns a true value if any item in LIST meets the criterion given through BLOCK. Sets $_ for each item in LIST in turn:

print "At least one value undefined"
if any { !defined($_) } @list;

Returns false otherwise, or undef if LIST is empty.

all BLOCK LIST

Returns a true value if all items in LIST meet the criterion given through BLOCK. Sets $_ for each item in LIST in turn:

print "All items defined"
if all { defined($_) } @list;

Returns false otherwise, or undef if LIST is empty.

none BLOCK LIST

Logically the negation of any. Returns a true value if no item in LIST meets the criterion given through BLOCK. Sets $_ for each item in LIST in turn:

print "No value defined"
if none { defined($_) } @list;

Returns false otherwise, or undef if LIST is empty.

notall BLOCK LIST

Logically the negation of all. Returns a true value if not all items in LIST meet the criterion given through BLOCK. Sets $_ for each item in LIST in turn:

print "Not all values defined"
if notall { defined($_) } @list;

Returns false otherwise, or undef if LIST is empty.

true BLOCK LIST

Counts the number of elements in LIST for which the criterion in BLOCK is true. Sets $_ for each item in LIST in turn:

printf "%i item(s) are defined", true { defined($_) } @list;

false BLOCK LIST

Counts the number of elements in LIST for which the criterion in BLOCK is false. Sets $_ for each item in LIST in turn:

printf "%i item(s) are not defined", false { defined($_) } @list;

firstidx BLOCK LIST

first_index BLOCK LIST

Returns the index of the first element in LIST for which the criterion in BLOCK is true. Sets $_ for each item in LIST in turn:

my @list = (1, 4, 3, 2, 4, 6);
printf "item with index %i in list is 4", firstidx { $_ == 4 } @list;
__END__
item with index 1 in list is 4

Returns -1 if no such item could be found.

first_index is an alias for firstidx.