Main > Free Download Search >

Free topological software for linux

topological

Sponsored Links
Sponsored Links
Sort by >> Relevance
rss
Secleted [ 0 ] software to compare
Results 1 - 15 of about 5
python-graph 1.6.0

python-graph 1.6.0


A library for working with graphs in Python more>> python-graph 1.6.0 is a useful software which functions as a library for working with graphs in Python. This software provides ?a suitable data structure for representing graphs and a whole set of important algorithms.

The code is appropriately documented and API reference is generated automatically by epydoc. Comments, bug reports and suggestions are welcome.

Major Features:

  1. Support for directed, undirected, weighted and non-weighted graphs
  2. Support for hypergraphs
  3. Canonical operations
  4. XML import and export
  5. DOT-Language output (for usage with Graphviz)
  6. Random graph generation
  7. Accessibility (transitive closure)
  8. Breadth-first search
  9. Cut-vertex and cut-edge identification
  10. Depth-first search
  11. Heuristic search (A* algorithm)
  12. Identification of connected components
  13. Minimum spanning tree (Prims algorithm)
  14. Mutual-accessibility (strongly connected components)
  15. Shortest path search (Dijkstras algorithm)
  16. Topological sorting

Enhancements: Fixes an installer bug.

Requirements: Python

<<less
Added: 2009-06-07 License: MIT/X Consortium Lic... Price: FREE
12 downloads
SQLAlchemy 0.3.10

SQLAlchemy 0.3.10


SQLAlchemy is a SQL toolkit and object relational mapper for Python. more>>
SQLAlchemy is a SQL toolkit and object relational mapper for Python.
The Python SQL toolkit and Object Relational Mapper that gives application developers the full power and flexibility of SQL. SQLAlchemy provides a full suite of well known enterprise-level persistence patterns, designed for efficient and high-performing database access, adapted into a simple and Pythonic domain language.
- extremely easy to use for all the basic tasks, such as: accessing thread-safe and pooled connections, constructing SQL from Python expressions, finding object instances, and commiting object modifications back to the database.
- powerful enough for complicated tasks, such as: eager load a graph of objects and their dependencies via joins; map recursive adjacency structures automatically; map objects to not just tables but to any arbitrary join or select statement; combine multiple tables together to load whole sets of otherwise unrelated objects from a single result set; commit entire graphs of object changes in one step.
- built to conform to what DBAs demand, including the ability to swap out generated SQL with hand-optimized statements, full usage of bind parameters for all literal values, fully transactionalized and consistent updates using Unit of Work.
- modular. Different parts of SQLAlchemy can be used independently of the rest, including the connection pool, SQL construction, and ORM. SQLAlchemy is constructed in an open style that allows plenty of customization, with an architecture that supports custom datatypes, custom SQL extensions, and ORM plugins which can augment or extend mapping functionality.
SQLAlchemys Philosophy:
- SQL databases behave less and less like object collections the more size and performance start to matter; object collections behave less and less like tables and rows the more abstraction starts to matter. SQLAlchemy aims to accomodate both of these principles.
- Your classes arent tables, and your objects arent rows. Databases arent just collections of tables; theyre relational algebra engines. You dont have to select from just tables, you can select from joins, subqueries, and unions. Database and domain concepts should be visibly decoupled from the beginning, allowing both sides to develop to their full potential.
- For example, table metadata (objects that describe tables) are declared distinctly from the classes theyre designed to store. That way database relationship concepts dont interfere with your object design concepts, and vice-versa; the transition from table-mapping to selectable-mapping is seamless; a class can be mapped against the database in more than one way. SQLAlchemy provides a powerful mapping layer that can work as automatically or as manually as you choose, determining relationships based on foreign keys or letting you define the join conditions explicitly, to bridge the gap between database and domain.
SQLAlchemys Advantages:
- The Unit Of Work system organizes pending CRUD operations into queues and commits them all in one batch. It then performs a topological "dependency sort" of all items to be committed and deleted and groups redundant statements together. This produces the maxiumum efficiency and transaction safety, and minimizes chances of deadlocks. Modeled after Fowlers "Unit of Work" pattern as well as Java Hibernate.
- Function-based query construction allows boolean expressions, operators, functions, table aliases, selectable subqueries, create/update/insert/delete queries, correlated updates, correlated EXISTS clauses, UNION clauses, inner and outer joins, bind parameters, free mixing of literal text within expressions, as little or as much as desired. Query-compilation is vendor-specific; the same query object can be compiled into any number of resulting SQL strings depending on its compilation algorithm.
- Database mapping and class design are totally separate. Persisted objects have no subclassing requirement (other than object) and are POPOs : plain old Python objects. They retain serializability (pickling) for usage in various caching systems and session objects. SQLAlchemy "decorates" classes with non-intrusive property accessors to automatically log object creates and modifications with the UnitOfWork engine, to lazyload related data, as well as to track attribute change histories.
- Custom list classes can be used with eagerly or lazily loaded child object lists, allowing rich relationships to be created on the fly as SQLAlchemy appends child objects to an object attribute.
- Composite (multiple-column) primary keys are supported, as are "association" objects that represent the middle of a "many-to-many" relationship.
- Self-referential tables and mappers are supported. Adjacency list structures can be created, saved, and deleted with proper cascading, with no extra programming.
- Data mapping can be used in a row-based manner. Any bizarre hyper-optimized query that you or your DBA can cook up, you can run in SQLAlchemy, and as long as it returns the expected columns within a rowset, you can get your objects from it. For a rowset that contains more than one kind of object per row, multiple mappers can be chained together to return multiple object instance lists from a single database round trip.
- The type system allows pre- and post- processing of data, both at the bind parameter and the result set level. User-defined types can be freely mixed with built-in types. Generic types as well as SQL-specific types are available.
<<less
Download (0.46MB)
Added: 2007-07-22 License: MIT/X Consortium License Price:
827 downloads
Bio::Tree::Compatible 1.5.2_102

Bio::Tree::Compatible 1.5.2_102


Bio::Tree::Compatible is a Perl module for testing compatibility of phylogenetic trees with nested taxa. more>>
Bio::Tree::Compatible is a Perl module for testing compatibility of phylogenetic trees with nested taxa.

SYNOPSIS

use Bio::Tree::Compatible;
use Bio::TreeIO;
my $input = new Bio::TreeIO(-format => newick,
-file => input.tre);
my $t1 = $input->next_tree;
my $t2 = $input->next_tree;

my ($incompat, $ilabels, $inodes) = $t1->is_compatible($t2);
if ($incompat) {
my %cluster1 = %{ $t1->cluster_representation };
my %cluster2 = %{ $t2->cluster_representation };
print "incompatible treesn";
if (scalar(@$ilabels)) {
foreach my $label (@$ilabels) {
my $node1 = $t1->find_node(-id => $label);
my $node2 = $t2->find_node(-id => $label);
my @c1 = sort @{ $cluster1{$node1} };
my @c2 = sort @{ $cluster2{$node2} };
print "label $label";
print " cluster"; map { print " ",$_ } @c1;
print " cluster"; map { print " ",$_ } @c2; print "n";
}
}
if (scalar(@$inodes)) {
while (@$inodes) {
my $node1 = shift @$inodes;
my $node2 = shift @$inodes;
my @c1 = sort @{ $cluster1{$node1} };
my @c2 = sort @{ $cluster2{$node2} };
print "cluster"; map { print " ",$_ } @c1;
print " properly intersects cluster";
map { print " ",$_ } @c2; print "n";
}
}
} else {
print "compatible treesn";
}

Bio::Tree::Compatible is a Perl tool for testing compatibility of phylogenetic trees with nested taxa represented as Bio::Tree::Tree objects. It is based on a recent characterization of ancestral compatibility of semi-labeled trees in terms of their cluster representations.

A semi-labeled tree is a phylogenetic tree with some of its internal nodes labeled, and it can represent a classification tree as well as a phylogenetic tree with nested taxa, with labeled internal nodes corresponding to taxa at a higher level of aggregation or nesting than that of their descendents.

Two semi-labeled trees are compatible if their topological restrictions to the common labels are such that for each node label, the smallest clusters containing it in each of the trees coincide and, furthermore, no cluster in one of the trees properly intersects a cluster of the other tree.

Future extensions of Bio::Tree::Compatible include a Bio::Tree::Supertree module for combining compatible phylogenetic trees with nested taxa into a common supertree.

<<less
Download (5.6MB)
Added: 2007-06-28 License: Perl Artistic License Price:
848 downloads
Bake 1.0

Bake 1.0


Bake is a small domain specific programming language for describing how to transform one file into another. more>>
Bake is a small domain specific programming language for describing how to transform one file into another. Bake uses the typical topological sort, but has features that make describing this relatively easy.

Bake has patterns, similar to make, but which are part of the dependency graph (unlike in make).

<<less
Download (0.092MB)
Added: 2006-06-06 License: GPL (GNU General Public License) Price:
1235 downloads
VCG TriMeshInfo 1.2

VCG TriMeshInfo 1.2


VCG TriMeshInfo is a tool designed to inspect 3D models and retrieve many types of topological and geometrical information. more>>
VCG TriMeshInfo is a tool designed to inspect 3D models and retrieve many types of topological and geometrical information from them.
It can be used to automate the process of decoding 3D mesh inherent properties and ease data classification and retrieval.
For each analyzed dataset, the following data are extracted:
- Number of Vertices (Unreferenced vertices are listed separately)
- Number of Faces
- Number of Edges
- Number of Connected Components
- Number of Boundaries
- Number of Isolated Vertices (i.e. Unreferenced)
- Manifold
- Genus (Computed only for Manifold Datasets)
- Orientability
- Orientation
- Regularity (We consider as regular those meshes generated through regular subdivision. Each non boundary vertex of a regular mesh has 6 incident edges, if there are only 5 incident edges the mesh is said to be semi-regular, irregular in all other cases)
- Number of Duplicated Vertices
- Self-Intersection (Currently computed only for Datasets with less than 3M faces)
Enhancements:
- This release included a major rewrite of the core component for computing geometrical and topological features of the analyzed mesh.
- Important changes included speeded up self-intersection tests, more robust (and correct) computation of topological genus and volume, and more flexible output with an HTML output option.
<<less
Download (0.12MB)
Added: 2005-12-27 License: GPL (GNU General Public License) Price:
1400 downloads
Secleted [ 0 ] software to compare
  • Page: 1 of 1
  • 1