Refinement

ShelXle is an instrument that manages to combine an editor with syntax highlighting for the SHELXL-associated .ins (input) and .res (output) files with an interactive graphical display for visualization of a three-dimensional structure including the electron density (Fo) and difference density... Platforms: Windows

NOC is a open source development toolkit and a powerful molecular explorer for protein structure visualizing,analysis,crystallographic mapping, modeling, and refinement, Gromacs/Amber MD trajectories displaying,movie making... Platforms: Windows, Mac, BSD, Linux

PARAMESH is a package of Fortran 90 subroutines designed to provide anapplication developer with an easy route to extend an existing serialcode which uses a logically cartesian structured mesh into a parallelcode with adaptive mesh refinement(AMR). Platforms: Mac, Linux

The Protein Geometry Database hosts the development code for a flexible database for searching protein geometry, as well as a library for accessing this data for protein modeling & refinement programs. Platforms: Windows, Mac, Linux

XD-shell - is a shell (console) interface to XD program which deals with experimental electron density refinement. Platforms: Windows, Mac, Linux

This script can handle multiple extrapolation steps, it can accommodate leading error terms and perform any uniform refinement scheme.The script can report a full extrapolation table, including comparing it against a previously known good solution. Key features "Richardson Extrapolation": - Able... Platforms: Windows, Mac, *nix, Matlab, BSD Solaris

Force Field X is a group of open source (GPL v. 3), platform independent (Java Runtime Environment) modules for molecular biophysics. Key methods include: Polarizable AMOEBA force fields Particle-mesh Ewald electrostatics Generalized Kirkwood continuum electrostatics X-ray and neutron... Platforms: Mac

Meshgen is a program designed to interactively generate 2D FEM meshes composed of triangular and quadrilateral elements. It supports three edge types (normal, parabolic and circle) for multiple refinement strategies and handles domains composed of more than one material. The output format is... Platforms: *nix

PyGTS is a python package used to construct, manipulate, and perform computations on 3D triangulated surfaces. It is a hand-crafted and pythonic binding for the GNU Triangulated Surface (GTS) Library. * Geometric primitives Point, Vertex, Segment, Edge, Triangle, Face, and Surface. *... Platforms: *nix

WebOb is an extraction and refinement of pieces from Paste. It is under active development. Discussion should happen on the Paste mailing lists, and bugs can go on the issue tracker. It was originally written by Ian Bicking, and the primary maintainer is now Sergey Schetinin. WebOb provides... Platforms: *nix

Volume.app is a small graphical software utility enabling quick and convenient control of a computer's audio volume level. It is intended for use on Linux/Unix systems in conjunction with an X window manager that supports dockable applications ("dockapps") such as AfterStep, BlackBox, or Window... Platforms: *nix

Statistics::CalinskiHarabasz is a Perl extension to the cluster stopping rule proposed by Calinski and Harabasz (C&H). SYNOPSIS use Statistics::CalinskiHarabasz; &ch(InputFile, "agglo", 10); Input file is expected in the "dense" format - Sample Input file: 6 5 1 1 0 0 1 1 0 0 0 0 1 1... Platforms: *nix

Statistics::Gap Perl module is an adaptation of the Gap Statistic. SYNOPSIS use Statistics::Gap; $predictedk = &gap("prefix", "vec", INPUTMATRIX, "rbr", "h2", 30, 10, rep, 90, 4); OR use Statistics::Gap; $predictedk = &gap("prefix", "vec", INPUTMATRIX, "rbr", "h2", 30, 10, rep, 90, 4,... Platforms: *nix

Volume.app is a small graphical software utility enabling quick and convenient control of a computers audio volume level. Volume.app is intended for use on Linux/Unix systems in conjunction with an X window manager that supports dockable applications ("dockapps") such as AfterStep, BlackBox, or... Platforms: *nix

The Getfem++ project focuses on the development of a generic and efficient C++ library for finite element methods elementary computations. The goal is to provide a library allowing the computation of any elementary matrix (even for mixed finite element methods) on the largest class of methods and... Platforms: *nix

Syntax::Highlight::Engine::Kate::Java is a Perl plugin for Java syntax highlighting. SYNOPSIS require Syntax::Highlight::Engine::Kate::Java; my $sh = new Syntax::Highlight::Engine::Kate::Java([ ]); Syntax::Highlight::Engine::Kate::Java is a plugin module that provides syntax highlighting... Platforms: *nix

Syntax::Highlight::Engine::Kate::C is a plugin for C syntax highlighting. SYNOPSIS require Syntax::Highlight::Engine::Kate::C; my $sh = new Syntax::Highlight::Engine::Kate::C([ ]); Syntax::Highlight::Engine::Kate::C is a plugin module that provides syntax highlighting for C to the... Platforms: *nix

JDave project is a behavior-driven development framework that provides an easy way to specify the behavior of your Java classes. Behavior Driven Development (BDD) is a refinement for Test Driven Development (TDD). It is not a radical change from TDD, in fact the actual process of doing BDD is... Platforms: *nix

Think if it as Konfabulator, Watson, and Deskshade all wrapped into one, without the price or the refinement. Platforms: Mac

JML or Java Modeling Language is a behavioral interface specification language that a user can use to specify the behavior of Java modules. The language combines the design by contract approach of Eiffel and the model-based specification approach of the Larch family of interface specification... Platforms: Windows