PDB2PQR is a Python software package that automates many of the common tasks of preparing structures for continuum electrostatics calculations, providing a platform-independent utility for converting protein files in PDB format to PQR format. These tasks include adding a limited number of missing heavy atoms to biomolecular structures, determining side-chain pKas, placing missing hydrogens, optimizing the protein for favorable hydrogen bonding, assigning charge and radius parameters from a variety of force fields.
gfit analyzes data using models. gfit lets the user create a model for virtually any type of system using a minimal amount of computer code. It is particularly useful for studying various systems in biophysics, biochemistry, and cell biology. The interface for gfit models specifies relationships between input and output variables in a rule-based fashion. It provides flexibility and allows the user to reuse same models for many related problems.
GaussianBeam is a Gaussian optics simulator. It features table-top display of the optical setup. It computes the beam parameters. You can move optics with the mouse. Available optics: lenses, flat and curved interfaces, mirrors, dielectric slab, and generic ABCD. Magic waist function: given a target waist, GaussianBeam finds the suitable arrangement of lenses. Fit waist function: measure the beam radius or diameter to define the input beam. The ability to save and load configurations.
Evolving Games for Unnatural Intelligence is a Java package for unsupervised machine learning based on Evolutionary Game Theory on directed graphs. It is able to segment data without any previuos information on the number of segments. It has no GUI, but implements generalizations of the original method proposed by Li, Chen, He and Jiang in the arxiv paper "A Novel Clustering Algorithm Based Upon Games on Evolving Network", published on 30 Dec 2008.
ODE is a high performance library for simulating rigid body dynamics. It is fully featured, stable, mature, and platform independent with an easy-to-use C/C++ API. It has advanced joint types and integrated collision detection with friction. ODE is useful for simulating vehicles, objects in virtual reality environments, and virtual creatures. It is currently used in many computer games, 3D authoring tools, and simulation tools.
Bullet is a 3D game multiphysics library that provides state of the art collision detection and soft body and rigid body dynamics. Bullet is integrated into Cinema 4D, Lightwave, and Blender. A Houdini and Maya Plugin is available. It has a modular extendible C++ design with hot-swap of most components. The back-ends were optimized for pthreads/Win32 Threads multi-threading and PS3 Cell SPU. Other features include discrete and continuous collision detection (CCD), swept collision queries, ray casting with custom collision filtering, generic convex support (using GJK), capsule, cylinder, cone, sphere, box, and non-convex triangle meshes. Rigid body dynamics include constraint solvers, generic constraints, ragdolls, hinges, and ball-sockets. Constraint limits and motors are supported. Soft body support includes cloth, rope, and deformable objects. Import and export into COLLADA 1.4 Physics format is supported. Dynamic deformation of non-convex triangle meshes is supported by refitting the acceleration structures.
The Particle System API allows C++ application developers to easily include dynamic simulations of groups of moving objects. The API is much lighter weight than a full physics engine. It is especially useful for eye candy in games and screen savers, but is also used in off-line animation software. With the Particle System API you create a group of particles, then describe the components of the particle effect using actions like Gravity(), Explosion(), and Bounce(). You apply the actions to the particle group at each time step, then read back the particle positions and other attributes into your app, or send them directly to the GPU as a vertex array or as geometry instances.
xylib is a portable C++ library for reading files that contain x-y data from powder diffraction, spectroscopy, or other experimental methods. Supported formats include plain text (CSV or TSV), Crystallographic Information File for Powder Diffraction (pdCIF), Siemens/Bruker UXD, Siemens/Bruker RAW v1/2/3, Philips UDF, Philips RD (raw scan) V3, Rigaku DAT, Sietronics Sieray CPI, DBWS/DMPLOT data file, Canberra MCA, XFIT/Koalariet XDD, RIET7/LHPM/CSRIET/ILL_D1A5/PSI_DMC DAT, Vamas ISO14976, and Princeton Instruments WinSpec SPE.