Force Field X 1.0.0-beta API

Packages

Package	Description
edu.rit.http	The HTTP package provides a lightweight HTTP/1.0 server.
edu.rit.io	The IO package provides the DataOutputStream and DataInputStream classes to read/write primitive data types and strings in binary form.
edu.rit.mp	The MP package provides low-level support for Message Passing.
edu.rit.mp.buf	The BUF package provides data buffers for Message Passing.
edu.rit.pj	The PJ package (Parallel Java) support shared memory, message passing and hybrid shared memory/message passing parallelization in pure Java.
edu.rit.pj.cluster	The Cluster package contains the Parallel Java cluster middleware and the main program for the PJ Job Scheduler Daemon process for a parallel computer.
edu.rit.pj.io	The IO package represents a file that resides in the user's account in the job frontend process of a PJ cluster parallel program.
edu.rit.pj.job	The Job package encapsulates a job and its attributes.
edu.rit.pj.reduction	The Reduction package provides a variety of reduction variables.
edu.rit.pj.replica	The Replica package provides replicated, shared reduction variables.
edu.rit.util	The Util package contains utilities that support the PJ API.
ffx	Force Field X implements fixed charge and polarizable atomic multipole molecular mechanics potentials, local and global optimization, molecular dynamics, free energy differences, etc, with special support for crystal space groups.
ffx.algorithms	The Algorithms package has support for local and global optimization, molecular dynamics simulations, and calculation of free energy differences.
ffx.algorithms.cli	The Algorithms CLI package defines options for PicoCLI command line scripts.
ffx.algorithms.dynamics	The Dynamics package implements molecular and stochastic dynamics using a pure Java code path and via OpenMM.
ffx.algorithms.dynamics.integrators	The Integrators package implements integrators for molecular dynamics simulations.
ffx.algorithms.dynamics.thermostats	The Thermostats package implements thermostats for molecular dynamics simulations.
ffx.algorithms.mc	The MC package implements a variety of Monte Carlo moves for optimization and simulation algorithms.
ffx.algorithms.misc	The Misc package contains a few miscellaneous algorithms.
ffx.algorithms.optimize	The Optimize package contains local and global optimization algorithms using pure Java and OpenMM code paths.
ffx.algorithms.optimize.anneal
ffx.algorithms.optimize.manybody
ffx.algorithms.thermodynamics	The Thermodynamics package computes free energy differences using Orthogonal Space Tempering (OST) sampling via pure Java or OpenMM (via Monte Carlo OST).
ffx.crystal	The Crystal package implements space group symmetry and periodic boundary condition support.
ffx.numerics	The Numerics package has support for atomic double arrays, FFTs (1D and 3D), numerical integration (1D), complex numbers, vector operations, multipole tensors, multi-dimensional optimization, special functions, splines and switching functions.
ffx.numerics.atomic	The Atomic package has implementations of a double array that can be safely operated on by multiple threads.
ffx.numerics.estimator
ffx.numerics.fft	The FFT package implements 1D and 3D FFTs of real or complex valued data, including SMP parallelization of 3D transforms and convolution using the Parallel Java library.
ffx.numerics.func1d
ffx.numerics.integrate	The Integrate package implements 1D numerical integration.
ffx.numerics.math	The Math package implements complex numbers, a software square root, and vector operations.
ffx.numerics.multipole	The Multipole package computes derivatives of 1/|r| via recursion to arbitrary order using Cartesian multipoles in either a global frame or a quasi-internal frame.
ffx.numerics.optimization	The Optimization package implements the limited-memory Broyden-Fletcher-Goldfarb-Shanno (L-BFGS) algorithm for large-scale multidimensional unconstrained optimization problems.
ffx.numerics.special	The Special package implements special functions including the complex error function (Erf) and the modified Bessel functions.
ffx.numerics.spline	The Spline package implements implements B-splines and Tricubic splines.
ffx.numerics.switching	The Switching package implements univariate switching functions.
ffx.numerics.tornado
ffx.potential	The Potential package implements molecular mechanics force fields with shared memory Parallel Java and via OpenMM.
ffx.potential.bonded	The Bonded package implements bonded molecular mechanics terms such as bonds, angles, torsions, etc.
ffx.potential.cli	The Potential CLI package defines reusable options for PicoCLI command line scripts.
ffx.potential.constraint
ffx.potential.extended	The Extended package is progress toward support for constant pH molecular dynamics using extended system variables (i.e.
ffx.potential.nonbonded	The Nonbonded package implements nonbonded molecular mechanics terms such as van der Waals and Particle Mesh Ewald electrostastics.
ffx.potential.nonbonded.implicit
ffx.potential.nonbonded.octree
ffx.potential.nonbonded.pme
ffx.potential.parameters	The Parameters package stores force field atom types, bond types, etc, and keywords that define the potential.
ffx.potential.parsers	The Parsers package handles reading/writing files to/from the internal data structure.
ffx.potential.utils	The Utils package implements core functionality needed for using the Potential package, such as opening and closing structure files, basic force field energy evaluations, etc.
ffx.realspace	The Real Space package implements real space structure refinement.
ffx.realspace.cli	The Real Space CLI package defines options for PicoCLI command line scripts.
ffx.realspace.parsers	The Parsers package reads and writes CCP4 map files.
ffx.ui	The UI package provides views and controllers for manipulating molecular systems.
ffx.ui.behaviors	The Behaviors package contains Java3D Behaviors that turn user actions into scenegraph changes.
ffx.ui.commands	The Commands package implements a Client/Server interface between Force Field X and simulations.
ffx.ui.properties	The Properties package will eventually encapsulate internationalization features.
ffx.utilities	The Utilities package implements a variety of useful Directory, File, Port, String, etc functionality.
ffx.xray	The X-ray package implements support for X-ray and Neutron refinement.
ffx.xray.cli	The X-ray CLI package defines options for PicoCLI command line scripts.
ffx.xray.parsers	The Parsers package reads CNS files and reads/writes MTZ files.