All Classes and Interfaces
Class
Description
AdderDoubleArray implements the AtomicDoubleArray interface using an array of
java.util.concurrent.atomic.DoubleAdder.The Adiabatic thermostat is for NVE simulations and does not alter particle velocities.
Represents command line options for scripts that utilize alchemistry on at least one topology.
AlgorithmFunctions, on top of the core functionality of PotentialsFunctions, describes additional
functionality such as molecular dynamics and L-BFGS local optimization.
The AlgorithmListener will be notified at regular intervals during an algorithm.
Base class for scripts in the Algorithms package, providing some key functions.
Base class for Algorithm tests.
AlgorithmUtils, on top of the core functionality of PotentialsUtils, implements additional
functionality such as molecular dynamics and L-BFGS local optimization.
Utilities for creating Amino Acid residues.
The 20 standard amino acids.
Constant
AIBConstant
ALASingle letter amino acid codes (need to
Constant
AminoAcidBackboneAtomsConstant
ARGConstant
ASDConstant
ASHConstant
ASNConstant
ASPConstant
CYDConstant
CYSConstant
CYSConstant
GLDConstant
GLHConstant
GlutamineAtomNamesConstant
GLUConstant
GLYConstant
GlycineBackboneAtomsConstant
HIDConstant
HIEConstant
HistidineAtomsConstant
ILEConstant
LEUConstant
LYDConstant
LYSConstant
MethionineAtomNamesConstant
ORNConstant
PCAConstant
PHEConstant
PROConstant
ProlineBackboneAtomsThe location of a residue within a chain.
Constant
SERThis interface is used by the "Build" routines.
Constant
THRConstant
TRPConstant
TYDConstant
TYRConstant
VALAmoebaCavitationForce.
AmoebaMultipoleForce.
OpenMM TorsionTorsion Force.
The Amoeba vdW Force.
This class uses the Andersen method to maintain constant temperature.
The Angle class represents an angle formed between three linearly bonded atoms.
OpenMM Angle Force.
The AngleTorsion class represents an angle torsion coupling between four bonded atoms.
OpenMM Angle-Torsion Force.
The AngleTorsionType class defines one angle-torsion energy type.
The AngleType class defines one harmonic angle bend energy term.
Angle function types include harmonic or sextic.
Angle modes include Normal or In-Plane
Temperature schedule for simulated annealing
Represents command line options for scripts that utilize simulated annealing.
The ARCFileFilter class is used to choose a TINKER Archive (*.ARC).
Class Arrays provides static methods for various operations on arrays and
matrices of primitive types and object types.
The AssemblyState class stores the chemical and coordinate state of a Molecular Assembly.
Enumeration of the different asymmetric unit limit operators.
The Atom class represents a single atom and defines its alternate conformations and molecular
mechanics atom type.
Element symbols for the first 109 elements.
This interface abstracts away the implementation of maintaining a 1D double array that is operated
on by multiple threads.
AtomicDoubleArray implementations (ADDER, MULTI, PJ).
Implementation of maintaining a 3D double array that is operated on by multiple threads.
Represents command line options for scripts that support atom selections.
The AtomType class represents one molecular mechanics atom type.
Class BackendClassLoader provides a class loader for a job backend process in
the PJ cluster middleware.
Class BackendFileInputStream provides an object in a job backend process that
reads a sequential file in the job frontend process.
Class BackendFileOutputStream provides an object in a job backend process
that writes a sequential file in the job frontend process.
Class BackendFileReader provides an object that reads sequential files in the
job backend process.
Class BackendFileWriter provides an object that writes sequential files in
the job backend process.
Class BackendInfo provides a record of information about one backend node in
the PJ cluster middleware.
The state of a backend node.
The BARFilter class parses TINKER bar(*.BAR) files.
The Barostat class maintains constant pressure using random trial moves in lattice parameters,
which are consistent with the space group.
Represents command line options for scripts that use a barostat/NPT.
Class BarrierAction is the abstract base class for an object containing code
that is executed as part of a barrier wait.
All force field types should extend the BaseType class.
Implements a bell-shaped switching function by stitching together a pair of
MultiplicativeSwitches.
The Bennett Acceptance Ratio class implements the Bennett Acceptance Ratio (BAR) statistical
estimator, based on the Tinker implementation.
Thermostat a molecular dynamics trajectory to an external bath using the Berendsen weak-coupling
thermostat.
Integrate Newton's equations of motion using a Beeman multistep recursion formula; the actual
coefficients are Brooks' "Better Beeman" values.
The BioType class maps PDB identifiers to atom types.
The BoltzmannMC abstract class is a skeleton for Boltzmann-weighted Metropolis Monte Carlo
simulations.
The Bond class represents a covalent bond formed between two atoms.
Bond Array.
The BondedEnergy interface.
The BondedTerm class is extended by all Valence Geometry classes (bond, angle, dihedral, torsion,
etc.).
Utilities for placing atoms.
This exception is thrown when an atom type could not be assigned.
This exception is thrown when a heavy atom is not found.
Bond Force.
The BondType class defines one harmonic bond stretch energy term.
Describes the function used by the bond.
Class BooleanArrayBuf provides a buffer for an array of Boolean items sent or
received using the Message Protocol (MP).
Class BooleanArrayBuf_1 provides a buffer for an array of Boolean items sent
or received using the Message Protocol (MP).
Class BooleanBuf is the abstract base class for a buffer of Boolean items
sent or received using the Message Protocol (MP).
Class BooleanItemBuf provides a buffer for a single Boolean item sent or
received using the Message Protocol (MP).
Class BooleanMatrixBuf provides a buffer for a matrix of Boolean items sent
or received using the Message Protocol (MP).
Class BooleanMatrixBuf_1 provides a buffer for a matrix of Boolean items sent
or received using the Message Protocol (MP).
Class BooleanOp is the abstract base class for a binary operation on Boolean
values, used to do reduction in a parallel program.
The BootstrappableEstimator interface describes a StatisticalEstimator which can use bootstrap
sampling as an additional method of calculating free energy and uncertainty.
The BootStrapStatistics class uses bootstrapping to estimate statistics from a
given population.
Parallel computation of Born radii chain rule terms via the Grycuk method.
Parallel computation of Born radii via the Grycuk method.
Rescale the Born radius integral to account for interstitial spaces.
Class Buf is the abstract base class for a buffer of items sent or received
using the Message Protocol (MP).
This class implements a spatial decomposition based on partitioning a grid into octants.
The BulkSolventList class builds a list of atoms in symmetry mates that are within a cutoff
distance of an atom in the asymmetric unit.
BulkSolventRowRegion class.
This class implements a spatial decomposition based on partitioning a grid into octants.
Thermostat a molecular dynamics trajectory to an external bath using the Bussi, Donadio, and
Parrinello method.
Class ByteArrayBuf provides a buffer for an array of byte items sent or
received using the Message Protocol (MP).
Class ByteArrayBuf_1 provides a buffer for an array of byte items sent or
received using the Message Protocol (MP).
Class ByteBuf is the abstract base class for a buffer of byte items sent or
received using the Message Protocol (MP).
Class ByteItemBuf provides a buffer for a single byte item sent or received
using the Message Protocol (MP).
Class ByteMatrixBuf provides a buffer for a matrix of byte items sent or
received using the Message Protocol (MP).
Class ByteMatrixBuf_1 provides a buffer for a matrix of byte items sent or
received using the Message Protocol (MP).
Class ByteOp is the abstract base class for a binary operation on byte
values, used to do reduction in a parallel program.
Class ByteSequence provides an abstraction for a sequence of bytes.
ByteSwap class.
CCP4MapFilter class.
CCP4MapWriter class.
Custom Centroid Bond Force.
The ChandlerCavitation class smoothly switches between a volume based dependence for small
solutes to a surface area dependence for large solutes.
Class Channel provides a channel for sending and receiving messages in the
Message Protocol (MP).
Class ChannelClosedException is thrown to indicate that an I/O operation
failed because the channel was closed.
Class ChannelGroup provides a group of Channels for sending and
receiving messages in the Message Protocol (MP).
Class ChannelGroupClosedException is thrown to indicate that an I/O operation
failed because the channel group was closed.
Class CharacterArrayBuf provides a buffer for an array of character items
sent or received using the Message Protocol (MP).
Class CharacterArrayBuf_1 provides a buffer for an array of character items
sent or received using the Message Protocol (MP).
Class CharacterBuf is the abstract base class for a buffer of character items
sent or received using the Message Protocol (MP).
Class CharacterItemBuf provides a buffer for a single character item sent or
received using the Message Protocol (MP).
Class CharacterMatrixBuf provides a buffer for a matrix of character items
sent or received using the Message Protocol (MP).
Class CharacterMatrixBuf_1 provides a buffer for a matrix of character items
sent or received using the Message Protocol (MP).
Class CharacterOp is the abstract base class for a binary operation on
character values, used to do reduction in a parallel program.
The ChargeType class defines a partial atomic charge type.
The CIFFilter class parses CIF coordinate (*.CIF) files.
CIF file reader
Cluster contains methods utilized in the
Cluster.groovy file.Class for cluster objects.
Center of Mass Motion Remover.
CNSFilter class.
The CNSMapWriter class writes an output map that covers the unit cell (not the asymmetric unit).
Class Comm provides a communicator for a PJ cluster parallel program.
Class CommPattern provides static methods for calculating communication
patterns for collective communication operations.
Class CommRequest provides an object for doing a non-blocking message passing
operation in a PJ cluster parallel program.
Class CommStatus provides the result of receiving a message from a
communicator (class Comm).
Compute the FFT of complex, double precision data of arbitrary length n.
Compute the 3D FFT of complex, double precision input of arbitrary dimensions via 1D Mixed Radix
FFTs.
Compute the 3D FFT of complex, double precision input of arbitrary dimensions via 1D Mixed Radix
FFTs in parallel.
ComplexNumber class.
A CompositeCurve represents points along a sum of functions which also extend FunctionDataCurve.
The CompositeSwitch uses a primary switch in the middle, and then two secondary switches at the
ends of the path to smoothly switch to the primary switch.
Restrain molecules to their center of mass.
Class Configuration provides configuration information about a parallel
computer running Parallel Java.
This class is for a configuration optimization of two small systems.
Interface ConnectListener specifies the interface for an object that is
notified whenever a Channel is connected in a ChannelGroup.
ConnollyRegion uses the algorithms from the AMS/VAM programs of Michael Connolly to compute the
analytical molecular surface area and volume of a collection of spherical atoms; thus it
implements Fred Richards' molecular surface definition as a set of analytically defined spherical
and toroidal polygons.
Class Constants contains various constants used in the PJ cluster middleware.
Library class containing constants such as Avogadro's number.
The ConstantSwitch returns a constant value for all input values x.
Defines a set of geometric constraints that must be applied self-consistently.
A Context stores the complete state of a simulation.
This ConvexHullOps class uses the QuickHull3D package by John E.
The CoordinateFileFilter class globally determines if a file is a valid coordinate file (PDB, XYZ,
INT, or ARC formats).
A CosineWave describes points along a sine wave of f(x) = a*sin(jx).
The CoulombTensorGlobal class computes derivatives of 1/|r| via recursion to arbitrary
order for Cartesian multipoles in the global frame.
The CoulombTensorQI class computes derivatives of 1/|r| via recursion to arbitrary order
for Cartesian multipoles in a quasi-internal frame.
The Crystal class encapsulates the lattice parameters and space group that describe the geometry
and symmetry of a crystal.
Minimize the energy of a system to an RMS gradient per atom convergence criteria.
The CrystalPotential interface extends Potential to provide methods that change the periodic
boundary conditions and symmetry via a Crystal instance.
Structure factor calculation (including bulk solvent structure factors)
The possible solvent model methods
Crystal statistics output/logger
Enumeration of the 7 crystal systems.
Custom Angle Force.
Custom Bond Force.
Custom Compound Bond Force.
Custom External Force.
Custom GB Force.
Custom Integrator.
OpenMM Custom MTS Integrator.
OpenMM Custom MTS Langevin Integrator.
Custom Non-bonded Force.
DataContainer interface.
Class DataInputStream provides an input stream that reads primitive data
types and strings in binary form.
Class DataOutputStream provides an output stream that writes primitive data
types and strings in binary form.
Represents command line options for scripts that utilize some form of crystallographic data.
A DataSet represents a set of points along a single dimension, and is able to be numerically
integrated.
Class DefaultRandom provides a default pseudorandom number generator (PRNG)
designed for use in parallel scientific programming.
DiffractionData class.
DiffractionFile class.
DiffractionFileFilter interface.
DiffractionRefinementData class.
DirectoryUtils class.
Parallel computation of induced dipoles due to the direct field.
Parallel calculation of continuum dispersion energy via pairwise descreening.
Calculates a residue-residue distance matrix.
The DistanceMatrixFileFilter class is used to choose a Distance Matrix (*.DST) file.
The DistanceMatrixFilter class parses a Distance Matrix (*.DST) files.
Compute the minimum distance between each pair of residues for all rotamer permutations.
Convenience class for working with 3D double vectors.
DoubleArray wrapper.
DoubleArray3D.
Class DoubleArrayBuf provides a buffer for an array of double items sent or
received using the Message Protocol (MP).
Class DoubleArrayBuf_1 provides a buffer for an array of double items sent or
received using the Message Protocol (MP).
Class DoubleBuf is the abstract base class for a buffer of double items sent
or received using the Message Protocol (MP).
DoubleIndexPair record.
Class DoubleItemBuf provides a buffer for a single double item sent or
received using the Message Protocol (MP).
The DoubleMath class is a simple math library that operates on 3-coordinate double arrays.
Class DoubleMatrixBuf provides a buffer for a matrix of double items sent or
received using the Message Protocol (MP).
Class DoubleMatrixBuf_1 provides a buffer for a matrix of double items sent
or received using the Message Protocol (MP).
Class DoubleMatrixFile provides an object for reading or writing a double
matrix from or to a file.
Class DoubleOp is the abstract base class for a binary operation on double
values, used to do reduction in a parallel program.
Describes a set of x, f(x) obtained by some mechanism; intended for numerical integration.
Convert a Double to a String and vice versa for use with JAXB.
Download utilities.
The DTDResolver class just points the DOM DocumentBuilder to the XML Document Type Definition
(DTD) files.
Compute the potential energy and derivatives for a dual-topology system.
Represents command line options for scripts that run molecular dynamics.
The DYNFileFilter class is used to choose a TINKER Restart (*.DYN) file.
The DYNFilter class parses TINKER Restart (*.DYN) files.
Class EmptyBooleanBuf provides a Boolean buffer that contains no items for
messages using the Message Protocol (MP).
Class EmptyByteBuf provides a byte buffer that contains no items for messages
using the Message Protocol (MP).
Class EmptyCharacterBuf provides a character buffer that contains no items
for messages using the Message Protocol (MP).
Class EmptyDoubleBuf provides a double buffer that contains no items for
messages using the Message Protocol (MP).
Class EmptyFloatBuf provides a float buffer that contains no items for
messages using the Message Protocol (MP).
Class EmptyIntegerBuf provides an integer buffer that contains no items for
messages using the Message Protocol (MP).
Class EmptyLongBuf provides a long buffer that contains no items for messages
using the Message Protocol (MP).
Class EmptyObjectBuf provides an object buffer that contains no items for
messages using the Message Protocol (MP).
Class EmptyShortBuf provides a short buffer that contains no items for
messages using the Message Protocol (MP).
Class EmptySigned16BitIntegerBuf provides a signed 16-bit integer buffer that
contains no items for messages using the Message Protocol (MP).
Class EmptySigned8BitIntegerBuf provides a signed 8-bit integer buffer that
contains no items for messages using the Message Protocol (MP).
Class EmptyUnsigned16BitIntegerBuf provides an unsigned 16-bit integer buffer
that contains no items for messages using the Message Protocol (MP).
Class EmptyUnsigned8BitIntegerBuf provides an unsigned 8-bit integer buffer
that contains no items for messages using the Message Protocol (MP).
The Energy script evaluates the energy of a system.
This Exception class indicates an error in calculating energy or gradients.
Static methods to evaluate erf(x) and erfc(x) for a real argument x.
Bootstrap Free Energy Estimate.
The ESVFileFilter class is used to choose a Extended System Restart (*.ESV) file.
The ESVFilter class parses Extended System Restart (*.ESV) files.
Mutable Particle Mesh Ewald constants.
The EwaldMultipoleTensorGlobal class computes derivatives of erfc(r)/|r| via
recursion to arbitrary order for Cartesian multipoles in the global frame.
The EwaldTensorQI class computes derivatives of erfc(r)/|r| via recursion to
arbitrary order for Cartesian multipoles in a quasi-internal frame.
Parallel expansion of the asymmetric unit induced dipoles to symmetry mates by applying symmetry
operator rotation matrices.
Exponential temperature schedule for simulated annealing
ExtendedSystem class.
The FFXClient class encapsulates a socket connection to an FFXServer started by an executing FFX
instance.
Base Command class.
This represents the context of an FFX MolecularAssembly.
FFXExec encapsulates a native replacement for the JDK System.exec() method.
The FFXFileFilter class is used to choose Force Field X script (*.FFX) files.
The FFXLocale class will encapsulate internationalization features.
The FFXProperty Annotation can be applied multiple times to some classes.
The FFXProperty Annotation should be used to document fields that are set using property files,
keyword files, force field parameter files and the Java property system.
BaseScript class.
The FFXServer is launched by an FFX instance to allow Force Field X Clients to connect.
The FFXSystem class contains extensions to the generic MolecularAssembly class.
The FFXTest configures the context for FFX tests.
Utility Routines to use the TornadoVM
The FileOpener interface specifies Runnable objects which can return one or more
MolecularAssemblies.
Class Files provides static methods for various file related operations.
FileUtils class.
Fixed Charge Alchemical Forces.
FixedChargeGBForce.
Define a fixed charge non-bonded force.
Composite annealing schedule with flat ends (i.e.
Convenience class for working with 3D float vectors.
Class FloatArrayBuf provides a buffer for an array of float items sent or
received using the Message Protocol (MP).
Class FloatArrayBuf_1 provides a buffer for an array of float items sent or
received using the Message Protocol (MP).
Class FloatBuf is the abstract base class for a buffer of float items sent or
received using the Message Protocol (MP).
Class FloatItemBuf provides a buffer for a single float item sent or received
using the Message Protocol (MP).
The FloatMath class is a simple math library that operates on 3-coordinate float arrays.
Class FloatMatrixBuf provides a buffer for a matrix of float items sent or
received using the Message Protocol (MP).
Class FloatMatrixBuf_1 provides a buffer for a matrix of float items sent or
received using the Message Protocol (MP).
Class FloatOp is the abstract base class for a binary operation on float
values, used to do reduction in a parallel program.
Force objects apply forces to the particles in a System, or alter their behavior in other
ways.
The ForceField class organizes parameters for a molecular mechanics force field.
Available force fields.
Compute the potential energy and derivatives of a molecular system described by a force field.
The ForceFieldFileFilter class is used to choose a TINKER Parameter file (*.PRM).
The ForceFieldFilter Class is used to parse and store molecular mechanics data from
keyword/property and parameter (*.PRM) files.
FormFactor interface.
Compute 4-Body energies.
Class FrontendFileReader provides an object that reads sequential files in
the job frontend process.
Class FrontendFileWriter provides an object that writes sequential files in
the job frontend process.
A FunctionDataCurve represents a set of points along a 1-dimensional, analytically integrable
function.
GaussVol implements a description molecular volume and surface area described by overlapping
Gaussian spheres.
This Generalized Kirkwood class implements GK for the AMOEBA polarizable atomic multipole force
field in parallel using a
NeighborList.Amoeba Generalized Kirkwood Force.
The GenerateRotamers class helps generate a rotamer library (particularly for nonstandard amino
acids) for a Residue.
Implicit Solvent Cavitation Force.
Parallel calculation of the Generalized Kirkwood reaction field energy.
The GK tensor can be constructed for a monopole potential (GB), a dipole potential or a
quadrupole potential.
The "mode" for the tensor (either POTENTIAL or BORN).
The GeneralizedKirkwoodTensor class contains utilities for generated Generalized Kirkwood
interaction tensors.
The GeneralizedKirkwoodTensor class contains utilities for generated Generalized Kirkwood
interaction tensors.
The GlobalBehavior class allows mouse control over camera position, adding a few functions to the
OrbitBehavior class.
Represents command line options for scripts that test gradients.
GradientSchedule class.
GradientUtils is a utility class for testing the gradient of a potential.
The GraphicsAxis class encapsulates the 3D Axis that is used to display and control
rotation/translation in the global frame.
The GraphicsCanvas class provides a Canvas on which to render 3D Graphics.
The ImageFormat enum lists supported image formats.
The LeftButtonMode enum describes what the left mouse button does.
The MouseMode enum describes what system is affected by mouse drags.
The GraphicsEvents class listens for mouse events over the Java3D GraphicsCanvas, dispatching
work to more specialized System Rotation and Translation Behaviors or to the GlobalOrbitBehavior.
The FullScreenWindow class controls full screen graphics.
The GraphicsPanel class contains the 3D Canvas and its status box.
The GraphicsPicking class is used to make selections and measurements.
The GraphicsPrefs class allows users to select graphics preferences.
The GraphicsSplitPane is an early attempt at working around issues caused by the heavyweight
Canvas3D inside a lightweight Swing SplitPane.
Harmonic Bond Force.
The HeadlessMain class is the entry point to the command line version of Force Field X.
Class Hex provides static methods for converting between hexadecimal strings
and numbers of various kinds.
The Hierarchy Class creates and manages a JTree view of the data structure.
HilbertCurveTransforms is a class that provides static methods for converting
between Hilbert indices and coordinates.
Write/read Histogram data to/from a String.
The HKL class represents a single reflection.
Class HttpRequest encapsulates an HTTP request received from a web browser.
Class HttpResponse encapsulates an HTTP response returned to a web browser.
Enumeration HttpResponse.Status enumerates the status codes for an HTTP
response message.
Class HttpServer provides a lightweight HTTP/1.0 server.
Java port of the hy36encode() and hy36decode() functions in the hybrid_36.py Python
prototype/reference implementation.
Class HybridTeam provides a team of threads, distributed across the processes
of a cluster parallel program, for executing a WorkerRegion in
parallel.
Initial implementation of a Hydrophobic PMF.
The ImproperTorsion class represents an Improper Torsion.
OpenMM Improper Torsion Force.
The ImproperTorsionType class defines an improper torsion.
The IndexIndexPair record.
Parallel summation and reduction of components of the induced dipole field at each atom.
Parallel calculation of the induced dipole field.
The InducedFileFilter class is used to choose a TINKER induced dipole (*.IND) file.
The InducedFilter class parses TINKER Induced Dipole (*.*U) files.
Parallel calculation of the Generalized Kirkwood induced reaction field.
Parallel initialization of accumulation arrays for Generalized Kirkwood.
Parallel initialization of accumulation arrays, expand atomic coordinates and rotation of
multipoles into the global frame.
OpenMM In-Plane Angle Force.
Class Instance provides static methods for creating instances of classes.
Int Array.
Class IntegerArrayBuf provides a buffer for an array of integer items sent or
received using the Message Protocol (MP).
Class IntegerArrayBuf_1 provides a buffer for an array of integer items sent
or received using the Message Protocol (MP).
Class IntegerBuf is the abstract base class for a buffer of integer items
sent or received using the Message Protocol (MP).
Class IntegerForLoop is the abstract base class for one variation of a
parallel for loop that is executed inside a ParallelRegion.
Class IntegerItemBuf provides a buffer for a single integer item sent or
received using the Message Protocol (MP).
Class IntegerMatrixBuf provides a buffer for a matrix of integer items sent
or received using the Message Protocol (MP).
Class IntegerMatrixBuf_1 provides a buffer for a matrix of integer items sent
or received using the Message Protocol (MP).
Class IntegerOp is the abstract base class for a binary operation on integer
values, used to do reduction in a parallel program.
Class IntegerSchedule provides an object that determines how to schedule the
iterations of a ParallelForLoop among the threads in a
ParallelTeam.
Class IntegerStrideForLoop is the abstract base class for one variation of a
parallel for loop that is executed inside a ParallelRegion.
This program integrates using four methods: rectangular integration, the trapezoidal method,
Simpson's Three Point Integration, and Boole's Five Point Integration.
Left vs right-hand integration; left-hand integration will start from the first available point,
run right as far as possible, and then clean up any remaining points using finishIntegration,
while right-hand integration will start from the last available point, run left as far as
possible, and then clean up any remaining points using finishIntegration.
Enumeration of implemented integration methods, and the number of points required by them.
This program integrates using three methods: the trapezoidal method, Simpson's Three Point
Integration, and Boole's Five Point Integration
The Integrator class is responsible for propagation of degrees of freedom through time.
An Integrator defines a method for simulating a System by integrating the equations of motion.
An enumeration of available integrators.
The INTFileFilter class is used to choose TINKER Internal Coordinate (*.INT) files.
The INTFilter class parses TINKER internal coordinate (*.INT) files.
Int Set.
Class InvalidMatrixFileException provides an exception thrown when the
contents of a matrix file are invalid.
Class IORequest encapsulates the state of a message being sent or received in
the Message Protocol (MP).
Class Job encapsulates a job and its attributes.
Class JobBackend is the main program for a job backend process in the PJ
cluster middleware.
Class JobBackendMessage provides a message sent to a Job Backend process
(interface JobBackendRef) in the PJ cluster middleware.
Class JobBackendProxy provides a proxy object for sending messages to a PJ
job backend process.
Interface JobBackendRef specifies the interface for the PJ job backend
process.
Class JobFrontend provides the message handler for the PJ job frontend
process.
Class JobFrontendMessage provides a message sent to a Job Frontend process
(interface JobFrontendRef) in the PJ cluster middleware.
Class JobFrontendProxy provides a proxy object for sending messages to a PJ
job frontend process.
Interface JobFrontendRef specifies the interface for the PJ job frontend
process.
Class JobGenerator is the abstract base class for an object that generates a
group of Jobs.
Class JobInfo provides a record of information about one job in a parallel
computer in the PJ cluster middleware.
The state of a job.
Class JobScheduler is the main program for the PJ Job Scheduler Daemon
process for a parallel computer.
Class JobSchedulerException is thrown to indicate that a job frontend process
was unable to contact the Job Scheduler Daemon.
Class JobSchedulerMessage provides a message sent to a Job Scheduler process
(interface JobSchedulerRef) in the PJ cluster middleware.
Class JobSchedulerProxy provides a proxy object for sending messages to a PJ
job scheduler process.
Interface JobSchedulerRef specifies the interface for the PJ Job Scheduler
Daemon process.
The Joint class contains the geometry produced by the FGroup Joiner method.
The KeyFileEditor class is a wrapper for the KeywordPanel to create a stand alone Key File Editor
(it needs updating).
The KeyFileFilter class is used to choose a Force Field X keyword (*.KEY) or property
(*.properties) file.
The KeyFilter class parses Force Field X Keyword (*.KEY) and Property (*.PROPERTIES) files.
The Keyword class holds a single Force Field X keyword entry.
The KeywordComponent class is used to represent one TINKER keyword.
The KeywordPanel class provides a View and Control of TINKER Keyword (*.KEY) files.
Provides a mechanism to shut down a ParallelTeam's threads, enabling garbage
collection.
The LambdaInterface should be implemented by potential energy terms that can accept a lambda
value from [0 ..
Define an MC move to update lambda.
Represents command line options for scripts that utilize a mobile lambda particle, such as
Thermodynamics.
Langevin Integrator.
Enumeration of the 7 lattice systems.
Enumeration of the different Laue systems.
This class implements the limited-memory Broyden-Fletcher-Goldfarb-Shanno (L-BFGS) algorithm for
large-scale multidimensional unconstrained optimization problems.
Linear temperature schedule for simulated annealing
A LinearDerivativeSwitch interpolates between 0 and 1 vi f(x) = 2*x - x^2.
Class LineBufferedOutputStream provides a line buffer layered on top of an
underlying output stream.
This class implements an algorithm for uni-dimensional line search.
The six possible line search results:
Class Lock provides an object used for synchronizing parallel team threads in
a critical region.
A minor extension to the SimpleFormatter to reduce verbosity if debugging is not turned on.
Interface Logger specifies the interface for an object that logs messages.
The default ConsoleHanlder publishes logging to System.err.
Class LongArrayBuf provides a buffer for an array of long items sent or
received using the Message Protocol (MP).
Class LongArrayBuf_1 provides a buffer for an array of long items sent or
received using the Message Protocol (MP).
Class LongBuf is the abstract base class for a buffer of long items sent or
received using the Message Protocol (MP).
Class LongForLoop is the abstract base class for one variation of a parallel
for loop that is executed inside a ParallelRegion.
Class LongItemBuf provides a buffer for a single long item sent or received
using the Message Protocol (MP).
Class LongMatrixBuf provides a buffer for a matrix of long items sent or
received using the Message Protocol (MP).
Class LongMatrixBuf_1 provides a buffer for a matrix of long items sent or
received using the Message Protocol (MP).
Class LongOp is the abstract base class for a binary operation on long
values, used to do reduction in a parallel program.
Class LongRange provides a range of type
long.Class LongSchedule provides an object that determines how to schedule the
iterations of a ParallelForLoop among the threads in a
ParallelTeam.
Class LongStrideForLoop is the abstract base class for one variation of a
parallel for loop that is executed inside a ParallelRegion.
Loop class.
LoopClosure class.
The Main class is the entry point to the graphical user interface version of Force Field X.
The MainMenu class creates the Force Field X Menu Bar
The MainPanel class is the main container for Force Field X, handles file input/output and is used
to pass references among the various sub-Panels.
A cell used for optimization of a subdomain, its residues, its extent in fractional coordinates,
its overall (linear) index, and its indices along the a, b, and c axes.
Represents command line options for scripts that use a many-body expansion for global
optimization.
By implementing the MaskingInterface interface, interaction pairs can be excluded during
NeighborList construction.Class Mathe provides useful mathematical operations.
The MatrixMath class is a simple matrix math library used mainly by the X-ray package.
The MBARFilter class parses mbar (*.mbar or *.bar) files.
Class Mcg1Random provides a default pseudorandom number generator (PRNG)
designed for use in parallel scientific programming.
MCLoop class.
The MCMove interface defines the basic functionality of a Monte Carlo move; that it can apply its
move and revert it.
Enumerates available molecular dynamics engines; presently limited to the FFX reference engine and
the OpenMM engine.
Use MD as a coordinate based MC move.
Define the verbosity of the MolecularDynamics class.
Describe actions taken by writeFilesForStep.
The MergeFilter class allows Force Field X to treat merging of Systems just like opening a file
from a hard disk or socket.
Class Message is the abstract base class for a message sent to a process in
the PJ cluster middleware.
The MetropolisMC interface defines the basic methods of a Metropolis Monte Carlo application.
Minimize the potential energy of a system to an RMS gradient per atom convergence criteria.
Enumerates available molecular minimization engines; presently limited to the FFX reference
engine and the OpenMM engine.
OpenMM accelerated L-BFGS minimization.
Represents command line options for scripts that involve local energy minimization.
The ModelingPanel class encapsulates functionality needed to run FFX Modeling Commands.
The ModelingShell is used to script Multiscale Modeling Routines via the Groovy scripting
language.
Implementation of the modified Bessel function of the first kind using Chebyshev polynomials.
The MolecularAssembly class is a collection of Polymers, Hetero Molecules, Ions and Water
Run NVE, NVT, or NPT molecular dynamics.
Runs Molecular Dynamics using OpenMM implementation
The MolecularMC class is a framework to take Monte Carlo steps on a molecular system.
The Molecule class is a general container used for simple compounds or in cases where more
specialized classes have not been implemented.
Monte Carlo Barostat.
The MonteCarloListener will be notified at regular intervals during an MC algorithm.
Sample a thermodynamic path using the OST method, with the time-dependent bias built up using
Metropolis Monte Carlo steps.
The MouseBehavior class is the Base class for all mouse manipulators.
The MouseBehaviorCallback interface is implemented by classes that want to receive callbacks when
transforms are updated.
The MouseOrbit class implements a mouse orbit behavior.
The MouseProperties class is simple extension of MouseBehavior.
The MouseRotate class implements a mouse rotation behavior.
The MouseSelection class implements a mouse selection behavior.
The MouseTranslate class implements a mouse translate behavior.
The MouseZoom class implements a Mouse Zoom behavior.
The MSGroup class has one sub-node containing atoms, and one that contains molecular
mechanics/geometry terms.
The MSNode class forms the basic unit that all data classes extend.
The MSRoot class is the root of the Force Field X data structure.
The MTZFileFilter class is used to choose CCP4 MTZ files
This class parses CCP4 MTZ files.
MTZWriter class.
The possible output "styles".
The MultiDoubleArray avoids the need for Atomic variables, but at the cost of storing a full size
double array for each thread.
Represents command line options for scripts that can create multiple walkers, such as multi-walker
OST.
Class MultipleParallelException is thrown to indicate that multiple threads
in a parallel team threw exceptions while executing a parallel construct.
The 6 coefficients of the multiplicative polynomial switch are unique given the distances "a" and
"b".
Amoeba Polarizable Multipole Force.
The abstract MultipoleTensor is extended by classes that compute derivatives of 1/|r| via
recursion to arbitrary order using Cartesian multipoles in either a global frame or a
quasi-internal frame.
Global and Quasi-Internal (QI) coordinate systems are supported.
Operators that are supported.
The MultipoleType class defines a multipole in its local frame.
The local multipole frame is defined by the Z-then-X or Bisector convention.
The MultiResidue class allows switching between residues for uses such as sequence optimization.
The MultistateBennettAcceptanceRatio class defines a statistical estimator based on a generalization
to the Bennett Acceptance Ratio (BAR) method for multiple lambda windows.
Harmonic oscillators test case generates data for testing the MBAR implementation
Enum of MBAR seed types.
Utilities for importing atoms from PDB files and checking their names.
Common HETATOM labels for water and ions.
The NCSCrystal class extends Crystal to support non-crystallographic symmetry (NCS).
Given unit cell parameters and symmetry operators, NCS copies are restrained to the asymmetric
unit atoms.
This class is used to compute interstitial space integrals of the form 1/r^6.
The NeighborList class builds Verlet lists in parallel via a spatial decomposition.
Hold the atom index and its symmetry operator.
Hold the atoms in each cell.
This implementation uses the coefficients from International Tables, Vol.
This class contains fields and methods for maintaining details of non-bonded cutoffs.
Nonbonded Force.
Class NonPjJobFrontend provides the message handler for a job frontend
process that communicates with the Job Scheduler to allocate backend nodes
but does not run a PJ program.
Utilities for creating Nucleic Acid residues.
The 4 RNA bases, 4 DNA bases, and mono- di- and triphosphate.
Since enumeration values must start with a letter, an 'M' is added to modified bases whose IUPAC
name starts with an integer.
Class ObjectArrayBuf provides a buffer for an array of object items sent or
received using the Message Protocol (MP).
Class ObjectArrayBuf_1 provides a buffer for an array of object items sent or
received using the Message Protocol (MP).
Class ObjectBuf is the abstract base class for a buffer of object items sent
or received using the Message Protocol (MP).
Class ObjectItemBuf provides a buffer for a single object item sent or
received using the Message Protocol (MP).
Class ObjectMatrixBuf provides a buffer for a matrix of object items sent or
received using the Message Protocol (MP).
Class ObjectMatrixBuf_1 provides a buffer for a matrix of object items sent
or received using the Message Protocol (MP).
Class ObjectOp is the abstract base class for a binary operation on object
values, used to do reduction in a parallel program.
ObjectPair record.
Octree method presented in the Fast Multipole Method (FMM) tutorial from the Barba Group:
https://github.com/barbagroup/FMM_tutorial
OctreeCell: Object class for Octree method presented in the Fast Multipole Method (FMM) tutorial
from the Barba Group: https://github.com/barbagroup/FMM_tutorial
OctreeParticle: Object class for Octree method presented in the Fast Multipole Method (FMM)
tutorial from the Barba Group: https://github.com/barbagroup/FMM_tutorial
OctreePoint: Object class for Octree method presented in the Fast Multipole Method (FMM) tutorial
from the Barba Group: https://github.com/barbagroup/FMM_tutorial
Class Op is the abstract base class for a binary operation used to do
reduction in a parallel program.
Creates and manage an OpenMM Context.
Compute the potential energy and derivatives using OpenMM.
Create and manage an OpenMM Integrator.
Retrieve state information from an OpenMM Simulation.
Create and manage an OpenMM System.
The OptimizationInterface defines methods required by an optimizer.
This interface allows the optimizer to notify registered instances of successful steps.
Parallel computation of the OPT induced dipoles.
An implementation of the Orthogonal Space Tempering algorithm.
Represents command line options for scripts that utilize variants of the Orthogonal Space
Tempering (OST) algorithm.
The OSXAdapter class was developed by following an example supplied on the OS X site.
The OutOfPlaneBend class represents an Out-Of-Plane Bend.
OpenMM Out-of-Plane Bend Force.
The OutOfPlaneBendType class defines one Allinger style out-of-plane angle bending energy type.
Class Packing provides static methods for packing and unpacking arrays of
bytes into and out of integers, long integers, and arrays thereof.
A fixed schedule that balances pairwise work across threads.
Class ParallelConstruct is the common base class for all parallel constructs
that are executed by a ParallelTeam.
Class ParallelForLoop is the abstract base class for a parallel for loop that
is executed inside a ParallelRegion.
Class ParallelIteration is the abstract base class for a parallel iteration
that is executed inside a ParallelRegion.
Class ParallelRegion is the abstract base class for a parallel region that is
executed by a ParallelTeam of threads.
Class ParallelSection is the abstract base class for a section of code to be
executed in parallel.
Class ParallelTeam provides a team of threads for executing a ParallelRegion in parallel.
This Particle Mesh Ewald class implements PME for the AMOEBA polarizable mutlipole force field in
parallel using a
NeighborList for any Crystal space group.Parallel pre-conditioned conjugate gradient solver for the self-consistent field.
The PDBFileFilter class is used to choose a Protein Databank (*.PDB) file.
The PDBFilter class parses data from a Protein DataBank (*.PDB) file.
Presently, VERSION3_3 is default, and VERSION3_2 is anything non-standard.
The PDBXFileFilter class is used to choose a PDBML File (*.XML).
PDBMLFilter class.
Periodic Torsion Force.
Parallel computation of the permanent field.
Parallel computation of the Generalized Kirkwood permanent reaction field.
Minimize the potential energy of a system to an RMS gradient per atom convergence criteria.
The PhReplicaExchange implements pH replica exchange.
The PickingCallback interface is implemented by classes wishing to recieve notification that a
picked object has moved.
The PickMouseBehavior class is the base class for mouse picking behaviors.
The PickOrbitBehavior class implements a mouse orbit behavior.
The PickPropertiesBehavior class.
The PickRotateBehavior class implements a mouse rotate behavior on a picked object.
The PickSelectionBehavior class implements a mouse based selections behavior.
The PickTranslateBehavior class implements a translation behavior on a picked scenegraph object.
The PickZoomBehavior class implements a scaling behavior on a picked scenegraph object.
The Pi-Orbital Torsion class.
OpenMM Pi-Orbital Torsion Force.
The PiOrbitalTorsionType class defines a Pi-Orbital Torsion energy term.
PJDoubleArray implements the AtomicDoubleArray interface using the Parallel Java class
SharedDoubleArray.
Class PJProperties provides static methods for reading Java system properties
that control the behavior of Parallel Java.
A Platform defines an implementation of all the kernels needed to perform some calculation.
Platform describes a set of force field implementations that include a pure Java reference
implementation (FFX), and two OpenMM implementations (OMM_CUDA and OMM_REF are supported)
The PolarizableMultipole class defines a polarizable multipole.
Parallel computation of the polarization energy as sum over atomic contributions (-1/2 u.E).
The PolarizeType class defines an isotropic atomic polarizability.
The Polymer class encapsulates a peptide or nucleotide chain.
Utilities for creating polymers.
A PolynomialCurve describes points along a polynomial function.
Port Utilities.
The Potential interface defines methods required by an optimizer or molecular dynamics.
Set the state of the Potential to include FAST varying energy terms, SLOW varying energy terms
or BOTH.
Recognized variables currently include Cartesian coordinates and OTHER.
Base class for scripts in the Potentials package, providing some key functions.
Base class for scripts in the Potentials package, providing some key functions.
The PotentialsFileOpener class specifies a Runnable object which is constructed with a File and,
when run, allows returning any opened MolecularAssembly objects and their associated properties.
PotentialsFunctions describes core functionality for many Force Field X algorithms and scripts,
such as opening and closing structure files, basic force field energy evaluations, etc.
PotentialsUtils implements core functionality for many Force Field X algorithms and scripts, such
as opening and closing structure files, basic force field evaluations, etc.
PotentialTest extends BaseFFXTest to include support for:
1) Creating a Groovy Binding before each test.
1) Creating a Groovy Binding before each test.
A PowerSwitch interpolates between 0 and 1 vi f(x) = (ax)^beta, where x must be between 0 and
1/a.
Class PrintStreamLogger provides an object that logs messages to a print
stream.
Class ProcessInfo provides a record of information about one job backend
process in the PJ cluster middleware.
The state of a job backend process.
Class ProgressiveAlignmentOfCrystals holds the majority of the functionality necessary to quantify
crystal similarity following the PAC method.
The Keyword Group for an FFX Keyword.
Log out FFXProperty Annotations for documentation purposes.
Class Proxy is the abstract base class for a proxy object for sending
messages to a PJ process.
The QIFrame class defines a quasi-internal frame between two atoms.
Implements an error-canceling quad topology, where two large dual-topology simulation legs are
run simultaneously to arrive at a small sum.
A QuasiLinearThetaMap implements a map of theta[-pi, +pi] to lambda[0,1] in a mostly-linear
fashion (i.e.
Class Random is the abstract base class for a pseudorandom number generator
(PRNG) designed for use in parallel scientific programming.
Class RandomSample provides objects that generate random samples from
discrete sets.
Class RandomSubset provides an object that generates a random subset of a set
of integers.
Represents command line options for scripts that create randomized unit cells.
Class Range provides a range of type
int.The Rattle classes implements the RATTLE distance constraint method.
Compute the FFT of real, double precision data of arbitrary length n using a Complex transform.
Compute the 3D FFT of real, double precision input of arbitrary dimensions.
Compute the 3D FFT of real, double precision input of arbitrary dimensions in parallel.
RealSpaceData class.
Combine the Real Space target and chemical potential energy.
Parallel evaluation of the PME real space energy and gradient.
RealSpaceFile class.
RealSpaceFileFilter interface.
Represents command line options for scripts that utilize a real-space density map.
RealSpaceRefinementData class.
Parallel evaluation of the PME reciprocal space energy and gradient.
The Reciprocal Space class computes the reciprocal space contribution to
ParticleMeshEwald
for the AMOEBA force field.Class ReduceArrays provides static methods for reduction operations on arrays
and matrices of primitive types and object types.
Parallel conversion of torques into forces, and then reduce them.
Combine the X-ray target and chemical potential energy using the
CrystalPotential interfaceRefinement minimization class using
OptimizationListener interface, constructs a RefinementEnergy object for this purposeDifferent refinement mode selection types.
RefinementModel class.
Class to represent a reflection list.
The ReflectionSpline class represents a reflection spline basis.
A relative solvation term for chemical perturbations.
Citations: Wolfenden et al: Wolfenden, R., Andersson, L., Cullis, P.
A BaseType for relative solvation energies (intended for nonstandard amino acids).
The Renderer class attempts to maximize throughput of graphics operations on MolecularAssembly
instances.
The RendererCache class defines constants related to rendering modes and caches primitives for
the Renderer.
An implementation of RepEx between Orthogonal Space Tempering potentials.
The ReplicaExchange implements temperature and lambda replica exchange methods.
Class ReplicatedBoolean provides a replicated, shared reduction variable for
a value of type
boolean.Class ReplicatedByte provides a replicated, shared reduction variable for a
value of type
byte.Class ReplicatedCharacter provides a replicated, shared reduction variable
for a value of type
char.Class ReplicatedDouble provides a replicated, shared reduction variable for a
value of type
double.Class ReplicatedFloat provides a replicated, shared reduction variable for a
value of type
float.Class ReplicatedInteger provides a replicated, shared reduction variable for
a value of type
int.Class ReplicatedLong provides a replicated, shared reduction variable for a
value of type
long.Class ReplicatedObject provides a replicated, shared reduction variable for a
value of type T (a nonprimitive type).
Class ReplicatedShort provides a replicated, shared reduction variable for a
value of type
short.The ReplicatesCrystal class extends Crystal to generate additional symmetry operators needed to
describe a "replicated" super-cell.
The Residue class represents individual amino acids or nucleic acid bases.
Residue type [NA, AA, UNK].
The ResidueState class encodes the current chemical and coordinate state of a Residue,
particularly a MultiResidue, for ease of reverting coordinates.
The Resolution class encapsulates the sampling limits and resolution limits for a given crystal
and/or data set.
Class ResourceCache provides a cache of resources, indexed by resource name.
Log resources.
Respa performs multiple time step molecular dynamics using the reversible reference system
propagation algorithm (r-RESPA) via a Verlet core with the potential split into fast- and
slow-evolving portions.
Restrain Bonds Force.
RestraintBond class.
Apply a restraint between groups.
Restrain Groups Force.
Restrain the position of atoms to their initial coordinates.
Restrain Positions Force.
Restrain Torsions Force.
The ROLS Interace defines "Recursive Over Length Scales" (ROLS) Methods.
The ROLSP class is used for Proof-Of-Concept Parallel Recusive Over Length Scales (ROLS) Methods
(currently only on shared memory systems).
Conformational Biased Monte Carlo (applied to ALL torsions of a peptide side-chain).
Represents a random chi[0] spin of the target residue.
Represents a Boltzmann-drawn spin of all residue torsions for use with RosenbluthCBMC
(Configurational-Bias Monte Carlo).
Mode of the RosenbluthChiAllMove instance.
Orientational Biased Monte Carlo (as applied to chi0 torsion of peptide side-chains).
The Rotamer Class usually represents one immutable amino acid Rotamer.
The Rotamer Library Class manages a library of side-chain Rotamers for amino acids, and a library
of backbone Rotamers for nucleic acids.
Monte Carlo driver for DEE-MC.
This implements single-rotamer changes in the framework of the rotamer energy matrices.
Optimize protein side-chain conformations and nucleic acid backbone conformations using rotamers.
Rotamer Optimization Methods.
Allows get2BodyDistance to find the shortest distance between any two rotamers or two residues.
The RowLoop class is used to parallelize placing onto a 3D grid
The RowRegion class is used to parallelize placing onto a 3D grid
RowSchedule class.
Class Runner is a parallel program that runs, in parallel, a group of
Jobs created by a JobGenerator.
The RunningStatistics class uses online, stable algorithms to calculate summary statistics from a
source of doubles, including mean, variance, standard deviation, max, min, sum, and count.
Represents command line options for scripts that save a structure to disc.
The ScalarMath class is a simple math library that operates on single variables
Fit bulk solvent and aniso B scaling terms to correct calculated structure factors against data
ScaleBulkMinimize class.
Scale factors and masking rules for electrostatics.
Describes available SCF algorithms, and whether they are supported by the FFX and/or CUDA
implementations.
Predict Mutual Induced Dipoles based on previous steps.
Class Schedule provides an object that determines how to schedule the
iterations of a ParallelForLoop among the threads in a
ParallelTeam.
Class Searching provides static methods for searching arrays of primitive
types and object types.
Class Searching.Byte is the base class for a helper object used to search
an array of type
byte[].Class Searching.Character is the base class for a helper object used to
search an array of type
char[].Class Searching.Double is the base class for a helper object used to
search an array of type
double[].Class Searching.Float is the base class for a helper object used to
search an array of type
float[].Class Searching.Integer is the base class for a helper object used to
search an array of type
int[].Class Searching.Long is the base class for a helper object used to search
an array of type
long[].Class Searching.Object is the base class for a helper object used to
search an array of type
T[].Class Searching.Short is the base class for a helper object used to
search an array of type
short[].The Selection class will be used to make recursive multiscale selections, however its
implementation is not yet complete.
Compute residue self-energy values in parallel across nodes.
Synchronous (blocking) communication of OST counts.
The SequentialEstimator abstract class defines a statistical estimator based on perturbative
potential energy differences between adjacent windows (e.g.
SETTLE triatomic distance constraints, intended for rigid water models.
Class SharedBoolean provides a reduction variable for a value of type
boolean.Class SharedBooleanArray provides an array reduction variable with elements
of type
boolean.Class SharedBooleanArrayBuf provides a buffer for a multiple thread safe
array of Boolean items sent or received using the Message Protocol (MP).
Class SharedBooleanArrayBuf_1 provides a buffer for a multiple thread safe
array of Boolean items sent or received using the Message Protocol (MP).
Class SharedBooleanBuf provides a buffer for a multiple thread safe Boolean
item sent or received using the Message Protocol (MP).
Class SharedByte provides a reduction variable for a value of type
byte.Class SharedByteArray provides an array reduction variable with elements of
type
byte.Class SharedByteArrayBuf provides a buffer for a multiple thread safe array
of byte items sent or received using the Message Protocol (MP).
Class SharedByteArrayBuf_1 provides a buffer for a multiple thread safe array
of byte items sent or received using the Message Protocol (MP).
Class SharedByteBuf provides a buffer for a multiple thread safe byte item
sent or received using the Message Protocol (MP).
Class SharedCharacter provides a reduction variable for a value of type
char.Class SharedCharacterArray provides an array reduction variable with elements
of type
char.Class SharedCharacterArrayBuf provides a buffer for a multiple thread safe
array of character items sent or received using the Message Protocol (MP).
Class SharedCharacterArrayBuf_1 provides a buffer for a multiple thread safe
array of character items sent or received using the Message Protocol (MP).
Class SharedCharacterBuf provides a buffer for a shared character item sent
or received using the Message Protocol (MP).
Class SharedDouble provides a reduction variable for a value of type
double.Class SharedDoubleArray provides an array reduction variable with elements of
type
double.Class SharedDoubleArrayBuf provides a buffer for a multiple thread safe array
of double items sent or received using the Message Protocol (MP).
Class SharedDoubleArrayBuf_1 provides a buffer for a multiple thread safe
array of double items sent or received using the Message Protocol (MP).
Class SharedDoubleBuf provides a buffer for a shared double item sent or
received using the Message Protocol (MP).
Class SharedFloat provides a reduction variable for a value of type
float.Class SharedFloatArray provides an array reduction variable with elements of
type
float.Class SharedFloatArrayBuf provides a buffer for a multiple thread safe array
of float items sent or received using the Message Protocol (MP).
Class SharedFloatArrayBuf_1 provides a buffer for a multiple thread safe
array of float items sent or received using the Message Protocol (MP).
Class SharedFloatBuf provides a buffer for a shared float item sent or
received using the Message Protocol (MP).
Class SharedInteger provides a reduction variable for a value of type
int.Class SharedIntegerArray provides an array reduction variable with elements
of type
int.Class SharedIntegerArrayBuf provides a buffer for a multiple thread safe
array of integer items sent or received using the Message Protocol (MP).
Class SharedIntegerArrayBuf_1 provides a buffer for a multiple thread safe
array of integer items sent or received using the Message Protocol (MP).
Class SharedIntegerBuf provides a buffer for a shared integer item sent or
received using the Message Protocol (MP).
Class SharedIntegerMatrix provides a matrix reduction variable with elements
of type
int.Class SharedLong provides a reduction variable for a value of type
long.Class SharedLongArray provides an array reduction variable with elements of
type
long.Class SharedLongArrayBuf provides a buffer for a multiple thread safe array
of long items sent or received using the Message Protocol (MP).
Class SharedLongArrayBuf_1 provides a buffer for a multiple thread safe array
of long items sent or received using the Message Protocol (MP).
Class SharedLongBuf provides a buffer for a shared long item sent or received
using the Message Protocol (MP).
Class SharedLongMatrix provides a matrix reduction variable with elements of
type
long.Class SharedObject provides a reduction variable for a value of an object
type.
Class SharedObjectArray provides an array reduction variable with elements of
an object type.
Class SharedObjectArrayBuf provides a buffer for a multiple thread safe array
of object items sent or received using the Message Protocol (MP).
Class SharedObjectArrayBuf_1 provides a buffer for a multiple thread safe
array of object items sent or received using the Message Protocol (MP).
Class SharedObjectBuf provides a buffer for a shared object item sent or
received using the Message Protocol (MP).
Class SharedShort provides a reduction variable for a value of type
short.Class SharedShortArray provides an array reduction variable with elements of
type
short.Class SharedShortArrayBuf provides a buffer for a multiple thread safe array
of short items sent or received using the Message Protocol (MP).
Class SharedShortArrayBuf_1 provides a buffer for a multiple thread safe
array of short items sent or received using the Message Protocol (MP).
Class SharedShortBuf provides a buffer for a shared short item sent or
received using the Message Protocol (MP).
Class SharedSigned16BitIntegerArrayBuf provides a buffer for a multiple
thread safe array of signed 16-bit integer items sent or received using the
Message Protocol (MP).
Class SharedSigned16BitIntegerArrayBuf_1 provides a buffer for a multiple
thread safe array of signed 16-bit integer items sent or received using the
Message Protocol (MP).
Class SharedSigned16BitIntegerBuf provides a buffer for a single signed
16-bit integer item sent or received using the Message Protocol (MP).
Class SharedSigned8BitIntegerArrayBuf provides a buffer for a multiple thread
safe array of signed 8-bit integer items sent or received using the Message
Protocol (MP).
Class SharedSigned8BitIntegerArrayBuf_1 provides a buffer for a multiple
thread safe array of signed 8-bit integer items sent or received using the
Message Protocol (MP).
Class SharedSigned8BitIntegerBuf provides a buffer for a shared signed 8-bit
integer item sent or received using the Message Protocol (MP).
Class SharedUnsigned16BitIntegerArrayBuf provides a buffer for a multiple
thread safe array of unsigned 16-bit integer items sent or received using the
Message Protocol (MP).
Class SharedUnsigned16BitIntegerArrayBuf_1 provides a buffer for a multiple
thread safe array of unsigned 16-bit integer items sent or received using the
Message Protocol (MP).
Class SharedUnsigned16BitIntegerBuf provides a buffer for a shared unsigned
16-bit integer item sent or received using the Message Protocol (MP).
Class SharedUnsigned8BitIntegerArrayBuf provides a buffer for a multiple
thread safe array of unsigned 8-bit integer items sent or received using the
Message Protocol (MP).
Class SharedUnsigned8BitIntegerArrayBuf_1 provides a buffer for a multiple
thread safe array of unsigned 8-bit integer items sent or received using the
Message Protocol (MP).
Class SharedUnsigned8BitIntegerBuf provides a buffer for a single unsigned
8-bit integer item sent or received using the Message Protocol (MP).
Class ShortArrayBuf provides a buffer for an array of short items sent or
received using the Message Protocol (MP).
Class ShortArrayBuf_1 provides a buffer for an array of short items sent or
received using the Message Protocol (MP).
Class ShortBuf is the abstract base class for a buffer of short items sent or
received using the Message Protocol (MP).
Class ShortItemBuf provides a buffer for a single short item sent or received
using the Message Protocol (MP).
Class ShortMatrixBuf provides a buffer for a matrix of short items sent or
received using the Message Protocol (MP).
Class ShortMatrixBuf_1 provides a buffer for a matrix of short items sent or
received using the Message Protocol (MP).
Class ShortOp is the abstract base class for a binary operation on short
values, used to do reduction in a parallel program.
Optimize SigmaA coefficients (using spline coefficients) and structure factor derivatives using a
likelihood target function.
SigmaAMinimize class.
Class Signed16BitIntegerArrayBuf provides a buffer for an array of signed
16-bit integer items sent or received using the Message Protocol (MP).
Class Signed16BitIntegerArrayBuf_1 provides a buffer for an array of signed
16-bit integer items sent or received using the Message Protocol (MP).
Class Signed16BitIntegerBuf is the abstract base class for a buffer of signed
16-bit integer items sent or received using the Message Protocol (MP).
Class Signed16BitIntegerItemBuf provides a buffer for a single signed 16-bit
integer item sent or received using the Message Protocol (MP).
Class Signed16BitIntegerMatrixBuf provides a buffer for a matrix of signed
16-bit integer items sent or received using the Message Protocol (MP).
Class Signed16BitIntegerMatrixBuf_1 provides a buffer for a matrix of signed
16-bit integer items sent or received using the Message Protocol (MP).
Class Signed8BitIntegerArrayBuf provides a buffer for an array of signed
8-bit integer items sent or received using the Message Protocol (MP).
Class Signed8BitIntegerArrayBuf_1 provides a buffer for an array of signed
8-bit integer items sent or received using the Message Protocol (MP).
Class Signed8BitIntegerBuf is the abstract base class for a buffer of signed
8-bit integer items sent or received using the Message Protocol (MP).
Class Signed8BitIntegerItemBuf provides a buffer for a single signed 8-bit
integer item sent or received using the Message Protocol (MP).
Class Signed8BitIntegerMatrixBuf provides a buffer for a matrix of signed
8-bit integer items sent or received using the Message Protocol (MP).
Class Signed8BitIntegerMatrixBuf_1 provides a buffer for a matrix of signed
8-bit integer items sent or received using the Message Protocol (MP).
Run NVT molecular dynamics at a series of temperatures to optimize a structure.
Represents non-composite AnnealingSchedules known (i.e.
The SimulationDefinition class is a serializable wrapper that specifies an FFX simulation.
The SimulationFilter class parses system data sent by FFXServer to FFXClient.
This SimulationLoader class oversees loading information from an executing FFX instance program
this instance of Force Field X.
The SimulationMessage class is used to pass simple messages between an FFXServer and its
FFXClient(s).
The SimulationUpdate class is a serializable wrapper for FFX simulation data that changes during
a simulation.
A SinWave describes points along a sine wave of f(x) = a*sin(jx).
The SliceLoop class is used to parallelize placing onto a 3D grid
The SliceLoop class is used to parallelize placing onto a 3D grid
SliceSchedule class.
The SoluteType class defines one implicit solvent radius.
SolventBinaryFormFactor class.
SolventGaussFormFactor class.
SolventPolyFormFactor class.
Parallel successive over-relaxation (SOR) solver for the self-consistent field.
Class Sorting provides static methods for sorting arrays of primitive types
and object types.
Class Sorting.Byte is the base class for a helper object used to sort an
array of type
byte[].Class Sorting.Character is the base class for a helper object used to
sort an array of type
char[].Class Sorting.Double is the base class for a helper object used to sort
an array of type
double[].Class Sorting.Float is the base class for a helper object used to sort an
array of type
float[].Class Sorting.Integer is the base class for a helper object used to sort
an array of type
int[].Class Sorting.Long is the base class for a helper object used to sort an
array of type
long[].Class Sorting.Object is the abstract base class for a helper object used
to sort an array of objects of type
T[].Class Sorting.Short is the base class for a helper object used to sort an
array of type
short[].The Spacegroup class defines the symmetry of a crystal.
This class holds the functionality to convert between equivalent space groups.
The SpaceGroupDefinitions class defines the 230 distinct space groups in three dimensions.
Loop over a list of atoms and assign their density to a grid.
This class implements a spatial decomposition based on partitioning a grid into octants.
A fixed schedule that load balances work chunks across threads.
Fit structure factors using spline coefficients
SplineMinimize class.
A SquaredTrigSwitch implements a 0-1 switch of form f(x) = sin^2(ax) or of form f(x) = cos^2(ax).
Software based computation of square root and inverse square root.
java -cp target/numerics-1.0.0-beta.jar -XX:+UnlockDiagnosticVMOptions -XX:+PrintAssembly
-Djava.library.path=hsdis-amd64.dylib ffx.numerics.math.SSETest
A State object records a snapshot of the current state of a simulation at a point in time.
The StatisticalEstimator interface defines a free energy estimator in the most generic sense.
Class Status provides the result of receiving a message in the Message
Protocol (MP).
Class Stdio provides standard I/O streams that can be redirected on a
per-thread basis.
Stochastic dynamics time step via a velocity Verlet integration algorithm.
Class StreamFile represents a file that resides in the user's account in the
job frontend process of a PJ cluster parallel program.
The StretchBend class represents a Stretch-Bend formed between three linearly bonded atoms.
OpenMM Stretch-Bend Force.
The StretchBendType class defines one out-of-plane angle bending energy type.
The StretchTorsion class represents a coupling between a torsional angle and the three bonds
contained in the torsion, as defined in the 2017 AMOEBA nucleic acid force field.
OpenMM Stretch-Torsion Force.
The StretchTorsionType class defines one stretch-torsion energy type.
String Array.
StringOutputStream class.
StringUtils class.
Structure Metrics contains functionality to calculate characteristics of coordinate systems.
SturmMethod class.
The SummaryStatistics class uses online, stable algorithms to calculate summary statistics from
double arrays/lists, including mean, variance, standard deviation, max, min, sum, and count.
SurfaceAreaRegion performs an analytical computation of the weighted solvent accessible surface
area of each atom and the first derivatives of the area with respect to Cartesian coordinates
This is the 3rd version of SwingWorker (also known as SwingWorker 3), an abstract class that you
subclass to perform GUI-related work in a dedicated thread.
The SymOp class defines the rotation and translation of a single symmetry operator.
This class represents a molecular system.
The SystemFilter class is the base class for most Force Field X file parsers.
The current state of the molecular dynamics simulation.
Algorithms that can be gracefully terminated early should implement this interface.
Represents command line options for scripts that calculate thermodynamics.
Represents categories of thermodynamics algorithms that must be handled differentially.
The abstract Thermostat class implements methods common to all thermostats for initializing
velocities from a Maxwell-Boltzmann distribution and computing the instantaneous temperature.
An enumeration of available Thermostats.
The TholeTensorGlobal class computes derivatives of Thole damping via recursion to order <= 4 for
Cartesian multipoles in either a global frame.
The TholeTensorQI class computes derivatives of Thole damping via recursion to order <= 4 for
Cartesian multipoles in a quasi-internal frame.
Compute 3-Body energy values in parallel across nodes.
Class Timer controls the execution of a TimerTask's timed
actions.
Represents command line options for scripts that perform timings for energy and optionally
gradients.
Interface TimerTask specifies the interface for an object that performs timed
actions under the control of a Timer.
A collection of Utility methods for compatibility with Tinker.
Utilities for interpolating between Amino Acid protonation and tautomer states.
Constant
CysteineAtomsConstant
HistidineAtomsConstant
lysineAtomsAmino acid protonation reactions.
Represents command line options for scripts that utilize multiple physical topologies.
Proof-of-concept use of the TornadoVM for parallelization of Java code.
The Torsion class represents a torsional angle formed between four bonded atoms.
TorsionSearch class for performing a torsion scan on a molecule in a molecular assembly.
The TorsionTorsion class represents two adjacent torsional angles formed by five bonded atoms.
Torsion-Torsion Force.
The TorsionTorsionType class defines a Torsion-Torsion spline.
The TorsionType class defines a torsional angle.
Torsion modes include Normal or In-Plane
The Trajectory class controls playback of a TINKER trajectory.
TriCubicSpline class.
Compute 2-Body energy values in parallel across nodes.
The UIFileCloser class wraps the closing of an FFXSystem within a thread.
The UIFileOpener class opens a file into Force Field X using a filter from the
ffx.potential.parsers package.
UIUtils implements core and extended functionality for many Force Field X algorithms and scripts,
such as opening and closing structure files, basic force field evaluations, molecular dynamics,
etc.
Static methods to generate and differentiate uniform b-Splines.
A UnivariateDiffFunction describes a function of a single value (often lambda).
Static class responsible for parsing String arrays into univariate switching functions.
A UnivariateSwitchingFunction describes a function of a single value (often lambda), where f(lb) =
0, f(ub) = 1, and df(x)/dx >= 0 for all x lb-ub.
A record class to hold the state of a system.
Class Unsigned16BitIntegerArrayBuf provides a buffer for an array of unsigned
16-bit integer items sent or received using the Message Protocol (MP).
Class Unsigned16BitIntegerArrayBuf_1 provides a buffer for an array of
unsigned 16-bit integer items sent or received using the Message Protocol
(MP).
Class Unsigned16BitIntegerBuf is the abstract base class for a buffer of
unsigned 16-bit integer items sent or received using the Message Protocol
(MP).
Class Unsigned16BitIntegerItemBuf provides a buffer for a single unsigned
16-bit integer item sent or received using the Message Protocol (MP).
Class Unsigned16BitIntegerMatrixBuf provides a buffer for a matrix of
unsigned 16-bit integer items sent or received using the Message Protocol
(MP).
Class Unsigned16BitIntegerMatrixBuf_1 provides a buffer for a matrix of
unsigned 16-bit integer items sent or received using the Message Protocol
(MP).
Class Unsigned8BitIntegerArrayBuf provides a buffer for an array of unsigned
8-bit integer items sent or received using the Message Protocol (MP).
Class Unsigned8BitIntegerArrayBuf_1 provides a buffer for an array of
unsigned 8-bit integer items sent or received using the Message Protocol
(MP).
Class Unsigned8BitIntegerBuf is the abstract base class for a buffer of
unsigned 8-bit integer items sent or received using the Message Protocol
(MP).
Class Unsigned8BitIntegerItemBuf provides a buffer for a single unsigned
8-bit integer item sent or received using the Message Protocol (MP).
Class Unsigned8BitIntegerMatrixBuf provides a buffer for a matrix of unsigned
8-bit integer items sent or received using the Message Protocol (MP).
Class Unsigned8BitIntegerMatrixBuf_1 provides a buffer for a matrix of
unsigned 8-bit integer items sent or received using the Message Protocol
(MP).
The UreyBradley class.
Urey-Bradley Force.
The UreyBradleyType class defines one harmonic UreyBradley cross term.
The Utilities class provides methods to locate functional units of an organic system.
An enumeration of recognized file types.
An enumeration of recognized organic polymers.
The Van der Waals class computes Van der Waals interaction in parallel using a
NeighborList for any Crystal.The trick: The setFactors(i,k) method is called every time through the inner VdW loop, avoiding
an "if (esv)" branch statement.
This class contains fields and methods for maintaining details of the van der Waals functional
form.
Epsilon combining rule.
Radius combining rule.
Radius size in the parameter file (radius or diameter).
Radius type in the parameter file (R-Min or Sigma).
VDW Type.
The Van der Waals class computes Van der Waals interaction in parallel using a
NeighborList for P1 (no symmetry) Crystal systems.Amoeba van der Waals Force.
The VDWPairType class defines a van der Waals Pair type.
The VDWType class defines van der Waals type for a normal interaction or a special 1-4
interaction.
Torsion modes include Normal or In-Plane
Vec3 Array.
Integrate Newton's equations of motion using a Velocity Verlet multistep recursion formula.
Verlet Integrator.
Class Version defines version information for the Parallel Java Library.
Weeks-Chandler-Andersen Dispersion Force.
Class WorkerConstruct is the common base class for all worker constructs that
are executed by a WorkerTeam.
Class WorkerForLoop is the abstract base class for a worker for loop that is
executed inside a WorkerRegion.
Class WorkerIntegerForLoop is the abstract base class for one variation of a
worker for loop that is executed inside a WorkerRegion.
Class WorkerIntegerStrideForLoop is the abstract base class for one variation
of a worker for loop that is executed inside a WorkerRegion.
Class WorkerIteration is the abstract base class for a worker iteration that
is executed inside a WorkerRegion.
Class WorkerLongForLoop is the abstract base class for one variation of a
worker for loop that is executed inside a WorkerRegion.
Class WorkerLongStrideForLoop is the abstract base class for one variation of
a worker for loop that is executed inside a WorkerRegion.
Class WorkerRegion is the abstract base class for a worker region that is
executed by a WorkerTeam of threads distributed across the
processes of a cluster parallel program.
Class WorkerTeam provides a team of threads, distributed across the processes
of a cluster parallel program, for executing a WorkerRegion in
parallel.
Represents command line options for scripts that periodically write out structures.
The XPHFileFilter class is used to choose a XPH Coordinate (*.XPH) file.
The XYZFilter class parses TINKER Cartesian coordinate (*.XYZ) files.
Combine the X-ray target and chemical potential energy.
This implementation uses the coefficients from Su and Coppens and 3 coefficient parameters derived
from CCTBX.
Represents command line options for scripts that utilize X-ray data with a maximum likelihood
target.
This class computes the energy and Cartesian coordinate gradient, plus finite difference
derivatives of lattice parameters.
The XYZFileFilter class is used to choose a TINKER Cartesian Coordinate (*.XYZ) file.
The XYZFilter class parses TINKER Cartesian coordinate (*.XYZ) files.
The Zwanzig class implements exponential averaging/free energy perturbation using the Zwanzig
relationship, in either the forwards or backwards direction (not both).
Directionality of the Zwanzig estimation (forwards perturbation or backwards perturbation).