Uses of Package
ffx.potential.bonded
Packages that use ffx.potential.bonded
Package
Description
The Algorithms CLI package defines options for PicoCLI command line scripts.
The MC package implements a variety of Monte Carlo moves for optimization and simulation
algorithms.
The Misc package contains a few miscellaneous algorithms.
The Optimize package contains local and global optimization algorithms using pure Java and OpenMM
code paths.
The manybody package implements many-body rotamer optimization infrastructure,
including distance matrices, an energy expansion (self, two-body, three-body,
and four-body), Dead-end elimination criteria, Goldstein elimination criteria,
and supporting data structures for efficient optimization.
The Thermodynamics package computes free energy differences using Orthogonal Space Tempering
(OST) sampling via pure Java or OpenMM (via Monte Carlo OST).
The Potential package implements molecular mechanics force fields with shared memory Parallel
Java and via OpenMM.
The Bonded package implements bonded molecular mechanics terms such as bonds, angles, torsions,
etc.
The Potential CLI package defines reusable options for PicoCLI command line scripts.
The constraint package implements holonomic constraint algorithms used during
molecular dynamics and minimization, including CCMA, SETTLE, and SHAKE-style
constraints (as well as charge constraints).
The Extended package is progress toward support for constant pH molecular dynamics using extended
system variables (i.e. lambda dynamics on protonation).
The Nonbonded package implements nonbonded molecular mechanics terms such as van der Waals and
Particle Mesh Ewald electrostastics.
The implicit package implements implicit solvent models and related terms,
including Generalized Kirkwood (GK) electrostatics, surface area terms,
dispersion/cavitation contributions, and supporting parallel regions for
Born radii and field evaluation.
The pme package implements polarization and permanent electrostatics using
Particle Mesh Ewald (PME).
The openmm package contains utilities to construct and run Force Field X
potentials on the OpenMM platform, including system builders, custom forces,
alchemical fixed-charge forces, and integrators tailored to FFX simulations.
The Parameters package stores force field atom types, bond types, etc, and keywords that define
the potential.
The Parsers package handles reading/writing files to/from the internal data structure.
The terms package contains analytical potential energy terms and their
gradients for bonded interactions (bond, angle, stretch-bend, torsions,
impropers, Urey-Bradley) and restraint terms used by Force Field X.
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.
The Real Space package implements real space structure refinement.
The UI package provides views and controllers for manipulating molecular systems.
The X-ray package implements support for X-ray and Neutron refinement.
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Classes in ffx.potential.bonded used by ffx.algorithms.cliClassDescriptionThe Residue class represents individual amino acids or nucleic acid bases.The Rotamer Library Class manages a library of side-chain Rotamers for amino acids, and a library of backbone Rotamers for nucleic acids.
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Classes in ffx.potential.bonded used by ffx.algorithms.mcClassDescriptionThe Residue class represents individual amino acids or nucleic acid bases.
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Classes in ffx.potential.bonded used by ffx.algorithms.miscClassDescriptionThe Residue class represents individual amino acids or nucleic acid bases.The Rotamer Library Class manages a library of side-chain Rotamers for amino acids, and a library of backbone Rotamers for nucleic acids.
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Classes in ffx.potential.bonded used by ffx.algorithms.optimizeClassDescriptionThe Atom class represents a single atom and defines its alternate conformations and molecular mechanics atom type.The Molecule class is a general container used for simple compounds or in cases where more specialized classes have not been implemented.The Residue class represents individual amino acids or nucleic acid bases.The Rotamer Library Class manages a library of side-chain Rotamers for amino acids, and a library of backbone Rotamers for nucleic acids.
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Classes in ffx.potential.bonded used by ffx.algorithms.optimize.manybody
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Classes in ffx.potential.bonded used by ffx.algorithms.thermodynamicsClassDescriptionThe LambdaInterface should be implemented by potential energy terms that can accept a lambda value from [0 .. 1] that defines a twice differentiable path between states 0 and 1.
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Classes in ffx.potential.bonded used by ffx.potentialClassDescriptionThe Angle class represents an angle formed between three linearly bonded atoms.The Atom class represents a single atom and defines its alternate conformations and molecular mechanics atom type.The LambdaInterface should be implemented by potential energy terms that can accept a lambda value from [0 .. 1] that defines a twice differentiable path between states 0 and 1.The Molecule class is a general container used for simple compounds or in cases where more specialized classes have not been implemented.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 Polymer class encapsulates a peptide or nucleotide chain.The Residue class represents individual amino acids or nucleic acid bases.The ROLS Interace defines "Recursive Over Length Scales" (ROLS) Methods.
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Classes in ffx.potential.bonded used by ffx.potential.bondedClassDescriptionThe 20 standard amino acids.Constant
AIBConstantALASingle letter amino acid codes (need toConstantAminoAcidBackboneAtomsConstantARGConstantASDConstantASHConstantASNConstantASPConstantCYDConstantCYSConstantCYSConstantGLDConstantGLHConstantGlutamineAtomNamesConstantGLUConstantGLYConstantGlycineBackboneAtomsConstantHIDConstantHIEConstantHistidineAtomsConstantILEConstantLEUConstantLYDConstantLYSConstantMethionineAtomNamesConstantORNConstantPCAConstantPHEConstantPROConstantProlineBackboneAtomsThe location of a residue within a chain.ConstantSERThis interface is used by the "Build" routines.ConstantTHRConstantTRPConstantTYDConstantTYRConstantVALThe Angle class represents an angle formed between three linearly bonded atoms.The AngleTorsion class represents an angle torsion coupling between four bonded atoms.The Atom class represents a single atom and defines its alternate conformations and molecular mechanics atom type.Element symbols for the first 109 elements.The Bond class represents a covalent bond formed between two atoms.The BondedEnergy interface.The BondedTerm class is extended by all Valence Geometry classes (bond, angle, dihedral, torsion, etc.).This exception is thrown when an atom type could not be assigned.This exception is thrown when a heavy atom is not found.The ImproperTorsion class represents an Improper Torsion.The Joint class contains the geometry produced by the FGroup Joiner method.The LambdaInterface should be implemented by potential energy terms that can accept a lambda value from [0 .. 1] that defines a twice differentiable path between states 0 and 1.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 MultiResidue class allows switching between residues for uses such as sequence optimization.Common HETATOM labels for water and ions.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.The OutOfPlaneBend class represents an Out-Of-Plane Bend.The Pi-Orbital Torsion class.The Polymer class encapsulates a peptide or nucleotide chain.Citations: Wolfenden et al: Wolfenden, R., Andersson, L., Cullis, P.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.Restrain the position of atoms to their initial coordinates.The ROLS Interace defines "Recursive Over Length Scales" (ROLS) Methods.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.The StretchBend class represents a Stretch-Bend formed between three linearly bonded atoms.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.The Torsion class represents a torsional angle formed between four bonded atoms.The TorsionTorsion class represents two adjacent torsional angles formed by five bonded atoms.The UreyBradley class. -
Classes in ffx.potential.bonded used by ffx.potential.cliClassDescriptionThe Atom class represents a single atom and defines its alternate conformations and molecular mechanics atom type.
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Classes in ffx.potential.bonded used by ffx.potential.constraint
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Classes in ffx.potential.bonded used by ffx.potential.extendedClassDescriptionThe Atom class represents a single atom and defines its alternate conformations and molecular mechanics atom type.The Residue class represents individual amino acids or nucleic acid bases.
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Classes in ffx.potential.bonded used by ffx.potential.nonbondedClassDescriptionThe Atom class represents a single atom and defines its alternate conformations and molecular mechanics atom type.The LambdaInterface should be implemented by potential energy terms that can accept a lambda value from [0 .. 1] that defines a twice differentiable path between states 0 and 1.
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Classes in ffx.potential.bonded used by ffx.potential.nonbonded.implicit
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Classes in ffx.potential.bonded used by ffx.potential.nonbonded.pmeClassDescriptionThe Atom class represents a single atom and defines its alternate conformations and molecular mechanics atom type.
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Classes in ffx.potential.bonded used by ffx.potential.openmmClassDescriptionThe Angle class represents an angle formed between three linearly bonded atoms.The Atom class represents a single atom and defines its alternate conformations and molecular mechanics atom type.The LambdaInterface should be implemented by potential energy terms that can accept a lambda value from [0 .. 1] that defines a twice differentiable path between states 0 and 1.
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Classes in ffx.potential.bonded used by ffx.potential.parametersClassDescriptionThe Atom class represents a single atom and defines its alternate conformations and molecular mechanics atom type.The Residue class represents individual amino acids or nucleic acid bases.The Rotamer Class usually represents one immutable amino acid Rotamer.
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Classes in ffx.potential.bonded used by ffx.potential.parsersClassDescriptionThe Atom class represents a single atom and defines its alternate conformations and molecular mechanics atom type.The Bond class represents a covalent bond formed between two atoms.The MSNode class forms the basic unit that all data classes extend.The Residue class represents individual amino acids or nucleic acid bases.
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Classes in ffx.potential.bonded used by ffx.potential.termsClassDescriptionThe Angle class represents an angle formed between three linearly bonded atoms.The AngleTorsion class represents an angle torsion coupling between four bonded atoms.The Bond class represents a covalent bond formed between two atoms.The BondedTerm class is extended by all Valence Geometry classes (bond, angle, dihedral, torsion, etc.).The ImproperTorsion class represents an Improper Torsion.The OutOfPlaneBend class represents an Out-Of-Plane Bend.The Pi-Orbital Torsion class.RestraintDistance class.Restrain the position of atoms to their initial coordinates.The StretchBend class represents a Stretch-Bend formed between three linearly bonded atoms.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.The Torsion class represents a torsional angle formed between four bonded atoms.The TorsionTorsion class represents two adjacent torsional angles formed by five bonded atoms.The UreyBradley class.
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Classes in ffx.potential.bonded used by ffx.potential.utils
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Classes in ffx.potential.bonded used by ffx.realspaceClassDescriptionThe Atom class represents a single atom and defines its alternate conformations and molecular mechanics atom type.The LambdaInterface should be implemented by potential energy terms that can accept a lambda value from [0 .. 1] that defines a twice differentiable path between states 0 and 1.The Molecule class is a general container used for simple compounds or in cases where more specialized classes have not been implemented.The Residue class represents individual amino acids or nucleic acid bases.
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Classes in ffx.potential.bonded used by ffx.uiClassDescriptionThe 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 ROLS Interace defines "Recursive Over Length Scales" (ROLS) Methods.
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Classes in ffx.potential.bonded used by ffx.xrayClassDescriptionThe Atom class represents a single atom and defines its alternate conformations and molecular mechanics atom type.The LambdaInterface should be implemented by potential energy terms that can accept a lambda value from [0 .. 1] that defines a twice differentiable path between states 0 and 1.The Molecule class is a general container used for simple compounds or in cases where more specialized classes have not been implemented.The Residue class represents individual amino acids or nucleic acid bases.