Uses of Package
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 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 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 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 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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ClassDescriptionThe 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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ClassDescriptionThe Residue class represents individual amino acids or nucleic acid bases.
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ClassDescriptionThe 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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ClassDescriptionThe 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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ClassDescriptionThe 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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ClassDescriptionThe 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.The Bond class represents a covalent bond formed between two atoms.The ImproperTorsion class represents an Improper Torsion.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 OutOfPlaneBend class represents an Out-Of-Plane Bend.The Pi-Orbital Torsion class.The Polymer class encapsulates a peptide or nucleotide chain.The Residue class represents individual amino acids or nucleic acid bases.RestraintDistance class.The ROLS Interace defines "Recursive Over Length Scales" (ROLS) Methods.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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ClassDescriptionThe 20 standard amino acids.Constant
AIB
ConstantALA
Single letter amino acid codes (need toConstantAminoAcidBackboneAtoms
ConstantARG
ConstantASD
ConstantASH
ConstantASN
ConstantASP
ConstantCYD
ConstantCYS
ConstantCYS
ConstantGLD
ConstantGLH
ConstantGlutamineAtomNames
ConstantGLU
ConstantGLY
ConstantGlycineBackboneAtoms
ConstantHID
ConstantHIE
ConstantHistidineAtoms
ConstantILE
ConstantLEU
ConstantLYD
ConstantLYS
ConstantMethionineAtomNames
ConstantORN
ConstantPCA
ConstantPHE
ConstantPRO
ConstantProlineBackboneAtoms
The location of a residue within a chain.ConstantSER
This interface is used by the "Build" routines.ConstantTHR
ConstantTRP
ConstantTYD
ConstantTYR
ConstantVAL
The 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.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. -
ClassDescriptionThe Atom class represents a single atom and defines its alternate conformations and molecular mechanics atom type.
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ClassDescriptionThe 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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ClassDescriptionThe Atom class represents a single atom and defines its alternate conformations and molecular mechanics atom type.The BondedEnergy interface.The BondedTerm class is extended by all Valence Geometry classes (bond, angle, dihedral, torsion, etc.).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 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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ClassDescriptionThe Atom class represents a single atom and defines its alternate conformations and molecular mechanics atom type.
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ClassDescriptionThe 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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ClassDescriptionThe 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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ClassDescriptionThe 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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ClassDescriptionThe 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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ClassDescriptionThe 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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ClassDescriptionThe 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.