Uses of Class
ffx.potential.bonded.Atom

Packages that use Atom

Package	Description
ffx.algorithms.optimize	The Optimize package contains local and global optimization algorithms using pure Java and OpenMM code paths.
ffx.algorithms.optimize.manybody	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.
ffx.potential	The Potential package implements molecular mechanics force fields with shared memory Parallel Java and via OpenMM.
ffx.potential.bonded	The Bonded package implements bonded molecular mechanics terms such as bonds, angles, torsions, etc.
ffx.potential.cli	The Potential CLI package defines reusable options for PicoCLI command line scripts.
ffx.potential.constraint	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).
ffx.potential.extended	The Extended package is progress toward support for constant pH molecular dynamics using extended system variables (i.e. lambda dynamics on protonation).
ffx.potential.nonbonded	The Nonbonded package implements nonbonded molecular mechanics terms such as van der Waals and Particle Mesh Ewald electrostastics.
ffx.potential.nonbonded.implicit	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.
ffx.potential.nonbonded.pme	The pme package implements polarization and permanent electrostatics using Particle Mesh Ewald (PME).
ffx.potential.openmm	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.
ffx.potential.parameters	The Parameters package stores force field atom types, bond types, etc, and keywords that define the potential.
ffx.potential.parsers	The Parsers package handles reading/writing files to/from the internal data structure.
ffx.potential.utils	The Utils package implements core functionality needed for using the Potential package, such as opening and closing structure files, basic force field energy evaluations, etc.
ffx.xray	The X-ray package implements support for X-ray and Neutron refinement.
ffx.xray.refine
ffx.xray.scatter
ffx.xray.solvent

Uses of Atom in ffx.algorithms.optimize

Methods in ffx.algorithms.optimize that return types with arguments of type Atom

Modifier and Type	Method	Description
Set<Atom>	TitrationManyBody.getExcludeAtoms()

Method parameters in ffx.algorithms.optimize with type arguments of type Atom

Modifier and Type	Method	Description
boolean	TitrationManyBody.excludeExcessAtoms(Set<Atom> excludeAtoms, int[] optimalRotamers, MolecularAssembly molecularAssembly, List<Residue> residueList)
boolean	TitrationManyBody.excludeExcessAtoms(Set<Atom> excludeAtoms, int[] optimalRotamers, List<Residue> residueList)
void	TitrationManyBody.setExcludeAtoms(Set<Atom> excludeAtoms)

Uses of Atom in ffx.algorithms.optimize.manybody

Methods in ffx.algorithms.optimize.manybody with parameters of type Atom

Modifier and Type	Method	Description
boolean	ManyBodyCell.atomInsideCell(Atom atom, Crystal crystal, SymOp symOp)	Checks if an Atom would be contained inside this cell.

Uses of Atom in ffx.potential

Methods in ffx.potential that return Atom

Modifier and Type	Method	Description
Atom	MolecularAssembly.findAtom(Atom atom)	findAtom
Atom	MolecularAssembly.findAtom(Atom atom, boolean matchDeuterium)	findAtom
static Atom	Utilities.findSeed(Atom end, Atom other)	Returns an atom bonded to the "end" atom, which is not equal to "other".
Atom[]	MolecularAssembly.getActiveAtomArray()	getActiveAtomArray
Atom[]	ForceFieldEnergy.getAtomArray()	Get all atoms that make up this ForceFieldEnergy.
Atom[]	MolecularAssembly.getAtomArray()	Return an Array of all atoms in the System.
Atom	MolecularAssembly.getAtomFromWireVertex(int i)	getAtomFromWireVertex
Atom	DualTopologyEnergy.getDualTopologyAtom(int topology, int index)	Get the atom from the dual-topology atom array corresponding to the specified topology and index.
Atom[]	DualTopologyEnergy.getDualTopologyAtoms(int topology)	Get the dual topology atoms for the specified topology.

Methods in ffx.potential that return types with arguments of type Atom

Modifier and Type	Method	Description
List<Atom>	MolecularAssembly.getBackBoneAtoms()	getBackBoneAtoms

Methods in ffx.potential with parameters of type Atom

Modifier and Type	Method	Description
Atom	MolecularAssembly.findAtom(Atom atom)	findAtom
Atom	MolecularAssembly.findAtom(Atom atom, boolean matchDeuterium)	findAtom
static Atom	Utilities.findSeed(Atom end, Atom other)	Returns an atom bonded to the "end" atom, which is not equal to "other".

Method parameters in ffx.potential with type arguments of type Atom

Modifier and Type	Method	Description
static void	Utilities.biochemistry(MolecularAssembly molecularAssembly, List<Atom> atoms)	This routine sub-divides a system into groups of ions, water, hetero molecules, and polynucleotides/polypeptides.

Uses of Atom in ffx.potential.bonded

Fields in ffx.potential.bonded declared as Atom

Modifier and Type	Field	Description
final Atom	BondedUtils.MissingAtomTypeException.atom
protected Atom[]	BondedTerm.atoms	Atoms that are used to form this term.

Fields in ffx.potential.bonded with type parameters of type Atom

Modifier and Type	Field	Description
static Comparator<Atom>	Atom.XYZIndexComparator	Compare two atoms (implementation of the Comparator interface).

Methods in ffx.potential.bonded that return Atom

Modifier and Type	Method	Description
static Atom	BondedUtils.buildH(MSGroup residue, AminoAcidUtils.SideChainType atomName, Atom ia, double bond, Atom ib, double angle1, Atom ic, double angle2, int chiral, ForceField forceField, List<Bond> bondList)	Build a hydrogen atom.
static Atom	BondedUtils.buildH(MSGroup residue, String atomName, Atom ia, double bond, Atom ib, double angle1, Atom ic, double angle2, int chiral, int lookUp, ForceField forceField, List<Bond> bondList)	Build a hydrogen atom.
static Atom	BondedUtils.buildHeavy(MSGroup residue, AminoAcidUtils.SideChainType atomName, Atom ia, double bond, Atom ib, double angle1, Atom ic, double angle2, int chiral, ForceField forceField, List<Bond> bondList)	Build a heavy atom.
static Atom	BondedUtils.buildHeavy(MSGroup residue, String atomName, Atom ia, double bond, Atom ib, double angle1, Atom ic, double angle2, int chiral, int lookUp, ForceField forceField)	Build a heavy atom.
static Atom	BondedUtils.buildHeavy(MSGroup residue, String atomName, Atom ia, double bond, Atom ib, double angle1, Atom ic, double angle2, int chiral, int lookUp, ForceField forceField, List<Bond> bondList)	Build a heavy atom.
static Atom	BondedUtils.buildHeavy(MSGroup residue, String atomName, Atom bondedTo, int key, ForceField forceField, List<Bond> bondList)	Build a heavy atom.
static Atom	BondedUtils.buildHydrogenAtom(MSGroup residue, String atomName, Atom ia, double bond, Atom ib, double angle1, Atom ic, double angle2, int chiral, AtomType atomType, ForceField forceField, List<Bond> bondList)	Build a hydrogen atom.
static Atom	BondedUtils.findNitrogenAtom(Residue residue)	Finds the backbone nitrogen of a residue.
Atom	Bond.get1_2(Atom a)	Find the other Atom in this Bond.
Atom	RestrainDistance.get1_2(Atom a)	Find the other Atom in this Bond.
Atom	Angle.get1_3(Atom a)	If the specified atom is not the central atom of this angle, the atom of the opposite leg is returned.
Atom	AngleTorsion.get1_4(Atom a)	If the specified atom is not a central atom of this torsion, the atom at the opposite end is returned.
Atom	StretchTorsion.get1_4(Atom a)	If the specified atom is not a central atom of this torsion, the atom at the opposite end is returned.
Atom	Torsion.get1_4(Atom a)	If the specified atom is not a central atom of this torsion, the atom at the opposite end is returned.
static Atom	BondedUtils.getAlphaCarbon(Residue residue, Atom N)	Finds the alpha carbon of a residue, and handles any C-terminal ACE caps while at it.
Atom	BondedTerm.getAtom(int index)	Get the constituent Atom specified by index.
Atom	Molecule.getAtom(String name)	getAtom
Atom	RestrainTorsion.getAtom(int index)
Atom	Angle.getAtom4()	Getter for the field atom4.
Atom[]	BondedTerm.getAtomArray()	Returns all Atoms contained in this BondedTerm, regardless of whether they are child nodes in the tree structure.
Atom[]	BondedTerm.getAtomArray(boolean returnCopy)	Returns all Atoms contained in this BondedTerm, regardless of whether they are child nodes in the tree structure.
Atom	MSGroup.getAtomByName(String n, boolean caseInsensitive)	getAtomByName.
Atom	Residue.getAtomInitial()
Atom[]	BondedTerm.getAtoms()	Returns a reference to the Atoms contained in this BondedTerm, regardless of whether they are child nodes in the tree structure.
Atom[]	ResidueState.getAtoms()	Getter for the field atoms.
Atom[]	RestrainPosition.getAtoms()	Returns a copy of the atoms array.
Atom[]	RestrainTorsion.getAtoms()
Atom	Angle.getCentralAtom()	getCentralAtom.
Atom	TorsionTorsion.getChiralAtom()	getChiralAtom.
Atom	MSNode.getFirstActiveHeavyAtom()	Returns the first active heavy atom in the list of atoms for the current structure.
Atom	OutOfPlaneBend.getFirstAngleAtom()	Get the first atom of the Angle.
Atom	OutOfPlaneBend.getFourthAtom()	The atom of this out-of-plane bend that was not part of the Angle.
Atom	Angle.getFourthAtomOfTrigonalCenter()	If the central atom of the angle is trigonal, the 4th member of the trigonal center (that is not a part of the angle) will be returned.
Atom	OutOfPlaneBend.getLastAngleAtom()	Get the first atom of the Angle.
Atom	Residue.getReferenceAtom()	Returns a reference Atom for a Residue, primarily intended for rough distance calculations.
Atom	OutOfPlaneBend.getTrigonalAtom()	Get the trigonal atom of this out-of-plane bend (central atom of the Angle).
static Atom[]	BondedUtils.sortAtomsByDistance(Atom reference, List<Atom> toCompare)	Sorts toCompare by distance to the reference Atom, returning a sorted array.

Methods in ffx.potential.bonded that return types with arguments of type Atom

Modifier and Type	Method	Description
static List<Atom>	BondedUtils.findAtomsOfElement(Residue residue, int element)	Finds all Atoms belonging to a Residue of a given atomic number.
static List<Atom>	BondedUtils.findBondedAtoms(Atom atom, int element)	Finds Atoms bonded to a given Atom that match a certain atomic number.
static List<Atom>	BondedUtils.findBondedAtoms(Atom atom, Atom toExclude, int element)	Finds Atoms bonded to a given Atom that match a certain atomic number that do not match an excluded atom.
static Optional<Atom>	BondedUtils.findNucleotideO4s(Residue residue)	Find the O4' of a nucleic acid Residue.
List<Atom>	Atom.get12List()	Get the list of 1-2 atoms ordered by XYZ index.
List<Atom>	Atom.get13List()	Get the list of 1-3 atoms ordered by XYZ index.
List<Atom>	Atom.get14List()	Get the list of 1-4 atoms ordered by XYZ index.
List<Atom>	Atom.get15List()	Get the list of 1-5 atoms ordered by XYZ index.
List<Atom>	Atom.getAtomList()	Returns a List of all Atoms below the present MSNode.
List<Atom>	MSNode.getAtomList()	Returns a List of all Atoms below the present MSNode.
List<Atom>	MSNode.getAtomList(boolean originalOrder)	getAtomList.
List<Atom>	Residue.getBackboneAtoms()	Returns a list of backbone atoms; for our purposes, nucleic acid backbone atoms are those of the nucleobase.
List<Atom>	MSGroup.getDanglingAtoms()	Returns the MultiScaleGroup's dangling Atoms list.
List<Atom>	MultiResidue.getDanglingAtoms()	Returns the MultiScaleGroup's dangling Atoms list.
List<Atom>	MultiResidue.getSideChainAtoms()	Returns a list of side chain atoms; for our purposes, nucleic acid side chain atoms are the sugar and the phosphate.
List<Atom>	Residue.getSideChainAtoms()	Returns a list of side chain atoms; for our purposes, nucleic acid side chain atoms are the sugar and the phosphate.
List<Atom>	MultiResidue.getVariableAtoms()	Returns a list of atoms liable to change during dead-end elimination repacking.
List<Atom>	Residue.getVariableAtoms()	Returns a list of atoms liable to change during dead-end elimination repacking.
static Optional<Atom>	NamingUtils.renameAlkyl(Atom carbon, Atom priorAtom, int protonOffset, char posName)	Renames an atom, its bonded hydrogen, and returns the next atom in the chain.
static Optional<Atom>	NamingUtils.renameBranchedAlkyl(Atom carbon, Atom priorAtom, int protonOffset, int branchNum, char posName)	Renames a numbered carbon, its bonded hydrogen, and returns the next atom in the chain.
static Map<String,Atom>	NamingUtils.renameCommonPurine(Atom N9, Atom C1s)	Renames atoms common to all standard purines (A, G)
static Map<String,Atom>	NamingUtils.renameCommonPyrimidine(Atom N1, Atom C1s)	Renames atoms common to all standard pyrimidines (C, T, U)

Methods in ffx.potential.bonded with parameters of type Atom

Modifier and Type	Method	Description
static boolean	BondedUtils.atomAttachedToAtom(Atom a1, Atom a2)	Checks if atom a1 is bonded to atom a2.
static Residue	AminoAcidUtils.buildAIB(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildAIB.
static Residue	AminoAcidUtils.buildAlanine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildAlanine.
static Residue	AminoAcidUtils.buildArginine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildArginine.
static Residue	AminoAcidUtils.buildAsparagine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildAsparagine.
static Residue	AminoAcidUtils.buildAspartate(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildAspartate.
static Bond	BondedUtils.buildBond(Atom a1, Atom a2, ForceField forceField, List<Bond> bondList)	Build a bond between two atoms.
static Residue	AminoAcidUtils.buildCysteine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildCysteine.
static Residue	AminoAcidUtils.buildCystine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildCystine.
static Residue	AminoAcidUtils.buildDeprotonatedCysteine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildDeprotonatedCysteine.
static Residue	AminoAcidUtils.buildDeprotonatedLysine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildDeprotonatedLysine.
static Residue	AminoAcidUtils.buildDeprotonatedTyrosine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildDeprotonatedTyrosine.
static Residue	AminoAcidUtils.buildGlutamate(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildGlutamate.
static Residue	AminoAcidUtils.buildGlutamine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildGlutamine.
static Residue	AminoAcidUtils.buildGlycine(Residue res, Atom CA, Atom N, Atom C, AminoAcidUtils.ResiduePosition position, ForceField ff, List<Bond> bonds)	buildGlycine.
static Atom	BondedUtils.buildH(MSGroup residue, AminoAcidUtils.SideChainType atomName, Atom ia, double bond, Atom ib, double angle1, Atom ic, double angle2, int chiral, ForceField forceField, List<Bond> bondList)	Build a hydrogen atom.
static Atom	BondedUtils.buildH(MSGroup residue, String atomName, Atom ia, double bond, Atom ib, double angle1, Atom ic, double angle2, int chiral, int lookUp, ForceField forceField, List<Bond> bondList)	Build a hydrogen atom.
static Atom	BondedUtils.buildHeavy(MSGroup residue, AminoAcidUtils.SideChainType atomName, Atom ia, double bond, Atom ib, double angle1, Atom ic, double angle2, int chiral, ForceField forceField, List<Bond> bondList)	Build a heavy atom.
static Atom	BondedUtils.buildHeavy(MSGroup residue, String atomName, Atom ia, double bond, Atom ib, double angle1, Atom ic, double angle2, int chiral, int lookUp, ForceField forceField)	Build a heavy atom.
static Atom	BondedUtils.buildHeavy(MSGroup residue, String atomName, Atom ia, double bond, Atom ib, double angle1, Atom ic, double angle2, int chiral, int lookUp, ForceField forceField, List<Bond> bondList)	Build a heavy atom.
static Atom	BondedUtils.buildHeavy(MSGroup residue, String atomName, Atom bondedTo, int key, ForceField forceField, List<Bond> bondList)	Build a heavy atom.
static Residue	AminoAcidUtils.buildHistidine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildHistidine.
static Atom	BondedUtils.buildHydrogenAtom(MSGroup residue, String atomName, Atom ia, double bond, Atom ib, double angle1, Atom ic, double angle2, int chiral, AtomType atomType, ForceField forceField, List<Bond> bondList)	Build a hydrogen atom.
static Residue	AminoAcidUtils.buildIsoleucine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildIsoleucine.
static Residue	AminoAcidUtils.buildLeucine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildLeucine.
static Residue	AminoAcidUtils.buildLysine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildLysine.
static Residue	AminoAcidUtils.buildMethionine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bond)	buildMethionine.
static Residue	AminoAcidUtils.buildNeutralAsparticAcid(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildNeutralAsparticAcid.
static Residue	AminoAcidUtils.buildNeutralGlutamicAcid(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildNeutralGlutamicAcid.
static Residue	AminoAcidUtils.buildNeutralHistidineD(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildNeutralHistidineD.
static Residue	AminoAcidUtils.buildNeutralHistidineE(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildNeutralHistidineE.
static Residue	AminoAcidUtils.buildOrnithine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildOrnithine.
static Residue	AminoAcidUtils.buildPCA(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildPCA.
static Residue	AminoAcidUtils.buildPhenylalanine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildPhenylalanine.
static Residue	AminoAcidUtils.buildProline(Residue res, Atom CA, Atom N, Atom C, AminoAcidUtils.ResiduePosition position, ForceField ff, List<Bond> bonds)	buildProline.
static Residue	AminoAcidUtils.buildSerine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildSerine.
static Residue	AminoAcidUtils.buildThreonine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildThreonine.
static Residue	AminoAcidUtils.buildTryptophan(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bond)	buildTryptophan.
static Residue	AminoAcidUtils.buildTwoProtonAsparticAcid(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildTwoProtonAsparticAcid.
static Residue	AminoAcidUtils.buildTwoProtonGlutamicAcid(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildTwoProtonGlutamicAcid.
static Residue	AminoAcidUtils.buildTyrosine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildTyrosine.
static Residue	AminoAcidUtils.buildValine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildValine.
boolean	AngleTorsion.compare(Atom a0, Atom a1, Atom a2, Atom a3)	compare
boolean	StretchTorsion.compare(Atom a0, Atom a1, Atom a2, Atom a3)	compare
boolean	Torsion.compare(Atom a0, Atom a1, Atom a2, Atom a3)	compare
int	Atom.compareTo(Atom a)
static List<Atom>	BondedUtils.findBondedAtoms(Atom atom, int element)	Finds Atoms bonded to a given Atom that match a certain atomic number.
static List<Atom>	BondedUtils.findBondedAtoms(Atom atom, Atom toExclude, int element)	Finds Atoms bonded to a given Atom that match a certain atomic number that do not match an excluded atom.
Atom	Bond.get1_2(Atom a)	Find the other Atom in this Bond.
Atom	RestrainDistance.get1_2(Atom a)	Find the other Atom in this Bond.
Atom	Angle.get1_3(Atom a)	If the specified atom is not the central atom of this angle, the atom of the opposite leg is returned.
Atom	AngleTorsion.get1_4(Atom a)	If the specified atom is not a central atom of this torsion, the atom at the opposite end is returned.
Atom	StretchTorsion.get1_4(Atom a)	If the specified atom is not a central atom of this torsion, the atom at the opposite end is returned.
Atom	Torsion.get1_4(Atom a)	If the specified atom is not a central atom of this torsion, the atom at the opposite end is returned.
static Atom	BondedUtils.getAlphaCarbon(Residue residue, Atom N)	Finds the alpha carbon of a residue, and handles any C-terminal ACE caps while at it.
Angle	Atom.getAngle(Atom centralAtom, Atom endAtom)	getAngle.
Bond	Atom.getBond(Atom a)	getBond
Torsion	Atom.getTorsion(Atom atom2, Atom atom3, Atom atom4)	Finds a Torsion which contains this atom, and atoms 2, 3, and 4.
static boolean	BondedUtils.hasAttachedAtom(Atom atom, int element)	Checks if there is an Atom of a given atomic number bonded to the provided Atom.
static void	BondedUtils.intxyz(Atom atom, Atom ia, double bond, Atom ib, double angle1, Atom ic, double angle2, int chiral)	This routine was derived from a similar routine in TINKER.
boolean	Atom.is_1_3(Atom atom)	is_1_3
boolean	Atom.is_1_4(Atom atom)	Are these atoms 1-4 bonded?
boolean	Atom.is_1_5(Atom atom)	Are these atoms 1-5 bonded?
boolean	Atom.is_1_6(Atom atom)	Are these atoms 1-6 bonded?
boolean	Atom.is_1_7(Atom atom)	Are these atoms 1-7 bonded?
boolean	Atom.is_1_8(Atom atom)	Are these atoms 1-8 bonded?
boolean	Atom.is_12_or_13(Atom a)	is_12_or_13
boolean	Atom.isBonded(Atom a)	Checks to see if an Atom is bonded to this Atom
boolean	Atom.isRing(Atom a2)	Determine if atom is in a ring with second atom WARNING: Does not work for 8+ membered rings...
static void	Angle.logNoAngleType(Atom a1, Atom a2, Atom a3, ForceField forceField)	Log that no AngleType exists.
static void	Bond.logNoBondType(Atom a1, Atom a2, ForceField forceField)	Log that no BondType exists.
static void	Torsion.logNoTorsionType(Atom a0, Atom a1, Atom a2, Atom a3, ForceField forceField)	Log that no TorsionType exists.
static void	NamingUtils.nameAcetylCap(Residue residue, Atom aceC)	Names the atoms in an N-terminal acetyl ACE capping group.
static RestrainPosition	RestrainPosition.parseRestrainPosition(String line, Atom[] atoms, boolean useLambda)	Parse a Restrain-Position line and return a RestrainPosition instance.
static Optional<Atom>	NamingUtils.renameAlkyl(Atom carbon, Atom priorAtom, int protonOffset, char posName)	Renames an atom, its bonded hydrogen, and returns the next atom in the chain.
static Optional<Atom>	NamingUtils.renameBranchedAlkyl(Atom carbon, Atom priorAtom, int protonOffset, int branchNum, char posName)	Renames a numbered carbon, its bonded hydrogen, and returns the next atom in the chain.
static void	NamingUtils.renameCommonAminoAcids(Residue residue, AminoAcidUtils.AminoAcid3 aa3, Atom CA, Atom CB)	Renames atoms in common amino acids to PDB standard.
static void	NamingUtils.renameCommonNucleobase(Atom N19, Atom C1s, NucleicAcidUtils.NucleicAcid3 na3)	Renames the atoms of the common nucleobases (A, C, G, T, U, and deoxy variants).
static Map<String,Atom>	NamingUtils.renameCommonPurine(Atom N9, Atom C1s)	Renames atoms common to all standard purines (A, G)
static Map<String,Atom>	NamingUtils.renameCommonPyrimidine(Atom N1, Atom C1s)	Renames atoms common to all standard pyrimidines (C, T, U)
static void	ResidueState.revertAtomicCoordinates(Atom[] atoms, double[][] coords)	Uses a double[nAtoms][3] to revert the coordinates of an array of atoms.
void	Residue.setAtomInitial(Atom atomInitial)
void	BondedTerm.setAtoms(Atom[] a)	Add a constituent Atom to the Term.
void	Atom.setAxisAtoms(Atom... set)	Setter for the field axisAtoms.
void	Bond.setColor(Atom a)	Set the color of this Bond's Java3D shapes based on the passed Atom.
static void	BondedUtils.sortAtomsByDistance(Atom reference, Atom[] toCompare)	In-place sorts toCompare by distance to the reference Atom.
static Atom[]	BondedUtils.sortAtomsByDistance(Atom reference, List<Atom> toCompare)	Sorts toCompare by distance to the reference Atom, returning a sorted array.
static double[][]	ResidueState.storeAtomicCoordinates(Atom[] atoms)	Returns a new double[nAtoms][3] with the coordinates of an array of atoms.

Method parameters in ffx.potential.bonded with type arguments of type Atom

Modifier and Type	Method	Description
static void	NamingUtils.renameArginineHydrogen(Residue residue, List<Atom> resAtoms)	renameArginineHydrogen.
static void	NamingUtils.renameAsparagineHydrogen(Residue residue, List<Atom> resAtoms)	renameAsparagineHydrogen.
static void	NamingUtils.renameBetaHydrogen(Residue residue, List<Atom> resAtoms, int indexes)	renameBetaHydrogen.
static void	NamingUtils.renameDeltaHydrogen(Residue residue, List<Atom> resAtoms, int indexes)	renameDeltaHydrogen.
static void	NamingUtils.renameEpsilonHydrogen(Residue residue, List<Atom> resAtoms, int indexes)	renameEpsilonHydrogen.
static void	NamingUtils.renameGammaHydrogen(Residue residue, List<Atom> resAtoms, int indexes)	renameGammaHydrogen.
static void	NamingUtils.renameGlutamineHydrogen(Residue residue, List<Atom> resAtoms)	renameGlutamineHydrogen.
static void	NamingUtils.renameGlycineAlphaHydrogen(Residue residue, List<Atom> resAtoms)	renameGlycineAlphaHydrogen.
static void	NamingUtils.renameIsoleucineHydrogen(Residue residue, List<Atom> resAtoms)	renameIsoleucineHydrogen.
static void	NamingUtils.renameZetaHydrogen(Residue residue, List<Atom> resAtoms, int indexes)	renameZetaHydrogen.
void	MSGroup.setDanglingAtoms(List<Atom> a)	Sets the MultiScaleGroup's danglingAtoms member to a.
void	MultiResidue.setDanglingAtoms(List<Atom> a)	Sets the MultiScaleGroup's danglingAtoms member to a.
static Atom[]	BondedUtils.sortAtomsByDistance(Atom reference, List<Atom> toCompare)	Sorts toCompare by distance to the reference Atom, returning a sorted array.

Constructors in ffx.potential.bonded with parameters of type Atom

Modifier	Constructor	Description
	Atom(int xyzIndex, Atom copyFrom, double[] xyz, int resSeq, char chainID, String segID)	Creates a new Atom similar to an existing Atom (e.g. for tiling a solvent box over a solute).
	Bond(Atom a1, Atom a2)	Bond constructor.
	MissingAtomTypeException(Residue residue, Atom atom)
	MissingHeavyAtomException(String atomName, AtomType atomType, Atom bondedTo)
	OutOfPlaneBend(Angle angle, Atom atom)	OutOfPlaneBend constructor.
	RestrainDistance(Atom a1, Atom a2, Crystal crystal, boolean lambdaTerm, double lamStart, double lamEnd, UnivariateSwitchingFunction sf)	Creates a distance restraint between two Atoms.
	RestrainPosition(Atom[] atoms, double[][] equilibriumCoordinates, double forceConst, double flatBottom, boolean lambdaTerm)	Restrain atoms to a position in the global coordinate frame.
	RestrainTorsion(Atom a1, Atom a2, Atom a3, Atom a4, TorsionType torsionType, boolean lambdaEnabled, boolean reverseLambda, double units)	Constructor for RestrainTorsion.

Uses of Atom in ffx.potential.cli

Method parameters in ffx.potential.cli with type arguments of type Atom

Modifier and Type	Method	Description
static void	AtomSelectionOptions.actOnAtoms(MolecularAssembly assembly, String selection, BiConsumer<Atom,Boolean> action, String description)
static void	AtomSelectionOptions.actOnResidueAtoms(MolecularAssembly assembly, String selection, BiConsumer<Atom,Boolean> action, String description)

Uses of Atom in ffx.potential.constraint

Methods in ffx.potential.constraint with parameters of type Atom

Modifier and Type	Method	Description
static CcmaConstraint	CcmaConstraint.ccmaFactory(List<Bond> constrainedBonds, List<Angle> constrainedAngles, Atom[] allAtoms, double[] masses, double nonzeroCutoff)	Constructs a set of bond length Constraints to be satisfied using the Constaint Constraint Matrix Approximation, a parallelizable stable numeric method.

Uses of Atom in ffx.potential.extended

Methods in ffx.potential.extended that return Atom

Modifier and Type	Method	Description
Atom[]	ExtendedSystem.getExtendedAtoms()	All atoms of the fully-protonated system (not just those affected by this system).

Uses of Atom in ffx.potential.nonbonded

Fields in ffx.potential.nonbonded declared as Atom

Modifier and Type	Field	Description
protected Atom[]	ParticleMeshEwald.atoms	An ordered array of atoms in the system.

Methods in ffx.potential.nonbonded with parameters of type Atom

Modifier and Type	Method	Description
double[]	ParticleMeshEwald.computeMoments(Atom[] activeAtoms, boolean forceEnergy)	Compute multipole moments for an array of atoms.
void	GeneralizedKirkwood.setAtoms(Atom[] atoms)	Setter for the field atoms.
void	NeighborList.setAtoms(Atom[] atoms)	The NeighborList will be re-configured, if necessary, for the supplied atom list.
void	ParticleMeshEwald.setAtoms(Atom[] atoms, int[] molecule)
void	ReciprocalSpace.setAtoms(Atom[] atoms)	Setter for the field atoms.
void	RowRegion.setAtoms(Atom[] atoms)	Setter for the field atoms.
void	SliceRegion.setAtoms(Atom[] atoms)	Setter for the field atoms.
void	SpatialDensityRegion.setAtoms(Atom[] atoms)	setAtoms.
void	VanDerWaals.setAtoms(Atom[] atoms, int[] molecule, boolean[] neuralNetwork)	Set the atoms and molecule arrays, and rebuild the neighbor list.
void	VanDerWaalsTornado.setAtoms(Atom[] atoms)	Setter for the field atoms.

Constructors in ffx.potential.nonbonded with parameters of type Atom

Modifier	Constructor	Description
	GeneralizedKirkwood(ForceField forceField, Atom[] atoms, ParticleMeshEwald particleMeshEwald, Crystal crystal, ParallelTeam parallelTeam, double gkCutoff)	Constructor for GeneralizedKirkwood.
	NCSRestraint(Atom[] atoms, ForceField forceField, Crystal crystal)	This NCSRestraint is based on the unit cell parameters and symmetry operators of the supplied crystal.
	NeighborList(Crystal crystal, Atom[] atoms, double cutoff, double buffer, ParallelTeam parallelTeam)	Constructor for the NeighborList class.
	ParticleMeshEwald(Atom[] atoms, int[] molecule, ForceField forceField, Crystal crystal, NeighborList neighborList, ForceField.ELEC_FORM elecForm, double ewaldCutoff, double gkCutoff, ParallelTeam parallelTeam)	ParticleMeshEwald constructor.
	ReciprocalSpace(ParticleMeshEwald particleMeshEwald, Crystal crystal, ForceField forceField, Atom[] atoms, double aewald, ParallelTeam fftTeam, ParallelTeam parallelTeam)	Reciprocal Space PME contribution.
	RowRegion(int gX, int gY, int gZ, double[] grid, int nSymm, int threadCount, Atom[] atoms, double[][][] coordinates)	Constructor for RowRegion.
	SliceRegion(int gX, int gY, int gZ, double[] grid, int nSymm, int threadCount, Atom[] atoms, double[][][] coordinates)	Constructor for SliceRegion.
	SpatialDensityRegion(int gX, int gY, int gZ, double[] grid, int basisSize, int nSymm, int minWork, int threadCount, Crystal crystal, Atom[] atoms, double[][][] coordinates)	Constructor for SpatialDensityRegion.
	VanDerWaals(Atom[] atoms, int[] molecule, boolean[] neuralNetwork, Crystal crystal, ForceField forceField, ParallelTeam parallelTeam, double vdwCutoff, double neighborListCutoff)	The VanDerWaals class constructor.
	VanDerWaalsTornado(Atom[] atoms, Crystal crystal, ForceField forceField, double vdwCutoff)	The VanDerWaalsTornado class constructor.

Uses of Atom in ffx.potential.nonbonded.implicit

Fields in ffx.potential.nonbonded.implicit declared as Atom

Modifier and Type	Field	Description
protected Atom[]	BornGradRegion.atoms	An ordered array of atoms in the system.
protected Atom[]	BornRadiiRegion.atoms	An ordered array of atoms in the system.
protected Atom[]	DispersionRegion.atoms	An ordered array of atoms in the system.
protected Atom[]	InducedGKFieldRegion.atoms	An ordered array of atoms in the system.
protected Atom[]	PermanentGKFieldRegion.atoms	An ordered array of atoms in the system.

Methods in ffx.potential.nonbonded.implicit with parameters of type Atom

Modifier and Type	Method	Description
void	DispersionRegion.allocate(Atom[] atoms)	Allocate storage given the Atom array.
void	GaussVol.allocate(Atom[] atoms)
void	BornGradRegion.init(Atom[] atoms, Crystal crystal, double[][][] sXYZ, int[][][] neighborLists, double[] baseRadius, double[] descreenRadius, double[] overlapScale, double[] neckScale, double descreenOffset, double[] unscaledBornIntegral, boolean[] use, double cut2, boolean nativeEnvironmentApproximation, double[] born, AtomicDoubleArray3D grad, AtomicDoubleArray sharedBornGrad)
void	BornRadiiRegion.init(Atom[] atoms, Crystal crystal, double[][][] sXYZ, int[][][] neighborLists, double[] baseRadius, double[] descreenRadius, double[] overlapScale, double[] neckScale, double descreenOffset, boolean[] use, double cut2, boolean nativeEnvironmentApproximation, double[] born)
void	ConnollyRegion.init(Atom[] atoms, boolean gradient)	Initialize this VolumeRegion instance for an energy evaluation.
void	DispersionRegion.init(Atom[] atoms, Crystal crystal, boolean[] use, int[][][] neighborLists, double[] x, double[] y, double[] z, double cut2, boolean gradient, AtomicDoubleArray3D grad)	Initialize the DispersionRegion for energy calculation.
void	GKEnergyRegion.init(Atom[] atoms, double[][][] globalMultipole, double[][][] inducedDipole, double[][][] inducedDipoleCR, Crystal crystal, double[][][] sXYZ, int[][][] neighborLists, boolean[] use, double cut2, double[] baseRadius, double[] born, boolean gradient, ParallelTeam parallelTeam, AtomicDoubleArray3D grad, AtomicDoubleArray3D torque, AtomicDoubleArray sharedBornGrad)
void	InducedGKFieldRegion.init(Atom[] atoms, double[][][] inducedDipole, double[][][] inducedDipoleCR, Crystal crystal, double[][][] sXYZ, int[][][] neighborLists, boolean[] use, double cut2, double[] born, AtomicDoubleArray3D sharedGKField, AtomicDoubleArray3D sharedGKFieldCR)
void	InitializationRegion.init(GeneralizedKirkwood generalizedKirkwood, Atom[] atoms, boolean lambdaTerm, AtomicDoubleArray3D grad, AtomicDoubleArray3D torque, AtomicDoubleArray sharedBornGrad)
void	PermanentGKFieldRegion.init(Atom[] atoms, double[][][] globalMultipole, Crystal crystal, double[][][] sXYZ, int[][][] neighborLists, boolean[] use, double cut2, double[] born, AtomicDoubleArray3D sharedGKField)

Constructors in ffx.potential.nonbonded.implicit with parameters of type Atom

Modifier	Constructor	Description
	ChandlerCavitation(Atom[] atoms, ConnollyRegion connollyRegion, ForceField forceField)
	ChandlerCavitation(Atom[] atoms, GaussVol gaussVol, ForceField forceField)
	ConnollyRegion(Atom[] atoms, double[] baseRadius, int nThreads)	ConnollyRegion constructor.
	DispersionRegion(int nt, Atom[] atoms, ForceField forceField)	DispersionRegion constructor.
	GaussVol(Atom[] atoms, ForceField forceField, ParallelTeam parallelTeam)	Creates/Initializes a GaussVol instance.
	HydrophobicPMFRegion(Atom[] atoms, double[] x, double[] y, double[] z, boolean[] use, double[][][] grad, int nt)
	SurfaceAreaRegion(Atom[] atoms, double[] x, double[] y, double[] z, boolean[] use, int[][][] neighborLists, AtomicDoubleArray3D grad, int nt, double probe, double surfaceTension)	This class is a port of the Cavitation code in TINKER.

Uses of Atom in ffx.potential.nonbonded.pme

Methods in ffx.potential.nonbonded.pme with parameters of type Atom

Modifier and Type	Method	Description
void	DirectRegion.init(Atom[] atoms, double[] polarizability, double[][][] globalMultipole, double[][] cartMultipolePhi, AtomicDoubleArray3D field, AtomicDoubleArray3D fieldCR, boolean generalizedKirkwoodTerm, GeneralizedKirkwood generalizedKirkwood, EwaldParameters ewaldParameters, double soluteDielectric, double[][][] inducedDipole, double[][][] inducedDipoleCR, double[][] directDipole, double[][] directDipoleCR, double[][] directField, double[][] directFieldCR)
void	ExpandInducedDipolesRegion.init(Atom[] atoms, Crystal crystal, double[][][] inducedDipole, double[][][] inducedDipoleCR)
void	InducedDipoleFieldReduceRegion.init(Atom[] atoms, double[][][] inducedDipole, double[][][] inducedDipoleCR, boolean generalizedKirkwoodTerm, GeneralizedKirkwood generalizedKirkwood, EwaldParameters ewaldParameters, double soluteDielectric, double[][] cartesianDipolePhi, double[][] cartesianDipolePhiCR, AtomicDoubleArray3D field, AtomicDoubleArray3D fieldCR)
void	InducedDipoleFieldRegion.init(Atom[] atoms, Crystal crystal, boolean[] use, int[] molecule, double[] ipdamp, double[] thole, double[][][] coordinates, RealSpaceNeighborParameters realSpaceNeighborParameters, double[][][] inducedDipole, double[][][] inducedDipoleCR, boolean reciprocalSpaceTerm, ReciprocalSpace reciprocalSpace, LambdaMode lambdaMode, EwaldParameters ewaldParameters, AtomicDoubleArray3D field, AtomicDoubleArray3D fieldCR, PMETimings pmeTimings)
void	InitializationRegion.init(boolean lambdaTerm, AlchemicalParameters alchemicalParameters, ExtendedSystem esvSystem, Atom[] atoms, double[][][] coordinates, Crystal crystal, MultipoleType.MultipoleFrameDefinition[] frame, int[][] axisAtom, double[][][] globalMultipole, double[][][] titrationMultipole, double[][][] tautomerMultipole, double[] polarizability, double[] titrationPolarizability, double[] tautomerPolarizability, double[] thole, double[] ipdamp, boolean[] use, int[][][] neighborLists, int[][][] realSpaceLists, AtomicDoubleArray3D grad, AtomicDoubleArray3D torque, AtomicDoubleArray3D lambdaGrad, AtomicDoubleArray3D lambdaTorque)
void	OPTRegion.init(int currentOptOrder, Atom[] atoms, double[] polarizability, double[][][] inducedDipole, double[][][] inducedDipoleCR, double[][] cartesianDipolePhi, double[][] cartesianDipolePhiCR, AtomicDoubleArray3D field, AtomicDoubleArray3D fieldCR, boolean generalizedKirkwoodTerm, GeneralizedKirkwood generalizedKirkwood, EwaldParameters ewaldParameters, double dielectric)
void	PCGSolver.init(Atom[] atoms, double[][][] coordinates, double[] polarizability, double[] ipdamp, double[] thole, boolean[] use, Crystal crystal, double[][][] inducedDipole, double[][][] inducedDipoleCR, double[][] directDipole, double[][] directDipoleCR, AtomicDoubleArray3D field, AtomicDoubleArray3D fieldCR, EwaldParameters ewaldParameters, double dieletric, ParallelTeam parallelTeam, IntegerSchedule realSpaceSchedule, PMETimings pmeTimings)
void	PermanentFieldRegion.init(Atom[] atoms, Crystal crystal, double[][][] coordinates, double[][][] globalMultipole, double[][][] inducedDipole, double[][][] inducedDipoleCR, int[][][] neighborLists, ScaleParameters scaleParameters, boolean[] use, int[] molecule, double[] ipdamp, double[] thole, int[][] ip11, int[][] mask12, int[][] mask13, int[][] mask14, LambdaMode lambdaMode, boolean reciprocalSpaceTerm, ReciprocalSpace reciprocalSpace, EwaldParameters ewaldParameters, PCGSolver pcgSolver, IntegerSchedule permanentSchedule, RealSpaceNeighborParameters realSpaceNeighborParameters, AtomicDoubleArray3D field, AtomicDoubleArray3D fieldCR)
void	PolarizationEnergyRegion.init(Atom[] atoms, double[] polarizability, double[][][] inducedDipole, double[][] directDipoleCR, double polarizationScale)
void	RealSpaceEnergyRegion.init(Atom[] atoms, Crystal crystal, ExtendedSystem extendedSystem, boolean esvTerm, double[][][] coordinates, MultipoleType.MultipoleFrameDefinition[] frame, int[][] axisAtom, double[][][] globalMultipole, double[][][] titrationMultipole, double[][][] tautomerMultipole, double[][][] inducedDipole, double[][][] inducedDipoleCR, boolean[] use, int[] molecule, int[][] ip11, int[][] mask12, int[][] mask13, int[][] mask14, int[][] mask15, boolean[] isSoft, double[] ipdamp, double[] thole, RealSpaceNeighborParameters realSpaceNeighborParameters, boolean gradient, boolean lambdaTerm, boolean nnTerm, LambdaMode lambdaMode, Polarization polarization, EwaldParameters ewaldParameters, ScaleParameters scaleParameters, AlchemicalParameters alchemicalParameters, long[] realSpaceEnergyTime, AtomicDoubleArray3D grad, AtomicDoubleArray3D torque, AtomicDoubleArray3D lambdaGrad, AtomicDoubleArray3D lambdaTorque, SharedDouble shareddEdLambda, SharedDouble sharedd2EdLambda2)
void	ReciprocalEnergyRegion.init(Atom[] atoms, Crystal crystal, boolean gradient, boolean lambdaTerm, boolean esvTerm, boolean[] use, double[][][] globalMultipole, double[][][] globalFracMultipole, double[][][] titrationMultipole, double[][][] tautomerMultipole, double[][] cartMultipolePhi, double[][] fracMultipolePhi, Polarization polarization, double[][][] inducedDipole, double[][][] inducedDipoleCR, double[][] cartesianDipolePhi, double[][] cartesianDipolePhiCR, double[][] fracInducedDipolePhi, double[][] fracInducedDipolePhiCR, ReciprocalSpace reciprocalSpace, AlchemicalParameters alchemicalParameters, ExtendedSystem extendedSystem, AtomicDoubleArray3D grad, AtomicDoubleArray3D torque, AtomicDoubleArray3D lambdaGrad, AtomicDoubleArray3D lambdaTorque, SharedDouble shareddEdLambda, SharedDouble sharedd2EdLambda2)
void	ReduceRegion.init(boolean lambdaTerm, boolean gradient, Atom[] atoms, double[][][] coordinates, MultipoleType.MultipoleFrameDefinition[] frame, int[][] axisAtom, AtomicDoubleArray3D grad, AtomicDoubleArray3D torque, AtomicDoubleArray3D lambdaGrad, AtomicDoubleArray3D lambdaTorque)
void	SORRegion.init(Atom[] atoms, double[] polarizability, double[][][] inducedDipole, double[][][] inducedDipoleCR, double[][] directDipole, double[][] directDipoleCR, double[][] cartesianDipolePhi, double[][] cartesianDipolePhiCR, AtomicDoubleArray3D field, AtomicDoubleArray3D fieldCR, boolean generalizedKirkwoodTerm, GeneralizedKirkwood generalizedKirkwood, EwaldParameters ewaldParameters)

Uses of Atom in ffx.potential.openmm

Fields in ffx.potential.openmm declared as Atom

Modifier and Type	Field	Description
protected Atom[]	OpenMMSystem.atoms	Array of atoms in the system.

Methods in ffx.potential.openmm that return Atom

Modifier and Type	Method	Description
Atom[]	OpenMMSystem.getAtoms()	Get the atoms in the system.

Methods in ffx.potential.openmm with parameters of type Atom

Modifier and Type	Method	Description
double[]	OpenMMState.getAccelerations(double[] a, Atom[] atoms)	The acceleration array will contain the acceleration information for all atoms.
double[]	OpenMMState.getActiveAccelerations(double[] a, Atom[] atoms)	The acceleration array will contain the acceleration information for all atoms.
double[]	OpenMMState.getActiveGradient(double[] g, Atom[] atoms)	The force array contains the OpenMM force information for active atoms.
double[]	OpenMMState.getActivePositions(double[] x, Atom[] atoms)	The position array contains the OpenMM atomic position information for active atoms.
double[]	OpenMMState.getActiveVelocities(double[] v, Atom[] atoms)	The velocity array contains the OpenMM atomic position information for active atoms.
void	AmoebaGeneralizedKirkwoodForce.updateForce(Atom[] atoms, OpenMMEnergy openMMEnergy)	Update the force.
void	AmoebaGKCavitationForce.updateForce(Atom[] atoms, OpenMMEnergy openMMEnergy)	Update the Cavitation force.
void	AmoebaMultipoleForce.updateForce(Atom[] atoms, int topology, OpenMMDualTopologyEnergy openMMDualTopologyEnergy)	Update the force parameters for the AMOEBA Multipole Force in a dual topology system.
void	AmoebaMultipoleForce.updateForce(Atom[] atoms, OpenMMEnergy openMMEnergy)	Update the force parameters for the AMOEBA Multipole Force.
void	AmoebaVdwForce.updateForce(Atom[] atoms, int topology, OpenMMDualTopologyEnergy openMMDualTopologyEnergy)	Update the vdW force.
void	AmoebaVdwForce.updateForce(Atom[] atoms, OpenMMEnergy openMMEnergy)	Update the vdW force.
void	AmoebaWcaDispersionForce.updateForce(Atom[] atoms, OpenMMEnergy openMMEnergy)	Update the WCA force.
void	FixedChargeGBForce.updateForce(Atom[] atoms, OpenMMEnergy openMMEnergy)	Update the GB force.
void	FixedChargeNonbondedForce.updateForce(Atom[] atoms, OpenMMEnergy openMMEnergy)	Update an existing non-bonded force for the OpenMM System.
void	OpenMMDualTopologyEnergy.updateParameters(Atom[] atoms)	Update parameters if the Use flags and/or Lambda value has changed.
void	OpenMMDualTopologySystem.updateParameters(Atom[] atoms)	Update parameters if the Use flags and/or Lambda value has changed.
void	OpenMMEnergy.updateParameters(Atom[] atoms)	Update parameters if the Use flags and/or Lambda value has changed.
void	OpenMMPotential.updateParameters(Atom[] atoms)	Update parameters if the Use flags and/or Lambda value has changed.
void	OpenMMSystem.updateParameters(Atom[] atoms)	Update parameters if the Use flags and/or Lambda value has changed.

Constructors in ffx.potential.openmm with parameters of type Atom

Modifier	Constructor	Description
	OpenMMContext(Platform platform, OpenMMSystem openMMSystem, Atom[] atoms)	Create an OpenMM Context for a single topology OpenMM system.

Uses of Atom in ffx.potential.parameters

Methods in ffx.potential.parameters with parameters of type Atom

Modifier and Type	Method	Description
static void	MultipoleType.assignAxisAtoms(Atom atom)	Assign local multipole frame defining atoms.
static boolean	MultipoleType.assignMultipole(ForceField.ELEC_FORM elecForm, Atom atom, ForceField forceField, double[] multipole, int i, int[][] axisAtom, MultipoleType.MultipoleFrameDefinition[] frame)	Assign the multipole type.
static void	PolarizeType.assignPolarizationGroups(Atom[] atoms, int[][] ip11, int[][] ip12, int[][] ip13)	Assign polarization groups to atoms based on their connectivity.
double[]	TitrationUtils.getMultipole(Atom atom, double titrationLambda, double tautomerLambda, double[] multipole)
double[]	TitrationUtils.getMultipoleTautomerDeriv(Atom atom, double titrationLambda, double tautomerLambda, double[] multipole)
double[]	TitrationUtils.getMultipoleTitrationDeriv(Atom atom, double titrationLambda, double tautomerLambda, double[] multipole)
double	TitrationUtils.getPolarizability(Atom atom, double titrationLambda, double tautomerLambda, double defaultPolarizability)
double	TitrationUtils.getPolarizabilityTautomerDeriv(Atom atom, double titrationLambda, double tautomerLambda)
double	TitrationUtils.getPolarizabilityTitrationDeriv(Atom atom, double titrationLambda, double tautomerLambda)
static SoluteType	SoluteType.getSoluteType(Atom atom, ForceField forceField, SoluteType.SOLUTE_RADII_TYPE soluteRadiiType)
static int	TitrationUtils.getTitratingHydrogenDirection(AminoAcidUtils.AminoAcid3 aminoAcid3, Atom atom)
static void	PolarizeType.growGroup(List<Integer> group, Atom seed)	A recursive method that checks all atoms bonded to the seed atom for inclusion in the polarization group.
static boolean	TitrationUtils.isTitratingHeavy(AminoAcidUtils.AminoAcid3 aminoAcid3, Atom atom)	Used to keep track of heavy atoms with changing polarizability.
static boolean	TitrationUtils.isTitratingHydrogen(AminoAcidUtils.AminoAcid3 aminoAcid3, Atom atom)
static MultipoleType	MultipoleType.multipoleTypeFactory(ForceField.ELEC_FORM elecForm, Atom atom, ForceField forceField)	multipoleTypeFactory.
static void	SoluteType.setSoluteRadii(ForceField forceField, Atom[] atoms, SoluteType.SOLUTE_RADII_TYPE soluteRadiiType)

Uses of Atom in ffx.potential.parsers

Fields in ffx.potential.parsers with type parameters of type Atom

Modifier and Type	Field	Description
protected List<Atom>	SystemFilter.atomList	The atomList is filled by filters that extend SystemFilter.

Methods in ffx.potential.parsers that return types with arguments of type Atom

Modifier and Type	Method	Description
static Set<Atom>	SystemFilter.atomListToSet(List<Integer> atomList, Atom[] atoms)	Converts a list of atom indices to an array of atoms.
List<Atom>	SystemFilter.getAtomList()	Getter for the field atomList.

Methods in ffx.potential.parsers with parameters of type Atom

Modifier and Type	Method	Description
void	PDBFilter.Mutation.addTors(Atom atom, int index)
static Set<Atom>	SystemFilter.atomListToSet(List<Integer> atomList, Atom[] atoms)	Converts a list of atom indices to an array of atoms.
static int	CIFFilter.bondAtoms(Atom[] atoms, double bondTolerance)	Add bonds between atoms.
static void	CIFFilter.collectAtoms(Atom seed, ArrayList<Atom> atoms)	Finds all atoms that are bonded to one another.
static String	CIFFilter.getAtomElement(Atom atom)	Parse atom name to determine atomic element.
static String	PDBFilter.toPDBAtomLine(Atom atom)	Simple method useful for converting files to PDB format.

Method parameters in ffx.potential.parsers with type arguments of type Atom

Modifier and Type	Method	Description
static void	CIFFilter.collectAtoms(Atom seed, ArrayList<Atom> atoms)	Finds all atoms that are bonded to one another.
boolean	PDBFilter.writeFile(File saveFile, boolean append, Set<Atom> toExclude, boolean writeEnd, boolean versioning)	writeFile
boolean	PDBFilter.writeFile(File saveFile, boolean append, Set<Atom> toExclude, boolean writeEnd, boolean versioning, String[] extraLines)	writeFile

Constructor parameters in ffx.potential.parsers with type arguments of type Atom

Modifier	Constructor	Description
	MergeFilter(MolecularAssembly f, ArrayList<Atom> a, ArrayList<Bond> b)	Constructor for MergeFilter.

Uses of Atom in ffx.potential.utils

Methods in ffx.potential.utils that return Atom

Modifier and Type	Method	Description
static Atom[]	ConvexHullOps.identifyHullAtoms(QuickHull3D quickHull3D, Atom[] allAtoms)	UNTESTED: Identifies atoms forming the convex hull.

Methods in ffx.potential.utils with parameters of type Atom

Modifier and Type	Method	Description
static QuickHull3D	ConvexHullOps.constructHull(Atom[] atoms)	Constructs a convex hull from a set of atoms.
static Atom[]	ConvexHullOps.identifyHullAtoms(QuickHull3D quickHull3D, Atom[] allAtoms)	UNTESTED: Identifies atoms forming the convex hull.
static double	ConvexHullOps.maxDist(Atom[] atoms)	Maximum pairwise distance between atoms in an array.
static double[][]	StructureMetrics.momentsOfInertia(Atom[] atoms, boolean moved, boolean print, boolean pma)	Compute the moments of inertia for all atoms in the supplied array.
static double	StructureMetrics.radiusOfGyration(Atom[] atoms)	Compute the radius of gyration for all atoms in the supplied array.
static double[]	StructureMetrics.radiusOfGyrationComponents(Atom[] atoms)	Compute the radius of gyration for all atoms in the supplied array.

Uses of Atom in ffx.xray

Method parameters in ffx.xray with type arguments of type Atom

Modifier and Type	Method	Description
void	DiffractionData.writeModel(String filename, Set<Atom> excludeAtoms, double pH)	Write current model to PDB file.

Constructors in ffx.xray with parameters of type Atom

Modifier	Constructor	Description
	CrystalReciprocalSpace(ReflectionList reflectionList, Atom[] scatteringAtoms, ParallelTeam fftTeam, ParallelTeam parallelTeam)	Crystal Reciprocal Space constructor, assumes this is not a bulk solvent mask and is not a neutron data set
	CrystalReciprocalSpace(ReflectionList reflectionList, Atom[] scatteringAtoms, ParallelTeam fftTeam, ParallelTeam parallelTeam, boolean solventMask)	Crystal Reciprocal Space constructor, assumes this is not a neutron data set and implements a polynomial bulk solvent mask if needed
	CrystalReciprocalSpace(ReflectionList reflectionlist, Atom[] scatteringAtoms, ParallelTeam fftTeam, ParallelTeam parallelTeam, boolean solventMask, boolean neutron, SolventModel solventModel, GridMethod gridMethod)	Crystal Reciprocal Space constructor, all parameters provided

Uses of Atom in ffx.xray.refine

Fields in ffx.xray.refine declared as Atom

Modifier and Type	Field	Description
protected final Atom	RefinedParameter.atom	The primary Atom that serves as the central reference in a refinement process.

Fields in ffx.xray.refine with type parameters of type Atom

Modifier and Type	Field	Description
protected final List<Atom>	RefinedOccupancy.complementList	A collection of atoms that are constrained in relation to a primary Atom.
protected final List<Atom>	RefinedOccupancy.complementScatterList	A collection of Atom instances that are both constrained with respect to a primary Atom and directly contribute to experimental scattering.
protected final List<Atom>	RefinedParameter.constrainedAtoms	A collection of atoms that are constrained in relation to a primary Atom.
protected final List<Atom>	RefinedParameter.constrainedAtomsThatScatter	A collection of Atom instances that are both constrained with respect to a primary Atom and directly contribute to experimental scattering.

Methods in ffx.xray.refine that return Atom

Modifier and Type	Method	Description
Atom[]	RefinementModel.getActiveAtoms()	Getter for the field activeAtomArray.
Atom[]	RefinementModel.getScatteringAtoms()	Getter for the field totalAtomArray.

Methods in ffx.xray.refine with parameters of type Atom

Modifier and Type	Method	Description
void	RefinedBFactor.addConstrainedAtom(Atom atom)	Adds the specified atom to the list of constrained atoms while applying specific constraints.
void	RefinedCoordinates.addConstrainedAtom(Atom atom)
void	RefinedOccupancy.addConstrainedAtom(Atom atom)
abstract void	RefinedParameter.addConstrainedAtom(Atom atom)	Adds an atom to the list of constrained atoms for the given primary atom.
void	RefinedOccupancy.addConstrainedAtomComplement(Atom atom)	Adds an atom constrained to this RefinedOccupancy instance.
void	RefinedBFactor.addConstrainedAtomThatScatters(Atom atom)	Adds the given atom to the list of constrained atoms that scatter in structural models.
void	RefinedCoordinates.addConstrainedAtomThatScatters(Atom atom)
void	RefinedOccupancy.addConstrainedAtomThatScatters(Atom atom)
abstract void	RefinedParameter.addConstrainedAtomThatScatters(Atom atom)	Adds an atom to the list of constrained atoms that contribute to experimental scattering.
void	RefinedOccupancy.addConstrainedAtomThatScattersComplement(Atom atom)	Adds an atom constrained to this RefinedOccupancy instance as a complementary, scattering atom.

Constructors in ffx.xray.refine with parameters of type Atom

Modifier	Constructor	Description
	RefinedBFactor(Atom atom)	Constructor for the RefinableBfactor class.
	RefinedCoordinates(Atom atom)	Constructs a new RefinableCoordinates instance for the specified atom.
	RefinedOccupancy(Atom atom)	Constructs a RefinableOccupancy instance for managing the specified atom.
	RefinedParameter(Atom atom)	Constructs a new RefinedParameters object for the specified primary Atom.

Uses of Atom in ffx.xray.scatter

Constructors in ffx.xray.scatter with parameters of type Atom

Modifier	Constructor	Description
	NeutronFormFactor(Atom atom)	Constructor for NeutronFormFactor.
	NeutronFormFactor(Atom atom, double badd)	Constructor for NeutronFormFactor.
	NeutronFormFactor(Atom atom, double badd, double[] xyz)	Constructor for NeutronFormFactor.
	SolventBinaryFormFactor(Atom atom, double probeRad)	Constructor for SolventBinaryFormFactor.
	SolventBinaryFormFactor(Atom atom, double probeRad, double[] xyz)	Constructor for SolventBinaryFormFactor.
	SolventGaussFormFactor(Atom atom, double sd)	Constructor for SolventGaussFormFactor.
	SolventGaussFormFactor(Atom atom, double sd, double[] xyz)	Constructor for SolventGaussFormFactor.
	SolventPolyFormFactor(Atom atom, double arad, double w)	Constructor for SolventPolyFormFactor.
	SolventPolyFormFactor(Atom atom, double arad, double w, double[] xyz)	Constructor for SolventPolyFormFactor.
	XRayFormFactor(Atom atom)	Constructor for XRayFormFactor.
	XRayFormFactor(Atom atom, boolean use3G)	Constructor for XRayFormFactor.
	XRayFormFactor(Atom atom, boolean use3G, double badd)	Constructor for XRayFormFactor.
	XRayFormFactor(Atom atom, boolean use3G, double badd, double[] xyz)	Constructor for XRayFormFactor.

Uses of Atom in ffx.xray.solvent

Constructors in ffx.xray.solvent with parameters of type Atom

Modifier	Constructor	Description
	BulkSolventDensityRegion(int gX, int gY, int gZ, double[] grid, int basisSize, int nSymm, int minWork, int threadCount, Crystal crystal, Atom[] atoms, double[][][] coordinates, double cutoff, ParallelTeam parallelTeam)	Constructor for BulkSolventDensityRegion.
	BulkSolventList(Crystal crystal, Atom[] atoms, double cutoff, ParallelTeam parallelTeam)	Constructor for the NeighborList class.
	BulkSolventRowRegion(int gX, int gY, int gZ, double[] grid, int nSymm, int threadCount, Crystal crystal, Atom[] atoms, double[][][] coordinates, double cutoff, ParallelTeam parallelTeam)	Constructor for BulkSolventDensityRegion.
	BulkSolventSliceRegion(int gX, int gY, int gZ, double[] grid, int nSymm, int threadCount, Crystal crystal, Atom[] atoms, double[][][] coordinates, double cutoff, ParallelTeam parallelTeam)	Constructor for BulkSolventDensityRegion.