Uses of Class
ffx.potential.parameters.AtomType

Packages that use AtomType

Package	Description
ffx.potential.bonded	The Bonded package implements bonded molecular mechanics terms such as bonds, angles, torsions, etc.
ffx.potential.parameters	The Parameters package stores force field atom types, bond types, etc, and keywords that define the potential.

Uses of AtomType in ffx.potential.bonded

Fields in ffx.potential.bonded declared as AtomType

Modifier and Type	Field	Description
final AtomType	BondedUtils.MissingHeavyAtomException.atomType

Methods in ffx.potential.bonded that return AtomType

Modifier and Type	Method	Description
static AtomType	BondedUtils.findAtomType(int key, ForceField forceField)	findAtomType.
AtomType	Atom.getAtomType()	Getter for the field atomType.

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

Modifier and Type	Method	Description
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.
void	Atom.setAtomType(AtomType atomType)	Setter for the field atomType.

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

Modifier	Constructor	Description
	Atom(int xyzIndex, String name, AtomType atomType, double[] xyz)	Constructor used when parsing XYZ files.
	MissingHeavyAtomException(String atomName, AtomType atomType, Atom bondedTo)

Uses of AtomType in ffx.potential.parameters

Methods in ffx.potential.parameters that return AtomType

Modifier and Type	Method	Description
AtomType	ForceField.getAtomType(String key)	getAtomType
AtomType	ForceField.getAtomType(String moleculeName, String atomName)	getAtomType
static AtomType	AtomType.parse(String input, String[] tokens)	Construct an AtomType from an input string.

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

Modifier and Type	Method	Description
HashMap<String,AtomType>	ForceField.getAtomTypes(String moleculeName)	Getter for the field atomTypes.
List<AtomType>	ForceField.getSimilarAtomTypes(AtomType atomType)	Getter for the field atomTypes.

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

Modifier and Type	Method	Description
AngleType	ForceField.getAngleType(AtomType a1, AtomType a2, AtomType a3)	getAngleType
BondType	ForceField.getBondType(AtomType a1, AtomType a2)	getBondType
OutOfPlaneBendType	ForceField.getOutOfPlaneBendType(AtomType a4, AtomType a0, AtomType a1, AtomType a2)	getOutOfPlaneBendType
PiOrbitalTorsionType	ForceField.getPiOrbitalTorsionType(AtomType a1, AtomType a2)	getPiOrbitalTorsionType
List<AtomType>	ForceField.getSimilarAtomTypes(AtomType atomType)	Getter for the field atomTypes.
StretchBendType	ForceField.getStretchBendType(AtomType a1, AtomType a2, AtomType a3)	getStretchBendType
TorsionType	ForceField.getTorsionType(AtomType a0, AtomType a1, AtomType a2, AtomType a3)	getTorsionType

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

Modifier and Type	Method	Description
AngleTorsionType	AngleTorsionType.patchClasses(HashMap<AtomType,AtomType> typeMap)	Remap new atom classes to known internal ones.
AngleTorsionType	AngleTorsionType.patchClasses(HashMap<AtomType,AtomType> typeMap)	Remap new atom classes to known internal ones.
AngleType	AngleType.patchClasses(HashMap<AtomType,AtomType> typeMap)	Remap new atom classes to known internal ones.
AngleType	AngleType.patchClasses(HashMap<AtomType,AtomType> typeMap)	Remap new atom classes to known internal ones.
BondType	BondType.patchClasses(HashMap<AtomType,AtomType> typeMap)	Remap new atom classes to known internal ones.
BondType	BondType.patchClasses(HashMap<AtomType,AtomType> typeMap)	Remap new atom classes to known internal ones.
void	ImproperTorsionType.patchClasses(HashMap<AtomType,AtomType> typeMap)	Remap new atom classes to known internal ones.
void	ImproperTorsionType.patchClasses(HashMap<AtomType,AtomType> typeMap)	Remap new atom classes to known internal ones.
OutOfPlaneBendType	OutOfPlaneBendType.patchClasses(HashMap<AtomType,AtomType> typeMap)	Remap new atom classes to known internal ones.
OutOfPlaneBendType	OutOfPlaneBendType.patchClasses(HashMap<AtomType,AtomType> typeMap)	Remap new atom classes to known internal ones.
PiOrbitalTorsionType	PiOrbitalTorsionType.patchClasses(HashMap<AtomType,AtomType> typeMap)	Remap new atom classes to known internal ones.
PiOrbitalTorsionType	PiOrbitalTorsionType.patchClasses(HashMap<AtomType,AtomType> typeMap)	Remap new atom classes to known internal ones.
StretchBendType	StretchBendType.patchClasses(HashMap<AtomType,AtomType> typeMap)	Remap new atom classes to known internal ones.
StretchBendType	StretchBendType.patchClasses(HashMap<AtomType,AtomType> typeMap)	Remap new atom classes to known internal ones.
StretchTorsionType	StretchTorsionType.patchClasses(HashMap<AtomType,AtomType> typeMap)	Remap new atom classes to known internal ones.
StretchTorsionType	StretchTorsionType.patchClasses(HashMap<AtomType,AtomType> typeMap)	Remap new atom classes to known internal ones.
void	TorsionTorsionType.patchClasses(HashMap<AtomType,AtomType> typeMap)	Remap new atom classes to known internal ones.
void	TorsionTorsionType.patchClasses(HashMap<AtomType,AtomType> typeMap)	Remap new atom classes to known internal ones.
TorsionType	TorsionType.patchClasses(HashMap<AtomType,AtomType> typeMap)	Remap new atom classes to known internal ones.
TorsionType	TorsionType.patchClasses(HashMap<AtomType,AtomType> typeMap)	Remap new atom classes to known internal ones.
void	UreyBradleyType.patchClasses(HashMap<AtomType,AtomType> typeMap)	Remap new atom classes to known internal ones.
void	UreyBradleyType.patchClasses(HashMap<AtomType,AtomType> typeMap)	Remap new atom classes to known internal ones.