Uses of Class
pl.poznan.put.atom.AtomName

Packages that use AtomName

Package	Description
pl.poznan.put.atom	Collection of utility classes to work with atom types, names and atomic bonds.
pl.poznan.put.pdb	Contains classes responsible for PDB/mmCIF data modelling and analysis.
pl.poznan.put.pdb.analysis	Contains classes which work on data from PDB or mmCIF files.
pl.poznan.put.protein
pl.poznan.put.rna
pl.poznan.put.torsion	Contains classes dealing with torsion angles handling.

Uses of AtomName in pl.poznan.put.atom

Methods in pl.poznan.put.atom that return AtomName

Modifier and Type	Method	Description
static AtomName	AtomName.fromString(String pdbName)	Creates an instance from String.
static AtomName	AtomName.valueOf(String name)	Returns the enum constant of this type with the specified name.
static AtomName[]	AtomName.values()	Returns an array containing the constants of this enum type, in the order they are declared.

Uses of AtomName in pl.poznan.put.pdb

Methods in pl.poznan.put.pdb that return AtomName

Modifier and Type	Method	Description
AtomName	PdbAtomLine.detectAtomName()

Uses of AtomName in pl.poznan.put.pdb.analysis

Methods in pl.poznan.put.pdb.analysis that return types with arguments of type AtomName

Modifier and Type	Method	Description
default Set<AtomName>	ResidueComponent.additionalAtoms()
Set<AtomName>	DefaultPdbResidue.atomNames()
Set<AtomName>	ImmutableDefaultPdbResidue.atomNames()
default Set<AtomName>	PdbResidue.atomNames()
Set<AtomName>	ResidueComponent.requiredAtoms()

Methods in pl.poznan.put.pdb.analysis with parameters of type AtomName

Modifier and Type	Method	Description
default PdbAtomLine	PdbResidue.findAtom(AtomName atomName)	Finds an atom of a given name.
default boolean	PdbResidue.hasAtom(AtomName atomName)	Checks whether this residue has atom of the given name.

Method parameters in pl.poznan.put.pdb.analysis with type arguments of type AtomName

Modifier and Type	Method	Description
static ResidueInformationProvider	ResidueTypeDetector.detectResidueType(String residueName, Set<AtomName> atomNames)	Detects the type of residue by its name or atom content.

Uses of AtomName in pl.poznan.put.protein

Methods in pl.poznan.put.protein that return types with arguments of type AtomName

Modifier and Type	Method	Description
default Set<AtomName>	Backbone.requiredAtoms()

Uses of AtomName in pl.poznan.put.rna

Methods in pl.poznan.put.rna that return types with arguments of type AtomName

Modifier and Type	Method	Description
Set<AtomName>	Phosphate.additionalAtoms()
org.apache.commons.lang3.tuple.Pair<AtomName,AtomName>	Nucleobase.edgeVectorAtoms(NucleobaseEdge edge)
org.apache.commons.lang3.tuple.Pair<AtomName,AtomName>	Nucleobase.edgeVectorAtoms(NucleobaseEdge edge)
default org.apache.commons.lang3.tuple.Pair<AtomName,AtomName>	Purine.edgeVectorAtoms(NucleobaseEdge edge)
default org.apache.commons.lang3.tuple.Pair<AtomName,AtomName>	Purine.edgeVectorAtoms(NucleobaseEdge edge)
default org.apache.commons.lang3.tuple.Pair<AtomName,AtomName>	Pyrimidine.edgeVectorAtoms(NucleobaseEdge edge)
default org.apache.commons.lang3.tuple.Pair<AtomName,AtomName>	Pyrimidine.edgeVectorAtoms(NucleobaseEdge edge)
Set<AtomName>	Phosphate.requiredAtoms()
Set<AtomName>	Ribose.requiredAtoms()
default Map<AtomName,PdbAtomLine>	Nucleobase.standardReferenceFrame()

Uses of AtomName in pl.poznan.put.torsion

Methods in pl.poznan.put.torsion that return types with arguments of type AtomName

Modifier and Type	Method	Description
Quadruple<AtomName>	AtomBasedTorsionAngleType.atoms()
Quadruple<AtomName>	ImmutableAtomBasedTorsionAngleType.atoms()

Method parameters in pl.poznan.put.torsion with type arguments of type AtomName

Modifier and Type	Method	Description
ImmutableAtomBasedTorsionAngleType.Builder	ImmutableAtomBasedTorsionAngleType.Builder.atoms(Quadruple<AtomName> atoms)	Initializes the value for the atoms attribute.
static ImmutableAtomBasedTorsionAngleType	ImmutableAtomBasedTorsionAngleType.of(MoleculeType moleculeType, String shortDisplayName, String exportName, Quadruple<AtomName> atoms, Quadruple<Integer> residueRule)	Construct a new immutable AtomBasedTorsionAngleType instance.
ImmutableAtomBasedTorsionAngleType	ImmutableAtomBasedTorsionAngleType.withAtoms(Quadruple<AtomName> value)	Copy the current immutable object by setting a value for the atoms attribute.