Uses of Interface
pl.poznan.put.pdb.analysis.PdbResidue

Packages that use PdbResidue

Package	Description
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.rna
pl.poznan.put.structure	Package contains classes useful in describing secondary structure (base pairs, helices, etc.)
pl.poznan.put.torsion	Contains classes dealing with torsion angles handling.

Uses of PdbResidue in pl.poznan.put.pdb

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

Modifier and Type	Method	Description
final PdbResidue	PdbRemark465Line.toResidue()	Creates an instance of DefaultPdbResidue marked as missing and without atoms.

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

Classes in pl.poznan.put.pdb.analysis that implement PdbResidue

Modifier and Type	Class	Description
class	DefaultPdbResidue	A default implementation of a residue (nucleotide or amino acid).
final class	ImmutableDefaultPdbResidue	Immutable implementation of DefaultPdbResidue.

Methods in pl.poznan.put.pdb.analysis that return PdbResidue

Modifier and Type	Method	Description
default PdbResidue	ResidueCollection.findResidue(ChainNumberICode query)	Finds a residue by a triplet (chain, number, icode).

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

Modifier and Type	Method	Description
List<PdbResidue>	AbstractPdbModel.residues()	Groups together atoms from the same residue and repeat that for every residue.
List<PdbResidue>	DefaultCifModel.residues()
List<PdbResidue>	DefaultPdbModel.residues()
abstract List<PdbResidue>	DefaultResidueCollection.residues()
List<PdbResidue>	ImmutableDefaultCifModel.residues()	Groups together atoms from the same residue and repeat that for every residue.
List<PdbResidue>	ImmutableDefaultPdbModel.residues()	Groups together atoms from the same residue and repeat that for every residue.
List<PdbResidue>	ImmutableDefaultResidueCollection.residues()
List<PdbResidue>	ImmutablePdbChain.residues()
List<PdbResidue>	ImmutablePdbCompactFragment.residues()
abstract List<PdbResidue>	PdbChain.residues()
abstract List<PdbResidue>	PdbCompactFragment.residues()
List<PdbResidue>	ResidueCollection.residues()

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

Modifier and Type	Method	Description
final ImmutableDefaultResidueCollection.Builder	ImmutableDefaultResidueCollection.Builder.addResidues(PdbResidue element)	Adds one element to residues list.
final ImmutableDefaultResidueCollection.Builder	ImmutableDefaultResidueCollection.Builder.addResidues(PdbResidue... elements)	Adds elements to residues list.
final ImmutablePdbChain.Builder	ImmutablePdbChain.Builder.addResidues(PdbResidue element)	Adds one element to residues list.
final ImmutablePdbChain.Builder	ImmutablePdbChain.Builder.addResidues(PdbResidue... elements)	Adds elements to residues list.
final ImmutablePdbCompactFragment.Builder	ImmutablePdbCompactFragment.Builder.addResidues(PdbResidue element)	Adds one element to residues list.
final ImmutablePdbCompactFragment.Builder	ImmutablePdbCompactFragment.Builder.addResidues(PdbResidue... elements)	Adds elements to residues list.
boolean	MoleculeType.areConnected(PdbResidue r1, PdbResidue r2)	Checks if two residues are connected.
final ImmutableDefaultPdbResidue.Builder	ImmutableDefaultPdbResidue.Builder.from(PdbResidue instance)	Fill a builder with attribute values from the provided pl.poznan.put.pdb.analysis.PdbResidue instance.
default boolean	PdbResidue.isConnectedTo(PdbResidue other)	Checks if this residue is connected with another one (see MoleculeType.areConnected(PdbResidue, PdbResidue)).
final ImmutableDefaultResidueCollection	ImmutableDefaultResidueCollection.withResidues(PdbResidue... elements)	Copy the current immutable object with elements that replace the content of residues.
final ImmutablePdbChain	ImmutablePdbChain.withResidues(PdbResidue... elements)	Copy the current immutable object with elements that replace the content of residues.
final ImmutablePdbCompactFragment	ImmutablePdbCompactFragment.withResidues(PdbResidue... elements)	Copy the current immutable object with elements that replace the content of residues.

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

Modifier and Type	Method	Description
final ImmutableDefaultResidueCollection.Builder	ImmutableDefaultResidueCollection.Builder.addAllResidues(Iterable<? extends PdbResidue> elements)	Adds elements to residues list.
final ImmutablePdbChain.Builder	ImmutablePdbChain.Builder.addAllResidues(Iterable<? extends PdbResidue> elements)	Adds elements to residues list.
final ImmutablePdbCompactFragment.Builder	ImmutablePdbCompactFragment.Builder.addAllResidues(Iterable<? extends PdbResidue> elements)	Adds elements to residues list.
static ResidueTorsionAngles	ResidueTorsionAngles.calculate(List<PdbResidue> residues, int index)	Calculates all torsion angles' values in the given residue.
static ImmutableDefaultResidueCollection	ImmutableDefaultResidueCollection.of(Iterable<? extends PdbResidue> residues)	Construct a new immutable DefaultResidueCollection instance.
static ImmutableDefaultResidueCollection	ImmutableDefaultResidueCollection.of(List<PdbResidue> residues)	Construct a new immutable DefaultResidueCollection instance.
static ImmutablePdbChain	ImmutablePdbChain.of(String identifier, Iterable<? extends PdbResidue> residues)	Construct a new immutable PdbChain instance.
static ImmutablePdbChain	ImmutablePdbChain.of(String identifier, List<PdbResidue> residues)	Construct a new immutable PdbChain instance.
static ImmutablePdbCompactFragment	ImmutablePdbCompactFragment.of(Iterable<? extends PdbResidue> residues)	Construct a new immutable PdbCompactFragment instance.
static ImmutablePdbCompactFragment	ImmutablePdbCompactFragment.of(List<PdbResidue> residues)	Construct a new immutable PdbCompactFragment instance.
final ImmutableDefaultResidueCollection.Builder	ImmutableDefaultResidueCollection.Builder.residues(Iterable<? extends PdbResidue> elements)	Sets or replaces all elements for residues list.
final ImmutablePdbChain.Builder	ImmutablePdbChain.Builder.residues(Iterable<? extends PdbResidue> elements)	Sets or replaces all elements for residues list.
final ImmutablePdbCompactFragment.Builder	ImmutablePdbCompactFragment.Builder.residues(Iterable<? extends PdbResidue> elements)	Sets or replaces all elements for residues list.
final ImmutableDefaultResidueCollection	ImmutableDefaultResidueCollection.withResidues(Iterable<? extends PdbResidue> elements)	Copy the current immutable object with elements that replace the content of residues.
final ImmutablePdbChain	ImmutablePdbChain.withResidues(Iterable<? extends PdbResidue> elements)	Copy the current immutable object with elements that replace the content of residues.
final ImmutablePdbCompactFragment	ImmutablePdbCompactFragment.withResidues(Iterable<? extends PdbResidue> elements)	Copy the current immutable object with elements that replace the content of residues.

Uses of PdbResidue in pl.poznan.put.rna

Methods in pl.poznan.put.rna with parameters of type PdbResidue

Modifier and Type	Method	Description
default org.apache.commons.math3.geometry.euclidean.threed.Vector3D	Nucleobase.edgeVector(PdbResidue residue, NucleobaseEdge edge)

Method parameters in pl.poznan.put.rna with type arguments of type PdbResidue

Modifier and Type	Method	Description
final TorsionAngleValue	PseudophasePuckerType.calculate(List<PdbResidue> residues, int currentIndex)	Calculates the value of pseudophase pucker according to the formula in Saenger's "Principles of ...".

Uses of PdbResidue in pl.poznan.put.structure

Methods in pl.poznan.put.structure with parameters of type PdbResidue

Modifier and Type	Method	Description
static boolean	BasePair.isCanonicalPair(PdbResidue left, PdbResidue right)	Checks if two residues are canonical base pairs by means of (1) distance between atoms which form hydrogen bonds and (2) checking if two bases face each other.

Uses of PdbResidue in pl.poznan.put.torsion

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

Modifier and Type	Method	Description
default TorsionAngleValue	AtomBasedTorsionAngleType.calculate(List<PdbResidue> residues, int currentIndex)	Calculates the value of this torsion angle (see Angle.torsionAngle(Vector3D, Vector3D, Vector3D, Vector3D)).
final TorsionAngleValue	AverageTorsionAngleType.calculate(List<PdbResidue> residues, int currentIndex)	Calculates the average torsion angle value by calculating basic angle values and creating an AngleSample out of them to get the mean direction.
TorsionAngleValue	TorsionAngleType.calculate(List<PdbResidue> residues, int currentIndex)	Calculates the value of this torsion angle.
default List<AtomPair>	AtomBasedTorsionAngleType.findAtomPairs(List<PdbResidue> residues, int currentIndex)	Applies residueRule() on the given list of residues to find three pairs of atoms: (a1, a2), (a2, a3), (a3, a4).