Uses of Interface pl.poznan.put.pdb.analysis.PdbResidue (BioCommons 3.0.4 API)

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
`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).
`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).
`static PdbResidue`	DefaultPdbResidue.`fromBioJavaGroup(org.biojava.nbio.structure.Group group)`	Creates an instance of this class from Group object defined in BioJava.

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
`ImmutableDefaultResidueCollection.Builder`	ImmutableDefaultResidueCollection.Builder.`addResidues(PdbResidue element)`	Adds one element to `residues` list.
`ImmutableDefaultResidueCollection.Builder`	ImmutableDefaultResidueCollection.Builder.`addResidues(PdbResidue... elements)`	Adds elements to `residues` list.
`ImmutablePdbChain.Builder`	ImmutablePdbChain.Builder.`addResidues(PdbResidue element)`	Adds one element to `residues` list.
`ImmutablePdbChain.Builder`	ImmutablePdbChain.Builder.`addResidues(PdbResidue... elements)`	Adds elements to `residues` list.
`ImmutablePdbCompactFragment.Builder`	ImmutablePdbCompactFragment.Builder.`addResidues(PdbResidue element)`	Adds one element to `residues` list.
`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.
`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)`).
`ImmutableDefaultResidueCollection`	ImmutableDefaultResidueCollection.`withResidues(PdbResidue... elements)`	Copy the current immutable object with elements that replace the content of `residues`.
`ImmutablePdbChain`	ImmutablePdbChain.`withResidues(PdbResidue... elements)`	Copy the current immutable object with elements that replace the content of `residues`.
`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
`ImmutableDefaultResidueCollection.Builder`	ImmutableDefaultResidueCollection.Builder.`addAllResidues(Iterable<? extends PdbResidue> elements)`	Adds elements to `residues` list.
`ImmutablePdbChain.Builder`	ImmutablePdbChain.Builder.`addAllResidues(Iterable<? extends PdbResidue> elements)`	Adds elements to `residues` list.
`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.
`ImmutableDefaultResidueCollection.Builder`	ImmutableDefaultResidueCollection.Builder.`residues(Iterable<? extends PdbResidue> elements)`	Sets or replaces all elements for `residues` list.
`ImmutablePdbChain.Builder`	ImmutablePdbChain.Builder.`residues(Iterable<? extends PdbResidue> elements)`	Sets or replaces all elements for `residues` list.
`ImmutablePdbCompactFragment.Builder`	ImmutablePdbCompactFragment.Builder.`residues(Iterable<? extends PdbResidue> elements)`	Sets or replaces all elements for `residues` list.
`ImmutableDefaultResidueCollection`	ImmutableDefaultResidueCollection.`withResidues(Iterable<? extends PdbResidue> elements)`	Copy the current immutable object with elements that replace the content of `residues`.
`ImmutablePdbChain`	ImmutablePdbChain.`withResidues(Iterable<? extends PdbResidue> elements)`	Copy the current immutable object with elements that replace the content of `residues`.
`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)`
`static StandardReferenceFrame`	StandardReferenceFrame.`ofResidue(PdbResidue residue)`

Method parameters in pl.poznan.put.rna with type arguments of type PdbResidue
Modifier and Type	Method	Description
`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)`).
`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).