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

Packages that use ResidueCollection

Package	Description
pl.poznan.put.pdb.analysis	Contains classes which work on data from PDB or mmCIF files.
pl.poznan.put.structure	Package contains classes useful in describing secondary structure (base pairs, helices, etc.)

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

Subinterfaces of ResidueCollection in pl.poznan.put.pdb.analysis

Modifier and Type	Interface	Description
interface	CifModel	A structure parsed from an mmCIF file.
interface	PdbModel	A structure parsed from a PDB file.
interface	SingleTypedResidueCollection	A collection of residues with a common molecule type (RNA or protein).

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

Modifier and Type	Class	Description
class	AbstractPdbModel	A structure which detects residues from atoms alone and then chains from residues.
class	DefaultCifModel	A default implementation of a structure parsed from an mmCIF file.
class	DefaultPdbModel	A default implementation of a structure parsed from a PDB file.
class	DefaultResidueCollection	A container for a list of residues.
final class	ImmutableDefaultCifModel	Immutable implementation of DefaultCifModel.
final class	ImmutableDefaultPdbModel	Immutable implementation of DefaultPdbModel.
final class	ImmutableDefaultResidueCollection	Immutable implementation of DefaultResidueCollection.
final class	ImmutablePdbChain	Immutable implementation of PdbChain.
final class	ImmutablePdbCompactFragment	Immutable implementation of PdbCompactFragment.
class	PdbChain	A chain in a structure.
class	PdbCompactFragment	A collection of residues such that (i, i+1) are connected.

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

Modifier and Type	Method	Description
default ResidueCollection	ResidueCollection.withoutAlternateLocations()	Creates a new instance of this class in which atoms with alternate locations are present only once.

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

Modifier and Type	Method	Description
ResidueCollection.CifBuilder	ResidueCollection.CifBuilder.add(ResidueCollection residueCollection)	Add a residue collection to be serialized into mmCIF format.
ResidueCollection.CifBuilder	ResidueCollection.CifBuilder.add(ResidueCollection residueCollection, String name)	Add a residue collection to be serialized into mmCIF format.
ResidueCollection.CifBuilder	ResidueCollection.CifBuilder.add(ResidueCollection residueCollection, String name, String description)	Add a residue collection to be serialized into mmCIF format.
ResidueCollection.CifBuilder	ResidueCollection.CifBuilder.add(ResidueCollection residueCollection, String name, String description, int modelNumber)	Add a residue collection to be serialized into mmCIF format.
ResidueCollection.PdbBuilder	ResidueCollection.PdbBuilder.add(ResidueCollection residueCollection)	Add a new residue collection to the builder.
ResidueCollection.PdbBuilder	ResidueCollection.PdbBuilder.add(ResidueCollection residueCollection, String name)	Add a new named residue collection to the builder.
final ImmutableDefaultResidueCollection.Builder	ImmutableDefaultResidueCollection.Builder.from(ResidueCollection instance)	Fill a builder with attribute values from the provided pl.poznan.put.pdb.analysis.ResidueCollection instance.
final ImmutablePdbChain.Builder	ImmutablePdbChain.Builder.from(ResidueCollection instance)	Fill a builder with attribute values from the provided pl.poznan.put.pdb.analysis.ResidueCollection instance.
final ImmutablePdbCompactFragment.Builder	ImmutablePdbCompactFragment.Builder.from(ResidueCollection instance)	Fill a builder with attribute values from the provided pl.poznan.put.pdb.analysis.ResidueCollection instance.

Uses of ResidueCollection in pl.poznan.put.structure

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

Modifier and Type	Method	Description
static Collection<ClassifiedBasePair>	CanonicalStructureExtractor.basePairs(ResidueCollection residueCollection)
static BpSeq	CanonicalStructureExtractor.bpSeq(ResidueCollection residueCollection)	Extracts the canonical secondary structure from the 3D data and outputs it in BPSEQ format.