Uses of Class
pl.poznan.put.pdb.PdbResidueIdentifier

Packages that use PdbResidueIdentifier

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.structure.formats

Uses of PdbResidueIdentifier in pl.poznan.put.pdb

Subclasses of PdbResidueIdentifier in pl.poznan.put.pdb

Modifier and Type	Class	Description
final class	ImmutablePdbResidueIdentifier	Immutable implementation of PdbResidueIdentifier.

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

Modifier and Type	Method	Description
static PdbResidueIdentifier	PdbResidueIdentifier.from(ChainNumberICode chainNumberICode)	Creates an instance of this class from any implementation of ChainNumberICode.
final PdbResidueIdentifier	PdbNamedResidueIdentifier.toResidueIdentifier()

Methods in pl.poznan.put.pdb with parameters of type PdbResidueIdentifier

Modifier and Type	Method	Description
static ImmutablePdbResidueIdentifier	ImmutablePdbResidueIdentifier.copyOf(PdbResidueIdentifier instance)	Creates an immutable copy of a PdbResidueIdentifier value.
final ImmutablePdbResidueIdentifier.Builder	ImmutablePdbResidueIdentifier.Builder.from(PdbResidueIdentifier instance)	Fill a builder with attribute values from the provided pl.poznan.put.pdb.PdbResidueIdentifier instance.

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

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

Modifier and Type	Method	Description
abstract PdbResidueIdentifier	DefaultPdbResidue.identifier()
PdbResidueIdentifier	ImmutableDefaultPdbResidue.identifier()
PdbResidueIdentifier	ImmutableResidueTorsionAngles.identifier()
PdbResidueIdentifier	PdbResidue.identifier()
abstract PdbResidueIdentifier	ResidueTorsionAngles.identifier()

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

Modifier and Type	Method	Description
abstract Set<PdbResidueIdentifier>	DefaultCifModel.chainTerminatedAfter()
abstract Set<PdbResidueIdentifier>	DefaultPdbModel.chainTerminatedAfter()
Set<PdbResidueIdentifier>	ImmutableDefaultCifModel.chainTerminatedAfter()
Set<PdbResidueIdentifier>	ImmutableDefaultPdbModel.chainTerminatedAfter()
Set<PdbResidueIdentifier>	PdbModel.chainTerminatedAfter()
default List<PdbResidueIdentifier>	ResidueCollection.residueIdentifiers()

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

Modifier and Type	Method	Description
final ImmutableDefaultCifModel.Builder	ImmutableDefaultCifModel.Builder.addChainTerminatedAfter(PdbResidueIdentifier element)	Adds one element to chainTerminatedAfter set.
final ImmutableDefaultCifModel.Builder	ImmutableDefaultCifModel.Builder.addChainTerminatedAfter(PdbResidueIdentifier... elements)	Adds elements to chainTerminatedAfter set.
final ImmutableDefaultPdbModel.Builder	ImmutableDefaultPdbModel.Builder.addChainTerminatedAfter(PdbResidueIdentifier element)	Adds one element to chainTerminatedAfter set.
final ImmutableDefaultPdbModel.Builder	ImmutableDefaultPdbModel.Builder.addChainTerminatedAfter(PdbResidueIdentifier... elements)	Adds elements to chainTerminatedAfter set.
final ImmutableDefaultPdbResidue.Builder	ImmutableDefaultPdbResidue.Builder.identifier(PdbResidueIdentifier identifier)	Initializes the value for the identifier attribute.
final ImmutableResidueTorsionAngles.Builder	ImmutableResidueTorsionAngles.Builder.identifier(PdbResidueIdentifier identifier)	Initializes the value for the identifier attribute.
default boolean	PdbModel.isModified(PdbResidueIdentifier query)	Checks if a given residue is modified (as stated in the PDB or mmCIF headers).
default PdbModresLine	PdbModel.modificationDetails(PdbResidueIdentifier query)	Provides details about modification of the residue.
static ImmutableDefaultPdbResidue	ImmutableDefaultPdbResidue.of(PdbResidueIdentifier identifier, String standardResidueName, String modifiedResidueName, Iterable<? extends PdbAtomLine> atoms)	Construct a new immutable DefaultPdbResidue instance.
static ImmutableDefaultPdbResidue	ImmutableDefaultPdbResidue.of(PdbResidueIdentifier identifier, String standardResidueName, String modifiedResidueName, List<PdbAtomLine> atoms)	Construct a new immutable DefaultPdbResidue instance.
static ImmutableResidueTorsionAngles	ImmutableResidueTorsionAngles.of(PdbResidueIdentifier identifier, Iterable<? extends TorsionAngleValue> values)	Construct a new immutable ResidueTorsionAngles instance.
static ImmutableResidueTorsionAngles	ImmutableResidueTorsionAngles.of(PdbResidueIdentifier identifier, List<TorsionAngleValue> values)	Construct a new immutable ResidueTorsionAngles instance.
final ResidueTorsionAngles	PdbCompactFragment.torsionAngles(PdbResidueIdentifier identifier)	Computes torsion angles' values for a given residue.
final ImmutableDefaultCifModel	ImmutableDefaultCifModel.withChainTerminatedAfter(PdbResidueIdentifier... elements)	Copy the current immutable object with elements that replace the content of chainTerminatedAfter.
final ImmutableDefaultPdbModel	ImmutableDefaultPdbModel.withChainTerminatedAfter(PdbResidueIdentifier... elements)	Copy the current immutable object with elements that replace the content of chainTerminatedAfter.
final ImmutableDefaultPdbResidue	ImmutableDefaultPdbResidue.withIdentifier(PdbResidueIdentifier value)	Copy the current immutable object by setting a value for the identifier attribute.
final ImmutableResidueTorsionAngles	ImmutableResidueTorsionAngles.withIdentifier(PdbResidueIdentifier value)	Copy the current immutable object by setting a value for the identifier attribute.

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

Modifier and Type	Method	Description
final ImmutableDefaultCifModel.Builder	ImmutableDefaultCifModel.Builder.addAllChainTerminatedAfter(Iterable<? extends PdbResidueIdentifier> elements)	Adds elements to chainTerminatedAfter set.
final ImmutableDefaultPdbModel.Builder	ImmutableDefaultPdbModel.Builder.addAllChainTerminatedAfter(Iterable<? extends PdbResidueIdentifier> elements)	Adds elements to chainTerminatedAfter set.
final ImmutableDefaultCifModel.Builder	ImmutableDefaultCifModel.Builder.chainTerminatedAfter(Iterable<? extends PdbResidueIdentifier> elements)	Sets or replaces all elements for chainTerminatedAfter set.
final ImmutableDefaultPdbModel.Builder	ImmutableDefaultPdbModel.Builder.chainTerminatedAfter(Iterable<? extends PdbResidueIdentifier> elements)	Sets or replaces all elements for chainTerminatedAfter set.
static ImmutableDefaultCifModel	ImmutableDefaultCifModel.of(PdbHeaderLine header, PdbExpdtaLine experimentalData, PdbRemark2Line resolution, int modelNumber, List<PdbAtomLine> atoms, List<PdbModresLine> modifiedResidues, List<PdbRemark465Line> missingResidues, String title, Set<PdbResidueIdentifier> chainTerminatedAfter, List<QuantifiedBasePair> basePairs)	Construct a new immutable DefaultCifModel instance.
static ImmutableDefaultPdbModel	ImmutableDefaultPdbModel.of(PdbHeaderLine header, PdbExpdtaLine experimentalData, PdbRemark2Line resolution, int modelNumber, List<PdbAtomLine> atoms, List<PdbModresLine> modifiedResidues, List<PdbRemark465Line> missingResidues, String title, Set<PdbResidueIdentifier> chainTerminatedAfter)	Construct a new immutable DefaultPdbModel instance.
final ImmutableDefaultCifModel	ImmutableDefaultCifModel.withChainTerminatedAfter(Iterable<? extends PdbResidueIdentifier> elements)	Copy the current immutable object with elements that replace the content of chainTerminatedAfter.
final ImmutableDefaultPdbModel	ImmutableDefaultPdbModel.withChainTerminatedAfter(Iterable<? extends PdbResidueIdentifier> elements)	Copy the current immutable object with elements that replace the content of chainTerminatedAfter.

Uses of PdbResidueIdentifier in pl.poznan.put.structure.formats

Methods in pl.poznan.put.structure.formats that return PdbResidueIdentifier

Modifier and Type	Method	Description
final PdbResidueIdentifier	CombinedStrandFromPdb.identifier(DotBracketSymbol symbol)
final PdbResidueIdentifier	DefaultDotBracketFromPdb.identifier(DotBracketSymbol symbol)
PdbResidueIdentifier	DotBracketFromPdb.identifier(DotBracketSymbol symbol)	Maps the given dot-bracket symbol to its corresponding residue identifier.

Methods in pl.poznan.put.structure.formats that return types with arguments of type PdbResidueIdentifier

Modifier and Type	Method	Description
final Set<PdbResidueIdentifier>	CombinedStrandFromPdb.identifierSet()
Set<PdbResidueIdentifier>	DotBracketFromPdb.identifierSet()
Set<PdbResidueIdentifier>	ImmutableDefaultDotBracketFromPdb.identifierSet()
protected abstract Map<DotBracketSymbol,PdbResidueIdentifier>	CombinedStrandFromPdb.inputSymbolToResidue()
protected Map<DotBracketSymbol,PdbResidueIdentifier>	ImmutableCombinedStrandFromPdb.inputSymbolToResidue()
protected org.apache.commons.collections4.BidiMap<DotBracketSymbol,PdbResidueIdentifier>	CombinedStrandFromPdb.mapping()
protected org.apache.commons.collections4.BidiMap<DotBracketSymbol,PdbResidueIdentifier>	ImmutableCombinedStrandFromPdb.mapping()
protected Map<PdbResidueIdentifier,DotBracketSymbol>	DefaultDotBracketFromPdb.residueToSymbol()
protected Map<PdbResidueIdentifier,DotBracketSymbol>	ImmutableDefaultDotBracketFromPdb.residueToSymbol()
protected Map<DotBracketSymbol,PdbResidueIdentifier>	CombinedStrandFromPdb.symbolToResidue()
protected Map<DotBracketSymbol,PdbResidueIdentifier>	DefaultDotBracketFromPdb.symbolToResidue()
protected Map<DotBracketSymbol,PdbResidueIdentifier>	ImmutableCombinedStrandFromPdb.symbolToResidue()
protected Map<DotBracketSymbol,PdbResidueIdentifier>	ImmutableDefaultDotBracketFromPdb.symbolToResidue()

Methods in pl.poznan.put.structure.formats with parameters of type PdbResidueIdentifier

Modifier and Type	Method	Description
final ImmutableDefaultDotBracketFromPdb.Builder	ImmutableDefaultDotBracketFromPdb.Builder.addIdentifierSet(PdbResidueIdentifier element)	Adds one element to identifierSet set.
final ImmutableDefaultDotBracketFromPdb.Builder	ImmutableDefaultDotBracketFromPdb.Builder.addIdentifierSet(PdbResidueIdentifier... elements)	Adds elements to identifierSet set.
final boolean	CombinedStrandFromPdb.contains(PdbResidueIdentifier residueIdentifier)
final boolean	DefaultDotBracketFromPdb.contains(PdbResidueIdentifier residueIdentifier)
boolean	DotBracketFromPdb.contains(PdbResidueIdentifier residueIdentifier)	Checks if this structure contains a mapping for the given residue identifier.
final ImmutableCombinedStrandFromPdb.Builder	ImmutableCombinedStrandFromPdb.Builder.putInputSymbolToResidue(DotBracketSymbol key, PdbResidueIdentifier value)	Put one entry to the inputSymbolToResidue map.
final DotBracketSymbol	CombinedStrandFromPdb.symbol(PdbResidueIdentifier residueIdentifier)
final DotBracketSymbol	DefaultDotBracketFromPdb.symbol(PdbResidueIdentifier residueIdentifier)
DotBracketSymbol	DotBracketFromPdb.symbol(PdbResidueIdentifier residueIdentifier)	Maps the given residue identifier to its corresponding dot-bracket symbol.
final ImmutableDefaultDotBracketFromPdb	ImmutableDefaultDotBracketFromPdb.withIdentifierSet(PdbResidueIdentifier... elements)	Copy the current immutable object with elements that replace the content of identifierSet.

Method parameters in pl.poznan.put.structure.formats with type arguments of type PdbResidueIdentifier

Modifier and Type	Method	Description
final ImmutableDefaultDotBracketFromPdb.Builder	ImmutableDefaultDotBracketFromPdb.Builder.addAllIdentifierSet(Iterable<? extends PdbResidueIdentifier> elements)	Adds elements to identifierSet set.
final ImmutableDefaultDotBracketFromPdb.Builder	ImmutableDefaultDotBracketFromPdb.Builder.identifierSet(Iterable<? extends PdbResidueIdentifier> elements)	Sets or replaces all elements for identifierSet set.
final ImmutableCombinedStrandFromPdb.Builder	ImmutableCombinedStrandFromPdb.Builder.inputSymbolToResidue(Map<? extends DotBracketSymbol,? extends PdbResidueIdentifier> entries)	Sets or replaces all mappings from the specified map as entries for the inputSymbolToResidue map.
static ImmutableCombinedStrandFromPdb	ImmutableCombinedStrandFromPdb.of(Iterable<? extends Strand> inputStrands, Map<? extends DotBracketSymbol,? extends PdbResidueIdentifier> inputSymbolToResidue)	Construct a new immutable CombinedStrandFromPdb instance.
static ImmutableCombinedStrandFromPdb	ImmutableCombinedStrandFromPdb.of(List<Strand> inputStrands, Map<DotBracketSymbol,PdbResidueIdentifier> inputSymbolToResidue)	Construct a new immutable CombinedStrandFromPdb instance.
final ImmutableCombinedStrandFromPdb.Builder	ImmutableCombinedStrandFromPdb.Builder.putAllInputSymbolToResidue(Map<? extends DotBracketSymbol,? extends PdbResidueIdentifier> entries)	Put all mappings from the specified map as entries to inputSymbolToResidue map.
final ImmutableCombinedStrandFromPdb.Builder	ImmutableCombinedStrandFromPdb.Builder.putInputSymbolToResidue(Map.Entry<? extends DotBracketSymbol,? extends PdbResidueIdentifier> entry)	Put one entry to the inputSymbolToResidue map.
final ImmutableDefaultDotBracketFromPdb	ImmutableDefaultDotBracketFromPdb.withIdentifierSet(Iterable<? extends PdbResidueIdentifier> elements)	Copy the current immutable object with elements that replace the content of identifierSet.
final ImmutableCombinedStrandFromPdb	ImmutableCombinedStrandFromPdb.withInputSymbolToResidue(Map<? extends DotBracketSymbol,? extends PdbResidueIdentifier> entries)	Copy the current immutable object by replacing the inputSymbolToResidue map with the specified map.