Uses of Interface
org.biojava.nbio.protmod.ProteinModification

Packages that use ProteinModification

Package	Description
org.biojava.nbio.protmod
org.biojava.nbio.protmod.structure

Uses of ProteinModification in org.biojava.nbio.protmod

Classes in org.biojava.nbio.protmod that implement ProteinModification

Modifier and Type	Class	Description
class	ProteinModificationImpl	This class contains information about a specific protein modification.

Methods in org.biojava.nbio.protmod that return ProteinModification

Modifier and Type	Method	Description
static ProteinModification	ProteinModificationRegistry.getById(String id)

Methods in org.biojava.nbio.protmod that return types with arguments of type ProteinModification

Modifier and Type	Method	Description
static Set<ProteinModification>	ProteinModificationRegistry.allModifications()
static Set<ProteinModification>	ProteinModificationRegistry.getByCategory(ModificationCategory cat)
static Set<ProteinModification>	ProteinModificationRegistry.getByComponent(Component comp1, Component... comps)	Get ProteinModifications that involves one or more components.
static Set<ProteinModification>	ProteinModificationRegistry.getByKeyword(String keyword)
static Set<ProteinModification>	ProteinModificationRegistry.getByOccurrenceType(ModificationOccurrenceType occ)
static Set<ProteinModification>	ProteinModificationRegistry.getByPdbccId(String pdbccId)
static Set<ProteinModification>	ProteinModificationRegistry.getByPsimodId(String psimodId)
static Set<ProteinModification>	ProteinModificationRegistry.getByResidId(String residId)

Methods in org.biojava.nbio.protmod with parameters of type ProteinModification

Modifier and Type	Method	Description
int	ProteinModificationImpl.compareTo(ProteinModification arg0)
static void	ProteinModificationRegistry.register(ProteinModification modification)	Register a new ProteinModification.
static void	ProteinModificationRegistry.unregister(ProteinModification modification)	Remove a modification from registry.

Constructors in org.biojava.nbio.protmod with parameters of type ProteinModification

Constructor	Description
Builder(ProteinModification copyFrom)	Create a Builder from an existing ProteinModification.

Uses of ProteinModification in org.biojava.nbio.protmod.structure

Methods in org.biojava.nbio.protmod.structure that return ProteinModification

Modifier and Type	Method	Description
ProteinModification	ModifiedCompound.getModification()
ProteinModification	ModifiedCompoundImpl.getModification()

Methods in org.biojava.nbio.protmod.structure with parameters of type ProteinModification

Modifier and Type	Method	Description
void	ModifiedCompound.setModification(ProteinModification modi)
void	ModifiedCompoundImpl.setModification(ProteinModification protmod)

Method parameters in org.biojava.nbio.protmod.structure with type arguments of type ProteinModification

Modifier and Type	Method	Description
void	ProteinModificationIdentifier.identify(List<Chain> chains, Set<ProteinModification> potentialModifications)	Identify a set of modifications in a a list of chains.
void	ProteinModificationIdentifier.identify(Chain chain, Set<ProteinModification> potentialModifications)	Identify a set of modifications in a a chains.
void	ProteinModificationIdentifier.identify(Structure structure, Set<ProteinModification> potentialModifications)	Identify a set of modifications in a structure.

Constructors in org.biojava.nbio.protmod.structure with parameters of type ProteinModification

Constructor	Description
ModifiedCompoundImpl(ProteinModification modification, Collection<StructureAtomLinkage> linkages)
ModifiedCompoundImpl(ProteinModification modification, StructureGroup modifiedResidue)	Create a ModifiedCompoundImpl that has only one involved component.