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 and 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 and 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 and 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 and 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 and Description
ProteinModificationImpl.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 and Description
ProteinModification	ModifiedCompoundImpl.getModification()
ProteinModification	ModifiedCompound.getModification()

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

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

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

Modifier and Type	Method and Description
void	ProteinModificationIdentifier.identify(Chain chain, Set<ProteinModification> potentialModifications) Identify a set of modifications in a a chains.
void	ProteinModificationIdentifier.identify(List<Chain> chains, Set<ProteinModification> potentialModifications) Identify a set of modifications in a a list of 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 and Description
ModifiedCompoundImpl(ProteinModification modification, Collection<StructureAtomLinkage> linkages)
ModifiedCompoundImpl(ProteinModification modification, StructureGroup modifiedResidue) Create a ModifiedCompoundImpl that has only one involved component.