org.biojava3.protmod.structure
Interface ModifiedCompound

All Known Implementing Classes:
ModifiedCompoundImpl

public interface ModifiedCompound

Root interface for all modifications in structure.

Since:
3.0
Author:
Jianjiong Gao

Method Summary
 boolean addAtomLinkage(StructureAtomLinkage linkage)
          Add a linkage.
 void addAtomLinkages(Collection<StructureAtomLinkage> linkages)
          Add a collections of linkages.
 boolean crossChains()
           
 Set<StructureAtomLinkage> getAtomLinkages()
           
 String getDescription()
          return a description of this compound
 Set<StructureGroup> getGroups()
           
 Set<StructureGroup> getGroups(boolean isAminoAcid)
           
 ProteinModification getModification()
           
 void setAtomLinkages(Set<StructureAtomLinkage> linkages)
          Set atom linkages
 void setDescription(String desc)
           
 void setGroups(Set<StructureGroup> groups)
           
 void setModification(ProteinModification modi)
           
 

Method Detail

getDescription

String getDescription()
return a description of this compound

Returns:
a description

setDescription

void setDescription(String desc)

getModification

ProteinModification getModification()
Returns:
ProteinModificationBean occurred on the residue.

setModification

void setModification(ProteinModification modi)

getGroups

Set<StructureGroup> getGroups()
Returns:
a set of involved group.

setGroups

void setGroups(Set<StructureGroup> groups)

getGroups

Set<StructureGroup> getGroups(boolean isAminoAcid)
Parameters:
isAminoAcid - true if amino acids.
Returns:
a set of involved group of the type.

getAtomLinkages

Set<StructureAtomLinkage> getAtomLinkages()
Returns:
a set of atom linkages.
See Also:
#getLinkedGroupPairs, StructureAtomLinkage

setAtomLinkages

void setAtomLinkages(Set<StructureAtomLinkage> linkages)
Set atom linkages


addAtomLinkage

boolean addAtomLinkage(StructureAtomLinkage linkage)
Add a linkage. Add new the involved groups first using addGroup.

Parameters:
linkage - an atom linkage.
Returns:
true if this linkage was not already contained.
See Also:
StructureAtomLinkage

addAtomLinkages

void addAtomLinkages(Collection<StructureAtomLinkage> linkages)
Add a collections of linkages.

Parameters:
linkages - an atom linkage.

crossChains

boolean crossChains()
Returns:
true if groups from multiple chains were involved