Package org.biojava.nbio.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

Modifier and Type	Method	Description
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 Details

getDescription

String getDescription()

return a description of this compound

Returns:

a description

setDescription

void setDescription(String desc)

getModification

ProteinModification getModification()

Returns:

ProteinModification 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:

• 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