Method Detail

• getDescription

  java.lang.String getDescription()

  return a description of this compound

  Returns:

  a description

• setDescription

  void setDescription​(java.lang.String desc)

• getModification

  ProteinModification getModification()

  Returns:

  ProteinModificationBean occurred on the residue.

• setModification

  void setModification​(ProteinModification modi)

• getGroups

  java.util.Set<StructureGroup> getGroups()

  Returns:

  a set of involved group.

• setGroups

  void setGroups​(java.util.Set<StructureGroup> groups)

• getGroups

  java.util.Set<StructureGroup> getGroups​(boolean isAminoAcid)

  Parameters:

  isAminoAcid - true if amino acids.

  Returns:

  a set of involved group of the type.

• getAtomLinkages

  java.util.Set<StructureAtomLinkage> getAtomLinkages()

  Returns:

  a set of atom linkages.

  See Also:

  #getLinkedGroupPairs, StructureAtomLinkage

• setAtomLinkages

  void setAtomLinkages​(java.util.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​(java.util.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