Class ModifiedCompoundImpl

Method Details

• setModification

  public void setModification(ProteinModification protmod)

  Specified by:

  setModification in interface ModifiedCompound

• getModification

  public ProteinModification getModification()

  Specified by:

  getModification in interface ModifiedCompound

  Returns:

  ProteinModificationBean occurred on the residue.

• getOriginalModificationId

  @Deprecated public String getOriginalModificationId()

  Deprecated.

  use getModification().getId()

  Returns:

  the original modification ID.

• getGroups

  public Set<StructureGroup> getGroups()

  Specified by:

  getGroups in interface ModifiedCompound

  Returns:

  a set of involved group.

• getGroups

  public Set<StructureGroup> getGroups(boolean isAminoAcid)

  Specified by:

  getGroups in interface ModifiedCompound

  Parameters:

  isAminoAcid - true if amino acids.

  Returns:

  a set of involved group of the type.

• setGroups

  public void setGroups(Set<StructureGroup> groups)

  Specified by:

  setGroups in interface ModifiedCompound

• getAtomLinkages

  public Set<StructureAtomLinkage> getAtomLinkages()

  Specified by:

  getAtomLinkages in interface ModifiedCompound

  Returns:

  a set of atom linkages.

  See Also:

  • #getLinkedGroupPairs
  • StructureAtomLinkage

• setAtomLinkages

  public void setAtomLinkages(Set<StructureAtomLinkage> linkages)

  Description copied from interface: ModifiedCompound

  Set atom linkages

  Specified by:

  setAtomLinkages in interface ModifiedCompound

• addAtomLinkage

  public boolean addAtomLinkage(StructureAtomLinkage linkage)

  Description copied from interface: ModifiedCompound

  Add a linkage. Add new the involved groups first using addGroup.

  Specified by:

  addAtomLinkage in interface ModifiedCompound

  Parameters:

  linkage - an atom linkage.

  Returns:

  true if this linkage was not already contained.

  See Also:

  • StructureAtomLinkage

• addAtomLinkages

  public void addAtomLinkages(Collection<StructureAtomLinkage> linkages)

  Description copied from interface: ModifiedCompound

  Add a collections of linkages.

  Specified by:

  addAtomLinkages in interface ModifiedCompound

  Parameters:

  linkages - an atom linkage.

• crossChains

  public boolean crossChains()

  Specified by:

  crossChains in interface ModifiedCompound

  Returns:

  true if groups from multiple chains were involved

• toString

  public String toString()

  Overrides:

  toString in class Object

• getDescription

  public String getDescription()

  Description copied from interface: ModifiedCompound

  return a description of this compound

  Specified by:

  getDescription in interface ModifiedCompound

  Returns:

  a description

• setDescription

  public void setDescription(String desc)

  Specified by:

  setDescription in interface ModifiedCompound

• compareTo

  public int compareTo(ModifiedCompound compound)

  Specified by:

  compareTo in interface Comparable<ModifiedCompound>

• equals

  public boolean equals(Object obj)

  Overrides:

  equals in class Object

  Returns:

  true if same modification and same components; false, otherwise.

• hashCode

  public int hashCode()

  Overrides:

  hashCode in class Object