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 Details

    • 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:

    • 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:

    • 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