Interface ModifiedCompound

  • All Known Implementing Classes:
    ModifiedCompoundImpl

    public interface ModifiedCompound
    Root interface for all modifications in structure.
    Since:
    3.0
    Author:
    Jianjiong Gao
    • 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.
      • getGroups

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

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