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ModifiedCompoundImpl (biojava 5.2.0 API)

  • java.lang.Object
    • org.biojava.nbio.protmod.structure.ModifiedCompoundImpl
  • All Implemented Interfaces:
    Serializable, Comparable<ModifiedCompound>, ModifiedCompound
    public class ModifiedCompoundImpl
extends Object
implements ModifiedCompound, Serializable, Comparable<ModifiedCompound>
    Since:
    3.0
    Author:
    Jianjiong Gao
    See Also:
    Serialized Form

    • Field Summary

      Fields 
      Modifier and Type Field Description
      static String newline  

    • Constructor Summary

      Constructors 
      Constructor Description
      ModifiedCompoundImpl()  
      ModifiedCompoundImpl​(ProteinModification modification, Collection<StructureAtomLinkage> linkages)  
      ModifiedCompoundImpl​(ProteinModification modification, StructureGroup modifiedResidue)

      Create a ModifiedCompoundImpl that has only one involved component.

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      boolean addAtomLinkage​(StructureAtomLinkage linkage)

      Add a linkage.
      void addAtomLinkages​(Collection<StructureAtomLinkage> linkages)

      Add a collections of linkages.
      int compareTo​(ModifiedCompound compound)  
      boolean crossChains()  
      boolean equals​(Object obj)  
      Set<StructureAtomLinkage> getAtomLinkages()  
      String getDescription()

      return a description of this compound
      Set<StructureGroup> getGroups()  
      Set<StructureGroup> getGroups​(boolean isAminoAcid)  
      ProteinModification getModification()  
      int hashCode()  
      void setAtomLinkages​(Set<StructureAtomLinkage> linkages)

      Set atom linkages
      void setDescription​(String desc)  
      void setGroups​(Set<StructureGroup> groups)  
      void setModification​(ProteinModification protmod)  
      String toString()  

      • Methods inherited from class java.lang.Object

        clone, finalize, getClass, notify, notifyAll, wait, wait, wait

    • Field Detail

      • newline

        public static final String newline

    • Constructor Detail

      • ModifiedCompoundImpl

        public ModifiedCompoundImpl()

      • ModifiedCompoundImpl

        public ModifiedCompoundImpl​(ProteinModification modification,
                            StructureGroup modifiedResidue)

        Create a ModifiedCompoundImpl that has only one involved component. Use this constructor for a modified residue.

        Parameters:
        modification - ProteinModification.
        modifiedResidue - modified group.
        Throws:
        IllegalArgumentException - if either argument is null.

      • ModifiedCompoundImpl

        public ModifiedCompoundImpl​(ProteinModification modification,
                            Collection<StructureAtomLinkage> linkages)
        Parameters:
        modification - ProteinModification.
        linkages - a collection of atom linkages.
        See Also:
        ProteinModification, StructureAtomLinkage

    • Method Detail

      • 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.

      • 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)

        Set atom linkages

        Specified by:
        setAtomLinkages in interface ModifiedCompound

      • addAtomLinkage

        public boolean addAtomLinkage​(StructureAtomLinkage linkage)

        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)

        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()

        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