Package org.biojava.nbio.protmod

Class ModificationLinkage

java.lang.Object
org.biojava.nbio.protmod.ModificationLinkage
public class ModificationLinkage extends Object

  • Constructor Details

    • ModificationLinkage

      public ModificationLinkage(List<Component> components, int indexOfComponent1, int indexOfComponent2)
      Parameters:
      components - Components involved in a modification.
      indexOfComponent1 - index of the first component.
      indexOfComponent2 - index of the second component.

    • ModificationLinkage

      public ModificationLinkage(List<Component> components, int indexOfComponent1, String pdbNameOfAtomsOnComponent1, int indexOfComponent2, String pdbNameOfAtomsOnComponent2)
      Parameters:
      components - Components involved in a modification.
      indexOfComponent1 - index of the first component.
      labelOfAtomOnComponent1 - label of the atom on the first component.
      indexOfComponent2 - index of the second component.
      labelOfAtomOnComponent2 - label of the atom on the second component.

    • ModificationLinkage

      public ModificationLinkage(List<Component> components, int indexOfComponent1, List<String> pdbNameOfPotentialAtomsOnComponent1, int indexOfComponent2, List<String> pdbNameOfPotentialAtomsOnComponent2)
      Parameters:
      components - Components involved in a modification.
      indexOfComponent1 - index of the first component.
      labelOfAtomOnComponent1 - label of the atom on the first component.
      indexOfComponent2 - index of the second component.
      labelOfAtomOnComponent2 - label of the atom on the second component.

    • ModificationLinkage

      public ModificationLinkage(List<Component> components, int indexOfComponent1, List<String> pdbNameOfPotentialAtomsOnComponent1, String labelOfAtomOnComponent1, int indexOfComponent2, List<String> pdbNameOfPotentialAtomsOnComponent2, String labelOfAtomOnComponent2)
      Parameters:
      components - Components involved in a modification.
      indexOfComponent1 - index of the first component.
      pdbNameOfPotentialAtomsOnComponent1 - a list of PDB names of potential atoms on the first component.
      labelOfAtomOnComponent1 - label of the atom on the first component.
      indexOfComponent2 - index of the second component.
      pdbNameOfPotentialAtomsOnComponent2 - a list of PDB names of potential atoms on the second component.
      labelOfAtomOnComponent2 - label of the atom on the second component.

  • Method Details

    • getIndexOfComponent1

      public int getIndexOfComponent1()
      Returns:
      index of the first component.

    • getIndexOfComponent2

      public int getIndexOfComponent2()
      Returns:
      index of the second component.

    • getComponent1

      public Component getComponent1()
      Returns:
      the first component.

    • getComponent2

      public Component getComponent2()
      Returns:
      the second component.

    • getPDBNameOfPotentialAtomsOnComponent1

      public List<String> getPDBNameOfPotentialAtomsOnComponent1()
      Returns:
      a list of PDB names of potential atoms on the first component.

    • getPDBNameOfPotentialAtomsOnComponent2

      public List<String> getPDBNameOfPotentialAtomsOnComponent2()
      Returns:
      a list of PDB names of potential atoms on the second component.

    • getLabelOfAtomOnComponent1

      public String getLabelOfAtomOnComponent1()
      Returns:
      label of the atom on the first component.

    • getLabelOfAtomOnComponent2

      public String getLabelOfAtomOnComponent2()
      Returns:
      label of the atom on the second component.

    • toString

      public String toString()
      Overrides:
      toString in class Object