Constructor Summary

Method Summary

• Methods inherited from class java.lang.Object

  clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

• 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 Detail

• 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