org.biojava3.protmod
Class ModificationLinkage

java.lang.Object
  extended by org.biojava3.protmod.ModificationLinkage

public class ModificationLinkage
extends Object


Constructor Summary
ModificationLinkage(List<Component> components, int indexOfComponent1, int indexOfComponent2)
           
ModificationLinkage(List<Component> components, int indexOfComponent1, List<String> pdbNameOfPotentialAtomsOnComponent1, int indexOfComponent2, List<String> pdbNameOfPotentialAtomsOnComponent2)
           
ModificationLinkage(List<Component> components, int indexOfComponent1, List<String> pdbNameOfPotentialAtomsOnComponent1, String labelOfAtomOnComponent1, int indexOfComponent2, List<String> pdbNameOfPotentialAtomsOnComponent2, String labelOfAtomOnComponent2)
           
ModificationLinkage(List<Component> components, int indexOfComponent1, String pdbNameOfAtomsOnComponent1, int indexOfComponent2, String pdbNameOfAtomsOnComponent2)
           
 
Method Summary
 Component getComponent1()
           
 Component getComponent2()
           
 int getIndexOfComponent1()
           
 int getIndexOfComponent2()
           
 String getLabelOfAtomOnComponent1()
           
 String getLabelOfAtomOnComponent2()
           
 List<String> getPDBNameOfPotentialAtomsOnComponent1()
           
 List<String> getPDBNameOfPotentialAtomsOnComponent2()
           
 String toString()
           
 
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