org.biojava3.protmod
Class ModificationLinkage

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

public class ModificationLinkage
extends java.lang.Object

Constructor Summary

ModificationLinkage(java.util.List<Component> components, int indexOfComponent1, int indexOfComponent2)

ModificationLinkage(java.util.List<Component> components, int indexOfComponent1, java.util.List<java.lang.String> pdbNameOfPotentialAtomsOnComponent1, int indexOfComponent2, java.util.List<java.lang.String> pdbNameOfPotentialAtomsOnComponent2)

ModificationLinkage(java.util.List<Component> components, int indexOfComponent1, java.util.List<java.lang.String> pdbNameOfPotentialAtomsOnComponent1, java.lang.String labelOfAtomOnComponent1, int indexOfComponent2, java.util.List<java.lang.String> pdbNameOfPotentialAtomsOnComponent2, java.lang.String labelOfAtomOnComponent2)

ModificationLinkage(java.util.List<Component> components, int indexOfComponent1, java.lang.String pdbNameOfAtomsOnComponent1, int indexOfComponent2, java.lang.String pdbNameOfAtomsOnComponent2)

Method Summary

Component	getComponent1()
Component	getComponent2()
int	getIndexOfComponent1()
int	getIndexOfComponent2()
java.lang.String	getLabelOfAtomOnComponent1()
java.lang.String	getLabelOfAtomOnComponent2()
java.util.List<java.lang.String>	getPDBNameOfPotentialAtomsOnComponent1()
java.util.List<java.lang.String>	getPDBNameOfPotentialAtomsOnComponent2()
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

ModificationLinkage

public ModificationLinkage(java.util.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(java.util.List<Component> components,
                           int indexOfComponent1,
                           java.lang.String pdbNameOfAtomsOnComponent1,
                           int indexOfComponent2,
                           java.lang.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(java.util.List<Component> components,
                           int indexOfComponent1,
                           java.util.List<java.lang.String> pdbNameOfPotentialAtomsOnComponent1,
                           int indexOfComponent2,
                           java.util.List<java.lang.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(java.util.List<Component> components,
                           int indexOfComponent1,
                           java.util.List<java.lang.String> pdbNameOfPotentialAtomsOnComponent1,
                           java.lang.String labelOfAtomOnComponent1,
                           int indexOfComponent2,
                           java.util.List<java.lang.String> pdbNameOfPotentialAtomsOnComponent2,
                           java.lang.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 java.util.List<java.lang.String> getPDBNameOfPotentialAtomsOnComponent1()

Returns:

a list of PDB names of potential atoms on the first component.

getPDBNameOfPotentialAtomsOnComponent2

public java.util.List<java.lang.String> getPDBNameOfPotentialAtomsOnComponent2()

Returns:

a list of PDB names of potential atoms on the second component.

getLabelOfAtomOnComponent1

public java.lang.String getLabelOfAtomOnComponent1()

Returns:

label of the atom on the first component.

getLabelOfAtomOnComponent2

public java.lang.String getLabelOfAtomOnComponent2()

Returns:

label of the atom on the second component.

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object