Package org.biojava.nbio.protmod

Class ModificationLinkage

java.lang.Object

org.biojava.nbio.protmod.ModificationLinkage

public class ModificationLinkage
extends Object

Constructor Summary

Constructors

Constructor	Description
ModificationLinkage(List<Component> components, int indexOfComponent1, int indexOfComponent2)
ModificationLinkage(List<Component> components, int indexOfComponent1, String pdbNameOfAtomsOnComponent1, int indexOfComponent2, String pdbNameOfAtomsOnComponent2)
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)

Method Summary

Modifier and Type	Method	Description
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 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.

pdbNameOfAtomsOnComponent1 - label of the atom on the first component.

indexOfComponent2 - index of the second component.

pdbNameOfAtomsOnComponent2 - 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.

pdbNameOfPotentialAtomsOnComponent1 - label of the atom on the first component.

indexOfComponent2 - index of the second component.

pdbNameOfPotentialAtomsOnComponent2 - 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