ClusterDiagram

java.lang.Object
- etomica.virial.cluster.ClusterDiagram

All Implemented Interfaces:

java.io.Serializable
```
public class ClusterDiagram
extends java.lang.Object
implements java.io.Serializable
```
Holds information about a cluster diagram, including the bonds, root points, and score.

See Also:

Serialized Form

Field Summary

Fields
Modifier and Type Field Description

int[][] mConnections

int mNumBody

int mNumIdenticalPermutations

int mReeHooverFactor

Fields
Modifier and Type	Field	Description
`int[][]`	`mConnections`
`int`	`mNumBody`
`int`	`mNumIdenticalPermutations`
`int`	`mReeHooverFactor`

Constructor Summary

Constructors
Constructor	Description
`ClusterDiagram(int numBody, int numRootPoints)`	Constructs a cluster having numBody points of which numRootPoints are root points, with bonds between each pair of points (full star).
`ClusterDiagram(int numBody, int numRootPoints, int[][] bonds)`	Constructs a cluster having numBody points of which numRootPoints are root points, with bonds as given by the array bonds.
`ClusterDiagram(int numBody, int numRootPoints, int[][] bonds, Rational weight)`
`ClusterDiagram(ClusterDiagram cluster)`	Creates a copy of the given cluster

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`addConnection(int node1, int node2)`	Adds a connection between the node1 and node2.
`void`	`calcScore(int[] score)`	compute a score for the cluster.
`void`	`copyTo(ClusterDiagram destCluster)`
`boolean`	`deleteConnection(int node1, int node2)`	Deletes a connection from one node1 to node2.
`int`	`getNumConnections()`	returns the number of active connections in the cluster.
`int`	`getNumRootPoints()`
`Rational`	`getWeight()`
`boolean`	`isIsomorphOf(ClusterDiagram anotherCluster)`	Returns true if this cluster is an isomorph of the given cluster.
`boolean`	`isRootPoint(int i)`	returns true if the given point is a root point
`static void`	`main(java.lang.String[] args)`
`void`	`makeFullStar()`	Turns this cluster into a full star -- each point in the cluster is connected to every other point in the cluster.
`void`	`reset()`	Resets the cluster to being fully connected except that root points are not connected to each other.
`protected boolean`	`scoreGreaterThan(int[] compareScore)`	Determines if the cluster's current configuration has a score greater than the given score.
`void`	`setWeight(Rational weight)`
`void`	`sort()`	Sorts list of connections for each node in the diagram such that mConnections[i][j] < mConnections[i][k] for k > j.
`void`	`swap(int point1, int point2)`	Swaps point1 and point2.
`java.lang.String`	`toString()`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Field Detail
  - mNumBody
```
public final int mNumBody
```
  - mConnections
```
public final int[][] mConnections
```
  - mNumIdenticalPermutations
```
public int mNumIdenticalPermutations
```
  - mReeHooverFactor
```
public int mReeHooverFactor
```
- Constructor Detail
  - ClusterDiagram
```
public ClusterDiagram(int numBody,
                      int numRootPoints)
```
    Constructs a cluster having numBody points of which numRootPoints are root points, with bonds between each pair of points (full star).
  - ClusterDiagram
```
public ClusterDiagram(int numBody,
                      int numRootPoints,
                      int[][] bonds)
```
    Constructs a cluster having numBody points of which numRootPoints are root points, with bonds as given by the array bonds.
    
    Parameters:
    
    bonds - array of integer pairs that specifies nodes that have a bond joining them
  - ClusterDiagram
```
public ClusterDiagram(int numBody,
                      int numRootPoints,
                      int[][] bonds,
                      Rational weight)
```
  - ClusterDiagram
```
public ClusterDiagram(ClusterDiagram cluster)
```
    Creates a copy of the given cluster
- Method Detail
  - copyTo
```
public void copyTo(ClusterDiagram destCluster)
```
  - getNumRootPoints
```
public int getNumRootPoints()
```
  - isRootPoint
```
public boolean isRootPoint(int i)
```
    returns true if the given point is a root point
  - getNumConnections
```
public int getNumConnections()
```
    returns the number of active connections in the cluster.
  - getWeight
```
public Rational getWeight()
```
  - setWeight
```
public void setWeight(Rational weight)
```
  - makeFullStar
```
public void makeFullStar()
```
    Turns this cluster into a full star -- each point in the cluster is connected to every other point in the cluster.
  - swap
```
public void swap(int point1,
                 int point2)
```
    Swaps point1 and point2. Point1 points to everything point2 pointed to and vice-versa. Also, everything that pointed to point1 points to point2 and vice-versa. Don't swap root and non-root points.
  - deleteConnection
```
public boolean deleteConnection(int node1,
                                int node2)
```
    Deletes a connection from one node1 to node2. The method should be called again to delete the connection from node2 to node1.
  - addConnection
```
public void addConnection(int node1,
                          int node2)
```
    Adds a connection between the node1 and node2. The method should be called again to create the connection from the node2 to node1.
  - toString
```
public java.lang.String toString()
```
    Overrides:
    
    toString in class java.lang.Object
  - scoreGreaterThan
```
protected boolean scoreGreaterThan(int[] compareScore)
```
    Determines if the cluster's current configuration has a score greater than the given score. The current score is computed only enough to determine if it is less than the current cluster.
  - calcScore
```
public void calcScore(int[] score)
```
    compute a score for the cluster. The score is returned as an array of integers. The first element is the score for connections between i and i+1 and the second element is the score for connections between i and i+2 (the zeroth element is always 0). The score puts more importance on early points (having a connection for point 0 will score one higher than having the same connection for every other point). The score is returned in the array passed in.
  - reset
```
public void reset()
```
    Resets the cluster to being fully connected except that root points are not connected to each other. If the cluster is being generated from a ClusterGenerator, ClusterGenerator.reset should be called instead of this method.
  - sort
```
public void sort()
```
    Sorts list of connections for each node in the diagram such that mConnections[i][j] < mConnections[i][k] for k > j.
  - isIsomorphOf
```
public boolean isIsomorphOf(ClusterDiagram anotherCluster)
```
    Returns true if this cluster is an isomorph of the given cluster. That is, returns true if the given cluster can be mapped onto this one by some permutation of the field points.
  - main
```
public static void main(java.lang.String[] args)
```

Class ClusterDiagram

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

mNumBody

mConnections

mNumIdenticalPermutations

mReeHooverFactor

Constructor Detail

ClusterDiagram

ClusterDiagram

ClusterDiagram

ClusterDiagram

Method Detail

copyTo

getNumRootPoints

isRootPoint

getNumConnections

getWeight

setWeight

makeFullStar

swap

deleteConnection

addConnection

toString

scoreGreaterThan

calcScore

reset

sort

isIsomorphOf

main