Package com.actelion.research.chem.descriptor.flexophore

Class DistHist

java.lang.Object

com.actelion.research.chem.descriptor.flexophore.DistHist

All Implemented Interfaces:

java.io.Serializable

Direct Known Subclasses:

MolDistHist, MolDistHistViz

public class DistHist
extends java.lang.Object
implements java.io.Serializable

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
protected byte[]	arrDistHists

Constructor Summary

Constructors

Constructor	Description
DistHist()
DistHist(int nPPNodes)
DistHist(DistHist distHist)

Method Summary

Modifier and Type	Method	Description
void	copy(DistHist copy)
int	getBonds()
java.util.List<ClusterNode>	getClusterCenter(int maxDistance)	Calculates for nodes cluster the node with the minimum rmsd to the cluster center.
byte[]	getDistHist(int indexAt1, int indexAt2)
byte[]	getDistHist(int indexAt1, int indexAt2, byte[] arr)
byte[]	getDistHists()
int	getIdentifier()
static int	getIndex(int indexNode1, int indexNode2, int size)
int	getIndexPosStartForDistHist(int indexAt1, int indexAt2)
double	getMaxDistInHist(int indexAt1, int indexAt2)
int	getMinDist(int indexAt1, int indexAt2)
int	getNumPPNodes()
double	getRelMaxDistInHist()	To get the distance in Angstrom the relative distance has to be multiplied with the histogram range CGMult.RANGE_HISTOGRAM.
double	getRelMaxDistInHist(int indexAt1, int indexAt2)	To get the distance in Angstrom the relative distance has to be multiplied with the histogram range CGMult.RANGE_HISTOGRAM.
int	getSizeBytes()
byte	getValueAtAbsolutePosition(int indexAbsolutePosition)
protected void	initHistogramArray(int nPPNodes)
void	setDistHist(int indexAt1, int indexAt2, byte[] arrHist)
void	setDistHists(byte[] arr, int size, int identifier)	Flat copy
void	setIdentifier(int identifier)
java.lang.String	toStringHistsIndexed()

Methods inherited from class java.lang.Object

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

Field Detail

arrDistHists

protected byte[] arrDistHists

Constructor Detail

DistHist

public DistHist()

DistHist

public DistHist(int nPPNodes)

DistHist

public DistHist(DistHist distHist)

Method Detail

copy

public void copy(DistHist copy)

Parameters:

copy - : This object is written into copy.

getBonds

public int getBonds()

getNumPPNodes

public int getNumPPNodes()

Returns:

number of pharmacophore points.

getSizeBytes

public int getSizeBytes()

initHistogramArray

protected void initHistogramArray(int nPPNodes)

getIndex

public static final int getIndex(int indexNode1,
                                 int indexNode2,
                                 int size)

Parameters:

indexNode1 -

indexNode2 -

size - number of nodes

Returns:

getMinDist

public int getMinDist(int indexAt1,
                      int indexAt2)

getClusterCenter

public java.util.List<ClusterNode> getClusterCenter(int maxDistance)

Calculates for nodes cluster the node with the minimum rmsd to the cluster center.

Parameters:

maxDistance - maximum distance that a node will become a cluster member

Returns:

List with cluster.

setDistHist

public void setDistHist(int indexAt1,
                        int indexAt2,
                        byte[] arrHist)

getDistHists

public byte[] getDistHists()

setDistHists

public void setDistHists(byte[] arr,
                         int size,
                         int identifier)

Flat copy

Parameters:

arr -

size -

identifier -

getDistHist

public byte[] getDistHist(int indexAt1,
                          int indexAt2)

Parameters:

indexAt1 -

indexAt2 -

Returns:

deep copy.

getIndexPosStartForDistHist

public int getIndexPosStartForDistHist(int indexAt1,
                                       int indexAt2)

getValueAtAbsolutePosition

public byte getValueAtAbsolutePosition(int indexAbsolutePosition)

getDistHist

public byte[] getDistHist(int indexAt1,
                          int indexAt2,
                          byte[] arr)

getRelMaxDistInHist

public double getRelMaxDistInHist(int indexAt1,
                                  int indexAt2)

To get the distance in Angstrom the relative distance has to be multiplied with the histogram range CGMult.RANGE_HISTOGRAM.

Parameters:

indexAt1 -

indexAt2 -

Returns:

relative distance 0: only the first bin is occupied, 1: the last bin is occupied.

getMaxDistInHist

public double getMaxDistInHist(int indexAt1,
                               int indexAt2)

getRelMaxDistInHist

public double getRelMaxDistInHist()

To get the distance in Angstrom the relative distance has to be multiplied with the histogram range CGMult.RANGE_HISTOGRAM. Maximum relative distance between two nodes in the object.

Returns:

toStringHistsIndexed

public java.lang.String toStringHistsIndexed()

getIdentifier

public int getIdentifier()

setIdentifier

public void setIdentifier(int identifier)