Package org.openmolecules.chem.conf.gen

Class TorsionSet

java.lang.Object

org.openmolecules.chem.conf.gen.TorsionSet

All Implemented Interfaces:

java.lang.Comparable<TorsionSet>

public class TorsionSet
extends java.lang.Object
implements java.lang.Comparable<TorsionSet>

Constructor Summary

Constructors

Constructor	Description
TorsionSet(int[] torsionIndex, int[] conformerIndex, int[] bitShift, int[] longIndex, double likelihood)	Creates a new conformer description from torsion and conformer indexes.
TorsionSet(TorsionSet ref)	Deep-Copy constructor not including collision intensities

Method Summary

Modifier and Type	Method	Description
int	compareTo(TorsionSet ts)	Allows to order TorsionSets in a unique way for quick uniqueness checking against a TreeSet.
boolean	equals(java.lang.Object ts)
double[][]	getCollisionIntensityMatrix()
double	getCollisionIntensitySum()
int[]	getConformerIndexes()
double	getLikelihood()
int[]	getTorsionIndexes()
boolean	isUsed()
boolean	matches(TorsionSetEliminationRule er, double tolerance)
void	setCollisionIntensity(double sum, double[][] matrix)
void	setUsed()
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

TorsionSet

public TorsionSet(int[] torsionIndex,
                  int[] conformerIndex,
                  int[] bitShift,
                  int[] longIndex,
                  double likelihood)

Creates a new conformer description from torsion and conformer indexes.

Parameters:

torsionIndex - torsion angle index for all rotatable bonds

conformerIndex - conformer index for every rigid fragment

bitShift - bit position of torsion and conformer indexes

longIndex - index on long array for shifted torsion and conformer indexes

likelihood - all individual index likelyhoods multiplied

TorsionSet

public TorsionSet(TorsionSet ref)

Deep-Copy constructor not including collision intensities

Parameters:

ref -

Method Detail

getTorsionIndexes

public int[] getTorsionIndexes()

getConformerIndexes

public int[] getConformerIndexes()

getLikelihood

public double getLikelihood()

getCollisionIntensitySum

public double getCollisionIntensitySum()

getCollisionIntensityMatrix

public double[][] getCollisionIntensityMatrix()

setCollisionIntensity

public void setCollisionIntensity(double sum,
                                  double[][] matrix)

isUsed

public boolean isUsed()

setUsed

public void setUsed()

matches

public boolean matches(TorsionSetEliminationRule er,
                       double tolerance)

compareTo

public int compareTo(TorsionSet ts)

Allows to order TorsionSets in a unique way for quick uniqueness checking against a TreeSet.

Specified by:

compareTo in interface java.lang.Comparable<TorsionSet>

equals

public boolean equals(java.lang.Object ts)

Overrides:

equals in class java.lang.Object

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object