Package org.openmolecules.chem.conf.gen
Class TorsionSet
- java.lang.Object
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- org.openmolecules.chem.conf.gen.TorsionSet
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- All Implemented Interfaces:
java.lang.Comparable<TorsionSet>
public class TorsionSet extends java.lang.Object implements java.lang.Comparable<TorsionSet>
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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
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Method Summary
All Methods Instance Methods Concrete Methods 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()
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Constructor Detail
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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 bondsconformerIndex
- conformer index for every rigid fragmentbitShift
- bit position of torsion and conformer indexeslongIndex
- index on long array for shifted torsion and conformer indexeslikelihood
- all individual index likelyhoods multiplied
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TorsionSet
public TorsionSet(TorsionSet ref)
Deep-Copy constructor not including collision intensities- Parameters:
ref
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Method Detail
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getTorsionIndexes
public int[] getTorsionIndexes()
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getConformerIndexes
public int[] getConformerIndexes()
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getLikelihood
public double getLikelihood()
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getCollisionIntensitySum
public double getCollisionIntensitySum()
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getCollisionIntensityMatrix
public double[][] getCollisionIntensityMatrix()
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setCollisionIntensity
public void setCollisionIntensity(double sum, double[][] matrix)
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isUsed
public boolean isUsed()
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setUsed
public void setUsed()
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matches
public boolean matches(TorsionSetEliminationRule er, double tolerance)
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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 interfacejava.lang.Comparable<TorsionSet>
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equals
public boolean equals(java.lang.Object ts)
- Overrides:
equals
in classjava.lang.Object
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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