Some useful math operations. More...

Static Public Member Functions
static double	calculateAngle (double[] a, double[] b)
	compute the angle between two vectors a & b of same length More...

static void	norm (double[] d, double[] ret)
	Normalizes a vector. More...

static Vector3d	normDist (Point3d p1, Point3d p2)
	Get normalized distance between two point. More...

static double[]	scale (double[] d, double a)
	Scales a vector. More...

static void	scalar (double[] d, double a, double[] ret)
	Scales a vector. More...

static double	length (double[] v)
	Return the norm of a vector. More...

static double	computeDotProduct (double[] v0, double[] v1)
	Compute the dot product (a scalar) between two vectors. More...

static double[]	computeCrossProduct (double[] v0, double[] v1)
	Compute the cross product of two vectors. More...

static double[]	subtract (double[] v0, double[] v1)
	Perform vector subtraction. More...

static double[]	add (double[] v0, double[] v1)
	Perform vector addition. More...

static double	computeDihedralAngle (Point3d p0, Point3d p1, Point3d p2, Point3d p3)
	Compute the dihedral angle. More...

static double	computeDihedralAngle (double[] v0, double[] v1, double[] v2, double[] v3)
	Compute the dihedral angle. More...

static double	log2 (double x)

static double	roundValue (double val, int decimalPlaces)

static double	angle (Point3d a, Point3d b, Point3d c)
	Calculate the angle between the 3 points. More...

static double	getAngle (double[] A, double[] B, double[] C)
	Calculates angle (in degrees) between vectors BA and BC. More...

static double	distance (Point3d a, Point3d b)
	Calculates distance between point a and point b. More...

static double	torsion (Point3d p1, Point3d p2, Point3d p3, Point3d p4)
	Calculate the torsion angle between the 4 points. More...

static double	sum (double[] a)
	Return sum of all values in array. More...

static double	mean (double[] a)
	Calculate mean value. More...

static double	mean (List< Double > vals)

static Vector3d	getNormalDirection (Vector3d vecA)
	Generate a vector that is perpendicular to the given one. More...

static double[]	centroidOf (Collection< double[]> points, int dimension)

Static Private Attributes
static final double[]	tp1 = new double[3]

static final double[]	tp2 = new double[3]

static final double[]	tp3 = new double[3]

static final double[]	tp4 = new double[3]

Detailed Description

Some useful math operations.

Author: Vishwesh Venkatraman; Marco Foscato

Definition at line 38 of file MathUtils.java.

Member Function Documentation

◆ add()

static double[] denoptim.utils.MathUtils.add	(	double[]	v0,
		double[]	v1
	)

static

Perform vector addition.

Parameters

v0	First vector
v1	Second vector

Returns: v0 + v1

Definition at line 198 of file MathUtils.java.

Referenced by denoptim.gui.FragmentViewPanel.updateAPsInJmolViewer().

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◆ angle()

static double denoptim.utils.MathUtils.angle	(	Point3d	a,
		Point3d	b,
		Point3d	c
	)

static

Calculate the angle between the 3 points.

Parameters

a
b
c

Returns: angle calculated

Definition at line 284 of file MathUtils.java.

References denoptim.utils.MathUtils.angle(), and denoptim.constants.DENOPTIMConstants.FLOATCOMPARISONTOLERANCE.

Referenced by denoptim.utils.DummyAtomHandler.addDummiesOnLinearities(), denoptim.utils.MathUtils.angle(), denoptim.utils.MathUtils.calculateAngle(), denoptim.graph.rings.RingClosureFinder.evaluateClosability(), denoptim.integration.tinker.TinkerUtils.getICFromIAC(), and denoptim.integration.tinker.TinkerUtils.getThirdRefAtomId().

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◆ calculateAngle()

static double denoptim.utils.MathUtils.calculateAngle	(	double[]	a,
		double[]	b
	)

static

compute the angle between two vectors a & b of same length

Parameters

a
b

Returns: angle in degrees

Definition at line 51 of file MathUtils.java.

References denoptim.utils.MathUtils.angle(), denoptim.utils.MathUtils.computeDotProduct(), and denoptim.utils.MathUtils.length().

Referenced by denoptim.utils.MathUtils.getAngle().

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◆ centroidOf()

static double[] denoptim.utils.MathUtils.centroidOf	(	Collection< double[]>	points,
		int	dimension
	)

static

Definition at line 457 of file MathUtils.java.

Referenced by denoptim.fragmenter.DynamicCentroidCluster.getCentroid(), and denoptim.fragmenter.FragmentClusterer.getRMSDStatsOfNoisyDistorsions().

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◆ computeCrossProduct()

static double[] denoptim.utils.MathUtils.computeCrossProduct	(	double[]	v0,
		double[]	v1
	)

static

Compute the cross product of two vectors.

Result is a vector

Parameters

v0	First vector
v1	Second vector

Returns: crossProduct Cross product of vectors [x,y,z].

Definition at line 162 of file MathUtils.java.

Referenced by denoptim.utils.MathUtils.computeDihedralAngle().

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◆ computeDihedralAngle() [1/2]

static double denoptim.utils.MathUtils.computeDihedralAngle	(	double[]	v0,
		double[]	v1,
		double[]	v2,
		double[]	v3
	)

static

Compute the dihedral angle.

Parameters

v0	3D coordinates
v1	3D coordinates
v2	3D coordinates
v3	3D coordinates

Returns: angle

Definition at line 241 of file MathUtils.java.

References denoptim.utils.MathUtils.computeCrossProduct(), denoptim.utils.MathUtils.computeDotProduct(), and denoptim.utils.MathUtils.subtract().

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◆ computeDihedralAngle() [2/2]

static double denoptim.utils.MathUtils.computeDihedralAngle	(	Point3d	p0,
		Point3d	p1,
		Point3d	p2,
		Point3d	p3
	)

static

Compute the dihedral angle.

Parameters

p0	point in 3D
p1	point in 3D
p2	point in 3D
p3	point in 3D

Returns: angle

Definition at line 218 of file MathUtils.java.

References denoptim.utils.MathUtils.computeDihedralAngle().

Referenced by denoptim.utils.MathUtils.computeDihedralAngle(), denoptim.graph.rings.RingClosureFinder.evaluateClosability(), and denoptim.utils.MathUtils.torsion().

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◆ computeDotProduct()

static double denoptim.utils.MathUtils.computeDotProduct	(	double[]	v0,
		double[]	v1
	)

static

Compute the dot product (a scalar) between two vectors.

Parameters

v0	First vector
v1	Second vector

Returns: Dot product of given vectors.

Definition at line 148 of file MathUtils.java.

Referenced by denoptim.utils.MathUtils.calculateAngle(), and denoptim.utils.MathUtils.computeDihedralAngle().

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◆ distance()

static double denoptim.utils.MathUtils.distance	(	Point3d	a,
		Point3d	b
	)

static

Calculates distance between point a and point b.

Parameters

a	Point
b	Point

Returns: Distance between a and b

Definition at line 342 of file MathUtils.java.

Referenced by denoptim.graph.Fragment.is3D(), and denoptim.molecularmodeling.ChemicalObjectModel.updateXYZFromINT().

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◆ getAngle()

static double denoptim.utils.MathUtils.getAngle	(	double[]	A,
		double[]	B,
		double[]	C
	)

static

Calculates angle (in degrees) between vectors BA and BC.

Parameters

A	Point
B	Point
C	Point

Returns: Angle (degrees)

Definition at line 324 of file MathUtils.java.

References denoptim.utils.MathUtils.calculateAngle().

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◆ getNormalDirection()

static Vector3d denoptim.utils.MathUtils.getNormalDirection ( Vector3d vecA )

static

Generate a vector that is perpendicular to the given one.

No control over which perpendicular direction will be chosen.

Parameters

vecA	input vector

Returns: a normal vector

Definition at line 426 of file MathUtils.java.

Referenced by denoptim.molecularmodeling.ThreeDimTreeBuilder.append3DFragmentsViaEdges().

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◆ length()

static double denoptim.utils.MathUtils.length ( double[] v )

static

Return the norm of a vector.

Parameters

v	Vector to compute length of.

Returns: Length of vector.

Definition at line 134 of file MathUtils.java.

Referenced by denoptim.utils.MathUtils.calculateAngle(), and denoptim.utils.MathUtils.norm().

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◆ log2()

static double denoptim.utils.MathUtils.log2 ( double x )

static

Definition at line 260 of file MathUtils.java.

◆ mean() [1/2]

static double denoptim.utils.MathUtils.mean ( double[] a )

static

Calculate mean value.

Parameters

a	Array to calculate mean from.

Returns: mean value of array, NaN if empty array.

Definition at line 396 of file MathUtils.java.

References denoptim.utils.MathUtils.sum().

Referenced by denoptim.fitness.FitnessProvider.getFitness(), and denoptim.utils.MathUtils.mean().

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◆ mean() [2/2]

static double denoptim.utils.MathUtils.mean ( List< Double > vals )

static

Definition at line 406 of file MathUtils.java.

References denoptim.utils.MathUtils.mean().

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◆ norm()

static void denoptim.utils.MathUtils.norm	(	double[]	d,
		double[]	ret
	)

static

Normalizes a vector.

Parameters

d	A vector to be normalized.
ret	The normalized vector.

Definition at line 67 of file MathUtils.java.

References denoptim.utils.MathUtils.length().

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◆ normDist()

static Vector3d denoptim.utils.MathUtils.normDist	(	Point3d	p1,
		Point3d	p2
	)

static

Get normalized distance between two point.

Parameters

p1	the first point
p2	the second point

Returns: the normalized vector

Definition at line 86 of file MathUtils.java.

Referenced by denoptim.molecularmodeling.ChemicalObjectModel.updateXYZFromINT().

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◆ roundValue()

static double denoptim.utils.MathUtils.roundValue	(	double	val,
		int	decimalPlaces
	)

static

Definition at line 268 of file MathUtils.java.

◆ scalar()

static void denoptim.utils.MathUtils.scalar	(	double[]	d,
		double	a,
		double[]	ret
	)

static

Scales a vector.

Parameters

d	A vector to be scaled
a	A scaling value
ret	The scaled vector

Definition at line 119 of file MathUtils.java.

◆ scale()

static double[] denoptim.utils.MathUtils.scale	(	double[]	d,
		double	a
	)

static

Scales a vector.

Parameters

d	A vector to be scaled
a	A scaling value

Definition at line 102 of file MathUtils.java.

Referenced by denoptim.gui.FragmentViewPanel.updateAPsInJmolViewer().

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◆ subtract()

static double[] denoptim.utils.MathUtils.subtract	(	double[]	v0,
		double[]	v1
	)

static

Perform vector subtraction.

Parameters

v0	Vector to subtract from
v1	Vector to subtract

Returns: v0 - v1

Definition at line 180 of file MathUtils.java.

Referenced by denoptim.utils.MathUtils.computeDihedralAngle(), and denoptim.gui.FragmentViewPanel.updateAPsInJmolViewer().

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◆ sum()

static double denoptim.utils.MathUtils.sum ( double[] a )

static

Return sum of all values in array.

Parameters

a	Array to sum elements of.

Returns: array sum.

Definition at line 380 of file MathUtils.java.

References denoptim.utils.MathUtils.sum().

Referenced by denoptim.utils.MathUtils.mean(), and denoptim.utils.MathUtils.sum().

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◆ torsion()

static double denoptim.utils.MathUtils.torsion	(	Point3d	p1,
		Point3d	p2,
		Point3d	p3,
		Point3d	p4
	)

static

Calculate the torsion angle between the 4 points.

Parameters

p1	Point
p2	Point
p3	Point
p4	Point

Returns: Torsion between arguments

Definition at line 363 of file MathUtils.java.

References denoptim.utils.MathUtils.computeDihedralAngle(), denoptim.utils.MathUtils.tp1, denoptim.utils.MathUtils.tp2, denoptim.utils.MathUtils.tp3, and denoptim.utils.MathUtils.tp4.

Referenced by denoptim.integration.tinker.TinkerUtils.getICFromIAC().

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Member Data Documentation

◆ tp1

final double [] denoptim.utils.MathUtils.tp1 = new double[3]

staticprivate

Definition at line 350 of file MathUtils.java.

Referenced by denoptim.utils.MathUtils.torsion().

◆ tp2

final double [] denoptim.utils.MathUtils.tp2 = new double[3]

staticprivate

Definition at line 351 of file MathUtils.java.

Referenced by denoptim.utils.MathUtils.torsion().

◆ tp3

final double [] denoptim.utils.MathUtils.tp3 = new double[3]

staticprivate

Definition at line 352 of file MathUtils.java.

Referenced by denoptim.utils.MathUtils.torsion().

◆ tp4

final double [] denoptim.utils.MathUtils.tp4 = new double[3]

staticprivate

Definition at line 353 of file MathUtils.java.

Referenced by denoptim.utils.MathUtils.torsion().

The documentation for this class was generated from the following file:

/github/workspace/src/main/java/denoptim/utils/MathUtils.java

Static Public Member Functions

Static Private Attributes

Detailed Description

Member Function Documentation

◆ add()

◆ angle()

◆ calculateAngle()

◆ centroidOf()

◆ computeCrossProduct()

◆ computeDihedralAngle() [1/2]

◆ computeDihedralAngle() [2/2]

◆ computeDotProduct()

◆ distance()

◆ getAngle()

◆ getNormalDirection()

◆ length()

◆ log2()

◆ mean() [1/2]

◆ mean() [2/2]

◆ norm()

◆ normDist()

◆ roundValue()

◆ scalar()

◆ scale()

◆ subtract()

◆ sum()

◆ torsion()

Member Data Documentation

◆ tp1

◆ tp2

◆ tp3

◆ tp4