Uses of Class
pl.poznan.put.circular.Angle

Packages that use Angle

Package	Description
pl.poznan.put.circular	Classes to deal with angular data and circular statistics.
pl.poznan.put.circular.conversion	Contains classes useful in conversion between Cartesian and trigonometric representations.
pl.poznan.put.circular.samples	Classes which deal with samples of data.
pl.poznan.put.pdb.analysis	Contains classes which work on data from PDB or mmCIF files.
pl.poznan.put.protein
pl.poznan.put.rna
pl.poznan.put.torsion	Contains classes dealing with torsion angles handling.
pl.poznan.put.torsion.range

Uses of Angle in pl.poznan.put.circular

Subclasses of Angle in pl.poznan.put.circular

Modifier and Type	Class	Description
final class	ImmutableAngle	Immutable implementation of Angle.

Methods in pl.poznan.put.circular that return Angle

Modifier and Type	Method	Description
static Angle	Angle.betweenPoints(org.apache.commons.math3.geometry.euclidean.threed.Vector3D coordA, org.apache.commons.math3.geometry.euclidean.threed.Vector3D coordB, org.apache.commons.math3.geometry.euclidean.threed.Vector3D coordC)	Calculates angle ABC.
static Angle	Angle.fromHourMinuteString(String hourMinute)	Parses a string in format HH.MM as a vector on a circular clock.
final Angle	Angle.multiply(double v)	Multiplies the angular value by a constant.
protected Angle	Angle.normalize()
final Angle	Angle.orderedSubtract(Angle other)	Returns an ordered difference between angles.
final Angle	Angle.subtract(Angle other)	Subtracts another angular value from this.
static Angle	Angle.torsionAngle(org.apache.commons.math3.geometry.euclidean.threed.Vector3D vec1, org.apache.commons.math3.geometry.euclidean.threed.Vector3D vec2, org.apache.commons.math3.geometry.euclidean.threed.Vector3D vec3)	Calculates torsion angle given three vectors.
static Angle	Angle.torsionAngle(org.apache.commons.math3.geometry.euclidean.threed.Vector3D coordA, org.apache.commons.math3.geometry.euclidean.threed.Vector3D coordB, org.apache.commons.math3.geometry.euclidean.threed.Vector3D coordC, org.apache.commons.math3.geometry.euclidean.threed.Vector3D coordD)	Calculates torsion angle given four points.
static Angle	Angle.torsionAngleByAcos(org.apache.commons.math3.geometry.euclidean.threed.Vector3D a1, org.apache.commons.math3.geometry.euclidean.threed.Vector3D a2, org.apache.commons.math3.geometry.euclidean.threed.Vector3D a3, org.apache.commons.math3.geometry.euclidean.threed.Vector3D a4)	Calculates torsion angle given four points.

Methods in pl.poznan.put.circular that return types with arguments of type Angle

Modifier and Type	Method	Description
abstract Collection<Angle>	Histogram.data()
Collection<Angle>	ImmutableHistogram.data()
final Collection<Angle>	Histogram.findBin(double radiansStart)	Finds a bin which starts at a given point.

Methods in pl.poznan.put.circular with parameters of type Angle

Modifier and Type	Method	Description
final int	Angle.compareTo(Angle t)
static ImmutableAngle	ImmutableAngle.copyOf(Angle instance)	Creates an immutable copy of a Angle value.
final double	Angle.distance(Angle other)	Computes a useful distance in range [0; 2] between two angular values.
final ImmutableAngle.Builder	ImmutableAngle.Builder.from(Angle instance)	Fill a builder with attribute values from the provided Angle instance.
final boolean	Angle.isBetween(Angle begin, Angle end)	Return strue if this instance is in range [begin; end).
final Angle	Angle.orderedSubtract(Angle other)	Returns an ordered difference between angles.
final Angle	Angle.subtract(Angle other)	Subtracts another angular value from this.

Method parameters in pl.poznan.put.circular with type arguments of type Angle

Modifier and Type	Method	Description
final ImmutableHistogram.Builder	ImmutableHistogram.Builder.data(Collection<Angle> data)	Initializes the value for the data attribute.
static ImmutableHistogram	ImmutableHistogram.of(Collection<Angle> data, double binWidth)	Construct a new immutable Histogram instance.
final ImmutableHistogram	ImmutableHistogram.withData(Collection<Angle> value)	Copy the current immutable object by setting a value for the data attribute.

Uses of Angle in pl.poznan.put.circular.conversion

Methods in pl.poznan.put.circular.conversion with parameters of type Angle

Modifier and Type	Method	Description
static org.apache.commons.math3.geometry.euclidean.threed.Vector3D	CartesianUtilities.nextPlacement(org.apache.commons.math3.geometry.euclidean.threed.Vector3D coordA, org.apache.commons.math3.geometry.euclidean.threed.Vector3D coordB, org.apache.commons.math3.geometry.euclidean.threed.Vector3D coordC, double lengthCD, Angle angleBCD, Angle torsionABCD)	Computes position of atom D, if you know positions of A, B and C, and the length of bond B-C, and the angle B-C-D and the torsion angle A-B-C-D.

Uses of Angle in pl.poznan.put.circular.samples

Methods in pl.poznan.put.circular.samples that return Angle

Modifier and Type	Method	Description
Angle	AngleSample.meanDirection()
Angle	ImmutableAngleSample.meanDirection()
Angle	ImmutableTrigonometricMoment.meanDirection()
abstract Angle	TrigonometricMoment.meanDirection()
Angle	AngleSample.medianDirection()
Angle	ImmutableAngleSample.medianDirection()

Methods in pl.poznan.put.circular.samples that return types with arguments of type Angle

Modifier and Type	Method	Description
abstract Collection<Angle>	AngleSample.data()
Collection<Angle>	ImmutableAngleSample.data()
protected org.apache.commons.lang3.tuple.Pair<Angle,Double>	AngleSample.medianAndMeanDeviation()
protected org.apache.commons.lang3.tuple.Pair<Angle,Double>	ImmutableAngleSample.medianAndMeanDeviation()
protected List<Angle>	AngleSample.sortedData()
protected List<Angle>	ImmutableAngleSample.sortedData()

Methods in pl.poznan.put.circular.samples with parameters of type Angle

Modifier and Type	Method	Description
double	AngleSample.circularRank(Angle datapoint)	Computes the rank (index) of the value in the current sample assuming that 0 is the beginning of the circle.
static TrigonometricMoment	TrigonometricMoment.computeCentered(Collection<Angle> data, int p, Angle theta)	Computes a centered moment i.e. relative to the mean value in the sample.
final ImmutableTrigonometricMoment.Builder	ImmutableTrigonometricMoment.Builder.meanDirection(Angle meanDirection)	Initializes the value for the meanDirection attribute.
static ImmutableTrigonometricMoment	ImmutableTrigonometricMoment.of(Angle meanDirection, double meanResultantLength)	Construct a new immutable TrigonometricMoment instance.
final ImmutableTrigonometricMoment	ImmutableTrigonometricMoment.withMeanDirection(Angle value)	Copy the current immutable object by setting a value for the meanDirection attribute.

Method parameters in pl.poznan.put.circular.samples with type arguments of type Angle

Modifier and Type	Method	Description
static TrigonometricMoment	TrigonometricMoment.computeCentered(Collection<Angle> data, int p, Angle theta)	Computes a centered moment i.e. relative to the mean value in the sample.
static TrigonometricMoment	TrigonometricMoment.computeUncentered(Collection<Angle> data, int p)	Computes an uncentered moment i.e. from the data points not relative to any specific point.
final ImmutableAngleSample.Builder	ImmutableAngleSample.Builder.data(Collection<Angle> data)	Initializes the value for the data attribute.
static ImmutableAngleSample	ImmutableAngleSample.of(Collection<Angle> data)	Construct a new immutable AngleSample instance.
final ImmutableAngleSample	ImmutableAngleSample.withData(Collection<Angle> value)	Copy the current immutable object by setting a value for the data attribute.

Uses of Angle in pl.poznan.put.pdb.analysis

Methods in pl.poznan.put.pdb.analysis that return Angle

Modifier and Type	Method	Description
final Angle	ResidueTorsionAngles.value(MasterTorsionAngleType masterType)	Finds the value of a master torsion angle type in this collection.
final Angle	ResidueTorsionAngles.value(TorsionAngleType type)	Finds the value of specific torsion angle type in this collection.

Uses of Angle in pl.poznan.put.protein

Methods in pl.poznan.put.protein with parameters of type Angle

Modifier and Type	Method	Description
Range	AminoAcidTorsionAngle.range(Angle angle)

Uses of Angle in pl.poznan.put.rna

Methods in pl.poznan.put.rna that return Angle

Modifier and Type	Method	Description
Angle	ChiRange.begin()
Angle	Pseudorotation.begin()
Angle	ChiRange.end()
Angle	Pseudorotation.end()

Methods in pl.poznan.put.rna with parameters of type Angle

Modifier and Type	Method	Description
Range	NucleotideTorsionAngle.range(Angle angle)

Uses of Angle in pl.poznan.put.torsion

Methods in pl.poznan.put.torsion that return Angle

Modifier and Type	Method	Description
Angle	ImmutableTorsionAngleDelta.delta()
abstract Angle	TorsionAngleDelta.delta()
Angle	ImmutableTorsionAngleValue.value()
abstract Angle	TorsionAngleValue.value()

Methods in pl.poznan.put.torsion with parameters of type Angle

Modifier and Type	Method	Description
final ImmutableTorsionAngleDelta.Builder	ImmutableTorsionAngleDelta.Builder.delta(Angle delta)	Initializes the value for the delta attribute.
static ImmutableTorsionAngleDelta	ImmutableTorsionAngleDelta.of(MasterTorsionAngleType angleType, TorsionAngleDelta.State state, Angle delta, RangeDifference rangeDifference)	Construct a new immutable TorsionAngleDelta instance.
static ImmutableTorsionAngleValue	ImmutableTorsionAngleValue.of(TorsionAngleType angleType, Angle value)	Construct a new immutable TorsionAngleValue instance.
final Range	AverageTorsionAngleType.range(Angle angle)
Range	MasterTorsionAngleType.range(Angle angle)	Finds a matching range for the given angle value.
static TorsionAngleDelta	TorsionAngleDelta.subtractTorsionAngleValues(MasterTorsionAngleType masterType, Angle target, Angle model)	Subtracts torsion angle values and creates an instance of this class.
final ImmutableTorsionAngleValue.Builder	ImmutableTorsionAngleValue.Builder.value(Angle value)	Initializes the value for the value attribute.
final ImmutableTorsionAngleDelta	ImmutableTorsionAngleDelta.withDelta(Angle value)	Copy the current immutable object by setting a value for the delta attribute.
final ImmutableTorsionAngleValue	ImmutableTorsionAngleValue.withValue(Angle value)	Copy the current immutable object by setting a value for the value attribute.

Uses of Angle in pl.poznan.put.torsion.range

Methods in pl.poznan.put.torsion.range that return Angle

Modifier and Type	Method	Description
Angle	Range.begin()
Angle	TorsionRange.begin()
Angle	Range.end()
Angle	TorsionRange.end()

Methods in pl.poznan.put.torsion.range with parameters of type Angle

Modifier and Type	Method	Description
Range	RangeProvider.fromAngle(Angle angle)	Provdes a Range instance for given angle value.