Uses of Class pl.poznan.put.circular.Angle (BioCommons 3.0.4 API)

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
`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.
`Angle`	Angle.`multiply(double v)`	Multiplies the angular value by a constant.
`protected Angle`	Angle.`normalize()`
`Angle`	Angle.`orderedSubtract(Angle other)`	Returns an ordered difference between angles.
`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()`
`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
`int`	Angle.`compareTo(Angle t)`
`static ImmutableAngle`	ImmutableAngle.`copyOf(Angle instance)`	Creates an immutable copy of a `Angle` value.
`double`	Angle.`distance(Angle other)`	Computes a useful distance in range [0; 2] between two angular values.
`ImmutableAngle.Builder`	ImmutableAngle.Builder.`from(Angle instance)`	Fill a builder with attribute values from the provided `Angle` instance.
`boolean`	Angle.`isBetween(Angle begin, Angle end)`	Return strue if this instance is in range [begin; end).
`Angle`	Angle.`orderedSubtract(Angle other)`	Returns an ordered difference between angles.
`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
`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.
`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.
`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.
`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.
`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.
`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
`Angle`	ResidueTorsionAngles.`value(MasterTorsionAngleType masterType)`	Finds the value of a master torsion angle type in this collection.
`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()`
`abstract Angle`	BasePairParameters.`buckle()`
`Angle`	ImmutableBasePairParameters.`buckle()`
`Angle`	ChiRange.`end()`
`Angle`	Pseudorotation.`end()`
`abstract Angle`	BasePairParameters.`interBaseAngle()`
`Angle`	ImmutableBasePairParameters.`interBaseAngle()`
`abstract Angle`	BasePairParameters.`opening()`
`Angle`	ImmutableBasePairParameters.`opening()`
`abstract Angle`	BasePairParameters.`propeller()`
`Angle`	ImmutableBasePairParameters.`propeller()`

Methods in pl.poznan.put.rna with parameters of type Angle
Modifier and Type	Method	Description
`ImmutableBasePairParameters.Builder`	ImmutableBasePairParameters.Builder.`buckle(Angle buckle)`	Initializes the value for the `buckle` attribute.
`ImmutableBasePairParameters.Builder`	ImmutableBasePairParameters.Builder.`interBaseAngle(Angle interBaseAngle)`	Initializes the value for the `interBaseAngle` attribute.
`static ImmutableBasePairParameters`	ImmutableBasePairParameters.`of(double shear, double stretch, double stagger, Angle buckle, Angle propeller, Angle opening, Angle interBaseAngle)`	Construct a new immutable `BasePairParameters` instance.
`ImmutableBasePairParameters.Builder`	ImmutableBasePairParameters.Builder.`opening(Angle opening)`	Initializes the value for the `opening` attribute.
`ImmutableBasePairParameters.Builder`	ImmutableBasePairParameters.Builder.`propeller(Angle propeller)`	Initializes the value for the `propeller` attribute.
`Range`	NucleotideTorsionAngle.`range(Angle angle)`
`ImmutableBasePairParameters`	ImmutableBasePairParameters.`withBuckle(Angle value)`	Copy the current immutable object by setting a value for the `buckle` attribute.
`ImmutableBasePairParameters`	ImmutableBasePairParameters.`withInterBaseAngle(Angle value)`	Copy the current immutable object by setting a value for the `interBaseAngle` attribute.
`ImmutableBasePairParameters`	ImmutableBasePairParameters.`withOpening(Angle value)`	Copy the current immutable object by setting a value for the `opening` attribute.
`ImmutableBasePairParameters`	ImmutableBasePairParameters.`withPropeller(Angle value)`	Copy the current immutable object by setting a value for the `propeller` attribute.

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
`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.
`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.
`ImmutableTorsionAngleValue.Builder`	ImmutableTorsionAngleValue.Builder.`value(Angle value)`	Initializes the value for the `value` attribute.
`ImmutableTorsionAngleDelta`	ImmutableTorsionAngleDelta.`withDelta(Angle value)`	Copy the current immutable object by setting a value for the `delta` attribute.
`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.