Package pl.poznan.put.torsion

Class AverageTorsionAngleType

java.lang.Object

pl.poznan.put.torsion.AverageTorsionAngleType

All Implemented Interfaces:

DisplayableExportable, MasterTorsionAngleType, TorsionAngleType

Direct Known Subclasses:

ImmutableAverageTorsionAngleType

@Immutable
public abstract class AverageTorsionAngleType
extends Object
implements TorsionAngleType, MasterTorsionAngleType

An average of one or more basic angle types.

Constructor Summary

Constructors

Constructor	Description
AverageTorsionAngleType()

Method Summary

Modifier and Type	Method	Description
List<TorsionAngleType>	angleTypes()
TorsionAngleValue	calculate(Collection<TorsionAngleValue> values)	Calculates the average torsion angle value by collecting basic angle values and creating an AngleSample out of them to get the mean direction.
TorsionAngleValue	calculate(List<PdbResidue> residues, int currentIndex)	Calculates the average torsion angle value by calculating basic angle values and creating an AngleSample out of them to get the mean direction.
abstract List<MasterTorsionAngleType>	consideredAngles()
protected Set<TorsionAngleType>	consideredBasicAngleTypes()
String	exportName()
static AverageTorsionAngleType	forNucleicAcid()
static AverageTorsionAngleType	forProtein()
String	longDisplayName()
abstract MoleculeType	moleculeType()
Range	range(Angle angle)	Finds a matching range for the given angle value.
String	shortDisplayName()

Methods inherited from class java.lang.Object

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

Constructor Detail

AverageTorsionAngleType

public AverageTorsionAngleType()

Method Detail

forProtein

public static AverageTorsionAngleType forProtein()

Returns:

The default instance for proteins based on AminoAcidTorsionAngle.PHI, AminoAcidTorsionAngle.PSI, and AminoAcidTorsionAngle.OMEGA.

forNucleicAcid

public static AverageTorsionAngleType forNucleicAcid()

Returns:

The default instance for nucleic acids based on NucleotideTorsionAngle.ALPHA, NucleotideTorsionAngle.BETA, NucleotideTorsionAngle.GAMMA, NucleotideTorsionAngle.DELTA, NucleotideTorsionAngle.EPSILON, NucleotideTorsionAngle.ZETA and NucleotideTorsionAngle.CHI.

moleculeType

@Parameter(order=1)
public abstract MoleculeType moleculeType()

Specified by:

moleculeType in interface TorsionAngleType

Returns:

The molecule this torsion angle is defined for.

calculate

public final TorsionAngleValue calculate(List<PdbResidue> residues,
                                         int currentIndex)

Calculates the average torsion angle value by calculating basic angle values and creating an AngleSample out of them to get the mean direction.

Specified by:

calculate in interface TorsionAngleType

Parameters:

residues - The list of residues.

currentIndex - The index of current residue.

Returns:

The average value of torsion angles condigured for this type.

consideredAngles

@Parameter(order=2)
public abstract List<MasterTorsionAngleType> consideredAngles()

Returns:

The list of angle types to calculate average from.

shortDisplayName

@Lazy
public String shortDisplayName()

Specified by:

shortDisplayName in interface DisplayableExportable

Returns:

A short name to be shown in UI summary.

longDisplayName

public String longDisplayName()

Specified by:

longDisplayName in interface DisplayableExportable

Returns:

A long name to be shown in UI, may contain Unicode.

exportName

@Lazy
public String exportName()

Specified by:

exportName in interface DisplayableExportable

Returns:

A name to be used during export to output file, should be ASCII only.

calculate

public final TorsionAngleValue calculate(Collection<TorsionAngleValue> values)

Calculates the average torsion angle value by collecting basic angle values and creating an AngleSample out of them to get the mean direction.

Parameters:

values - The collection of torsion angle values.

Returns:

The average value of torsion angles condigured for this type.

angleTypes

public final List<TorsionAngleType> angleTypes()

Specified by:

angleTypes in interface MasterTorsionAngleType

Returns:

The list of basic angle types this type consists of.

range

public final Range range(Angle angle)

Description copied from interface: MasterTorsionAngleType

Finds a matching range for the given angle value.

Specified by:

range in interface MasterTorsionAngleType

Parameters:

angle - The angle value to find the range for.

Returns:

An instance of Range which incorporates this angle.

consideredBasicAngleTypes

@Lazy
protected Set<TorsionAngleType> consideredBasicAngleTypes()