Package pl.poznan.put.rna

Class PseudophasePuckerType

java.lang.Object

pl.poznan.put.rna.PseudophasePuckerType

All Implemented Interfaces:

DisplayableExportable, TorsionAngleType

Direct Known Subclasses:

ImmutablePseudophasePuckerType

@Immutable(singleton=true)
public abstract class PseudophasePuckerType
extends Object
implements TorsionAngleType

An angle describing the pseudophase pucker.

Constructor Summary

Constructors

Constructor	Description
PseudophasePuckerType()

Method Summary

Modifier and Type	Method	Description
TorsionAngleValue	calculate(List<PdbResidue> residues, int currentIndex)	Calculates the value of pseudophase pucker according to the formula in Saenger's "Principles of ...".
String	exportName()
String	longDisplayName()
MoleculeType	moleculeType()
String	shortDisplayName()

Methods inherited from class java.lang.Object

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

Constructor Detail

PseudophasePuckerType

public PseudophasePuckerType()

Method Detail

shortDisplayName

public final String shortDisplayName()

Specified by:

shortDisplayName in interface DisplayableExportable

Returns:

A short name to be shown in UI summary.

longDisplayName

public final String longDisplayName()

Specified by:

longDisplayName in interface DisplayableExportable

Returns:

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

exportName

public final String exportName()

Specified by:

exportName in interface DisplayableExportable

Returns:

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

moleculeType

public final 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 value of pseudophase pucker according to the formula in Saenger's "Principles of ...". Namely: atan2((nu1 + nu4) - (nu0 - nu3), nu2 * 2.0 * sin(36 deg) + sin(72 deg))

Specified by:

calculate in interface TorsionAngleType

Parameters:

residues - The list of residues.

currentIndex - The index of residue on the list.

Returns:

The value of pseudophase pucker angle.