Package pl.poznan.put.torsion

Interface AtomBasedTorsionAngleType

All Superinterfaces:

DisplayableExportable, TorsionAngleType

All Known Implementing Classes:

ImmutableAtomBasedTorsionAngleType

@Immutable
public interface AtomBasedTorsionAngleType
extends TorsionAngleType

A torsion angle which is defined upon four atomic coordinates.

Method Summary

Modifier and Type	Method	Description
Quadruple<AtomName>	atoms()
default TorsionAngleValue	calculate(List<PdbResidue> residues, int currentIndex)	Calculates the value of this torsion angle (see Angle.torsionAngle(Vector3D, Vector3D, Vector3D, Vector3D)).
default TorsionAngleValue	calculate(PdbAtomLine a1, PdbAtomLine a2, PdbAtomLine a3, PdbAtomLine a4)	Calculates a value of this torsion angle type given atoms explicitly.
String	exportName()
default List<AtomPair>	findAtomPairs(List<PdbResidue> residues, int currentIndex)	Applies residueRule() on the given list of residues to find three pairs of atoms: (a1, a2), (a2, a3), (a3, a4).
default boolean	isPseudoTorsion()
default String	longDisplayName()
MoleculeType	moleculeType()
Quadruple<Integer>	residueRule()
String	shortDisplayName()

Method Detail

moleculeType

@Parameter(order=1)
MoleculeType moleculeType()

Specified by:

moleculeType in interface TorsionAngleType

Returns:

The molecule this torsion angle is defined for.

calculate

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

Calculates the value of this torsion angle (see Angle.torsionAngle(Vector3D, Vector3D, Vector3D, Vector3D)).

Specified by:

calculate in interface TorsionAngleType

Parameters:

residues - The list of residues.

currentIndex - The index of current residue.

Returns:

The value of torsion angle of this type.

shortDisplayName

@Parameter(order=2)
String shortDisplayName()

Specified by:

shortDisplayName in interface DisplayableExportable

Returns:

A short name to be shown in UI summary.

longDisplayName

default String longDisplayName()

Specified by:

longDisplayName in interface DisplayableExportable

Returns:

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

exportName

@Parameter(order=3)
String exportName()

Specified by:

exportName in interface DisplayableExportable

Returns:

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

atoms

@Parameter(order=4)
Quadruple<AtomName> atoms()

Returns:

The quadruple of atoms defining this torsion angle type.

residueRule

@Parameter(order=5)
Quadruple<Integer> residueRule()

Returns:

The quadruple of relative indices to take atoms from. For example, a rule (0, 0, 0, 0) means that all atoms are from the same residue, while a rule (-1, 0, 0, 0) means that the first atom is taken from the preceding residue.

isPseudoTorsion

@Default
default boolean isPseudoTorsion()

Returns:

True if this is an instance of a pseudo-torsion angle type. A pseudo-torsion angle type is defined on a quadruple of atoms which are not connected (See NucleotideTorsionAngle.ETA or AminoAcidTorsionAngle.CALPHA).

calculate

default TorsionAngleValue calculate(PdbAtomLine a1,
                                    PdbAtomLine a2,
                                    PdbAtomLine a3,
                                    PdbAtomLine a4)

Calculates a value of this torsion angle type given atoms explicitly.

Parameters:

a1 - The first atom.

a2 - The second atom.

a3 - The third atom.

a4 - The fourth atom.

Returns:

A value of this torsion angle type.

findAtomPairs

default List<AtomPair> findAtomPairs(List<PdbResidue> residues,
                                     int currentIndex)

Applies residueRule() on the given list of residues to find three pairs of atoms: (a1, a2), (a2, a3), (a3, a4).

Parameters:

residues - The list of residues.

currentIndex - Index of the current residue.

Returns:

The list of atom pairs with three entries: (a1, a2), (a2, a3), (a3, a4)