Package pl.poznan.put.rna

Interface Nucleobase

All Superinterfaces:

NucleicAcidResidueComponent, ResidueComponent, ResidueInformationProvider

All Known Subinterfaces:

Purine, Pyrimidine

public interface Nucleobase
extends NucleicAcidResidueComponent, ResidueInformationProvider

A nucleobase (adenine, cytosine, guanine, uracil or thymine).

Method Summary

Modifier and Type	Method	Description
default org.apache.commons.math3.geometry.euclidean.threed.Vector3D	edgeVector(PdbResidue residue, NucleobaseEdge edge)
org.apache.commons.lang3.tuple.Pair<AtomName,AtomName>	edgeVectorAtoms(NucleobaseEdge edge)
default MoleculeType	moleculeType()
default NucleotideComponentType	nucleotideComponentType()
default Map<AtomName,PdbAtomLine>	standardReferenceFrame()
String	standardReferenceFrameString()

Methods inherited from interface pl.poznan.put.pdb.analysis.ResidueComponent

additionalAtoms, requiredAtoms

Methods inherited from interface pl.poznan.put.pdb.analysis.ResidueInformationProvider

aliases, defaultName, moleculeComponents, oneLetterName, torsionAngleTypes

Method Details

standardReferenceFrameString

String standardReferenceFrameString()

edgeVectorAtoms

org.apache.commons.lang3.tuple.Pair<AtomName,AtomName> edgeVectorAtoms(NucleobaseEdge edge)

standardReferenceFrame

default Map<AtomName,PdbAtomLine> standardReferenceFrame()

edgeVector

default org.apache.commons.math3.geometry.euclidean.threed.Vector3D edgeVector(PdbResidue residue,
 NucleobaseEdge edge)

moleculeType

default MoleculeType moleculeType()

Specified by:

moleculeType in interface ResidueInformationProvider

Returns:

The type of molecule of this residue (RNA or protein).

nucleotideComponentType

default NucleotideComponentType nucleotideComponentType()

Specified by:

nucleotideComponentType in interface NucleicAcidResidueComponent

Returns:

The type of this nucleotide component.