Uses of Interface
pl.poznan.put.structure.ClassifiedBasePair
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Packages that use ClassifiedBasePair Package Description pl.poznan.put.rna pl.poznan.put.structure Package contains classes useful in describing secondary structure (base pairs, helices, etc.)pl.poznan.put.structure.formats -
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Uses of ClassifiedBasePair in pl.poznan.put.rna
Method parameters in pl.poznan.put.rna with type arguments of type ClassifiedBasePair Modifier and Type Method Description static PdbModelChainReorderer. reorderAtoms(PdbModel model, Collection<? extends ClassifiedBasePair> basePairs)Reorders chains according to given canonical base pairs to keep connected chains together while minimizing the overall pseudoknot order. -
Uses of ClassifiedBasePair in pl.poznan.put.structure
Classes in pl.poznan.put.structure that implement ClassifiedBasePair Modifier and Type Class Description classAnalyzedBasePairA pair of residues with metadata taken from analysis tool.classImmutableAnalyzedBasePairImmutable implementation ofAnalyzedBasePair.classImmutableQuantifiedBasePairImmutable implementation ofQuantifiedBasePair.classQuantifiedBasePairA base pair which is classified and quantified with numerical parameters.Methods in pl.poznan.put.structure that return ClassifiedBasePair Modifier and Type Method Description ClassifiedBasePairAnalyzedBasePair. invert()ClassifiedBasePairClassifiedBasePair. invert()ClassifiedBasePairQuantifiedBasePair. invert()Methods in pl.poznan.put.structure that return types with arguments of type ClassifiedBasePair Modifier and Type Method Description static Collection<ClassifiedBasePair>CanonicalStructureExtractor. basePairs(ResidueCollection residueCollection)Methods in pl.poznan.put.structure with parameters of type ClassifiedBasePair Modifier and Type Method Description default intClassifiedBasePair. compareTo(ClassifiedBasePair t)ImmutableAnalyzedBasePair.BuilderImmutableAnalyzedBasePair.Builder. from(ClassifiedBasePair instance)Fill a builder with attribute values from the providedpl.poznan.put.structure.ClassifiedBasePairinstance.ImmutableQuantifiedBasePair.BuilderImmutableQuantifiedBasePair.Builder. from(ClassifiedBasePair instance)Fill a builder with attribute values from the providedpl.poznan.put.structure.ClassifiedBasePairinstance. -
Uses of ClassifiedBasePair in pl.poznan.put.structure.formats
Methods in pl.poznan.put.structure.formats that return types with arguments of type ClassifiedBasePair Modifier and Type Method Description Collection<? extends ClassifiedBasePair>ImmutableMultiLineDotBracket. basePairs()abstract Collection<? extends ClassifiedBasePair>MultiLineDotBracket. basePairs()protected Collection<ClassifiedBasePair>ImmutableMultiLineDotBracket. basePairs5to3()protected Collection<ClassifiedBasePair>MultiLineDotBracket. basePairs5to3()Method parameters in pl.poznan.put.structure.formats with type arguments of type ClassifiedBasePair Modifier and Type Method Description ImmutableMultiLineDotBracket.BuilderImmutableMultiLineDotBracket.Builder. basePairs(Collection<? extends ClassifiedBasePair> basePairs)Initializes the value for thebasePairsattribute.List<DotBracketFromPdb>CombinedStrandFromPdb. combineStrands(List<ClassifiedBasePair> unused)List<DotBracketFromPdb>DefaultDotBracketFromPdb. combineStrands(List<ClassifiedBasePair> nonCanonical)List<DotBracketFromPdb>DotBracketFromPdb. combineStrands(List<ClassifiedBasePair> nonCanonical)Combines strands which are connected via canonical or non-canonical base pairs.static BpSeqBpSeq. fromBasePairs(List<PdbNamedResidueIdentifier> residues, Collection<? extends ClassifiedBasePair> basePairs)Creates an instance of BPSEQ from a list of residue identifiers and a list of base pairs.static ImmutableMultiLineDotBracketImmutableMultiLineDotBracket. of(String sequence, Collection<? extends ClassifiedBasePair> basePairs)Construct a new immutableMultiLineDotBracketinstance.ImmutableMultiLineDotBracketImmutableMultiLineDotBracket. withBasePairs(Collection<? extends ClassifiedBasePair> value)Copy the current immutable object by setting a value for thebasePairsattribute.
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