Index (BioCommons 3.1.8 API)

A B C D E F G H I K L M N O P Q R S T U V W X Y Z _
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

A

a() - Method in class pl.poznan.put.types.ImmutableQuadruple
a() - Method in interface pl.poznan.put.types.Quadruple
a(T) - Method in class pl.poznan.put.types.ImmutableQuadruple.Builder: Initializes the value for the a attribute.
AbstractCombinedStrand - Class in pl.poznan.put.structure.formats
AbstractCombinedStrand() - Constructor for class pl.poznan.put.structure.formats.AbstractCombinedStrand
AbstractPdbModel - Class in pl.poznan.put.pdb.analysis: A structure which detects residues from atoms alone and then chains from residues.
AbstractPdbModel() - Constructor for class pl.poznan.put.pdb.analysis.AbstractPdbModel
AbstractRegionRemover - Class in pl.poznan.put.structure.pseudoknots.elimination: Java implementation of region removal algorithm as presented in: Smit, S. et al., 2008.
AbstractRegionRemover() - Constructor for class pl.poznan.put.structure.pseudoknots.elimination.AbstractRegionRemover
add(ResidueCollection) - Method in class pl.poznan.put.pdb.analysis.ResidueCollection.CifBuilder: Add a residue collection to be serialized into mmCIF format.
add(ResidueCollection) - Method in class pl.poznan.put.pdb.analysis.ResidueCollection.PdbBuilder: Add a new residue collection to the builder.
add(ResidueCollection, String) - Method in class pl.poznan.put.pdb.analysis.ResidueCollection.CifBuilder: Add a residue collection to be serialized into mmCIF format.
add(ResidueCollection, String) - Method in class pl.poznan.put.pdb.analysis.ResidueCollection.PdbBuilder: Add a new named residue collection to the builder.
add(ResidueCollection, String, String) - Method in class pl.poznan.put.pdb.analysis.ResidueCollection.CifBuilder: Add a residue collection to be serialized into mmCIF format.
add(ResidueCollection, String, String, int) - Method in class pl.poznan.put.pdb.analysis.ResidueCollection.CifBuilder: Add a residue collection to be serialized into mmCIF format.
addAllArguments(Iterable<String>) - Method in class pl.poznan.put.utility.ImmutableExecHelper.Builder: Adds elements to arguments list.
addAllAtoms(Iterable<? extends PdbAtomLine>) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel.Builder: Adds elements to atoms list.
addAllAtoms(Iterable<? extends PdbAtomLine>) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbModel.Builder: Adds elements to atoms list.
addAllAtoms(Iterable<? extends PdbAtomLine>) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbResidue.Builder: Adds elements to atoms list.
addAllBasePairs(Iterable<? extends QuantifiedBasePair>) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel.Builder: Adds elements to basePairs list.
addAllChainTerminatedAfter(Iterable<? extends PdbResidueIdentifier>) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel.Builder: Adds elements to chainTerminatedAfter set.
addAllChainTerminatedAfter(Iterable<? extends PdbResidueIdentifier>) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbModel.Builder: Adds elements to chainTerminatedAfter set.
addAllCombineStrands(Iterable<? extends DotBracket>) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultStrand.Builder: Adds elements to combineStrands list.
addAllCombineStrands(Iterable<? extends DotBracket>) - Method in class pl.poznan.put.structure.formats.ImmutableStrandView.Builder: Adds elements to combineStrands list.
addAllConsideredAngles(Iterable<? extends MasterTorsionAngleType>) - Method in class pl.poznan.put.torsion.ImmutableAverageTorsionAngleType.Builder: Adds elements to consideredAngles list.
addAllEntries(Iterable<? extends BpSeq.Entry>) - Method in class pl.poznan.put.structure.formats.ImmutableBpSeq.Builder: Adds elements to entries sortedSet.
addAllEntries(Iterable<? extends BpSeq.Entry>) - Method in class pl.poznan.put.structure.pseudoknots.ImmutableRegion.Builder: Adds elements to entries list.
addAllEntries(Iterable<? extends Ct.ExtendedEntry>) - Method in class pl.poznan.put.structure.formats.ImmutableCt.Builder: Adds elements to entries sortedSet.
addAllExperimentalTechniques(Iterable<? extends ExperimentalTechnique>) - Method in class pl.poznan.put.pdb.ImmutablePdbExpdtaLine.Builder: Adds elements to experimentalTechniques list.
addAllIdentifierSet(Iterable<? extends PdbResidueIdentifier>) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracketFromPdb.Builder: Adds elements to identifierSet set.
addAllInputStrands(Iterable<? extends Strand>) - Method in class pl.poznan.put.structure.formats.ImmutableCombinedStrand.Builder: Adds elements to inputStrands list.
addAllInputStrands(Iterable<? extends Strand>) - Method in class pl.poznan.put.structure.formats.ImmutableCombinedStrandFromPdb.Builder: Adds elements to inputStrands list.
addAllMissingResidues(Iterable<? extends PdbRemark465Line>) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel.Builder: Adds elements to missingResidues list.
addAllMissingResidues(Iterable<? extends PdbRemark465Line>) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbModel.Builder: Adds elements to missingResidues list.
addAllModifiedResidues(Iterable<? extends PdbModresLine>) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel.Builder: Adds elements to modifiedResidues list.
addAllModifiedResidues(Iterable<? extends PdbModresLine>) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbModel.Builder: Adds elements to modifiedResidues list.
addAllNames(Iterable<String>) - Method in class pl.poznan.put.types.ImmutableDistanceMatrix.Builder: Adds elements to names list.
addAllNucleotides(Iterable<? extends Nucleotide>) - Method in class pl.poznan.put.external.dssr.ImmutableDssrJson.Builder: Adds elements to nucleotides list.
addAllPairs(Iterable<? extends Pair>) - Method in class pl.poznan.put.external.dssr.ImmutableDssrJson.Builder: Adds elements to pairs list.
addAllRegions(Iterable<? extends Region>) - Method in class pl.poznan.put.structure.pseudoknots.dp.ImmutableConflictClique.Builder: Adds elements to regions set.
addAllRegions(Iterable<? extends Region>) - Method in class pl.poznan.put.structure.pseudoknots.ImmutableConflictGraph.Builder: Adds elements to regions list.
addAllResidues(Iterable<? extends PdbResidue>) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultResidueCollection.Builder: Adds elements to residues list.
addAllResidues(Iterable<? extends PdbResidue>) - Method in class pl.poznan.put.pdb.analysis.ImmutablePdbChain.Builder: Adds elements to residues list.
addAllResidues(Iterable<? extends PdbResidue>) - Method in class pl.poznan.put.pdb.analysis.ImmutablePdbCompactFragment.Builder: Adds elements to residues list.
addAllStrands(Iterable<? extends Strand>) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracket.Builder: Adds elements to strands list.
addAllStrands(Iterable<? extends Strand>) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracketFromPdb.Builder: Adds elements to strands list.
addAllSymbols(Iterable<? extends DotBracketSymbol>) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultStrand.Builder: Adds elements to symbols list.
addAllSymbols(Iterable<? extends DotBracketSymbol>) - Method in class pl.poznan.put.structure.formats.ImmutableTerminalMissing.Builder: Adds elements to symbols list.
addAllValues(Iterable<? extends TorsionAngleValue>) - Method in class pl.poznan.put.pdb.analysis.ImmutableResidueTorsionAngles.Builder: Adds elements to values list.
addArguments(String) - Method in class pl.poznan.put.utility.ImmutableExecHelper.Builder: Adds one element to arguments list.
addArguments(String...) - Method in class pl.poznan.put.utility.ImmutableExecHelper.Builder: Adds elements to arguments list.
addAtoms(PdbAtomLine) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel.Builder: Adds one element to atoms list.
addAtoms(PdbAtomLine) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbModel.Builder: Adds one element to atoms list.
addAtoms(PdbAtomLine) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbResidue.Builder: Adds one element to atoms list.
addAtoms(PdbAtomLine...) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel.Builder: Adds elements to atoms list.
addAtoms(PdbAtomLine...) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbModel.Builder: Adds elements to atoms list.
addAtoms(PdbAtomLine...) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbResidue.Builder: Adds elements to atoms list.
addBasePairs(QuantifiedBasePair) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel.Builder: Adds one element to basePairs list.
addBasePairs(QuantifiedBasePair...) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel.Builder: Adds elements to basePairs list.
addChainTerminatedAfter(PdbResidueIdentifier) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel.Builder: Adds one element to chainTerminatedAfter set.
addChainTerminatedAfter(PdbResidueIdentifier) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbModel.Builder: Adds one element to chainTerminatedAfter set.
addChainTerminatedAfter(PdbResidueIdentifier...) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel.Builder: Adds elements to chainTerminatedAfter set.
addChainTerminatedAfter(PdbResidueIdentifier...) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbModel.Builder: Adds elements to chainTerminatedAfter set.
addCombineStrands(DotBracket) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultStrand.Builder: Adds one element to combineStrands list.
addCombineStrands(DotBracket) - Method in class pl.poznan.put.structure.formats.ImmutableStrandView.Builder: Adds one element to combineStrands list.
addCombineStrands(DotBracket...) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultStrand.Builder: Adds elements to combineStrands list.
addCombineStrands(DotBracket...) - Method in class pl.poznan.put.structure.formats.ImmutableStrandView.Builder: Adds elements to combineStrands list.
addConsideredAngles(MasterTorsionAngleType) - Method in class pl.poznan.put.torsion.ImmutableAverageTorsionAngleType.Builder: Adds one element to consideredAngles list.
addConsideredAngles(MasterTorsionAngleType...) - Method in class pl.poznan.put.torsion.ImmutableAverageTorsionAngleType.Builder: Adds elements to consideredAngles list.
addEntries(BpSeq.Entry) - Method in class pl.poznan.put.structure.formats.ImmutableBpSeq.Builder: Adds one element to entries sortedSet.
addEntries(BpSeq.Entry) - Method in class pl.poznan.put.structure.pseudoknots.ImmutableRegion.Builder: Adds one element to entries list.
addEntries(BpSeq.Entry...) - Method in class pl.poznan.put.structure.formats.ImmutableBpSeq.Builder: Adds elements to entries sortedSet.
addEntries(BpSeq.Entry...) - Method in class pl.poznan.put.structure.pseudoknots.ImmutableRegion.Builder: Adds elements to entries list.
addEntries(Ct.ExtendedEntry) - Method in class pl.poznan.put.structure.formats.ImmutableCt.Builder: Adds one element to entries sortedSet.
addEntries(Ct.ExtendedEntry...) - Method in class pl.poznan.put.structure.formats.ImmutableCt.Builder: Adds elements to entries sortedSet.
addExperimentalTechniques(ExperimentalTechnique) - Method in class pl.poznan.put.pdb.ImmutablePdbExpdtaLine.Builder: Adds one element to experimentalTechniques list.
addExperimentalTechniques(ExperimentalTechnique...) - Method in class pl.poznan.put.pdb.ImmutablePdbExpdtaLine.Builder: Adds elements to experimentalTechniques list.
addIdentifierSet(PdbResidueIdentifier) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracketFromPdb.Builder: Adds one element to identifierSet set.
addIdentifierSet(PdbResidueIdentifier...) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracketFromPdb.Builder: Adds elements to identifierSet set.
addInputStrands(Strand) - Method in class pl.poznan.put.structure.formats.ImmutableCombinedStrand.Builder: Adds one element to inputStrands list.
addInputStrands(Strand) - Method in class pl.poznan.put.structure.formats.ImmutableCombinedStrandFromPdb.Builder: Adds one element to inputStrands list.
addInputStrands(Strand...) - Method in class pl.poznan.put.structure.formats.ImmutableCombinedStrand.Builder: Adds elements to inputStrands list.
addInputStrands(Strand...) - Method in class pl.poznan.put.structure.formats.ImmutableCombinedStrandFromPdb.Builder: Adds elements to inputStrands list.
additionalAtoms() - Method in interface pl.poznan.put.pdb.analysis.ResidueComponent
additionalAtoms() - Method in class pl.poznan.put.rna.Phosphate
addMissingResidues(PdbRemark465Line) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel.Builder: Adds one element to missingResidues list.
addMissingResidues(PdbRemark465Line) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbModel.Builder: Adds one element to missingResidues list.
addMissingResidues(PdbRemark465Line...) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel.Builder: Adds elements to missingResidues list.
addMissingResidues(PdbRemark465Line...) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbModel.Builder: Adds elements to missingResidues list.
addModifiedResidues(PdbModresLine) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel.Builder: Adds one element to modifiedResidues list.
addModifiedResidues(PdbModresLine) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbModel.Builder: Adds one element to modifiedResidues list.
addModifiedResidues(PdbModresLine...) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel.Builder: Adds elements to modifiedResidues list.
addModifiedResidues(PdbModresLine...) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbModel.Builder: Adds elements to modifiedResidues list.
addNames(String) - Method in class pl.poznan.put.types.ImmutableDistanceMatrix.Builder: Adds one element to names list.
addNames(String...) - Method in class pl.poznan.put.types.ImmutableDistanceMatrix.Builder: Adds elements to names list.
addNucleotides(Nucleotide) - Method in class pl.poznan.put.external.dssr.ImmutableDssrJson.Builder: Adds one element to nucleotides list.
addNucleotides(Nucleotide...) - Method in class pl.poznan.put.external.dssr.ImmutableDssrJson.Builder: Adds elements to nucleotides list.
addPairs(Pair) - Method in class pl.poznan.put.external.dssr.ImmutableDssrJson.Builder: Adds one element to pairs list.
addPairs(Pair...) - Method in class pl.poznan.put.external.dssr.ImmutableDssrJson.Builder: Adds elements to pairs list.
addRegions(Region) - Method in class pl.poznan.put.structure.pseudoknots.dp.ImmutableConflictClique.Builder: Adds one element to regions set.
addRegions(Region) - Method in class pl.poznan.put.structure.pseudoknots.ImmutableConflictGraph.Builder: Adds one element to regions list.
addRegions(Region...) - Method in class pl.poznan.put.structure.pseudoknots.dp.ImmutableConflictClique.Builder: Adds elements to regions set.
addRegions(Region...) - Method in class pl.poznan.put.structure.pseudoknots.ImmutableConflictGraph.Builder: Adds elements to regions list.
addResidues(PdbResidue) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultResidueCollection.Builder: Adds one element to residues list.
addResidues(PdbResidue) - Method in class pl.poznan.put.pdb.analysis.ImmutablePdbChain.Builder: Adds one element to residues list.
addResidues(PdbResidue) - Method in class pl.poznan.put.pdb.analysis.ImmutablePdbCompactFragment.Builder: Adds one element to residues list.
addResidues(PdbResidue...) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultResidueCollection.Builder: Adds elements to residues list.
addResidues(PdbResidue...) - Method in class pl.poznan.put.pdb.analysis.ImmutablePdbChain.Builder: Adds elements to residues list.
addResidues(PdbResidue...) - Method in class pl.poznan.put.pdb.analysis.ImmutablePdbCompactFragment.Builder: Adds elements to residues list.
addStrands(Strand) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracket.Builder: Adds one element to strands list.
addStrands(Strand) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracketFromPdb.Builder: Adds one element to strands list.
addStrands(Strand...) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracket.Builder: Adds elements to strands list.
addStrands(Strand...) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracketFromPdb.Builder: Adds elements to strands list.
addSymbols(DotBracketSymbol) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultStrand.Builder: Adds one element to symbols list.
addSymbols(DotBracketSymbol) - Method in class pl.poznan.put.structure.formats.ImmutableTerminalMissing.Builder: Adds one element to symbols list.
addSymbols(DotBracketSymbol...) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultStrand.Builder: Adds elements to symbols list.
addSymbols(DotBracketSymbol...) - Method in class pl.poznan.put.structure.formats.ImmutableTerminalMissing.Builder: Adds elements to symbols list.
addValues(TorsionAngleValue) - Method in class pl.poznan.put.pdb.analysis.ImmutableResidueTorsionAngles.Builder: Adds one element to values list.
addValues(TorsionAngleValue...) - Method in class pl.poznan.put.pdb.analysis.ImmutableResidueTorsionAngles.Builder: Adds elements to values list.
ADENINE - Enum constant in enum pl.poznan.put.rna.Nucleotide
after() - Method in class pl.poznan.put.structure.formats.Ct.ExtendedEntry
after() - Method in class pl.poznan.put.structure.formats.ImmutableExtendedEntry
after(int) - Method in class pl.poznan.put.structure.formats.ImmutableExtendedEntry.Builder: Initializes the value for the after attribute.
ALANINE - Enum constant in enum pl.poznan.put.protein.AminoAcid
aliases() - Method in interface pl.poznan.put.pdb.analysis.ResidueInformationProvider
aliases() - Method in enum pl.poznan.put.protein.AminoAcid
aliases() - Method in enum pl.poznan.put.rna.Nucleotide
allAngleTypes() - Method in enum pl.poznan.put.pdb.analysis.MoleculeType: Generates a list of all atom-based torsion angle types for this molecule type.
ALPHA - Enum constant in enum pl.poznan.put.rna.NucleotideTorsionAngle
ALPHA - Static variable in class pl.poznan.put.constant.Unicode
alternateLocation() - Method in class pl.poznan.put.pdb.ImmutablePdbAtomLine
alternateLocation() - Method in class pl.poznan.put.pdb.PdbAtomLine
alternateLocation(String) - Method in class pl.poznan.put.pdb.ImmutablePdbAtomLine.Builder: Initializes the optional value alternateLocation to alternateLocation.
alternateLocation(Optional<String>) - Method in class pl.poznan.put.pdb.ImmutablePdbAtomLine.Builder: Initializes the optional value alternateLocation to alternateLocation.
AminoAcid - Enum in pl.poznan.put.protein: An amino acid with all details regarding its atoms, torsion angles, etc.
AminoAcidTorsionAngle - Enum in pl.poznan.put.protein: A torsion angle defined for proteins.
AnalyzedBasePair - Class in pl.poznan.put.structure: A pair of residues with metadata taken from analysis tool.
AnalyzedBasePair() - Constructor for class pl.poznan.put.structure.AnalyzedBasePair
Angle - Class in pl.poznan.put.circular: A measurement for which one can distinguish a direction (i.e. [0..360) degrees)
Angle() - Constructor for class pl.poznan.put.circular.Angle
AngleFormat - Class in pl.poznan.put.utility: A collection of formatting methods for angular values.
AngleSample - Class in pl.poznan.put.circular.samples: A sample of angular values and computed statistics.
AngleSample() - Constructor for class pl.poznan.put.circular.samples.AngleSample
AngleTransformation - Enum in pl.poznan.put.circular.enums: A transformation used to display circular diagrams.
angleType() - Method in enum pl.poznan.put.rna.Chi
angleType() - Method in class pl.poznan.put.torsion.ImmutableTorsionAngleDelta
angleType() - Method in class pl.poznan.put.torsion.ImmutableTorsionAngleValue
angleType() - Method in class pl.poznan.put.torsion.TorsionAngleDelta
angleType() - Method in class pl.poznan.put.torsion.TorsionAngleValue
angleType(MasterTorsionAngleType) - Method in class pl.poznan.put.torsion.ImmutableTorsionAngleDelta.Builder: Initializes the value for the angleType attribute.
angleType(TorsionAngleType) - Method in class pl.poznan.put.torsion.ImmutableTorsionAngleValue.Builder: Initializes the value for the angleType attribute.
angleTypes() - Method in class pl.poznan.put.pdb.analysis.ImmutablePdbCompactFragment
angleTypes() - Method in class pl.poznan.put.pdb.analysis.PdbCompactFragment
angleTypes() - Method in enum pl.poznan.put.protein.AminoAcidTorsionAngle
angleTypes() - Method in enum pl.poznan.put.rna.NucleotideTorsionAngle
angleTypes() - Method in class pl.poznan.put.torsion.AverageTorsionAngleType
angleTypes() - Method in interface pl.poznan.put.torsion.MasterTorsionAngleType
angleValues() - Method in class pl.poznan.put.pdb.analysis.ImmutablePdbCompactFragment
angleValues() - Method in class pl.poznan.put.pdb.analysis.PdbCompactFragment
ANGSTROM - Static variable in class pl.poznan.put.constant.Unicode
ANTI - Enum constant in enum pl.poznan.put.rna.ChiRange
ANTI_TRANS - Enum constant in enum pl.poznan.put.torsion.range.TorsionRange
ANTICLINAL_MINUS - Enum constant in enum pl.poznan.put.torsion.range.TorsionRange
ANTICLINAL_PLUS - Enum constant in enum pl.poznan.put.torsion.range.TorsionRange
areConnected(PdbResidue, PdbResidue) - Method in enum pl.poznan.put.pdb.analysis.MoleculeType: Checks if two residues are connected.
ARGININE - Enum constant in enum pl.poznan.put.protein.AminoAcid
arguments() - Method in class pl.poznan.put.utility.ExecHelper
arguments() - Method in class pl.poznan.put.utility.ImmutableExecHelper
arguments(Iterable<String>) - Method in class pl.poznan.put.utility.ImmutableExecHelper.Builder: Sets or replaces all elements for arguments list.
asDisplayableTableModel() - Method in interface pl.poznan.put.interfaces.Tabular: Generates tabular data to be exported to output file i.e. raw numbers with maximum precision and ASCII only.
asExportableTableModel() - Method in interface pl.poznan.put.interfaces.Tabular: Generates tabular data which are formatted for UI, so they might be long, complex and with Unicode characters.
ASPARAGINE - Enum constant in enum pl.poznan.put.protein.AminoAcid
ASPARTIC_ACID - Enum constant in enum pl.poznan.put.protein.AminoAcid
assumeCanonical(BasePair) - Static method in enum pl.poznan.put.notation.Saenger: Checks which one of Saenger instances matches a canonical base pair of provided sequence.
AtomBasedTorsionAngleType - Interface in pl.poznan.put.torsion: A torsion angle which is defined upon four atomic coordinates.
atomName() - Method in class pl.poznan.put.pdb.ImmutablePdbAtomLine
atomName() - Method in class pl.poznan.put.pdb.PdbAtomLine
atomName(String) - Method in class pl.poznan.put.pdb.ImmutablePdbAtomLine.Builder: Initializes the value for the atomName attribute.
AtomName - Enum in pl.poznan.put.atom: A unified atom name found in PDB and mmCIF files with a list of alternative names.
atomNames() - Method in class pl.poznan.put.pdb.analysis.DefaultPdbResidue
atomNames() - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbResidue
atomNames() - Method in interface pl.poznan.put.pdb.analysis.PdbResidue
AtomPair - Class in pl.poznan.put.torsion: A pair of atoms.
AtomPair() - Constructor for class pl.poznan.put.torsion.AtomPair
atoms() - Method in class pl.poznan.put.pdb.analysis.DefaultCifModel
atoms() - Method in class pl.poznan.put.pdb.analysis.DefaultPdbModel
atoms() - Method in class pl.poznan.put.pdb.analysis.DefaultPdbResidue
atoms() - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel
atoms() - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbModel
atoms() - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbResidue
atoms() - Method in interface pl.poznan.put.pdb.analysis.PdbModel
atoms() - Method in interface pl.poznan.put.pdb.analysis.PdbResidue
atoms() - Method in interface pl.poznan.put.torsion.AtomBasedTorsionAngleType
atoms() - Method in class pl.poznan.put.torsion.ImmutableAtomBasedTorsionAngleType
atoms(Iterable<? extends PdbAtomLine>) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel.Builder: Sets or replaces all elements for atoms list.
atoms(Iterable<? extends PdbAtomLine>) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbModel.Builder: Sets or replaces all elements for atoms list.
atoms(Iterable<? extends PdbAtomLine>) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbResidue.Builder: Sets or replaces all elements for atoms list.
atoms(Quadruple<AtomName>) - Method in class pl.poznan.put.torsion.ImmutableAtomBasedTorsionAngleType.Builder: Initializes the value for the atoms attribute.
AtomType - Enum in pl.poznan.put.atom: An atom type (carbon, hydrogen, etc.) to be found in PDB and mmCIF files.
AverageTorsionAngleType - Class in pl.poznan.put.torsion: An average of one or more basic angle types.
AverageTorsionAngleType() - Constructor for class pl.poznan.put.torsion.AverageTorsionAngleType
avg() - Method in interface pl.poznan.put.atom.BondLength
avg() - Method in class pl.poznan.put.atom.ImmutableBondLength
avg(double) - Method in class pl.poznan.put.atom.ImmutableBondLength.Builder: Initializes the value for the avg attribute.

B

b() - Method in class pl.poznan.put.types.ImmutableQuadruple
b() - Method in interface pl.poznan.put.types.Quadruple
b(T) - Method in class pl.poznan.put.types.ImmutableQuadruple.Builder: Initializes the value for the b attribute.
Backbone - Interface in pl.poznan.put.protein: A backbone in a protein.
BASE - Enum constant in enum pl.poznan.put.rna.NucleotideComponentType
BASE_BASE - Static variable in class pl.poznan.put.rna.InteractionType: A base-base interaction, base pair.
BASE_BASE_1H - Static variable in class pl.poznan.put.rna.InteractionType: A weak base-base interaction, based on a single hydrogen bond only.
BASE_PHOSPHATE - Static variable in class pl.poznan.put.rna.InteractionType: A base-phosphate interaction (see BPh).
BASE_RIBOSE - Static variable in class pl.poznan.put.rna.InteractionType: A base-ribose interaction (see BR).
basePair() - Method in class pl.poznan.put.structure.AnalyzedBasePair
basePair() - Method in interface pl.poznan.put.structure.ClassifiedBasePair
basePair() - Method in class pl.poznan.put.structure.ImmutableAnalyzedBasePair
basePair() - Method in class pl.poznan.put.structure.ImmutableQuantifiedBasePair
basePair() - Method in class pl.poznan.put.structure.QuantifiedBasePair
basePair(BasePair) - Method in class pl.poznan.put.structure.ImmutableAnalyzedBasePair.Builder: Initializes the value for the basePair attribute.
basePair(BasePair) - Method in class pl.poznan.put.structure.ImmutableQuantifiedBasePair.Builder: Initializes the value for the basePair attribute.
BasePair - Class in pl.poznan.put.structure: A pairing between two nucleotides' bases.
BasePair() - Constructor for class pl.poznan.put.structure.BasePair
basePairs() - Method in interface pl.poznan.put.pdb.analysis.CifModel
basePairs() - Method in class pl.poznan.put.pdb.analysis.DefaultCifModel
basePairs() - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel
basePairs() - Method in class pl.poznan.put.structure.formats.ImmutableMultiLineDotBracket
basePairs() - Method in class pl.poznan.put.structure.formats.MultiLineDotBracket
basePairs(Iterable<? extends QuantifiedBasePair>) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel.Builder: Sets or replaces all elements for basePairs list.
basePairs(Collection<? extends ClassifiedBasePair>) - Method in class pl.poznan.put.structure.formats.ImmutableMultiLineDotBracket.Builder: Initializes the value for the basePairs attribute.
basePairs(ResidueCollection) - Static method in class pl.poznan.put.structure.CanonicalStructureExtractor
basePairs5to3() - Method in class pl.poznan.put.structure.formats.ImmutableMultiLineDotBracket
basePairs5to3() - Method in class pl.poznan.put.structure.formats.MultiLineDotBracket
before() - Method in class pl.poznan.put.structure.formats.Ct.ExtendedEntry
before() - Method in class pl.poznan.put.structure.formats.ImmutableExtendedEntry
before(int) - Method in class pl.poznan.put.structure.formats.ImmutableExtendedEntry.Builder: Initializes the value for the before attribute.
begin() - Method in enum pl.poznan.put.rna.ChiRange
begin() - Method in enum pl.poznan.put.rna.Pseudorotation
begin() - Method in class pl.poznan.put.structure.formats.ImmutableStrandView
begin() - Method in interface pl.poznan.put.structure.formats.Strand
begin() - Method in class pl.poznan.put.structure.formats.StrandView
begin() - Method in class pl.poznan.put.structure.pseudoknots.ImmutableRegion
begin() - Method in class pl.poznan.put.structure.pseudoknots.Region
begin() - Method in interface pl.poznan.put.torsion.range.Range
begin() - Method in enum pl.poznan.put.torsion.range.TorsionRange
begin(int) - Method in class pl.poznan.put.structure.formats.ImmutableStrandView.Builder: Initializes the value for the begin attribute.
begin(int) - Method in class pl.poznan.put.structure.pseudoknots.ImmutableRegion.Builder: Initializes the value for the begin attribute.
BETA - Enum constant in enum pl.poznan.put.rna.NucleotideTorsionAngle
BETA - Static variable in class pl.poznan.put.constant.Unicode
betweenPoints(Vector3D, Vector3D, Vector3D) - Static method in class pl.poznan.put.circular.Angle: Calculates angle ABC.
bins() - Method in class pl.poznan.put.circular.Histogram
bins() - Method in class pl.poznan.put.circular.ImmutableHistogram
binWidth() - Method in class pl.poznan.put.circular.Histogram
binWidth() - Method in class pl.poznan.put.circular.ImmutableHistogram
binWidth(double) - Method in class pl.poznan.put.circular.ImmutableHistogram.Builder: Initializes the value for the binWidth attribute.
Bond - Class in pl.poznan.put.atom: An atomic bond and corresponding length.
bondLength() - Method in class pl.poznan.put.torsion.AtomPair
bondLength() - Method in class pl.poznan.put.torsion.ImmutableAtomPair
BondLength - Interface in pl.poznan.put.atom: An atomic bond length.
BOTH_INVALID - Enum constant in enum pl.poznan.put.torsion.TorsionAngleDelta.State
BOTH_VALID - Enum constant in enum pl.poznan.put.torsion.TorsionAngleDelta.State
bothInvalidInstance(MasterTorsionAngleType) - Static method in class pl.poznan.put.torsion.TorsionAngleDelta: Creates an instance of torsion angle delta, where both input angles were invalid.
bph() - Method in class pl.poznan.put.structure.AnalyzedBasePair
bph() - Method in interface pl.poznan.put.structure.ClassifiedBasePair
bph() - Method in class pl.poznan.put.structure.ImmutableAnalyzedBasePair
bph() - Method in class pl.poznan.put.structure.ImmutableQuantifiedBasePair
bph() - Method in class pl.poznan.put.structure.QuantifiedBasePair
bph(BPh) - Method in class pl.poznan.put.structure.ImmutableAnalyzedBasePair.Builder: Initializes the value for the bph attribute.
bph(BPh) - Method in class pl.poznan.put.structure.ImmutableQuantifiedBasePair.Builder: Initializes the value for the bph attribute.
BPh - Enum in pl.poznan.put.notation: A base-phosphate notation described in: Classification and Energetics of the Base-Phosphate Interactions in RNA.
bpSeq(ResidueCollection) - Static method in class pl.poznan.put.structure.CanonicalStructureExtractor: Extracts the canonical secondary structure from the 3D data and outputs it in BPSEQ format.
BpSeq - Class in pl.poznan.put.structure.formats: RNA secondary structure in BPSEQ format.
BpSeq() - Constructor for class pl.poznan.put.structure.formats.BpSeq
BpSeq.Entry - Class in pl.poznan.put.structure.formats: An entry of a BPSEQ data.
br() - Method in class pl.poznan.put.structure.AnalyzedBasePair
br() - Method in interface pl.poznan.put.structure.ClassifiedBasePair
br() - Method in class pl.poznan.put.structure.ImmutableAnalyzedBasePair
br() - Method in class pl.poznan.put.structure.ImmutableQuantifiedBasePair
br() - Method in class pl.poznan.put.structure.QuantifiedBasePair
br(BR) - Method in class pl.poznan.put.structure.ImmutableAnalyzedBasePair.Builder: Initializes the value for the br attribute.
br(BR) - Method in class pl.poznan.put.structure.ImmutableQuantifiedBasePair.Builder: Initializes the value for the br attribute.
BR - Enum in pl.poznan.put.notation: A base-ribose notation described in: Classification and Energetics of the Base-Phosphate Interactions in RNA.
buckle() - Method in class pl.poznan.put.structure.ImmutableQuantifiedBasePair
buckle() - Method in class pl.poznan.put.structure.QuantifiedBasePair
buckle(double) - Method in class pl.poznan.put.structure.ImmutableQuantifiedBasePair.Builder: Initializes the value for the buckle attribute.
build() - Method in class pl.poznan.put.atom.ImmutableBondLength.Builder: Builds a new ImmutableBondLength.
build() - Method in class pl.poznan.put.circular.ImmutableAngle.Builder: Builds a new ImmutableAngle.
build() - Method in class pl.poznan.put.circular.ImmutableHistogram.Builder: Builds a new ImmutableHistogram.
build() - Method in class pl.poznan.put.circular.samples.ImmutableAngleSample.Builder: Builds a new ImmutableAngleSample.
build() - Method in class pl.poznan.put.circular.samples.ImmutableTrigonometricMoment.Builder: Builds a new ImmutableTrigonometricMoment.
build() - Method in class pl.poznan.put.external.dssr.ImmutableDssrJson.Builder: Builds a new ImmutableDssrJson.
build() - Method in class pl.poznan.put.external.dssr.ImmutableNucleotide.Builder: Builds a new ImmutableNucleotide.
build() - Method in class pl.poznan.put.external.dssr.ImmutablePair.Builder: Builds a new ImmutablePair.
build() - Method in class pl.poznan.put.pdb.analysis.ImmutableCifContainer.Builder: Builds a new ImmutableCifContainer.
build() - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel.Builder: Builds a new ImmutableDefaultCifModel.
build() - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbModel.Builder: Builds a new ImmutableDefaultPdbModel.
build() - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbResidue.Builder: Builds a new ImmutableDefaultPdbResidue.
build() - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultResidueCollection.Builder: Builds a new ImmutableDefaultResidueCollection.
build() - Method in class pl.poznan.put.pdb.analysis.ImmutablePdbChain.Builder: Builds a new ImmutablePdbChain.
build() - Method in class pl.poznan.put.pdb.analysis.ImmutablePdbCompactFragment.Builder: Builds a new ImmutablePdbCompactFragment.
build() - Method in class pl.poznan.put.pdb.analysis.ImmutableResidueTorsionAngles.Builder: Builds a new ImmutableResidueTorsionAngles.
build() - Method in class pl.poznan.put.pdb.analysis.ResidueCollection.CifBuilder
build() - Method in class pl.poznan.put.pdb.analysis.ResidueCollection.PdbBuilder
build() - Method in class pl.poznan.put.pdb.ImmutablePdbAtomLine.Builder: Builds a new ImmutablePdbAtomLine.
build() - Method in class pl.poznan.put.pdb.ImmutablePdbExpdtaLine.Builder: Builds a new ImmutablePdbExpdtaLine.
build() - Method in class pl.poznan.put.pdb.ImmutablePdbHeaderLine.Builder: Builds a new ImmutablePdbHeaderLine.
build() - Method in class pl.poznan.put.pdb.ImmutablePdbModresLine.Builder: Builds a new ImmutablePdbModresLine.
build() - Method in class pl.poznan.put.pdb.ImmutablePdbNamedResidueIdentifier.Builder: Builds a new ImmutablePdbNamedResidueIdentifier.
build() - Method in class pl.poznan.put.pdb.ImmutablePdbRemark2Line.Builder: Builds a new ImmutablePdbRemark2Line.
build() - Method in class pl.poznan.put.pdb.ImmutablePdbRemark465Line.Builder: Builds a new ImmutablePdbRemark465Line.
build() - Method in class pl.poznan.put.pdb.ImmutablePdbResidueIdentifier.Builder: Builds a new ImmutablePdbResidueIdentifier.
build() - Method in class pl.poznan.put.pdb.ImmutablePdbTitleLine.Builder: Builds a new ImmutablePdbTitleLine.
build() - Method in class pl.poznan.put.protein.ImmutableBackbone.Builder: Builds a new ImmutableBackbone.
build() - Method in class pl.poznan.put.rna.ImmutableInteractionType.Builder: Builds a new ImmutableInteractionType.
build() - Method in class pl.poznan.put.rna.ImmutablePhosphate.Builder: Builds a new ImmutablePhosphate.
build() - Method in class pl.poznan.put.rna.ImmutablePseudophasePuckerType.Builder: Builds a new ImmutablePseudophasePuckerType.
build() - Method in class pl.poznan.put.rna.ImmutableRibose.Builder: Builds a new ImmutableRibose.
build() - Method in class pl.poznan.put.structure.formats.ImmutableBpSeq.Builder: Builds a new ImmutableBpSeq.
build() - Method in class pl.poznan.put.structure.formats.ImmutableCombinedStrand.Builder: Builds a new ImmutableCombinedStrand.
build() - Method in class pl.poznan.put.structure.formats.ImmutableCombinedStrandFromPdb.Builder: Builds a new ImmutableCombinedStrandFromPdb.
build() - Method in class pl.poznan.put.structure.formats.ImmutableCt.Builder: Builds a new ImmutableCt.
build() - Method in class pl.poznan.put.structure.formats.ImmutableDefaultConverter.Builder: Builds a new ImmutableDefaultConverter.
build() - Method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracket.Builder: Builds a new ImmutableDefaultDotBracket.
build() - Method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracketFromPdb.Builder: Builds a new ImmutableDefaultDotBracketFromPdb.
build() - Method in class pl.poznan.put.structure.formats.ImmutableDefaultStrand.Builder: Builds a new ImmutableDefaultStrand.
build() - Method in class pl.poznan.put.structure.formats.ImmutableEntry.Builder: Builds a new ImmutableEntry.
build() - Method in class pl.poznan.put.structure.formats.ImmutableExtendedEntry.Builder: Builds a new ImmutableExtendedEntry.
build() - Method in class pl.poznan.put.structure.formats.ImmutableMultiLineDotBracket.Builder: Builds a new ImmutableMultiLineDotBracket.
build() - Method in class pl.poznan.put.structure.formats.ImmutableStrandView.Builder: Builds a new ImmutableStrandView.
build() - Method in class pl.poznan.put.structure.formats.ImmutableTerminalMissing.Builder: Builds a new ImmutableTerminalMissing.
build() - Method in class pl.poznan.put.structure.ImmutableAnalyzedBasePair.Builder: Builds a new ImmutableAnalyzedBasePair.
build() - Method in class pl.poznan.put.structure.ImmutableBasePair.Builder: Builds a new ImmutableBasePair.
build() - Method in class pl.poznan.put.structure.ImmutableDotBracketSymbol.Builder: Builds a new ImmutableDotBracketSymbol.
build() - Method in class pl.poznan.put.structure.ImmutableQuantifiedBasePair.Builder: Builds a new ImmutableQuantifiedBasePair.
build() - Method in class pl.poznan.put.structure.pseudoknots.dp.ImmutableConflictClique.Builder: Builds a new ImmutableConflictClique.
build() - Method in class pl.poznan.put.structure.pseudoknots.dp.ImmutableDynamicProgrammingAll.Builder: Builds a new ImmutableDynamicProgrammingAll.
build() - Method in class pl.poznan.put.structure.pseudoknots.elimination.ImmutableMaxConflicts.Builder: Builds a new ImmutableMaxConflicts.
build() - Method in class pl.poznan.put.structure.pseudoknots.elimination.ImmutableMinGain.Builder: Builds a new ImmutableMinGain.
build() - Method in class pl.poznan.put.structure.pseudoknots.ImmutableConflictGraph.Builder: Builds a new ImmutableConflictGraph.
build() - Method in class pl.poznan.put.structure.pseudoknots.ImmutableRegion.Builder: Builds a new ImmutableRegion.
build() - Method in class pl.poznan.put.torsion.ImmutableAtomBasedTorsionAngleType.Builder: Builds a new ImmutableAtomBasedTorsionAngleType.
build() - Method in class pl.poznan.put.torsion.ImmutableAtomPair.Builder: Builds a new ImmutableAtomPair.
build() - Method in class pl.poznan.put.torsion.ImmutableAverageTorsionAngleType.Builder: Builds a new ImmutableAverageTorsionAngleType.
build() - Method in class pl.poznan.put.torsion.ImmutableTorsionAngleDelta.Builder: Builds a new ImmutableTorsionAngleDelta.
build() - Method in class pl.poznan.put.torsion.ImmutableTorsionAngleValue.Builder: Builds a new ImmutableTorsionAngleValue.
build() - Method in class pl.poznan.put.types.ImmutableDistanceMatrix.Builder: Builds a new ImmutableDistanceMatrix.
build() - Method in class pl.poznan.put.types.ImmutableQuadruple.Builder: Builds a new ImmutableQuadruple.
build() - Method in class pl.poznan.put.utility.ImmutableExecHelper.Builder: Builds a new ImmutableExecHelper.
build() - Method in class pl.poznan.put.utility.ImmutableExecutionResult.Builder: Builds a new ImmutableExecutionResult.
builder() - Static method in class pl.poznan.put.atom.ImmutableBondLength: Creates a builder for ImmutableBondLength.
builder() - Static method in class pl.poznan.put.circular.ImmutableAngle: Creates a builder for ImmutableAngle.
builder() - Static method in class pl.poznan.put.circular.ImmutableHistogram: Creates a builder for ImmutableHistogram.
builder() - Static method in class pl.poznan.put.circular.samples.ImmutableAngleSample: Creates a builder for ImmutableAngleSample.
builder() - Static method in class pl.poznan.put.circular.samples.ImmutableTrigonometricMoment: Creates a builder for ImmutableTrigonometricMoment.
builder() - Static method in class pl.poznan.put.external.dssr.ImmutableDssrJson: Creates a builder for ImmutableDssrJson.
builder() - Static method in class pl.poznan.put.external.dssr.ImmutableNucleotide: Creates a builder for ImmutableNucleotide.
builder() - Static method in class pl.poznan.put.external.dssr.ImmutablePair: Creates a builder for ImmutablePair.
builder() - Static method in class pl.poznan.put.pdb.analysis.ImmutableCifContainer: Creates a builder for ImmutableCifContainer.
builder() - Static method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel: Creates a builder for ImmutableDefaultCifModel.
builder() - Static method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbModel: Creates a builder for ImmutableDefaultPdbModel.
builder() - Static method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbResidue: Creates a builder for ImmutableDefaultPdbResidue.
builder() - Static method in class pl.poznan.put.pdb.analysis.ImmutableDefaultResidueCollection: Creates a builder for ImmutableDefaultResidueCollection.
builder() - Static method in class pl.poznan.put.pdb.analysis.ImmutablePdbChain: Creates a builder for ImmutablePdbChain.
builder() - Static method in class pl.poznan.put.pdb.analysis.ImmutablePdbCompactFragment: Creates a builder for ImmutablePdbCompactFragment.
builder() - Static method in class pl.poznan.put.pdb.analysis.ImmutableResidueTorsionAngles: Creates a builder for ImmutableResidueTorsionAngles.
builder() - Static method in class pl.poznan.put.pdb.ImmutablePdbAtomLine: Creates a builder for ImmutablePdbAtomLine.
builder() - Static method in class pl.poznan.put.pdb.ImmutablePdbExpdtaLine: Creates a builder for ImmutablePdbExpdtaLine.
builder() - Static method in class pl.poznan.put.pdb.ImmutablePdbHeaderLine: Creates a builder for ImmutablePdbHeaderLine.
builder() - Static method in class pl.poznan.put.pdb.ImmutablePdbModresLine: Creates a builder for ImmutablePdbModresLine.
builder() - Static method in class pl.poznan.put.pdb.ImmutablePdbNamedResidueIdentifier: Creates a builder for ImmutablePdbNamedResidueIdentifier.
builder() - Static method in class pl.poznan.put.pdb.ImmutablePdbRemark2Line: Creates a builder for ImmutablePdbRemark2Line.
builder() - Static method in class pl.poznan.put.pdb.ImmutablePdbRemark465Line: Creates a builder for ImmutablePdbRemark465Line.
builder() - Static method in class pl.poznan.put.pdb.ImmutablePdbResidueIdentifier: Creates a builder for ImmutablePdbResidueIdentifier.
builder() - Static method in class pl.poznan.put.pdb.ImmutablePdbTitleLine: Creates a builder for ImmutablePdbTitleLine.
builder() - Static method in class pl.poznan.put.protein.ImmutableBackbone: Creates a builder for ImmutableBackbone.
builder() - Static method in class pl.poznan.put.rna.ImmutableInteractionType: Creates a builder for ImmutableInteractionType.
builder() - Static method in class pl.poznan.put.rna.ImmutablePhosphate: Creates a builder for ImmutablePhosphate.
builder() - Static method in class pl.poznan.put.rna.ImmutablePseudophasePuckerType: Creates a builder for ImmutablePseudophasePuckerType.
builder() - Static method in class pl.poznan.put.rna.ImmutableRibose: Creates a builder for ImmutableRibose.
builder() - Static method in class pl.poznan.put.structure.formats.ImmutableBpSeq: Creates a builder for ImmutableBpSeq.
builder() - Static method in class pl.poznan.put.structure.formats.ImmutableCombinedStrand: Creates a builder for ImmutableCombinedStrand.
builder() - Static method in class pl.poznan.put.structure.formats.ImmutableCombinedStrandFromPdb: Creates a builder for ImmutableCombinedStrandFromPdb.
builder() - Static method in class pl.poznan.put.structure.formats.ImmutableCt: Creates a builder for ImmutableCt.
builder() - Static method in class pl.poznan.put.structure.formats.ImmutableDefaultConverter: Creates a builder for ImmutableDefaultConverter.
builder() - Static method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracket: Creates a builder for ImmutableDefaultDotBracket.
builder() - Static method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracketFromPdb: Creates a builder for ImmutableDefaultDotBracketFromPdb.
builder() - Static method in class pl.poznan.put.structure.formats.ImmutableDefaultStrand: Creates a builder for ImmutableDefaultStrand.
builder() - Static method in class pl.poznan.put.structure.formats.ImmutableEntry: Creates a builder for ImmutableEntry.
builder() - Static method in class pl.poznan.put.structure.formats.ImmutableExtendedEntry: Creates a builder for ImmutableExtendedEntry.
builder() - Static method in class pl.poznan.put.structure.formats.ImmutableMultiLineDotBracket: Creates a builder for ImmutableMultiLineDotBracket.
builder() - Static method in class pl.poznan.put.structure.formats.ImmutableStrandView: Creates a builder for ImmutableStrandView.
builder() - Static method in class pl.poznan.put.structure.formats.ImmutableTerminalMissing: Creates a builder for ImmutableTerminalMissing.
builder() - Static method in class pl.poznan.put.structure.ImmutableAnalyzedBasePair: Creates a builder for ImmutableAnalyzedBasePair.
builder() - Static method in class pl.poznan.put.structure.ImmutableBasePair: Creates a builder for ImmutableBasePair.
builder() - Static method in class pl.poznan.put.structure.ImmutableDotBracketSymbol: Creates a builder for ImmutableDotBracketSymbol.
builder() - Static method in class pl.poznan.put.structure.ImmutableQuantifiedBasePair: Creates a builder for ImmutableQuantifiedBasePair.
builder() - Static method in class pl.poznan.put.structure.pseudoknots.dp.ImmutableConflictClique: Creates a builder for ImmutableConflictClique.
builder() - Static method in class pl.poznan.put.structure.pseudoknots.dp.ImmutableDynamicProgrammingAll: Creates a builder for ImmutableDynamicProgrammingAll.
builder() - Static method in class pl.poznan.put.structure.pseudoknots.elimination.ImmutableMaxConflicts: Creates a builder for ImmutableMaxConflicts.
builder() - Static method in class pl.poznan.put.structure.pseudoknots.elimination.ImmutableMinGain: Creates a builder for ImmutableMinGain.
builder() - Static method in class pl.poznan.put.structure.pseudoknots.ImmutableConflictGraph: Creates a builder for ImmutableConflictGraph.
builder() - Static method in class pl.poznan.put.structure.pseudoknots.ImmutableRegion: Creates a builder for ImmutableRegion.
builder() - Static method in class pl.poznan.put.torsion.ImmutableAtomBasedTorsionAngleType: Creates a builder for ImmutableAtomBasedTorsionAngleType.
builder() - Static method in class pl.poznan.put.torsion.ImmutableAtomPair: Creates a builder for ImmutableAtomPair.
builder() - Static method in class pl.poznan.put.torsion.ImmutableAverageTorsionAngleType: Creates a builder for ImmutableAverageTorsionAngleType.
builder() - Static method in class pl.poznan.put.torsion.ImmutableTorsionAngleDelta: Creates a builder for ImmutableTorsionAngleDelta.
builder() - Static method in class pl.poznan.put.torsion.ImmutableTorsionAngleValue: Creates a builder for ImmutableTorsionAngleValue.
builder() - Static method in class pl.poznan.put.types.ImmutableDistanceMatrix: Creates a builder for ImmutableDistanceMatrix.
builder() - Static method in class pl.poznan.put.types.ImmutableQuadruple: Creates a builder for ImmutableQuadruple.
builder() - Static method in class pl.poznan.put.utility.ImmutableExecHelper: Creates a builder for ImmutableExecHelper.
builder() - Static method in class pl.poznan.put.utility.ImmutableExecutionResult: Creates a builder for ImmutableExecutionResult.

C

c() - Method in class pl.poznan.put.types.ImmutableQuadruple
c() - Method in interface pl.poznan.put.types.Quadruple
c(T) - Method in class pl.poznan.put.types.ImmutableQuadruple.Builder: Initializes the value for the c attribute.
C - Enum constant in enum pl.poznan.put.atom.AtomName
C - Enum constant in enum pl.poznan.put.atom.AtomType
C1 - Enum constant in enum pl.poznan.put.atom.AtomName
C10 - Enum constant in enum pl.poznan.put.atom.AtomName
C11 - Enum constant in enum pl.poznan.put.atom.AtomName
C12 - Enum constant in enum pl.poznan.put.atom.AtomName
C13 - Enum constant in enum pl.poznan.put.atom.AtomName
C14 - Enum constant in enum pl.poznan.put.atom.AtomName
C15 - Enum constant in enum pl.poznan.put.atom.AtomName
C16 - Enum constant in enum pl.poznan.put.atom.AtomName
C19 - Enum constant in enum pl.poznan.put.atom.AtomName
C1p - Enum constant in enum pl.poznan.put.atom.AtomName
C2 - Enum constant in enum pl.poznan.put.atom.AtomName
C21 - Enum constant in enum pl.poznan.put.atom.AtomName
C23 - Enum constant in enum pl.poznan.put.atom.AtomName
C24 - Enum constant in enum pl.poznan.put.atom.AtomName
C2p - Enum constant in enum pl.poznan.put.atom.AtomName
C3 - Enum constant in enum pl.poznan.put.atom.AtomName
C3p - Enum constant in enum pl.poznan.put.atom.AtomName
C3T - Enum constant in enum pl.poznan.put.atom.AtomName
C4 - Enum constant in enum pl.poznan.put.atom.AtomName
C4p - Enum constant in enum pl.poznan.put.atom.AtomName
C5 - Enum constant in enum pl.poznan.put.atom.AtomName
C5M - Enum constant in enum pl.poznan.put.atom.AtomName
C5p - Enum constant in enum pl.poznan.put.atom.AtomName
C5T - Enum constant in enum pl.poznan.put.atom.AtomName
C6 - Enum constant in enum pl.poznan.put.atom.AtomName
C8 - Enum constant in enum pl.poznan.put.atom.AtomName
CA - Enum constant in enum pl.poznan.put.atom.AtomName
calculate(Collection<TorsionAngleValue>) - Method in class pl.poznan.put.torsion.AverageTorsionAngleType: Calculates the average torsion angle value by collecting basic angle values and creating an AngleSample out of them to get the mean direction.
calculate(List<PdbResidue>, int) - Static method in class pl.poznan.put.pdb.analysis.ResidueTorsionAngles: Calculates all torsion angles' values in the given residue.
calculate(List<PdbResidue>, int) - Method in class pl.poznan.put.rna.PseudophasePuckerType: Calculates the value of pseudophase pucker according to the formula in Saenger's "Principles of ...".
calculate(List<PdbResidue>, int) - Method in interface pl.poznan.put.torsion.AtomBasedTorsionAngleType: Calculates the value of this torsion angle (see Angle.torsionAngle(Vector3D, Vector3D, Vector3D, Vector3D)).
calculate(List<PdbResidue>, int) - Method in class pl.poznan.put.torsion.AverageTorsionAngleType: Calculates the average torsion angle value by calculating basic angle values and creating an AngleSample out of them to get the mean direction.
calculate(List<PdbResidue>, int) - Method in interface pl.poznan.put.torsion.TorsionAngleType: Calculates the value of this torsion angle.
calculate(PdbAtomLine, PdbAtomLine, PdbAtomLine, PdbAtomLine) - Method in interface pl.poznan.put.torsion.AtomBasedTorsionAngleType: Calculates a value of this torsion angle type given atoms explicitly.
calculateBoundingBox(Document) - Static method in class pl.poznan.put.utility.svg.SVGHelper: Calculates a bounding box for given node of SVG document.
CALPHA - Enum constant in enum pl.poznan.put.protein.AminoAcidTorsionAngle
CALPHA - Static variable in class pl.poznan.put.constant.Unicode
candidatesToCombine() - Method in class pl.poznan.put.structure.formats.DefaultDotBracketFromPdb
CanonicalStructureExtractor - Class in pl.poznan.put.structure: A set of methods to analyze 3D data to extract the canonical 2D structure.
CartesianUtilities - Class in pl.poznan.put.circular.conversion: A set of utility functions on the edge between cartesian and trigonometric representations.
CAT - Enum constant in enum pl.poznan.put.atom.AtomName
CAY - Enum constant in enum pl.poznan.put.atom.AtomName
CB - Enum constant in enum pl.poznan.put.atom.AtomName
CB1 - Enum constant in enum pl.poznan.put.atom.AtomName
CB2 - Enum constant in enum pl.poznan.put.atom.AtomName
CD - Enum constant in enum pl.poznan.put.atom.AtomName
CD1 - Enum constant in enum pl.poznan.put.atom.AtomName
CD2 - Enum constant in enum pl.poznan.put.atom.AtomName
CE - Enum constant in enum pl.poznan.put.atom.AtomName
CE1 - Enum constant in enum pl.poznan.put.atom.AtomName
CE2 - Enum constant in enum pl.poznan.put.atom.AtomName
CE3 - Enum constant in enum pl.poznan.put.atom.AtomName
CG - Enum constant in enum pl.poznan.put.atom.AtomName
CG1 - Enum constant in enum pl.poznan.put.atom.AtomName
CG2 - Enum constant in enum pl.poznan.put.atom.AtomName
CH2 - Enum constant in enum pl.poznan.put.atom.AtomName
chainIdentifier() - Method in interface pl.poznan.put.pdb.analysis.PdbResidue
chainIdentifier() - Method in interface pl.poznan.put.pdb.ChainNumberICode
chainIdentifier() - Method in class pl.poznan.put.pdb.ImmutablePdbAtomLine
chainIdentifier() - Method in class pl.poznan.put.pdb.ImmutablePdbModresLine
chainIdentifier() - Method in class pl.poznan.put.pdb.ImmutablePdbNamedResidueIdentifier
chainIdentifier() - Method in class pl.poznan.put.pdb.ImmutablePdbRemark465Line
chainIdentifier() - Method in class pl.poznan.put.pdb.ImmutablePdbResidueIdentifier
chainIdentifier() - Method in class pl.poznan.put.pdb.PdbAtomLine
chainIdentifier() - Method in class pl.poznan.put.pdb.PdbModresLine
chainIdentifier() - Method in class pl.poznan.put.pdb.PdbNamedResidueIdentifier
chainIdentifier() - Method in class pl.poznan.put.pdb.PdbRemark465Line
chainIdentifier() - Method in class pl.poznan.put.pdb.PdbResidueIdentifier
chainIdentifier(String) - Method in class pl.poznan.put.pdb.ImmutablePdbAtomLine.Builder: Initializes the value for the chainIdentifier attribute.
chainIdentifier(String) - Method in class pl.poznan.put.pdb.ImmutablePdbModresLine.Builder: Initializes the value for the chainIdentifier attribute.
chainIdentifier(String) - Method in class pl.poznan.put.pdb.ImmutablePdbNamedResidueIdentifier.Builder: Initializes the value for the chainIdentifier attribute.
chainIdentifier(String) - Method in class pl.poznan.put.pdb.ImmutablePdbRemark465Line.Builder: Initializes the value for the chainIdentifier attribute.
chainIdentifier(String) - Method in class pl.poznan.put.pdb.ImmutablePdbResidueIdentifier.Builder: Initializes the value for the chainIdentifier attribute.
chainName() - Method in class pl.poznan.put.external.dssr.ImmutableNucleotide
chainName() - Method in interface pl.poznan.put.external.dssr.Nucleotide
chainName(String) - Method in class pl.poznan.put.external.dssr.ImmutableNucleotide.Builder: Initializes the value for the chainName attribute.
ChainNumberICode - Interface in pl.poznan.put.pdb: A set of methods that allow to address a residue by its chain name, residue number and insertion code.
ChainReorderer - Class in pl.poznan.put.rna: A set of methods to reorder chains in an RNA structure.
chains() - Method in class pl.poznan.put.pdb.analysis.AbstractPdbModel: Groups together residues in the same chain and repeat that for every chain.
chains() - Method in class pl.poznan.put.pdb.analysis.DefaultCifModel
chains() - Method in class pl.poznan.put.pdb.analysis.DefaultPdbModel
chains() - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel: Groups together residues in the same chain and repeat that for every chain.
chains() - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbModel: Groups together residues in the same chain and repeat that for every chain.
chains() - Method in interface pl.poznan.put.pdb.analysis.PdbModel
chainTerminatedAfter() - Method in class pl.poznan.put.pdb.analysis.DefaultCifModel
chainTerminatedAfter() - Method in class pl.poznan.put.pdb.analysis.DefaultPdbModel
chainTerminatedAfter() - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel
chainTerminatedAfter() - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbModel
chainTerminatedAfter() - Method in interface pl.poznan.put.pdb.analysis.PdbModel
chainTerminatedAfter(Iterable<? extends PdbResidueIdentifier>) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel.Builder: Sets or replaces all elements for chainTerminatedAfter set.
chainTerminatedAfter(Iterable<? extends PdbResidueIdentifier>) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbModel.Builder: Sets or replaces all elements for chainTerminatedAfter set.
charge() - Method in class pl.poznan.put.pdb.ImmutablePdbAtomLine
charge() - Method in class pl.poznan.put.pdb.PdbAtomLine
charge(String) - Method in class pl.poznan.put.pdb.ImmutablePdbAtomLine.Builder: Initializes the value for the charge attribute.
check() - Method in class pl.poznan.put.circular.Histogram
check() - Method in class pl.poznan.put.circular.samples.AngleSample
CHH - Enum constant in enum pl.poznan.put.notation.LeontisWesthof
Chi - Enum in pl.poznan.put.rna: A glycosidic bond torsion angle (chi), which is defined differently for purines and pyrimidines.
CHI - Enum constant in enum pl.poznan.put.rna.NucleotideTorsionAngle
CHI - Static variable in class pl.poznan.put.constant.Unicode
CHI1 - Enum constant in enum pl.poznan.put.protein.AminoAcidTorsionAngle
CHI1 - Static variable in class pl.poznan.put.constant.Unicode
CHI2 - Enum constant in enum pl.poznan.put.protein.AminoAcidTorsionAngle
CHI2 - Static variable in class pl.poznan.put.constant.Unicode
CHI3 - Enum constant in enum pl.poznan.put.protein.AminoAcidTorsionAngle
CHI3 - Static variable in class pl.poznan.put.constant.Unicode
CHI4 - Enum constant in enum pl.poznan.put.protein.AminoAcidTorsionAngle
CHI4 - Static variable in class pl.poznan.put.constant.Unicode
CHI5 - Enum constant in enum pl.poznan.put.protein.AminoAcidTorsionAngle
CHI5 - Static variable in class pl.poznan.put.constant.Unicode
ChiRange - Enum in pl.poznan.put.rna: A range description for chi torsion angle type as defined in Saenger's "Principles...".
CHS - Enum constant in enum pl.poznan.put.notation.LeontisWesthof
CHW - Enum constant in enum pl.poznan.put.notation.LeontisWesthof
CifBuilder() - Constructor for class pl.poznan.put.pdb.analysis.ResidueCollection.CifBuilder: Creates an instance of this build and initializes it with an audit, citation and citation_author headers.
CifContainer - Class in pl.poznan.put.pdb.analysis: A container of one or more PDB files converted from a single mmCIF file.
CifContainer() - Constructor for class pl.poznan.put.pdb.analysis.CifContainer
CifConverter - Class in pl.poznan.put.pdb.analysis: A converter from mmCIF to one or more PDB files.
cifFile() - Method in class pl.poznan.put.pdb.analysis.CifContainer
cifFile() - Method in class pl.poznan.put.pdb.analysis.ImmutableCifContainer
cifFile(File) - Method in class pl.poznan.put.pdb.analysis.ImmutableCifContainer.Builder: Initializes the value for the cifFile attribute.
CifModel - Interface in pl.poznan.put.pdb.analysis: A structure parsed from an mmCIF file.
CifParser - Class in pl.poznan.put.pdb.analysis: A parser of mmCIF format.
CifParser() - Constructor for class pl.poznan.put.pdb.analysis.CifParser
CifPdbIncompatibilityException - Exception in pl.poznan.put.pdb: When it is impossible to convert from mmCIF to PDB.
circularDispersion() - Method in class pl.poznan.put.circular.samples.AngleSample
circularDispersion() - Method in class pl.poznan.put.circular.samples.ImmutableAngleSample
circularRank(Angle) - Method in class pl.poznan.put.circular.samples.AngleSample: Computes the rank (index) of the value in the current sample assuming that 0 is the beginning of the circle.
circularStandardDeviation() - Method in class pl.poznan.put.circular.samples.AngleSample
circularStandardDeviation() - Method in class pl.poznan.put.circular.samples.ImmutableAngleSample
circularVariance() - Method in class pl.poznan.put.circular.samples.AngleSample
circularVariance() - Method in class pl.poznan.put.circular.samples.ImmutableAngleSample
CIS - Enum constant in enum pl.poznan.put.notation.Stericity
CL - Enum constant in enum pl.poznan.put.atom.AtomName
classification() - Method in class pl.poznan.put.pdb.ImmutablePdbHeaderLine
classification() - Method in class pl.poznan.put.pdb.PdbHeaderLine
classification(String) - Method in class pl.poznan.put.pdb.ImmutablePdbHeaderLine.Builder: Initializes the value for the classification attribute.
ClassifiedBasePair - Interface in pl.poznan.put.structure: A pair of interacting nucleotides with classification info.
CLOCK - Enum constant in enum pl.poznan.put.circular.enums.AngleTransformation: 0 degree is on top, 90 degree is on the right.
close() - Method in class pl.poznan.put.pdb.analysis.CifContainer: Deletes all files (PDB and mmCIF) maintained by this instance.
CLP - Enum constant in enum pl.poznan.put.atom.AtomName
Clusterable - Interface in pl.poznan.put.interfaces: A set of methods that a data structure must implement to be clustered.
CM1 - Enum constant in enum pl.poznan.put.atom.AtomName
cm2() - Method in class pl.poznan.put.circular.samples.AngleSample
cm2() - Method in class pl.poznan.put.circular.samples.ImmutableAngleSample
CM2 - Enum constant in enum pl.poznan.put.atom.AtomName
CM5 - Enum constant in enum pl.poznan.put.atom.AtomName
CM7 - Enum constant in enum pl.poznan.put.atom.AtomName
Colors - Class in pl.poznan.put.constant: A set of utility functions to work with palettes and color interpolation.
CombinedStrand - Class in pl.poznan.put.structure.formats: A dot-bracket encoded structure made from combining one or more strands.
CombinedStrand() - Constructor for class pl.poznan.put.structure.formats.CombinedStrand
CombinedStrandFromPdb - Class in pl.poznan.put.structure.formats: A dot-bracket encoded structure made from combining one or more strands.
CombinedStrandFromPdb() - Constructor for class pl.poznan.put.structure.formats.CombinedStrandFromPdb
combineStrands() - Method in class pl.poznan.put.structure.formats.AbstractCombinedStrand
combineStrands() - Method in class pl.poznan.put.structure.formats.CombinedStrand
combineStrands() - Method in class pl.poznan.put.structure.formats.DefaultDotBracket
combineStrands() - Method in class pl.poznan.put.structure.formats.DefaultDotBracketFromPdb
combineStrands() - Method in interface pl.poznan.put.structure.formats.DotBracket: Combines strands which share a base pair into a new dot-bracket instance and returns a list of those.
combineStrands() - Method in class pl.poznan.put.structure.formats.ImmutableDefaultStrand: Combines strands which share a base pair into a new dot-bracket instance and returns a list of those.
combineStrands() - Method in class pl.poznan.put.structure.formats.ImmutableStrandView: Combines strands which share a base pair into a new dot-bracket instance and returns a list of those.
combineStrands(Iterable<? extends DotBracket>) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultStrand.Builder: Sets or replaces all elements for combineStrands list.
combineStrands(Iterable<? extends DotBracket>) - Method in class pl.poznan.put.structure.formats.ImmutableStrandView.Builder: Sets or replaces all elements for combineStrands list.
combineStrands(List<ClassifiedBasePair>) - Method in class pl.poznan.put.structure.formats.CombinedStrandFromPdb
combineStrands(List<ClassifiedBasePair>) - Method in class pl.poznan.put.structure.formats.DefaultDotBracketFromPdb
combineStrands(List<ClassifiedBasePair>) - Method in interface pl.poznan.put.structure.formats.DotBracketFromPdb: Combines strands which are connected via canonical or non-canonical base pairs.
command() - Method in class pl.poznan.put.utility.ExecHelper
command() - Method in class pl.poznan.put.utility.ImmutableExecHelper
command(String) - Method in class pl.poznan.put.utility.ImmutableExecHelper.Builder: Initializes the value for the command attribute.
comment() - Method in class pl.poznan.put.pdb.ImmutablePdbModresLine
comment() - Method in class pl.poznan.put.pdb.PdbModresLine
comment() - Method in class pl.poznan.put.structure.formats.BpSeq.Entry
comment() - Method in class pl.poznan.put.structure.formats.Ct.ExtendedEntry
comment() - Method in class pl.poznan.put.structure.formats.ImmutableEntry
comment() - Method in class pl.poznan.put.structure.formats.ImmutableExtendedEntry
comment(String) - Method in class pl.poznan.put.pdb.ImmutablePdbModresLine.Builder: Initializes the value for the comment attribute.
comment(String) - Method in class pl.poznan.put.structure.formats.ImmutableEntry.Builder: Initializes the value for the comment attribute.
comment(String) - Method in class pl.poznan.put.structure.formats.ImmutableExtendedEntry.Builder: Initializes the value for the comment attribute.
compare(Range) - Method in enum pl.poznan.put.rna.ChiRange
compare(Range) - Method in enum pl.poznan.put.rna.Pseudorotation
compare(Range) - Method in interface pl.poznan.put.torsion.range.Range: Compares with another range object.
compare(Range) - Method in enum pl.poznan.put.torsion.range.TorsionRange: Calculate difference between two angle ranges.
compareTo(Angle) - Method in class pl.poznan.put.circular.Angle
compareTo(PdbChain) - Method in class pl.poznan.put.pdb.analysis.PdbChain
compareTo(ChainNumberICode) - Method in interface pl.poznan.put.pdb.ChainNumberICode
compareTo(InteractionType) - Method in class pl.poznan.put.rna.InteractionType
compareTo(BasePair) - Method in class pl.poznan.put.structure.BasePair
compareTo(ClassifiedBasePair) - Method in interface pl.poznan.put.structure.ClassifiedBasePair
compareTo(DotBracketSymbol) - Method in class pl.poznan.put.structure.DotBracketSymbol
compareTo(BpSeq.Entry) - Method in class pl.poznan.put.structure.formats.BpSeq.Entry
compareTo(Ct.ExtendedEntry) - Method in class pl.poznan.put.structure.formats.Ct.ExtendedEntry
compareTo(Region) - Method in class pl.poznan.put.structure.pseudoknots.Region
compareTo(AtomPair) - Method in class pl.poznan.put.torsion.AtomPair
computeCentered(Collection<Angle>, int, Angle) - Static method in class pl.poznan.put.circular.samples.TrigonometricMoment: Computes a centered moment i.e. relative to the mean value in the sample.
computeUncentered(Collection<Angle>, int) - Static method in class pl.poznan.put.circular.samples.TrigonometricMoment: Computes an uncentered moment i.e. from the data points not relative to any specific point.
ConflictClique - Class in pl.poznan.put.structure.pseudoknots.dp: A collection of regions conflicting with each other.
ConflictClique() - Constructor for class pl.poznan.put.structure.pseudoknots.dp.ConflictClique
conflictCliques() - Method in class pl.poznan.put.structure.pseudoknots.ConflictGraph: Searches for connected components (named conflict cliques, although they are not real cliques).
ConflictGraph - Class in pl.poznan.put.structure.pseudoknots: A graph of conflicts between regions.
ConflictGraph() - Constructor for class pl.poznan.put.structure.pseudoknots.ConflictGraph
conflicts() - Method in class pl.poznan.put.structure.pseudoknots.ConflictGraph
conflicts() - Method in class pl.poznan.put.structure.pseudoknots.ImmutableConflictGraph
conflictsWith(Region) - Method in class pl.poznan.put.structure.pseudoknots.ConflictGraph: Returns all regions that conflict with a given one.
consideredAngles() - Method in class pl.poznan.put.torsion.AverageTorsionAngleType
consideredAngles() - Method in class pl.poznan.put.torsion.ImmutableAverageTorsionAngleType
consideredAngles(Iterable<? extends MasterTorsionAngleType>) - Method in class pl.poznan.put.torsion.ImmutableAverageTorsionAngleType.Builder: Sets or replaces all elements for consideredAngles list.
consideredBasicAngleTypes() - Method in class pl.poznan.put.torsion.AverageTorsionAngleType
consideredBasicAngleTypes() - Method in class pl.poznan.put.torsion.ImmutableAverageTorsionAngleType
contains(int) - Method in class pl.poznan.put.structure.formats.BpSeq.Entry: Checks for a paired BPSEQ entry (i, j) if a given index k lies between them: i < k < j.
contains(PdbResidueIdentifier) - Method in class pl.poznan.put.structure.formats.CombinedStrandFromPdb
contains(PdbResidueIdentifier) - Method in class pl.poznan.put.structure.formats.DefaultDotBracketFromPdb
contains(PdbResidueIdentifier) - Method in interface pl.poznan.put.structure.formats.DotBracketFromPdb: Checks if this structure contains a mapping for the given residue identifier.
containsAny(MoleculeType) - Method in interface pl.poznan.put.pdb.analysis.PdbModel: Checks if any chain is of a given type.
containsMissing() - Method in interface pl.poznan.put.structure.formats.DotBracket
continuation() - Method in class pl.poznan.put.pdb.ImmutablePdbTitleLine
continuation() - Method in class pl.poznan.put.pdb.PdbTitleLine
continuation(String) - Method in class pl.poznan.put.pdb.ImmutablePdbTitleLine.Builder: Initializes the value for the continuation attribute.
convert(File) - Static method in class pl.poznan.put.pdb.analysis.CifConverter: Parses a file in mmCIF format and convert it into a container of multiple PDB files.
convert(DefaultCifModel) - Static method in class pl.poznan.put.pdb.analysis.CifConverter: Converts a parsed mmCIF model into a set of PDB files with mapped chain names.
convert(BpSeq) - Method in interface pl.poznan.put.structure.formats.Converter: Converts the secondary structure from BPSEQ to dot-bracket format.
convert(BpSeq) - Method in class pl.poznan.put.structure.formats.DefaultConverter: Converts the secondary structure in BPSEQ format to dot-bracket.
convertedPdbChainName(File, String) - Method in class pl.poznan.put.pdb.analysis.CifContainer
convertedPdbChainName(File, String) - Method in interface pl.poznan.put.pdb.analysis.ModelContainer: Checks mapping of chains to get the generated PDB chain name from the original mmCIF chain name.
Converter - Interface in pl.poznan.put.structure.formats: A converter from BPSEQ to dot-bracket.
copyOf(BondLength) - Static method in class pl.poznan.put.atom.ImmutableBondLength: Creates an immutable copy of a BondLength value.
copyOf(Angle) - Static method in class pl.poznan.put.circular.ImmutableAngle: Creates an immutable copy of a Angle value.
copyOf(Histogram) - Static method in class pl.poznan.put.circular.ImmutableHistogram: Creates an immutable copy of a Histogram value.
copyOf(AngleSample) - Static method in class pl.poznan.put.circular.samples.ImmutableAngleSample: Creates an immutable copy of a AngleSample value.
copyOf(TrigonometricMoment) - Static method in class pl.poznan.put.circular.samples.ImmutableTrigonometricMoment: Creates an immutable copy of a TrigonometricMoment value.
copyOf(DssrJson) - Static method in class pl.poznan.put.external.dssr.ImmutableDssrJson: Creates an immutable copy of a DssrJson value.
copyOf(Nucleotide) - Static method in class pl.poznan.put.external.dssr.ImmutableNucleotide: Creates an immutable copy of a Nucleotide value.
copyOf(Pair) - Static method in class pl.poznan.put.external.dssr.ImmutablePair: Creates an immutable copy of a Pair value.
copyOf(CifContainer) - Static method in class pl.poznan.put.pdb.analysis.ImmutableCifContainer: Creates an immutable copy of a CifContainer value.
copyOf(DefaultCifModel) - Static method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel: Creates an immutable copy of a DefaultCifModel value.
copyOf(DefaultPdbModel) - Static method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbModel: Creates an immutable copy of a DefaultPdbModel value.
copyOf(DefaultPdbResidue) - Static method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbResidue: Creates an immutable copy of a DefaultPdbResidue value.
copyOf(DefaultResidueCollection) - Static method in class pl.poznan.put.pdb.analysis.ImmutableDefaultResidueCollection: Creates an immutable copy of a DefaultResidueCollection value.
copyOf(PdbChain) - Static method in class pl.poznan.put.pdb.analysis.ImmutablePdbChain: Creates an immutable copy of a PdbChain value.
copyOf(PdbCompactFragment) - Static method in class pl.poznan.put.pdb.analysis.ImmutablePdbCompactFragment: Creates an immutable copy of a PdbCompactFragment value.
copyOf(ResidueTorsionAngles) - Static method in class pl.poznan.put.pdb.analysis.ImmutableResidueTorsionAngles: Creates an immutable copy of a ResidueTorsionAngles value.
copyOf(PdbAtomLine) - Static method in class pl.poznan.put.pdb.ImmutablePdbAtomLine: Creates an immutable copy of a PdbAtomLine value.
copyOf(PdbExpdtaLine) - Static method in class pl.poznan.put.pdb.ImmutablePdbExpdtaLine: Creates an immutable copy of a PdbExpdtaLine value.
copyOf(PdbHeaderLine) - Static method in class pl.poznan.put.pdb.ImmutablePdbHeaderLine: Creates an immutable copy of a PdbHeaderLine value.
copyOf(PdbModresLine) - Static method in class pl.poznan.put.pdb.ImmutablePdbModresLine: Creates an immutable copy of a PdbModresLine value.
copyOf(PdbNamedResidueIdentifier) - Static method in class pl.poznan.put.pdb.ImmutablePdbNamedResidueIdentifier: Creates an immutable copy of a PdbNamedResidueIdentifier value.
copyOf(PdbRemark2Line) - Static method in class pl.poznan.put.pdb.ImmutablePdbRemark2Line: Creates an immutable copy of a PdbRemark2Line value.
copyOf(PdbRemark465Line) - Static method in class pl.poznan.put.pdb.ImmutablePdbRemark465Line: Creates an immutable copy of a PdbRemark465Line value.
copyOf(PdbResidueIdentifier) - Static method in class pl.poznan.put.pdb.ImmutablePdbResidueIdentifier: Creates an immutable copy of a PdbResidueIdentifier value.
copyOf(PdbTitleLine) - Static method in class pl.poznan.put.pdb.ImmutablePdbTitleLine: Creates an immutable copy of a PdbTitleLine value.
copyOf(Backbone) - Static method in class pl.poznan.put.protein.ImmutableBackbone: Creates an immutable copy of a Backbone value.
copyOf(InteractionType) - Static method in class pl.poznan.put.rna.ImmutableInteractionType: Creates an immutable copy of a InteractionType value.
copyOf(Phosphate) - Static method in class pl.poznan.put.rna.ImmutablePhosphate: Creates an immutable copy of a Phosphate value.
copyOf(PseudophasePuckerType) - Static method in class pl.poznan.put.rna.ImmutablePseudophasePuckerType: Creates an immutable copy of a PseudophasePuckerType value.
copyOf(Ribose) - Static method in class pl.poznan.put.rna.ImmutableRibose: Creates an immutable copy of a Ribose value.
copyOf(AnalyzedBasePair) - Static method in class pl.poznan.put.structure.ImmutableAnalyzedBasePair: Creates an immutable copy of a AnalyzedBasePair value.
copyOf(BasePair) - Static method in class pl.poznan.put.structure.ImmutableBasePair: Creates an immutable copy of a BasePair value.
copyOf(DotBracketSymbol) - Static method in class pl.poznan.put.structure.ImmutableDotBracketSymbol: Creates an immutable copy of a DotBracketSymbol value.
copyOf(BpSeq) - Static method in class pl.poznan.put.structure.formats.ImmutableBpSeq: Creates an immutable copy of a BpSeq value.
copyOf(BpSeq.Entry) - Static method in class pl.poznan.put.structure.formats.ImmutableEntry: Creates an immutable copy of a BpSeq.Entry value.
copyOf(CombinedStrand) - Static method in class pl.poznan.put.structure.formats.ImmutableCombinedStrand: Creates an immutable copy of a CombinedStrand value.
copyOf(CombinedStrandFromPdb) - Static method in class pl.poznan.put.structure.formats.ImmutableCombinedStrandFromPdb: Creates an immutable copy of a CombinedStrandFromPdb value.
copyOf(Ct) - Static method in class pl.poznan.put.structure.formats.ImmutableCt: Creates an immutable copy of a Ct value.
copyOf(Ct.ExtendedEntry) - Static method in class pl.poznan.put.structure.formats.ImmutableExtendedEntry: Creates an immutable copy of a Ct.ExtendedEntry value.
copyOf(DefaultConverter) - Static method in class pl.poznan.put.structure.formats.ImmutableDefaultConverter: Creates an immutable copy of a DefaultConverter value.
copyOf(DefaultDotBracket) - Static method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracket: Creates an immutable copy of a DefaultDotBracket value.
copyOf(DefaultDotBracketFromPdb) - Static method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracketFromPdb: Creates an immutable copy of a DefaultDotBracketFromPdb value.
copyOf(DefaultStrand) - Static method in class pl.poznan.put.structure.formats.ImmutableDefaultStrand: Creates an immutable copy of a DefaultStrand value.
copyOf(MultiLineDotBracket) - Static method in class pl.poznan.put.structure.formats.ImmutableMultiLineDotBracket: Creates an immutable copy of a MultiLineDotBracket value.
copyOf(StrandView) - Static method in class pl.poznan.put.structure.formats.ImmutableStrandView: Creates an immutable copy of a StrandView value.
copyOf(TerminalMissing) - Static method in class pl.poznan.put.structure.formats.ImmutableTerminalMissing: Creates an immutable copy of a TerminalMissing value.
copyOf(ConflictGraph) - Static method in class pl.poznan.put.structure.pseudoknots.ImmutableConflictGraph: Creates an immutable copy of a ConflictGraph value.
copyOf(ConflictClique) - Static method in class pl.poznan.put.structure.pseudoknots.dp.ImmutableConflictClique: Creates an immutable copy of a ConflictClique value.
copyOf(DynamicProgrammingAll) - Static method in class pl.poznan.put.structure.pseudoknots.dp.ImmutableDynamicProgrammingAll: Creates an immutable copy of a DynamicProgrammingAll value.
copyOf(MaxConflicts) - Static method in class pl.poznan.put.structure.pseudoknots.elimination.ImmutableMaxConflicts: Creates an immutable copy of a MaxConflicts value.
copyOf(MinGain) - Static method in class pl.poznan.put.structure.pseudoknots.elimination.ImmutableMinGain: Creates an immutable copy of a MinGain value.
copyOf(Region) - Static method in class pl.poznan.put.structure.pseudoknots.ImmutableRegion: Creates an immutable copy of a Region value.
copyOf(QuantifiedBasePair) - Static method in class pl.poznan.put.structure.ImmutableQuantifiedBasePair: Creates an immutable copy of a QuantifiedBasePair value.
copyOf(AtomBasedTorsionAngleType) - Static method in class pl.poznan.put.torsion.ImmutableAtomBasedTorsionAngleType: Creates an immutable copy of a AtomBasedTorsionAngleType value.
copyOf(AtomPair) - Static method in class pl.poznan.put.torsion.ImmutableAtomPair: Creates an immutable copy of a AtomPair value.
copyOf(AverageTorsionAngleType) - Static method in class pl.poznan.put.torsion.ImmutableAverageTorsionAngleType: Creates an immutable copy of a AverageTorsionAngleType value.
copyOf(TorsionAngleDelta) - Static method in class pl.poznan.put.torsion.ImmutableTorsionAngleDelta: Creates an immutable copy of a TorsionAngleDelta value.
copyOf(TorsionAngleValue) - Static method in class pl.poznan.put.torsion.ImmutableTorsionAngleValue: Creates an immutable copy of a TorsionAngleValue value.
copyOf(DistanceMatrix) - Static method in class pl.poznan.put.types.ImmutableDistanceMatrix: Creates an immutable copy of a DistanceMatrix value.
copyOf(Quadruple<T>) - Static method in class pl.poznan.put.types.ImmutableQuadruple: Creates an immutable copy of a Quadruple value.
copyOf(ExecHelper) - Static method in class pl.poznan.put.utility.ImmutableExecHelper: Creates an immutable copy of a ExecHelper value.
copyOf(ExecHelper.ExecutionResult) - Static method in class pl.poznan.put.utility.ImmutableExecutionResult: Creates an immutable copy of a ExecHelper.ExecutionResult value.
copyWithoutIsolatedBasePairs(DotBracket) - Static method in class pl.poznan.put.structure.formats.DefaultDotBracket: Creates a copy of existing instance, but removes isolated base pairs from it.
copyWithStrands(DotBracket, Ct) - Static method in class pl.poznan.put.structure.formats.DefaultDotBracket: Creates a copy of existing instance and applies the information in CT format to divide strands accordingly.
CR - Enum constant in enum pl.poznan.put.atom.AtomName
createRandomDirectory() - Static method in class pl.poznan.put.utility.ExecHelper: Generates a random name and creates a directory named like that in system temporary directory.
createRegions(BpSeq) - Static method in class pl.poznan.put.structure.pseudoknots.Region: Creates a list of regions from a secondary structure in BPSEQ format.
CRP - Enum constant in enum pl.poznan.put.atom.AtomName
CSH - Enum constant in enum pl.poznan.put.notation.LeontisWesthof
CSS - Enum constant in enum pl.poznan.put.notation.LeontisWesthof
CSW - Enum constant in enum pl.poznan.put.notation.LeontisWesthof
Ct - Class in pl.poznan.put.structure.formats: An RNA secondary structure encoded in CT (connect) format.
Ct() - Constructor for class pl.poznan.put.structure.formats.Ct
CT - Enum constant in enum pl.poznan.put.atom.AtomName
Ct.ExtendedEntry - Class in pl.poznan.put.structure.formats: A single entry in the CT formatted structure.
CWH - Enum constant in enum pl.poznan.put.notation.LeontisWesthof
CWS - Enum constant in enum pl.poznan.put.notation.LeontisWesthof
CWW - Enum constant in enum pl.poznan.put.notation.LeontisWesthof
CY - Enum constant in enum pl.poznan.put.atom.AtomName
CYSTEINE - Enum constant in enum pl.poznan.put.protein.AminoAcid
CYTOSINE - Enum constant in enum pl.poznan.put.rna.Nucleotide
CZ - Enum constant in enum pl.poznan.put.atom.AtomName
CZ2 - Enum constant in enum pl.poznan.put.atom.AtomName
CZ3 - Enum constant in enum pl.poznan.put.atom.AtomName

D

d() - Method in class pl.poznan.put.types.ImmutableQuadruple
d() - Method in interface pl.poznan.put.types.Quadruple
d(T) - Method in class pl.poznan.put.types.ImmutableQuadruple.Builder: Initializes the value for the d attribute.
data() - Method in class pl.poznan.put.circular.Histogram
data() - Method in class pl.poznan.put.circular.ImmutableHistogram
data() - Method in class pl.poznan.put.circular.samples.AngleSample
data() - Method in class pl.poznan.put.circular.samples.ImmutableAngleSample
data(Collection<Angle>) - Method in class pl.poznan.put.circular.ImmutableHistogram.Builder: Initializes the value for the data attribute.
data(Collection<Angle>) - Method in class pl.poznan.put.circular.samples.ImmutableAngleSample.Builder: Initializes the value for the data attribute.
DefaultCifModel - Class in pl.poznan.put.pdb.analysis: A default implementation of a structure parsed from an mmCIF file.
DefaultCifModel() - Constructor for class pl.poznan.put.pdb.analysis.DefaultCifModel
DefaultConverter - Class in pl.poznan.put.structure.formats: A default converter from BPSEQ to dot-bracket which iteratively (1) finds non-pseudoknots and assigns the current lowest level, then (2) increases level and (3) treats pseudoknots as the next input to (1) until there are base pairs without level assigned.
DefaultConverter() - Constructor for class pl.poznan.put.structure.formats.DefaultConverter
DefaultDotBracket - Class in pl.poznan.put.structure.formats: A default implementation of a dot-bracket.
DefaultDotBracket() - Constructor for class pl.poznan.put.structure.formats.DefaultDotBracket
DefaultDotBracketFromPdb - Class in pl.poznan.put.structure.formats: A default implementation of a dot-bracket structure which is mapped to data from 3D coordinates.
DefaultDotBracketFromPdb() - Constructor for class pl.poznan.put.structure.formats.DefaultDotBracketFromPdb
defaultName() - Method in interface pl.poznan.put.pdb.analysis.ResidueInformationProvider
DefaultPdbModel - Class in pl.poznan.put.pdb.analysis: A default implementation of a structure parsed from a PDB file.
DefaultPdbModel() - Constructor for class pl.poznan.put.pdb.analysis.DefaultPdbModel
DefaultPdbResidue - Class in pl.poznan.put.pdb.analysis: A default implementation of a residue (nucleotide or amino acid).
DefaultPdbResidue() - Constructor for class pl.poznan.put.pdb.analysis.DefaultPdbResidue
DefaultResidueCollection - Class in pl.poznan.put.pdb.analysis: A container for a list of residues.
DefaultResidueCollection() - Constructor for class pl.poznan.put.pdb.analysis.DefaultResidueCollection
DefaultStrand - Class in pl.poznan.put.structure.formats: A default implementation of a strand.
DefaultStrand() - Constructor for class pl.poznan.put.structure.formats.DefaultStrand
DEGREE - Static variable in class pl.poznan.put.constant.Unicode
degrees() - Method in class pl.poznan.put.circular.Angle
degrees(double) - Static method in class pl.poznan.put.utility.AngleFormat: Format an angle value given in radians.
degrees360() - Method in class pl.poznan.put.circular.Angle
degreesRoundedToHundredth(double) - Static method in class pl.poznan.put.utility.AngleFormat: Format an angle value given in radians.
degreesRoundedToOne(double) - Static method in class pl.poznan.put.utility.AngleFormat: Format an angle value given in radians.
delta() - Method in class pl.poznan.put.torsion.ImmutableTorsionAngleDelta
delta() - Method in class pl.poznan.put.torsion.TorsionAngleDelta
delta(Angle) - Method in class pl.poznan.put.torsion.ImmutableTorsionAngleDelta.Builder: Initializes the value for the delta attribute.
DELTA - Enum constant in enum pl.poznan.put.rna.NucleotideTorsionAngle
DELTA - Static variable in class pl.poznan.put.constant.Unicode
depositionDate() - Method in class pl.poznan.put.pdb.ImmutablePdbHeaderLine
depositionDate() - Method in class pl.poznan.put.pdb.PdbHeaderLine
depositionDate(Date) - Method in class pl.poznan.put.pdb.ImmutablePdbHeaderLine.Builder: Initializes the value for the depositionDate attribute.
description() - Method in class pl.poznan.put.rna.ImmutableInteractionType
description() - Method in class pl.poznan.put.rna.InteractionType
description() - Method in interface pl.poznan.put.structure.formats.Strand: Prepares description of strand in RNAComposer format.
description() - Method in class pl.poznan.put.structure.formats.StrandView
description(String) - Method in class pl.poznan.put.rna.ImmutableInteractionType.Builder: Initializes the value for the description attribute.
detectAtomName() - Method in class pl.poznan.put.pdb.PdbAtomLine
detectResidueType(String, Set<AtomName>) - Static method in class pl.poznan.put.pdb.analysis.ResidueTypeDetector: Detects the type of residue by its name or atom content.
DIFFERENT - Enum constant in enum pl.poznan.put.torsion.range.RangeDifference
DisplayableExportable - Interface in pl.poznan.put.interfaces: A set of methods that any kind of result has to implement to be displayable in UI or exportable to output file.
displayName() - Method in enum pl.poznan.put.notation.BPh
displayName() - Method in enum pl.poznan.put.notation.BR
displayName() - Method in enum pl.poznan.put.notation.StackingTopology
displayName() - Method in enum pl.poznan.put.rna.ChiRange
displayName() - Method in enum pl.poznan.put.rna.Pseudorotation
displayName() - Method in interface pl.poznan.put.torsion.range.Range
displayName() - Method in enum pl.poznan.put.torsion.range.TorsionRange
distance() - Method in class pl.poznan.put.torsion.AtomPair
distance() - Method in class pl.poznan.put.torsion.ImmutableAtomPair
distance(Angle) - Method in class pl.poznan.put.circular.Angle: Computes a useful distance in range [0; 2] between two angular values.
distanceMatrix() - Method in interface pl.poznan.put.interfaces.Clusterable
DistanceMatrix - Interface in pl.poznan.put.types
distanceTo(PdbAtomLine) - Method in class pl.poznan.put.pdb.PdbAtomLine: Calculates the euclidean distance to another atom.
DotBracket - Interface in pl.poznan.put.structure.formats: An RNA structure encoded in dot-bracket format.
DotBracketFromPdb - Interface in pl.poznan.put.structure.formats: A dot-bracket structure with correspondence to a 3D structure.
DotBracketSymbol - Class in pl.poznan.put.structure: A single symbol in a dot-bracket structure.
DotBracketSymbol() - Constructor for class pl.poznan.put.structure.DotBracketSymbol
DOWNWARD - Enum constant in enum pl.poznan.put.notation.StackingTopology
DssrJson - Class in pl.poznan.put.external.dssr
DssrJson() - Constructor for class pl.poznan.put.external.dssr.DssrJson
DynamicProgrammingAll - Class in pl.poznan.put.structure.pseudoknots.dp: Java implementation of OPT ALL algorithm as presented in: Smit, S. et al., 2008.
DynamicProgrammingAll() - Constructor for class pl.poznan.put.structure.pseudoknots.dp.DynamicProgrammingAll

E

edge3() - Method in enum pl.poznan.put.notation.LeontisWesthof
edge5() - Method in enum pl.poznan.put.notation.LeontisWesthof
edgeVector(PdbResidue, NucleobaseEdge) - Method in interface pl.poznan.put.rna.Nucleobase
edgeVectorAtoms(NucleobaseEdge) - Method in interface pl.poznan.put.rna.Nucleobase
edgeVectorAtoms(NucleobaseEdge) - Method in interface pl.poznan.put.rna.Purine
edgeVectorAtoms(NucleobaseEdge) - Method in interface pl.poznan.put.rna.Pyrimidine
ELECTRON_CRYSTALLOGRAPHY - Enum constant in enum pl.poznan.put.pdb.ExperimentalTechnique
ELECTRON_MICROSCOPY - Enum constant in enum pl.poznan.put.pdb.ExperimentalTechnique
elementSymbol() - Method in class pl.poznan.put.pdb.ImmutablePdbAtomLine
elementSymbol() - Method in class pl.poznan.put.pdb.PdbAtomLine
elementSymbol(String) - Method in class pl.poznan.put.pdb.ImmutablePdbAtomLine.Builder: Initializes the value for the elementSymbol attribute.
emptyDocument() - Static method in class pl.poznan.put.utility.svg.SVGHelper
emptyInstance(File) - Static method in class pl.poznan.put.pdb.analysis.CifContainer: Creates an empty instance (without any chain mapping).
end() - Method in enum pl.poznan.put.rna.ChiRange
end() - Method in enum pl.poznan.put.rna.Pseudorotation
end() - Method in class pl.poznan.put.structure.formats.ImmutableStrandView
end() - Method in interface pl.poznan.put.structure.formats.Strand
end() - Method in class pl.poznan.put.structure.formats.StrandView
end() - Method in class pl.poznan.put.structure.pseudoknots.ImmutableRegion
end() - Method in class pl.poznan.put.structure.pseudoknots.Region
end() - Method in interface pl.poznan.put.torsion.range.Range
end() - Method in enum pl.poznan.put.torsion.range.TorsionRange
end(int) - Method in class pl.poznan.put.structure.formats.ImmutableStrandView.Builder: Initializes the value for the end attribute.
end(int) - Method in class pl.poznan.put.structure.pseudoknots.ImmutableRegion.Builder: Initializes the value for the end attribute.
endpoint(int) - Method in class pl.poznan.put.structure.pseudoknots.dp.ConflictClique: Returns the endpoint of the given index.
endpointCount() - Method in class pl.poznan.put.structure.pseudoknots.dp.ConflictClique
entries() - Method in class pl.poznan.put.structure.formats.BpSeq
entries() - Method in class pl.poznan.put.structure.formats.Ct
entries() - Method in class pl.poznan.put.structure.formats.ImmutableBpSeq
entries() - Method in class pl.poznan.put.structure.formats.ImmutableCt
entries() - Method in class pl.poznan.put.structure.pseudoknots.ImmutableRegion
entries() - Method in class pl.poznan.put.structure.pseudoknots.Region
entries(Iterable<? extends BpSeq.Entry>) - Method in class pl.poznan.put.structure.formats.ImmutableBpSeq.Builder: Sets or replaces all elements for entries sortedSet.
entries(Iterable<? extends BpSeq.Entry>) - Method in class pl.poznan.put.structure.pseudoknots.ImmutableRegion.Builder: Sets or replaces all elements for entries list.
entries(Iterable<? extends Ct.ExtendedEntry>) - Method in class pl.poznan.put.structure.formats.ImmutableCt.Builder: Sets or replaces all elements for entries sortedSet.
Entry() - Constructor for class pl.poznan.put.structure.formats.BpSeq.Entry
ENVELOPE_1_ENDO - Enum constant in enum pl.poznan.put.rna.Pseudorotation
ENVELOPE_1_EXO - Enum constant in enum pl.poznan.put.rna.Pseudorotation
ENVELOPE_2_ENDO - Enum constant in enum pl.poznan.put.rna.Pseudorotation
ENVELOPE_2_EXO - Enum constant in enum pl.poznan.put.rna.Pseudorotation
ENVELOPE_3_ENDO - Enum constant in enum pl.poznan.put.rna.Pseudorotation
ENVELOPE_3_EXO - Enum constant in enum pl.poznan.put.rna.Pseudorotation
ENVELOPE_4_ENDO - Enum constant in enum pl.poznan.put.rna.Pseudorotation
ENVELOPE_4_EXO - Enum constant in enum pl.poznan.put.rna.Pseudorotation
ENVELOPE_O_ENDO - Enum constant in enum pl.poznan.put.rna.Pseudorotation
ENVELOPE_O_EXO - Enum constant in enum pl.poznan.put.rna.Pseudorotation
environment() - Method in class pl.poznan.put.utility.ExecHelper
environment() - Method in class pl.poznan.put.utility.ImmutableExecHelper
environment(Map<String, ? extends String>) - Method in class pl.poznan.put.utility.ImmutableExecHelper.Builder: Sets or replaces all mappings from the specified map as entries for the environment map.
EPR - Enum constant in enum pl.poznan.put.pdb.ExperimentalTechnique
EPS - Enum constant in enum pl.poznan.put.utility.svg.Format
EPSILON - Enum constant in enum pl.poznan.put.rna.NucleotideTorsionAngle
EPSILON - Static variable in class pl.poznan.put.constant.Unicode
EQUAL - Enum constant in enum pl.poznan.put.torsion.range.RangeDifference
equals(Object) - Method in class pl.poznan.put.atom.ImmutableBondLength: This instance is equal to all instances of ImmutableBondLength that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.circular.Angle
equals(Object) - Method in class pl.poznan.put.circular.ImmutableHistogram: This instance is equal to all instances of ImmutableHistogram that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.circular.samples.ImmutableAngleSample: This instance is equal to all instances of ImmutableAngleSample that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.circular.samples.ImmutableTrigonometricMoment: This instance is equal to all instances of ImmutableTrigonometricMoment that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.external.dssr.ImmutableDssrJson: This instance is equal to all instances of ImmutableDssrJson that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.external.dssr.ImmutableNucleotide: This instance is equal to all instances of ImmutableNucleotide that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.external.dssr.ImmutablePair: This instance is equal to all instances of ImmutablePair that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.pdb.analysis.ImmutableCifContainer: This instance is equal to all instances of ImmutableCifContainer that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel: This instance is equal to all instances of ImmutableDefaultCifModel that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbModel: This instance is equal to all instances of ImmutableDefaultPdbModel that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbResidue: This instance is equal to all instances of ImmutableDefaultPdbResidue that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultResidueCollection: This instance is equal to all instances of ImmutableDefaultResidueCollection that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.pdb.analysis.ImmutablePdbChain: This instance is equal to all instances of ImmutablePdbChain that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.pdb.analysis.ImmutablePdbCompactFragment: This instance is equal to all instances of ImmutablePdbCompactFragment that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.pdb.analysis.ImmutableResidueTorsionAngles: This instance is equal to all instances of ImmutableResidueTorsionAngles that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.pdb.ImmutablePdbAtomLine: This instance is equal to all instances of ImmutablePdbAtomLine that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.pdb.ImmutablePdbExpdtaLine: This instance is equal to all instances of ImmutablePdbExpdtaLine that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.pdb.ImmutablePdbHeaderLine: This instance is equal to all instances of ImmutablePdbHeaderLine that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.pdb.ImmutablePdbModresLine: This instance is equal to all instances of ImmutablePdbModresLine that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.pdb.ImmutablePdbNamedResidueIdentifier: This instance is equal to all instances of ImmutablePdbNamedResidueIdentifier that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.pdb.ImmutablePdbRemark2Line: This instance is equal to all instances of ImmutablePdbRemark2Line that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.pdb.ImmutablePdbRemark465Line: This instance is equal to all instances of ImmutablePdbRemark465Line that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.pdb.ImmutablePdbResidueIdentifier: This instance is equal to all instances of ImmutablePdbResidueIdentifier that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.pdb.ImmutablePdbTitleLine: This instance is equal to all instances of ImmutablePdbTitleLine that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.protein.ImmutableBackbone: This instance is equal to all instances of ImmutableBackbone that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.rna.ImmutableInteractionType: This instance is equal to all instances of ImmutableInteractionType that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.rna.ImmutablePhosphate: This instance is equal to all instances of ImmutablePhosphate that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.rna.ImmutablePseudophasePuckerType: This instance is equal to all instances of ImmutablePseudophasePuckerType that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.rna.ImmutableRibose: This instance is equal to all instances of ImmutableRibose that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.structure.formats.ImmutableBpSeq: This instance is equal to all instances of ImmutableBpSeq that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.structure.formats.ImmutableCombinedStrand: This instance is equal to all instances of ImmutableCombinedStrand that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.structure.formats.ImmutableCombinedStrandFromPdb: This instance is equal to all instances of ImmutableCombinedStrandFromPdb that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.structure.formats.ImmutableCt: This instance is equal to all instances of ImmutableCt that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultConverter: This instance is equal to all instances of ImmutableDefaultConverter that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracket: This instance is equal to all instances of ImmutableDefaultDotBracket that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracketFromPdb: This instance is equal to all instances of ImmutableDefaultDotBracketFromPdb that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultStrand: This instance is equal to all instances of ImmutableDefaultStrand that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.structure.formats.ImmutableEntry: This instance is equal to all instances of ImmutableEntry that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.structure.formats.ImmutableExtendedEntry: This instance is equal to all instances of ImmutableExtendedEntry that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.structure.formats.ImmutableMultiLineDotBracket: This instance is equal to all instances of ImmutableMultiLineDotBracket that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.structure.formats.ImmutableStrandView: This instance is equal to all instances of ImmutableStrandView that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.structure.formats.ImmutableTerminalMissing: This instance is equal to all instances of ImmutableTerminalMissing that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.structure.ImmutableAnalyzedBasePair: This instance is equal to all instances of ImmutableAnalyzedBasePair that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.structure.ImmutableBasePair: This instance is equal to all instances of ImmutableBasePair that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.structure.ImmutableDotBracketSymbol: This instance is equal to all instances of ImmutableDotBracketSymbol that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.structure.ImmutableQuantifiedBasePair: This instance is equal to all instances of ImmutableQuantifiedBasePair that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.structure.pseudoknots.dp.ImmutableConflictClique: This instance is equal to all instances of ImmutableConflictClique that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.structure.pseudoknots.dp.ImmutableDynamicProgrammingAll: This instance is equal to all instances of ImmutableDynamicProgrammingAll that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.structure.pseudoknots.elimination.ImmutableMaxConflicts: This instance is equal to all instances of ImmutableMaxConflicts that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.structure.pseudoknots.elimination.ImmutableMinGain: This instance is equal to all instances of ImmutableMinGain that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.structure.pseudoknots.ImmutableConflictGraph: This instance is equal to all instances of ImmutableConflictGraph that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.structure.pseudoknots.ImmutableRegion: This instance is equal to all instances of ImmutableRegion that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.torsion.ImmutableAtomBasedTorsionAngleType: This instance is equal to all instances of ImmutableAtomBasedTorsionAngleType that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.torsion.ImmutableAtomPair: This instance is equal to all instances of ImmutableAtomPair that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.torsion.ImmutableAverageTorsionAngleType: This instance is equal to all instances of ImmutableAverageTorsionAngleType that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.torsion.ImmutableTorsionAngleDelta: This instance is equal to all instances of ImmutableTorsionAngleDelta that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.torsion.ImmutableTorsionAngleValue: This instance is equal to all instances of ImmutableTorsionAngleValue that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.types.ImmutableDistanceMatrix: This instance is equal to all instances of ImmutableDistanceMatrix that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.types.ImmutableQuadruple: This instance is equal to all instances of ImmutableQuadruple that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.utility.ImmutableExecHelper: This instance is equal to all instances of ImmutableExecHelper that have equal attribute values.
equals(Object) - Method in class pl.poznan.put.utility.ImmutableExecutionResult: This instance is equal to all instances of ImmutableExecutionResult that have equal attribute values.
ETA - Enum constant in enum pl.poznan.put.rna.NucleotideTorsionAngle
ETA - Static variable in class pl.poznan.put.constant.Unicode
ETA_PRIM - Enum constant in enum pl.poznan.put.rna.NucleotideTorsionAngle
ETA_PRIM - Static variable in class pl.poznan.put.constant.Unicode
ExecHelper - Class in pl.poznan.put.utility: An executor of external processes.
ExecHelper() - Constructor for class pl.poznan.put.utility.ExecHelper
ExecHelper.ExecutionResult - Interface in pl.poznan.put.utility: A result of running external command.
execute() - Method in class pl.poznan.put.utility.ExecHelper: Executes the command in a working directory (if provided) with environment setting (if provided).
exitCode() - Method in interface pl.poznan.put.utility.ExecHelper.ExecutionResult
exitCode() - Method in class pl.poznan.put.utility.ImmutableExecutionResult
exitCode(int) - Method in class pl.poznan.put.utility.ImmutableExecutionResult.Builder: Initializes the value for the exitCode attribute.
experimentalData() - Method in class pl.poznan.put.pdb.analysis.DefaultCifModel
experimentalData() - Method in class pl.poznan.put.pdb.analysis.DefaultPdbModel
experimentalData() - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel
experimentalData() - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbModel
experimentalData() - Method in interface pl.poznan.put.pdb.analysis.PdbModel
experimentalData(PdbExpdtaLine) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel.Builder: Initializes the value for the experimentalData attribute.
experimentalData(PdbExpdtaLine) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbModel.Builder: Initializes the value for the experimentalData attribute.
ExperimentalTechnique - Enum in pl.poznan.put.pdb: An experimental technique used to solve a structure (according to the PDB sources).
experimentalTechniques() - Method in class pl.poznan.put.pdb.ImmutablePdbExpdtaLine
experimentalTechniques() - Method in class pl.poznan.put.pdb.PdbExpdtaLine
experimentalTechniques(Iterable<? extends ExperimentalTechnique>) - Method in class pl.poznan.put.pdb.ImmutablePdbExpdtaLine.Builder: Sets or replaces all elements for experimentalTechniques list.
export(OutputStream) - Method in interface pl.poznan.put.interfaces.Exportable: Exports the result to a provided output stream.
export(TableModel, OutputStream) - Static method in class pl.poznan.put.utility.TabularExporter: Exports the tabular data in CSV format and pushed it to an output stream.
export(SVGDocument, Format) - Static method in class pl.poznan.put.utility.svg.SVGHelper: Exports SVG image to a given output image format.
Exportable - Interface in pl.poznan.put.interfaces: A set of methods that any kind of result must implement to be exported to output file.
exportName() - Method in interface pl.poznan.put.interfaces.DisplayableExportable
exportName() - Method in enum pl.poznan.put.protein.AminoAcidTorsionAngle
exportName() - Method in enum pl.poznan.put.rna.NucleotideTorsionAngle
exportName() - Method in class pl.poznan.put.rna.PseudophasePuckerType
exportName() - Method in interface pl.poznan.put.torsion.AtomBasedTorsionAngleType
exportName() - Method in class pl.poznan.put.torsion.AverageTorsionAngleType
exportName() - Method in class pl.poznan.put.torsion.ImmutableAtomBasedTorsionAngleType
exportName() - Method in class pl.poznan.put.torsion.ImmutableAverageTorsionAngleType
exportName() - Method in class pl.poznan.put.torsion.TorsionAngleDelta
exportName() - Method in class pl.poznan.put.torsion.TorsionAngleValue
exportName(String) - Method in class pl.poznan.put.torsion.ImmutableAtomBasedTorsionAngleType.Builder: Initializes the value for the exportName attribute.
ExtendedEntry() - Constructor for class pl.poznan.put.structure.formats.Ct.ExtendedEntry

F

FALSE - Enum constant in enum pl.poznan.put.structure.HelixOrigin
FIBER_DIFFRACTION - Enum constant in enum pl.poznan.put.pdb.ExperimentalTechnique
fileChainMap() - Method in class pl.poznan.put.pdb.analysis.CifContainer
fileChainMap() - Method in class pl.poznan.put.pdb.analysis.ImmutableCifContainer
fileChainMap(Map<? extends File, ? extends BidiMap<String, String>>) - Method in class pl.poznan.put.pdb.analysis.ImmutableCifContainer.Builder: Sets or replaces all mappings from the specified map as entries for the fileChainMap map.
filteredAtoms(MoleculeType) - Method in interface pl.poznan.put.pdb.analysis.ResidueCollection: Filters atoms in this residue collection.
filteredMissing(MoleculeType) - Method in interface pl.poznan.put.pdb.analysis.PdbModel: Finds all missing residues of the given type.
filteredNewInstance(MoleculeType) - Method in class pl.poznan.put.pdb.analysis.DefaultCifModel
filteredNewInstance(MoleculeType) - Method in class pl.poznan.put.pdb.analysis.DefaultPdbModel
filteredNewInstance(MoleculeType) - Method in interface pl.poznan.put.pdb.analysis.PdbModel: Filters out residues of a given molecule type (RNA or protein) and creates a new instance of this class.
findAtom(AtomName) - Method in interface pl.poznan.put.pdb.analysis.PdbResidue: Finds an atom of a given name.
findAtomPairs(List<PdbResidue>, int) - Method in interface pl.poznan.put.torsion.AtomBasedTorsionAngleType: Applies residueRule() on the given list of residues to find three pairs of atoms: (a1, a2), (a2, a3), (a3, a4).
findBin(double) - Method in class pl.poznan.put.circular.Histogram: Finds a bin which starts at a given point.
findBondLengthViolations() - Method in interface pl.poznan.put.pdb.analysis.ResidueCollection: Analyzes atomic bond lenths to find violations (too long or too short) and generates a report in a form of a list of validation messages.
findChainContainingResidue(ChainNumberICode) - Method in interface pl.poznan.put.pdb.analysis.PdbModel: Finds a chain which has a given residue.
findNucleotide(String) - Method in class pl.poznan.put.external.dssr.DssrJson
findOptimalSolutions(ConflictClique) - Method in class pl.poznan.put.structure.pseudoknots.dp.DynamicProgrammingAll
findPseudoknots(BpSeq) - Method in class pl.poznan.put.structure.pseudoknots.dp.DynamicProgrammingAll
findPseudoknots(BpSeq) - Method in class pl.poznan.put.structure.pseudoknots.elimination.AbstractRegionRemover: Finds pseudoknots by removing one region at a time until there are any conflicts.
findPseudoknots(BpSeq) - Method in interface pl.poznan.put.structure.pseudoknots.PseudoknotFinder: Finds pseudoknots in BPSEQ data.
findRegion(int, int) - Method in class pl.poznan.put.structure.pseudoknots.dp.ConflictClique: Searches for a region given its begin and end indices.
findResidue(ChainNumberICode) - Method in interface pl.poznan.put.pdb.analysis.ResidueCollection: Finds a residue by a triplet (chain, number, icode).
findStrand(DotBracketSymbol) - Method in interface pl.poznan.put.structure.formats.DotBracket: Finds a strand which contains the given symbol.
FLUORESCENCE_TRANSFER - Enum constant in enum pl.poznan.put.pdb.ExperimentalTechnique
Format - Enum in pl.poznan.put.utility.svg: An image format which can be used to export SVG images to.
forNucleicAcid() - Static method in class pl.poznan.put.torsion.AverageTorsionAngleType
forProtein() - Static method in class pl.poznan.put.torsion.AverageTorsionAngleType
from(BondLength) - Method in class pl.poznan.put.atom.ImmutableBondLength.Builder: Fill a builder with attribute values from the provided BondLength instance.
from(Angle) - Method in class pl.poznan.put.circular.ImmutableAngle.Builder: Fill a builder with attribute values from the provided Angle instance.
from(Histogram) - Method in class pl.poznan.put.circular.ImmutableHistogram.Builder: Fill a builder with attribute values from the provided Histogram instance.
from(AngleSample) - Method in class pl.poznan.put.circular.samples.ImmutableAngleSample.Builder: Fill a builder with attribute values from the provided AngleSample instance.
from(TrigonometricMoment) - Method in class pl.poznan.put.circular.samples.ImmutableTrigonometricMoment.Builder: Fill a builder with attribute values from the provided TrigonometricMoment instance.
from(DssrJson) - Method in class pl.poznan.put.external.dssr.ImmutableDssrJson.Builder: Fill a builder with attribute values from the provided DssrJson instance.
from(Nucleotide) - Method in class pl.poznan.put.external.dssr.ImmutableNucleotide.Builder: Fill a builder with attribute values from the provided Nucleotide instance.
from(Pair) - Method in class pl.poznan.put.external.dssr.ImmutablePair.Builder: Fill a builder with attribute values from the provided Pair instance.
from(DisplayableExportable) - Method in class pl.poznan.put.torsion.ImmutableAtomBasedTorsionAngleType.Builder: Fill a builder with attribute values from the provided pl.poznan.put.interfaces.DisplayableExportable instance.
from(AbstractPdbModel) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel.Builder: Fill a builder with attribute values from the provided pl.poznan.put.pdb.analysis.AbstractPdbModel instance.
from(AbstractPdbModel) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbModel.Builder: Fill a builder with attribute values from the provided pl.poznan.put.pdb.analysis.AbstractPdbModel instance.
from(CifContainer) - Method in class pl.poznan.put.pdb.analysis.ImmutableCifContainer.Builder: Fill a builder with attribute values from the provided CifContainer instance.
from(CifModel) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel.Builder: Fill a builder with attribute values from the provided pl.poznan.put.pdb.analysis.CifModel instance.
from(DefaultCifModel) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel.Builder: Fill a builder with attribute values from the provided pl.poznan.put.pdb.analysis.DefaultCifModel instance.
from(DefaultPdbModel) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbModel.Builder: Fill a builder with attribute values from the provided pl.poznan.put.pdb.analysis.DefaultPdbModel instance.
from(DefaultPdbResidue) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbResidue.Builder: Fill a builder with attribute values from the provided pl.poznan.put.pdb.analysis.DefaultPdbResidue instance.
from(DefaultResidueCollection) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultResidueCollection.Builder: Fill a builder with attribute values from the provided pl.poznan.put.pdb.analysis.DefaultResidueCollection instance.
from(PdbChain) - Method in class pl.poznan.put.pdb.analysis.ImmutablePdbChain.Builder: Fill a builder with attribute values from the provided pl.poznan.put.pdb.analysis.PdbChain instance.
from(PdbCompactFragment) - Method in class pl.poznan.put.pdb.analysis.ImmutablePdbCompactFragment.Builder: Fill a builder with attribute values from the provided pl.poznan.put.pdb.analysis.PdbCompactFragment instance.
from(PdbModel) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel.Builder: Fill a builder with attribute values from the provided pl.poznan.put.pdb.analysis.PdbModel instance.
from(PdbModel) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbModel.Builder: Fill a builder with attribute values from the provided pl.poznan.put.pdb.analysis.PdbModel instance.
from(PdbResidue) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbResidue.Builder: Fill a builder with attribute values from the provided pl.poznan.put.pdb.analysis.PdbResidue instance.
from(ResidueCollection) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultResidueCollection.Builder: Fill a builder with attribute values from the provided pl.poznan.put.pdb.analysis.ResidueCollection instance.
from(ResidueCollection) - Method in class pl.poznan.put.pdb.analysis.ImmutablePdbChain.Builder: Fill a builder with attribute values from the provided pl.poznan.put.pdb.analysis.ResidueCollection instance.
from(ResidueCollection) - Method in class pl.poznan.put.pdb.analysis.ImmutablePdbCompactFragment.Builder: Fill a builder with attribute values from the provided pl.poznan.put.pdb.analysis.ResidueCollection instance.
from(ResidueTorsionAngles) - Method in class pl.poznan.put.pdb.analysis.ImmutableResidueTorsionAngles.Builder: Fill a builder with attribute values from the provided ResidueTorsionAngles instance.
from(SingleTypedResidueCollection) - Method in class pl.poznan.put.pdb.analysis.ImmutablePdbChain.Builder: Fill a builder with attribute values from the provided pl.poznan.put.pdb.analysis.SingleTypedResidueCollection instance.
from(SingleTypedResidueCollection) - Method in class pl.poznan.put.pdb.analysis.ImmutablePdbCompactFragment.Builder: Fill a builder with attribute values from the provided pl.poznan.put.pdb.analysis.SingleTypedResidueCollection instance.
from(ChainNumberICode) - Method in class pl.poznan.put.pdb.ImmutablePdbAtomLine.Builder: Fill a builder with attribute values from the provided pl.poznan.put.pdb.ChainNumberICode instance.
from(ChainNumberICode) - Method in class pl.poznan.put.pdb.ImmutablePdbModresLine.Builder: Fill a builder with attribute values from the provided pl.poznan.put.pdb.ChainNumberICode instance.
from(ChainNumberICode) - Method in class pl.poznan.put.pdb.ImmutablePdbNamedResidueIdentifier.Builder: Fill a builder with attribute values from the provided pl.poznan.put.pdb.ChainNumberICode instance.
from(ChainNumberICode) - Method in class pl.poznan.put.pdb.ImmutablePdbRemark465Line.Builder: Fill a builder with attribute values from the provided pl.poznan.put.pdb.ChainNumberICode instance.
from(ChainNumberICode) - Method in class pl.poznan.put.pdb.ImmutablePdbResidueIdentifier.Builder: Fill a builder with attribute values from the provided pl.poznan.put.pdb.ChainNumberICode instance.
from(ChainNumberICode) - Static method in class pl.poznan.put.pdb.PdbResidueIdentifier: Creates an instance of this class from any implementation of ChainNumberICode.
from(PdbAtomLine) - Method in class pl.poznan.put.pdb.ImmutablePdbAtomLine.Builder: Fill a builder with attribute values from the provided pl.poznan.put.pdb.PdbAtomLine instance.
from(PdbExpdtaLine) - Method in class pl.poznan.put.pdb.ImmutablePdbExpdtaLine.Builder: Fill a builder with attribute values from the provided PdbExpdtaLine instance.
from(PdbHeaderLine) - Method in class pl.poznan.put.pdb.ImmutablePdbHeaderLine.Builder: Fill a builder with attribute values from the provided PdbHeaderLine instance.
from(PdbModresLine) - Method in class pl.poznan.put.pdb.ImmutablePdbModresLine.Builder: Fill a builder with attribute values from the provided pl.poznan.put.pdb.PdbModresLine instance.
from(PdbNamedResidueIdentifier) - Method in class pl.poznan.put.pdb.ImmutablePdbNamedResidueIdentifier.Builder: Fill a builder with attribute values from the provided pl.poznan.put.pdb.PdbNamedResidueIdentifier instance.
from(PdbRemark2Line) - Method in class pl.poznan.put.pdb.ImmutablePdbRemark2Line.Builder: Fill a builder with attribute values from the provided PdbRemark2Line instance.
from(PdbRemark465Line) - Method in class pl.poznan.put.pdb.ImmutablePdbRemark465Line.Builder: Fill a builder with attribute values from the provided pl.poznan.put.pdb.PdbRemark465Line instance.
from(PdbResidueIdentifier) - Method in class pl.poznan.put.pdb.ImmutablePdbResidueIdentifier.Builder: Fill a builder with attribute values from the provided pl.poznan.put.pdb.PdbResidueIdentifier instance.
from(PdbTitleLine) - Method in class pl.poznan.put.pdb.ImmutablePdbTitleLine.Builder: Fill a builder with attribute values from the provided PdbTitleLine instance.
from(Backbone) - Method in class pl.poznan.put.protein.ImmutableBackbone.Builder: Fill a builder with attribute values from the provided Backbone instance.
from(InteractionType) - Method in class pl.poznan.put.rna.ImmutableInteractionType.Builder: Fill a builder with attribute values from the provided InteractionType instance.
from(Phosphate) - Method in class pl.poznan.put.rna.ImmutablePhosphate.Builder: Fill a builder with attribute values from the provided Phosphate instance.
from(PseudophasePuckerType) - Method in class pl.poznan.put.rna.ImmutablePseudophasePuckerType.Builder: Fill a builder with attribute values from the provided PseudophasePuckerType instance.
from(Ribose) - Method in class pl.poznan.put.rna.ImmutableRibose.Builder: Fill a builder with attribute values from the provided Ribose instance.
from(AnalyzedBasePair) - Method in class pl.poznan.put.structure.ImmutableAnalyzedBasePair.Builder: Fill a builder with attribute values from the provided pl.poznan.put.structure.AnalyzedBasePair instance.
from(BasePair) - Method in class pl.poznan.put.structure.ImmutableBasePair.Builder: Fill a builder with attribute values from the provided BasePair instance.
from(ClassifiedBasePair) - Method in class pl.poznan.put.structure.ImmutableAnalyzedBasePair.Builder: Fill a builder with attribute values from the provided pl.poznan.put.structure.ClassifiedBasePair instance.
from(ClassifiedBasePair) - Method in class pl.poznan.put.structure.ImmutableQuantifiedBasePair.Builder: Fill a builder with attribute values from the provided pl.poznan.put.structure.ClassifiedBasePair instance.
from(DotBracketSymbol) - Method in class pl.poznan.put.structure.ImmutableDotBracketSymbol.Builder: Fill a builder with attribute values from the provided DotBracketSymbol instance.
from(AbstractCombinedStrand) - Method in class pl.poznan.put.structure.formats.ImmutableCombinedStrand.Builder: Fill a builder with attribute values from the provided pl.poznan.put.structure.formats.AbstractCombinedStrand instance.
from(AbstractCombinedStrand) - Method in class pl.poznan.put.structure.formats.ImmutableCombinedStrandFromPdb.Builder: Fill a builder with attribute values from the provided pl.poznan.put.structure.formats.AbstractCombinedStrand instance.
from(AbstractDotBracket) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracket.Builder: Fill a builder with attribute values from the provided pl.poznan.put.structure.formats.AbstractDotBracket instance.
from(AbstractDotBracket) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracketFromPdb.Builder: Fill a builder with attribute values from the provided pl.poznan.put.structure.formats.AbstractDotBracket instance.
from(BpSeq) - Method in class pl.poznan.put.structure.formats.ImmutableBpSeq.Builder: Fill a builder with attribute values from the provided BpSeq instance.
from(BpSeq.Entry) - Method in class pl.poznan.put.structure.formats.ImmutableEntry.Builder: Fill a builder with attribute values from the provided Entry instance.
from(CombinedStrand) - Method in class pl.poznan.put.structure.formats.ImmutableCombinedStrand.Builder: Fill a builder with attribute values from the provided pl.poznan.put.structure.formats.CombinedStrand instance.
from(CombinedStrandFromPdb) - Method in class pl.poznan.put.structure.formats.ImmutableCombinedStrandFromPdb.Builder: Fill a builder with attribute values from the provided pl.poznan.put.structure.formats.CombinedStrandFromPdb instance.
from(Ct) - Method in class pl.poznan.put.structure.formats.ImmutableCt.Builder: Fill a builder with attribute values from the provided Ct instance.
from(Ct.ExtendedEntry) - Method in class pl.poznan.put.structure.formats.ImmutableExtendedEntry.Builder: Fill a builder with attribute values from the provided ExtendedEntry instance.
from(DefaultConverter) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultConverter.Builder: Fill a builder with attribute values from the provided DefaultConverter instance.
from(DefaultDotBracket) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracket.Builder: Fill a builder with attribute values from the provided pl.poznan.put.structure.formats.DefaultDotBracket instance.
from(DefaultDotBracketFromPdb) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracketFromPdb.Builder: Fill a builder with attribute values from the provided pl.poznan.put.structure.formats.DefaultDotBracketFromPdb instance.
from(DefaultStrand) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultStrand.Builder: Fill a builder with attribute values from the provided pl.poznan.put.structure.formats.DefaultStrand instance.
from(DotBracket) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracket.Builder: Fill a builder with attribute values from the provided pl.poznan.put.structure.formats.DotBracket instance.
from(DotBracket) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracketFromPdb.Builder: Fill a builder with attribute values from the provided pl.poznan.put.structure.formats.DotBracket instance.
from(DotBracket) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultStrand.Builder: Fill a builder with attribute values from the provided pl.poznan.put.structure.formats.DotBracket instance.
from(DotBracket) - Method in class pl.poznan.put.structure.formats.ImmutableStrandView.Builder: Fill a builder with attribute values from the provided pl.poznan.put.structure.formats.DotBracket instance.
from(DotBracketFromPdb) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracketFromPdb.Builder: Fill a builder with attribute values from the provided pl.poznan.put.structure.formats.DotBracketFromPdb instance.
from(MultiLineDotBracket) - Method in class pl.poznan.put.structure.formats.ImmutableMultiLineDotBracket.Builder: Fill a builder with attribute values from the provided MultiLineDotBracket instance.
from(Strand) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultStrand.Builder: Fill a builder with attribute values from the provided pl.poznan.put.structure.formats.Strand instance.
from(Strand) - Method in class pl.poznan.put.structure.formats.ImmutableStrandView.Builder: Fill a builder with attribute values from the provided pl.poznan.put.structure.formats.Strand instance.
from(StrandView) - Method in class pl.poznan.put.structure.formats.ImmutableStrandView.Builder: Fill a builder with attribute values from the provided pl.poznan.put.structure.formats.StrandView instance.
from(TerminalMissing) - Method in class pl.poznan.put.structure.formats.ImmutableTerminalMissing.Builder: Fill a builder with attribute values from the provided TerminalMissing instance.
from(ConflictGraph) - Method in class pl.poznan.put.structure.pseudoknots.ImmutableConflictGraph.Builder: Fill a builder with attribute values from the provided ConflictGraph instance.
from(ConflictClique) - Method in class pl.poznan.put.structure.pseudoknots.dp.ImmutableConflictClique.Builder: Fill a builder with attribute values from the provided ConflictClique instance.
from(DynamicProgrammingAll) - Method in class pl.poznan.put.structure.pseudoknots.dp.ImmutableDynamicProgrammingAll.Builder: Fill a builder with attribute values from the provided DynamicProgrammingAll instance.
from(MaxConflicts) - Method in class pl.poznan.put.structure.pseudoknots.elimination.ImmutableMaxConflicts.Builder: Fill a builder with attribute values from the provided MaxConflicts instance.
from(MinGain) - Method in class pl.poznan.put.structure.pseudoknots.elimination.ImmutableMinGain.Builder: Fill a builder with attribute values from the provided MinGain instance.
from(Region) - Method in class pl.poznan.put.structure.pseudoknots.ImmutableRegion.Builder: Fill a builder with attribute values from the provided Region instance.
from(QuantifiedBasePair) - Method in class pl.poznan.put.structure.ImmutableQuantifiedBasePair.Builder: Fill a builder with attribute values from the provided pl.poznan.put.structure.QuantifiedBasePair instance.
from(AtomBasedTorsionAngleType) - Method in class pl.poznan.put.torsion.ImmutableAtomBasedTorsionAngleType.Builder: Fill a builder with attribute values from the provided pl.poznan.put.torsion.AtomBasedTorsionAngleType instance.
from(AtomPair) - Method in class pl.poznan.put.torsion.ImmutableAtomPair.Builder: Fill a builder with attribute values from the provided AtomPair instance.
from(AverageTorsionAngleType) - Method in class pl.poznan.put.torsion.ImmutableAverageTorsionAngleType.Builder: Fill a builder with attribute values from the provided pl.poznan.put.torsion.AverageTorsionAngleType instance.
from(TorsionAngleDelta) - Method in class pl.poznan.put.torsion.ImmutableTorsionAngleDelta.Builder: Fill a builder with attribute values from the provided TorsionAngleDelta instance.
from(TorsionAngleType) - Method in class pl.poznan.put.torsion.ImmutableAtomBasedTorsionAngleType.Builder: Fill a builder with attribute values from the provided pl.poznan.put.torsion.TorsionAngleType instance.
from(TorsionAngleType) - Method in class pl.poznan.put.torsion.ImmutableAverageTorsionAngleType.Builder: Fill a builder with attribute values from the provided pl.poznan.put.torsion.TorsionAngleType instance.
from(TorsionAngleValue) - Method in class pl.poznan.put.torsion.ImmutableTorsionAngleValue.Builder: Fill a builder with attribute values from the provided TorsionAngleValue instance.
from(DistanceMatrix) - Method in class pl.poznan.put.types.ImmutableDistanceMatrix.Builder: Fill a builder with attribute values from the provided DistanceMatrix instance.
from(Quadruple<T>) - Method in class pl.poznan.put.types.ImmutableQuadruple.Builder: Fill a builder with attribute values from the provided Quadruple instance.
from(ExecHelper) - Method in class pl.poznan.put.utility.ImmutableExecHelper.Builder: Fill a builder with attribute values from the provided ExecHelper instance.
from(ExecHelper.ExecutionResult) - Method in class pl.poznan.put.utility.ImmutableExecutionResult.Builder: Fill a builder with attribute values from the provided ExecutionResult instance.
fromAngle(Angle) - Method in interface pl.poznan.put.torsion.range.RangeProvider: Provdes a Range instance for given angle value.
fromBasePairs(List<PdbNamedResidueIdentifier>, Collection<? extends ClassifiedBasePair>) - Static method in class pl.poznan.put.structure.formats.BpSeq: Creates an instance of BPSEQ from a list of residue identifiers and a list of base pairs.
fromBpSeq(BpSeq) - Static method in class pl.poznan.put.structure.formats.Ct: Converts RNA secondary structure in BPSEQ format to CT format.
fromBpSeqAndPdbModel(BpSeq, PdbModel) - Static method in class pl.poznan.put.structure.formats.Ct: Converts RNA secondary structure in BPSEQ format to CT format, taking into account information from 3D coordinates (residue numbering, chain sizes).
fromCt(Ct) - Static method in class pl.poznan.put.structure.formats.BpSeq: Converts RNA secondary structure in CT format to BPSEQ format.
fromDotBracket(DotBracket) - Static method in class pl.poznan.put.structure.formats.BpSeq: Converts RNA secondary structure in dot-bracket format to BPSEQ format.
fromDotBracket(DotBracket) - Static method in class pl.poznan.put.structure.formats.Ct: Converts RNA secondary structure in dot-bracket format to CT format.
fromEntry(BpSeq.Entry) - Static method in class pl.poznan.put.structure.formats.Ct.ExtendedEntry: Converts a BPSEQ entry into an instance of this class.
fromFile(File) - Static method in class pl.poznan.put.utility.svg.SVGHelper: Loads an SVG image from file.
fromFullName(String) - Static method in enum pl.poznan.put.pdb.ExperimentalTechnique: Finds a matching instance of this enum in case-insensitive manner.
fromHourMinuteString(String) - Static method in class pl.poznan.put.circular.Angle: Parses a string in format HH.MM as a vector on a circular clock.
fromNumber(int) - Static method in enum pl.poznan.put.notation.LeontisWesthof: Matches a number in range 1-12 to one of the constants.
fromNumber(int) - Static method in enum pl.poznan.put.notation.Saenger: Matches a value in range 1-28 to an instance of this class with the same value written as a Roman numeral.
fromString(CharSequence) - Static method in enum pl.poznan.put.notation.LeontisWesthof: Finds a constant that matches a given name in case-insensitive manner or return UNKNOWN otherwise.
fromString(String) - Static method in enum pl.poznan.put.atom.AtomName: Creates an instance from String.
fromString(String) - Static method in enum pl.poznan.put.notation.BPh: Finds an enum constant that matches the given one or return a predefined UNKNOWN value.
fromString(String) - Static method in enum pl.poznan.put.notation.BR: Finds an enum constant that matches the given one or return a predefined UNKNOWN value.
fromString(String) - Static method in enum pl.poznan.put.notation.Saenger: Finds an enum that matches the given name or return UNKNOWN otherwise.
fromString(String) - Static method in enum pl.poznan.put.notation.StackingTopology: Finds an enum constant that matches the given one or return a predefined UNKNOWN value.
fromString(String) - Static method in class pl.poznan.put.structure.formats.BpSeq.Entry: Parses a string into a BPSEQ entry.
fromString(String) - Static method in class pl.poznan.put.structure.formats.BpSeq: Parses string into an instance of this class.
fromString(String) - Static method in class pl.poznan.put.structure.formats.Ct.ExtendedEntry: Creates an instance from a string in format: int string int int int int.
fromString(String) - Static method in class pl.poznan.put.structure.formats.Ct: Parses string into an instance of this class.
fromString(String) - Static method in class pl.poznan.put.structure.formats.DefaultDotBracket: Parses a string into an instance of this class.
fromString(String) - Static method in class pl.poznan.put.structure.formats.MultiLineDotBracket: Creates an instance by reading a set of lines in dot-bracket notation.
fromUri(URI) - Static method in class pl.poznan.put.utility.svg.SVGHelper: Loads an SVG image from URI.
fromValue(int) - Static method in enum pl.poznan.put.torsion.range.RangeDifference: Parses value 0, 1, 2, or 3 as EQUAL, SIMILAR, DIFFERENT and OPPOSITE respectively.
fullName() - Method in enum pl.poznan.put.notation.LeontisWesthof: Generates a full name representation.

G

GAMMA - Enum constant in enum pl.poznan.put.rna.NucleotideTorsionAngle
GAMMA - Static variable in class pl.poznan.put.constant.Unicode
generateComment() - Method in interface pl.poznan.put.structure.ClassifiedBasePair
generateValidationMessage() - Method in class pl.poznan.put.torsion.AtomPair: Generate a validation message if the distance between this atom pair is larger than 150% of the maximum expected bond length (see Bond.length(AtomType, AtomType)).
get(int) - Method in interface pl.poznan.put.types.Quadruple
getDistinctColors() - Static method in class pl.poznan.put.constant.Colors
getExtension() - Method in enum pl.poznan.put.utility.svg.Format
getHeight(SVGDocument) - Static method in class pl.poznan.put.utility.svg.SVGHelper: Retrieves the height of the SVG document.
getIsRepresented() - Method in class pl.poznan.put.structure.AnalyzedBasePair: Returns the value of isRepresented(), but this naming is required by Spring.
getLineMetrics(SVGGraphics2D) - Static method in class pl.poznan.put.utility.svg.SVGHelper: Gets metrics for a line of ASCII letters in the context of SVG image.
getName() - Method in enum pl.poznan.put.atom.AtomName: Gets the default atom name (if more than one is configured).
getPdbName() - Method in enum pl.poznan.put.pdb.ExperimentalTechnique
getProvider() - Static method in enum pl.poznan.put.rna.ChiRange
getProvider() - Static method in enum pl.poznan.put.rna.Pseudorotation
getTranscoder() - Method in enum pl.poznan.put.utility.svg.Format
getType() - Method in enum pl.poznan.put.atom.AtomName: Gets enum describing the type of atom that this constant represents.
getValue() - Method in enum pl.poznan.put.torsion.range.RangeDifference
getWidth(SVGDocument) - Static method in class pl.poznan.put.utility.svg.SVGHelper: Retrieves the width of the SVG document.
GLUTAMIC_ACID - Enum constant in enum pl.poznan.put.protein.AminoAcid
GLUTAMINE - Enum constant in enum pl.poznan.put.protein.AminoAcid
GLYCINE - Enum constant in enum pl.poznan.put.protein.AminoAcid
GUANINE - Enum constant in enum pl.poznan.put.rna.Nucleotide

H

H - Enum constant in enum pl.poznan.put.atom.AtomType
H1 - Enum constant in enum pl.poznan.put.atom.AtomName
H1p - Enum constant in enum pl.poznan.put.atom.AtomName
H2 - Enum constant in enum pl.poznan.put.atom.AtomName
H21 - Enum constant in enum pl.poznan.put.atom.AtomName
H22 - Enum constant in enum pl.poznan.put.atom.AtomName
H2p - Enum constant in enum pl.poznan.put.atom.AtomName
H2pp - Enum constant in enum pl.poznan.put.atom.AtomName
H3 - Enum constant in enum pl.poznan.put.atom.AtomName
H3p - Enum constant in enum pl.poznan.put.atom.AtomName
H3T - Enum constant in enum pl.poznan.put.atom.AtomName
H3T1 - Enum constant in enum pl.poznan.put.atom.AtomName
H3T2 - Enum constant in enum pl.poznan.put.atom.AtomName
H3T3 - Enum constant in enum pl.poznan.put.atom.AtomName
H41 - Enum constant in enum pl.poznan.put.atom.AtomName
H42 - Enum constant in enum pl.poznan.put.atom.AtomName
H4p - Enum constant in enum pl.poznan.put.atom.AtomName
H5 - Enum constant in enum pl.poznan.put.atom.AtomName
H51 - Enum constant in enum pl.poznan.put.atom.AtomName
H52 - Enum constant in enum pl.poznan.put.atom.AtomName
H53 - Enum constant in enum pl.poznan.put.atom.AtomName
H53p - Enum constant in enum pl.poznan.put.atom.AtomName
H5p - Enum constant in enum pl.poznan.put.atom.AtomName
H5pp - Enum constant in enum pl.poznan.put.atom.AtomName
H5T - Enum constant in enum pl.poznan.put.atom.AtomName
H5T1 - Enum constant in enum pl.poznan.put.atom.AtomName
H5T2 - Enum constant in enum pl.poznan.put.atom.AtomName
H5T3 - Enum constant in enum pl.poznan.put.atom.AtomName
H6 - Enum constant in enum pl.poznan.put.atom.AtomName
H61 - Enum constant in enum pl.poznan.put.atom.AtomName
H62 - Enum constant in enum pl.poznan.put.atom.AtomName
H8 - Enum constant in enum pl.poznan.put.atom.AtomName
HA - Enum constant in enum pl.poznan.put.atom.AtomName
HA1 - Enum constant in enum pl.poznan.put.atom.AtomName
HA2 - Enum constant in enum pl.poznan.put.atom.AtomName
hasAllHeavyAtoms() - Method in class pl.poznan.put.pdb.analysis.DefaultPdbResidue
hasAllHeavyAtoms() - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbResidue: Compares the set of actual atoms in this residue with the set of expected atoms derived from the detected type of residue.
hasAllHeavyAtoms() - Method in interface pl.poznan.put.pdb.analysis.PdbResidue: Compares the set of actual atoms in this residue with the set of expected atoms derived from the detected type of residue.
hasAnyHydrogen() - Method in interface pl.poznan.put.pdb.analysis.PdbResidue
hasAnyPair() - Method in class pl.poznan.put.structure.formats.BpSeq
hasAtom(AtomName) - Method in interface pl.poznan.put.pdb.analysis.PdbResidue: Checks whether this residue has atom of the given name.
hasConflicts() - Method in class pl.poznan.put.structure.pseudoknots.ConflictGraph
hasConflicts(Region) - Method in class pl.poznan.put.structure.pseudoknots.ConflictGraph: Checks if a given region has any conflicts.
hashCode() - Method in class pl.poznan.put.atom.ImmutableBondLength: Computes a hash code from attributes: min, max, avg.
hashCode() - Method in class pl.poznan.put.circular.ImmutableAngle: Computes a hash code from attributes: radians.
hashCode() - Method in class pl.poznan.put.circular.ImmutableHistogram: Computes a hash code from attributes: data, binWidth.
hashCode() - Method in class pl.poznan.put.circular.samples.ImmutableAngleSample: Computes a hash code from attributes: data.
hashCode() - Method in class pl.poznan.put.circular.samples.ImmutableTrigonometricMoment: Computes a hash code from attributes: meanDirection, meanResultantLength.
hashCode() - Method in class pl.poznan.put.external.dssr.ImmutableDssrJson: Computes a hash code from attributes: pairs, nucleotides.
hashCode() - Method in class pl.poznan.put.external.dssr.ImmutableNucleotide: Computes a hash code from attributes: id, chainName, oneLetterName, residueNumber.
hashCode() - Method in class pl.poznan.put.external.dssr.ImmutablePair: Computes a hash code from attributes: nt1, nt2, saenger, lw.
hashCode() - Method in class pl.poznan.put.pdb.analysis.ImmutableCifContainer: Computes a hash code from attributes: fileChainMap, cifFile.
hashCode() - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel: Computes a hash code from attributes: atoms.
hashCode() - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbModel: Computes a hash code from attributes: atoms.
hashCode() - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbResidue: Computes a hash code from attributes: identifier, standardResidueName, modifiedResidueName, atoms.
hashCode() - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultResidueCollection: Computes a hash code from attributes: residues.
hashCode() - Method in class pl.poznan.put.pdb.analysis.ImmutablePdbChain: Computes a hash code from attributes: identifier, residues.
hashCode() - Method in class pl.poznan.put.pdb.analysis.ImmutablePdbCompactFragment: Computes a hash code from attributes: residues, name.
hashCode() - Method in class pl.poznan.put.pdb.analysis.ImmutableResidueTorsionAngles: Computes a hash code from attributes: identifier, values.
hashCode() - Method in class pl.poznan.put.pdb.ImmutablePdbAtomLine: Computes a hash code from attributes: atomName, residueName, chainIdentifier, residueNumber, insertionCode, x, y, z.
hashCode() - Method in class pl.poznan.put.pdb.ImmutablePdbExpdtaLine: Computes a hash code from attributes: experimentalTechniques.
hashCode() - Method in class pl.poznan.put.pdb.ImmutablePdbHeaderLine: Computes a hash code from attributes: classification, depositionDate, idCode.
hashCode() - Method in class pl.poznan.put.pdb.ImmutablePdbModresLine: Computes a hash code from attributes: idCode, residueName, chainIdentifier, residueNumber, insertionCode, standardResidueName, comment.
hashCode() - Method in class pl.poznan.put.pdb.ImmutablePdbNamedResidueIdentifier: Computes a hash code from attributes: chainIdentifier, residueNumber, insertionCode, oneLetterName.
hashCode() - Method in class pl.poznan.put.pdb.ImmutablePdbRemark2Line: Computes a hash code from attributes: resolution.
hashCode() - Method in class pl.poznan.put.pdb.ImmutablePdbRemark465Line: Computes a hash code from attributes: modelNumber, residueName, chainIdentifier, residueNumber, insertionCode.
hashCode() - Method in class pl.poznan.put.pdb.ImmutablePdbResidueIdentifier: Computes a hash code from attributes: chainIdentifier, residueNumber, insertionCode.
hashCode() - Method in class pl.poznan.put.pdb.ImmutablePdbTitleLine: Computes a hash code from attributes: continuation, title.
hashCode() - Method in class pl.poznan.put.protein.ImmutableBackbone: Returns a constant hash code value.
hashCode() - Method in class pl.poznan.put.rna.ImmutableInteractionType: Computes a hash code from attributes: left, right, isPairing, description.
hashCode() - Method in class pl.poznan.put.rna.ImmutablePhosphate: Returns a constant hash code value.
hashCode() - Method in class pl.poznan.put.rna.ImmutablePseudophasePuckerType: Returns a constant hash code value.
hashCode() - Method in class pl.poznan.put.rna.ImmutableRibose: Returns a constant hash code value.
hashCode() - Method in class pl.poznan.put.structure.formats.ImmutableBpSeq: Computes a hash code from attributes: entries.
hashCode() - Method in class pl.poznan.put.structure.formats.ImmutableCombinedStrand: Computes a hash code from attributes: inputStrands.
hashCode() - Method in class pl.poznan.put.structure.formats.ImmutableCombinedStrandFromPdb: Computes a hash code from attributes: inputStrands, inputSymbolToResidue.
hashCode() - Method in class pl.poznan.put.structure.formats.ImmutableCt: Computes a hash code from attributes: entries.
hashCode() - Method in class pl.poznan.put.structure.formats.ImmutableDefaultConverter: Computes a hash code from attributes: pseudoknotFinder, maxSolutions.
hashCode() - Method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracket: Computes a hash code from attributes: sequence, structure.
hashCode() - Method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracketFromPdb: Computes a hash code from attributes: identifierSet, model, sequence, structure.
hashCode() - Method in class pl.poznan.put.structure.formats.ImmutableDefaultStrand: Computes a hash code from attributes: combineStrands, name, symbols.
hashCode() - Method in class pl.poznan.put.structure.formats.ImmutableEntry: Computes a hash code from attributes: index, seq, pair, comment.
hashCode() - Method in class pl.poznan.put.structure.formats.ImmutableExtendedEntry: Computes a hash code from attributes: index, seq, before, after, pair, original, comment.
hashCode() - Method in class pl.poznan.put.structure.formats.ImmutableMultiLineDotBracket: Computes a hash code from attributes: sequence, basePairs.
hashCode() - Method in class pl.poznan.put.structure.formats.ImmutableStrandView: Computes a hash code from attributes: combineStrands, name, begin, end, parent.
hashCode() - Method in class pl.poznan.put.structure.formats.ImmutableTerminalMissing: Computes a hash code from attributes: symbols.
hashCode() - Method in class pl.poznan.put.structure.ImmutableAnalyzedBasePair: Computes a hash code from attributes: basePair, interactionType, saenger, leontisWesthof, bph, br, stackingTopology.
hashCode() - Method in class pl.poznan.put.structure.ImmutableBasePair: Computes a hash code from attributes: left, right.
hashCode() - Method in class pl.poznan.put.structure.ImmutableDotBracketSymbol: Computes a hash code from attributes: sequence, structure, index.
hashCode() - Method in class pl.poznan.put.structure.ImmutableQuantifiedBasePair: Computes a hash code from attributes: basePair, interactionType, saenger, leontisWesthof, bph, br, stackingTopology.
hashCode() - Method in class pl.poznan.put.structure.pseudoknots.dp.ImmutableConflictClique: Computes a hash code from attributes: regions.
hashCode() - Method in class pl.poznan.put.structure.pseudoknots.dp.ImmutableDynamicProgrammingAll: Computes a hash code from attributes: regionRemover, maxCliqueSize.
hashCode() - Method in class pl.poznan.put.structure.pseudoknots.elimination.ImmutableMaxConflicts: Returns a constant hash code value.
hashCode() - Method in class pl.poznan.put.structure.pseudoknots.elimination.ImmutableMinGain: Returns a constant hash code value.
hashCode() - Method in class pl.poznan.put.structure.pseudoknots.ImmutableConflictGraph: Computes a hash code from attributes: regions.
hashCode() - Method in class pl.poznan.put.structure.pseudoknots.ImmutableRegion: Computes a hash code from attributes: entries, begin, end.
hashCode() - Method in class pl.poznan.put.torsion.ImmutableAtomBasedTorsionAngleType: Computes a hash code from attributes: moleculeType, shortDisplayName, exportName, atoms, residueRule, isPseudoTorsion.
hashCode() - Method in class pl.poznan.put.torsion.ImmutableAtomPair: Computes a hash code from attributes: leftAtom, rightAtom.
hashCode() - Method in class pl.poznan.put.torsion.ImmutableAverageTorsionAngleType: Computes a hash code from attributes: moleculeType, consideredAngles.
hashCode() - Method in class pl.poznan.put.torsion.ImmutableTorsionAngleDelta: Computes a hash code from attributes: angleType, state, delta, rangeDifference.
hashCode() - Method in class pl.poznan.put.torsion.ImmutableTorsionAngleValue: Computes a hash code from attributes: angleType, value.
hashCode() - Method in class pl.poznan.put.types.ImmutableDistanceMatrix: Computes a hash code from attributes: names, matrix.
hashCode() - Method in class pl.poznan.put.types.ImmutableQuadruple: Computes a hash code from attributes: a, b, c, d.
hashCode() - Method in class pl.poznan.put.utility.ImmutableExecHelper: Computes a hash code from attributes: workingDirectory, command, environment, arguments.
hashCode() - Method in class pl.poznan.put.utility.ImmutableExecutionResult: Computes a hash code from attributes: exitCode, standardOutput, standardError.
hasInvalidBeforeOrAfter() - Method in class pl.poznan.put.structure.formats.Ct.ExtendedEntry
hasResidue(ChainNumberICode) - Method in interface pl.poznan.put.pdb.analysis.ResidueCollection: Checks if a given (chain, number, icode) is present in this collection of residues.
HB - Enum constant in enum pl.poznan.put.atom.AtomName
HB1 - Enum constant in enum pl.poznan.put.atom.AtomName
HB2 - Enum constant in enum pl.poznan.put.atom.AtomName
HB3 - Enum constant in enum pl.poznan.put.atom.AtomName
HD1 - Enum constant in enum pl.poznan.put.atom.AtomName
HD11 - Enum constant in enum pl.poznan.put.atom.AtomName
HD12 - Enum constant in enum pl.poznan.put.atom.AtomName
HD13 - Enum constant in enum pl.poznan.put.atom.AtomName
HD2 - Enum constant in enum pl.poznan.put.atom.AtomName
HD21 - Enum constant in enum pl.poznan.put.atom.AtomName
HD22 - Enum constant in enum pl.poznan.put.atom.AtomName
HD23 - Enum constant in enum pl.poznan.put.atom.AtomName
HD3 - Enum constant in enum pl.poznan.put.atom.AtomName
HE - Enum constant in enum pl.poznan.put.atom.AtomName
HE1 - Enum constant in enum pl.poznan.put.atom.AtomName
HE2 - Enum constant in enum pl.poznan.put.atom.AtomName
HE21 - Enum constant in enum pl.poznan.put.atom.AtomName
HE22 - Enum constant in enum pl.poznan.put.atom.AtomName
HE3 - Enum constant in enum pl.poznan.put.atom.AtomName
header() - Method in class pl.poznan.put.pdb.analysis.DefaultCifModel
header() - Method in class pl.poznan.put.pdb.analysis.DefaultPdbModel
header() - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel
header() - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbModel
header() - Method in interface pl.poznan.put.pdb.analysis.PdbModel
header(PdbHeaderLine) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel.Builder: Initializes the value for the header attribute.
header(PdbHeaderLine) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbModel.Builder: Initializes the value for the header attribute.
HelixOrigin - Enum in pl.poznan.put.structure: An information whether a base pair originated from a helix.
HG - Enum constant in enum pl.poznan.put.atom.AtomName
HG1 - Enum constant in enum pl.poznan.put.atom.AtomName
HG11 - Enum constant in enum pl.poznan.put.atom.AtomName
HG12 - Enum constant in enum pl.poznan.put.atom.AtomName
HG13 - Enum constant in enum pl.poznan.put.atom.AtomName
HG2 - Enum constant in enum pl.poznan.put.atom.AtomName
HG21 - Enum constant in enum pl.poznan.put.atom.AtomName
HG22 - Enum constant in enum pl.poznan.put.atom.AtomName
HG23 - Enum constant in enum pl.poznan.put.atom.AtomName
HH - Enum constant in enum pl.poznan.put.atom.AtomName
HH11 - Enum constant in enum pl.poznan.put.atom.AtomName
HH12 - Enum constant in enum pl.poznan.put.atom.AtomName
HH2 - Enum constant in enum pl.poznan.put.atom.AtomName
HH21 - Enum constant in enum pl.poznan.put.atom.AtomName
HH22 - Enum constant in enum pl.poznan.put.atom.AtomName
HIGH_ANTI - Enum constant in enum pl.poznan.put.rna.ChiRange
HISTIDINE - Enum constant in enum pl.poznan.put.protein.AminoAcid
Histogram - Class in pl.poznan.put.circular: A collection of angular observations put into bins of specified width.
Histogram() - Constructor for class pl.poznan.put.circular.Histogram
HL - Enum constant in enum pl.poznan.put.atom.AtomName
HL1 - Enum constant in enum pl.poznan.put.atom.AtomName
HL2 - Enum constant in enum pl.poznan.put.atom.AtomName
HL3 - Enum constant in enum pl.poznan.put.atom.AtomName
HN - Enum constant in enum pl.poznan.put.atom.AtomName
HN1 - Enum constant in enum pl.poznan.put.atom.AtomName
HN2 - Enum constant in enum pl.poznan.put.atom.AtomName
HNT - Enum constant in enum pl.poznan.put.atom.AtomName
HO2p - Enum constant in enum pl.poznan.put.atom.AtomName
HOOGSTEEN - Enum constant in enum pl.poznan.put.notation.NucleobaseEdge
HR - Enum constant in enum pl.poznan.put.atom.AtomName
HR1 - Enum constant in enum pl.poznan.put.atom.AtomName
HR2 - Enum constant in enum pl.poznan.put.atom.AtomName
HR3 - Enum constant in enum pl.poznan.put.atom.AtomName
HT1 - Enum constant in enum pl.poznan.put.atom.AtomName
HT2 - Enum constant in enum pl.poznan.put.atom.AtomName
HT3 - Enum constant in enum pl.poznan.put.atom.AtomName
HY1 - Enum constant in enum pl.poznan.put.atom.AtomName
HY2 - Enum constant in enum pl.poznan.put.atom.AtomName
HY3 - Enum constant in enum pl.poznan.put.atom.AtomName
HZ - Enum constant in enum pl.poznan.put.atom.AtomName
HZ1 - Enum constant in enum pl.poznan.put.atom.AtomName
HZ2 - Enum constant in enum pl.poznan.put.atom.AtomName
HZ3 - Enum constant in enum pl.poznan.put.atom.AtomName

I

I - Enum constant in enum pl.poznan.put.notation.Saenger
id() - Method in class pl.poznan.put.external.dssr.ImmutableNucleotide
id() - Method in interface pl.poznan.put.external.dssr.Nucleotide
id(String) - Method in class pl.poznan.put.external.dssr.ImmutableNucleotide.Builder: Initializes the value for the id attribute.
idCode() - Method in interface pl.poznan.put.pdb.analysis.PdbModel
idCode() - Method in class pl.poznan.put.pdb.ImmutablePdbHeaderLine
idCode() - Method in class pl.poznan.put.pdb.ImmutablePdbModresLine
idCode() - Method in class pl.poznan.put.pdb.PdbHeaderLine
idCode() - Method in class pl.poznan.put.pdb.PdbModresLine
idCode(String) - Method in class pl.poznan.put.pdb.ImmutablePdbHeaderLine.Builder: Initializes the value for the idCode attribute.
idCode(String) - Method in class pl.poznan.put.pdb.ImmutablePdbModresLine.Builder: Initializes the value for the idCode attribute.
identifier() - Method in class pl.poznan.put.pdb.analysis.DefaultPdbResidue
identifier() - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbResidue
identifier() - Method in class pl.poznan.put.pdb.analysis.ImmutablePdbChain
identifier() - Method in class pl.poznan.put.pdb.analysis.ImmutableResidueTorsionAngles
identifier() - Method in class pl.poznan.put.pdb.analysis.PdbChain
identifier() - Method in interface pl.poznan.put.pdb.analysis.PdbResidue
identifier() - Method in class pl.poznan.put.pdb.analysis.ResidueTorsionAngles
identifier(String) - Method in class pl.poznan.put.pdb.analysis.ImmutablePdbChain.Builder: Initializes the value for the identifier attribute.
identifier(PdbResidueIdentifier) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbResidue.Builder: Initializes the value for the identifier attribute.
identifier(PdbResidueIdentifier) - Method in class pl.poznan.put.pdb.analysis.ImmutableResidueTorsionAngles.Builder: Initializes the value for the identifier attribute.
identifier(DotBracketSymbol) - Method in class pl.poznan.put.structure.formats.CombinedStrandFromPdb
identifier(DotBracketSymbol) - Method in class pl.poznan.put.structure.formats.DefaultDotBracketFromPdb
identifier(DotBracketSymbol) - Method in interface pl.poznan.put.structure.formats.DotBracketFromPdb: Maps the given dot-bracket symbol to its corresponding residue identifier.
identifierSet() - Method in class pl.poznan.put.structure.formats.CombinedStrandFromPdb
identifierSet() - Method in interface pl.poznan.put.structure.formats.DotBracketFromPdb
identifierSet() - Method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracketFromPdb
identifierSet(Iterable<? extends PdbResidueIdentifier>) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracketFromPdb.Builder: Sets or replaces all elements for identifierSet set.
idNucleotideMap() - Method in class pl.poznan.put.external.dssr.DssrJson
idNucleotideMap() - Method in class pl.poznan.put.external.dssr.ImmutableDssrJson
II - Enum constant in enum pl.poznan.put.notation.Saenger
III - Enum constant in enum pl.poznan.put.notation.Saenger
ImmutableAnalyzedBasePair - Class in pl.poznan.put.structure: Immutable implementation of AnalyzedBasePair.
ImmutableAnalyzedBasePair.Builder - Class in pl.poznan.put.structure: Builds instances of type ImmutableAnalyzedBasePair.
ImmutableAngle - Class in pl.poznan.put.circular: Immutable implementation of Angle.
ImmutableAngle.Builder - Class in pl.poznan.put.circular: Builds instances of type ImmutableAngle.
ImmutableAngleSample - Class in pl.poznan.put.circular.samples: Immutable implementation of AngleSample.
ImmutableAngleSample.Builder - Class in pl.poznan.put.circular.samples: Builds instances of type ImmutableAngleSample.
ImmutableAtomBasedTorsionAngleType - Class in pl.poznan.put.torsion: Immutable implementation of AtomBasedTorsionAngleType.
ImmutableAtomBasedTorsionAngleType.Builder - Class in pl.poznan.put.torsion: Builds instances of type ImmutableAtomBasedTorsionAngleType.
ImmutableAtomPair - Class in pl.poznan.put.torsion: Immutable implementation of AtomPair.
ImmutableAtomPair.Builder - Class in pl.poznan.put.torsion: Builds instances of type ImmutableAtomPair.
ImmutableAverageTorsionAngleType - Class in pl.poznan.put.torsion: Immutable implementation of AverageTorsionAngleType.
ImmutableAverageTorsionAngleType.Builder - Class in pl.poznan.put.torsion: Builds instances of type ImmutableAverageTorsionAngleType.
ImmutableBackbone - Class in pl.poznan.put.protein: Immutable implementation of Backbone.
ImmutableBackbone.Builder - Class in pl.poznan.put.protein: Builds instances of type ImmutableBackbone.
ImmutableBasePair - Class in pl.poznan.put.structure: Immutable implementation of BasePair.
ImmutableBasePair.Builder - Class in pl.poznan.put.structure: Builds instances of type ImmutableBasePair.
ImmutableBondLength - Class in pl.poznan.put.atom: Immutable implementation of BondLength.
ImmutableBondLength.Builder - Class in pl.poznan.put.atom: Builds instances of type ImmutableBondLength.
ImmutableBpSeq - Class in pl.poznan.put.structure.formats: Immutable implementation of BpSeq.
ImmutableBpSeq.Builder - Class in pl.poznan.put.structure.formats: Builds instances of type ImmutableBpSeq.
ImmutableCifContainer - Class in pl.poznan.put.pdb.analysis: Immutable implementation of CifContainer.
ImmutableCifContainer.Builder - Class in pl.poznan.put.pdb.analysis: Builds instances of type ImmutableCifContainer.
ImmutableCombinedStrand - Class in pl.poznan.put.structure.formats: Immutable implementation of CombinedStrand.
ImmutableCombinedStrand.Builder - Class in pl.poznan.put.structure.formats: Builds instances of type ImmutableCombinedStrand.
ImmutableCombinedStrandFromPdb - Class in pl.poznan.put.structure.formats: Immutable implementation of CombinedStrandFromPdb.
ImmutableCombinedStrandFromPdb.Builder - Class in pl.poznan.put.structure.formats: Builds instances of type ImmutableCombinedStrandFromPdb.
ImmutableConflictClique - Class in pl.poznan.put.structure.pseudoknots.dp: Immutable implementation of ConflictClique.
ImmutableConflictClique.Builder - Class in pl.poznan.put.structure.pseudoknots.dp: Builds instances of type ImmutableConflictClique.
ImmutableConflictGraph - Class in pl.poznan.put.structure.pseudoknots: Immutable implementation of ConflictGraph.
ImmutableConflictGraph.Builder - Class in pl.poznan.put.structure.pseudoknots: Builds instances of type ImmutableConflictGraph.
ImmutableCt - Class in pl.poznan.put.structure.formats: Immutable implementation of Ct.
ImmutableCt.Builder - Class in pl.poznan.put.structure.formats: Builds instances of type ImmutableCt.
ImmutableDefaultCifModel - Class in pl.poznan.put.pdb.analysis: Immutable implementation of DefaultCifModel.
ImmutableDefaultCifModel.Builder - Class in pl.poznan.put.pdb.analysis: Builds instances of type ImmutableDefaultCifModel.
ImmutableDefaultConverter - Class in pl.poznan.put.structure.formats: Immutable implementation of DefaultConverter.
ImmutableDefaultConverter.Builder - Class in pl.poznan.put.structure.formats: Builds instances of type ImmutableDefaultConverter.
ImmutableDefaultDotBracket - Class in pl.poznan.put.structure.formats: Immutable implementation of DefaultDotBracket.
ImmutableDefaultDotBracket.Builder - Class in pl.poznan.put.structure.formats: Builds instances of type ImmutableDefaultDotBracket.
ImmutableDefaultDotBracketFromPdb - Class in pl.poznan.put.structure.formats: Immutable implementation of DefaultDotBracketFromPdb.
ImmutableDefaultDotBracketFromPdb.Builder - Class in pl.poznan.put.structure.formats: Builds instances of type ImmutableDefaultDotBracketFromPdb.
ImmutableDefaultPdbModel - Class in pl.poznan.put.pdb.analysis: Immutable implementation of DefaultPdbModel.
ImmutableDefaultPdbModel.Builder - Class in pl.poznan.put.pdb.analysis: Builds instances of type ImmutableDefaultPdbModel.
ImmutableDefaultPdbResidue - Class in pl.poznan.put.pdb.analysis: Immutable implementation of DefaultPdbResidue.
ImmutableDefaultPdbResidue.Builder - Class in pl.poznan.put.pdb.analysis: Builds instances of type ImmutableDefaultPdbResidue.
ImmutableDefaultResidueCollection - Class in pl.poznan.put.pdb.analysis: Immutable implementation of DefaultResidueCollection.
ImmutableDefaultResidueCollection.Builder - Class in pl.poznan.put.pdb.analysis: Builds instances of type ImmutableDefaultResidueCollection.
ImmutableDefaultStrand - Class in pl.poznan.put.structure.formats: Immutable implementation of DefaultStrand.
ImmutableDefaultStrand.Builder - Class in pl.poznan.put.structure.formats: Builds instances of type ImmutableDefaultStrand.
ImmutableDistanceMatrix - Class in pl.poznan.put.types: Immutable implementation of DistanceMatrix.
ImmutableDistanceMatrix.Builder - Class in pl.poznan.put.types: Builds instances of type ImmutableDistanceMatrix.
ImmutableDotBracketSymbol - Class in pl.poznan.put.structure: Immutable implementation of DotBracketSymbol.
ImmutableDotBracketSymbol.Builder - Class in pl.poznan.put.structure: Builds instances of type ImmutableDotBracketSymbol.
ImmutableDssrJson - Class in pl.poznan.put.external.dssr: Immutable implementation of DssrJson.
ImmutableDssrJson.Builder - Class in pl.poznan.put.external.dssr: Builds instances of type ImmutableDssrJson.
ImmutableDynamicProgrammingAll - Class in pl.poznan.put.structure.pseudoknots.dp: Immutable implementation of DynamicProgrammingAll.
ImmutableDynamicProgrammingAll.Builder - Class in pl.poznan.put.structure.pseudoknots.dp: Builds instances of type ImmutableDynamicProgrammingAll.
ImmutableEntry - Class in pl.poznan.put.structure.formats: Immutable implementation of BpSeq.Entry.
ImmutableEntry.Builder - Class in pl.poznan.put.structure.formats: Builds instances of type ImmutableEntry.
ImmutableExecHelper - Class in pl.poznan.put.utility: Immutable implementation of ExecHelper.
ImmutableExecHelper.Builder - Class in pl.poznan.put.utility: Builds instances of type ImmutableExecHelper.
ImmutableExecutionResult - Class in pl.poznan.put.utility: Immutable implementation of ExecHelper.ExecutionResult.
ImmutableExecutionResult.Builder - Class in pl.poznan.put.utility: Builds instances of type ImmutableExecutionResult.
ImmutableExtendedEntry - Class in pl.poznan.put.structure.formats: Immutable implementation of Ct.ExtendedEntry.
ImmutableExtendedEntry.Builder - Class in pl.poznan.put.structure.formats: Builds instances of type ImmutableExtendedEntry.
ImmutableHistogram - Class in pl.poznan.put.circular: Immutable implementation of Histogram.
ImmutableHistogram.Builder - Class in pl.poznan.put.circular: Builds instances of type ImmutableHistogram.
ImmutableInteractionType - Class in pl.poznan.put.rna: Immutable implementation of InteractionType.
ImmutableInteractionType.Builder - Class in pl.poznan.put.rna: Builds instances of type ImmutableInteractionType.
ImmutableMaxConflicts - Class in pl.poznan.put.structure.pseudoknots.elimination: Immutable implementation of MaxConflicts.
ImmutableMaxConflicts.Builder - Class in pl.poznan.put.structure.pseudoknots.elimination: Builds instances of type ImmutableMaxConflicts.
ImmutableMinGain - Class in pl.poznan.put.structure.pseudoknots.elimination: Immutable implementation of MinGain.
ImmutableMinGain.Builder - Class in pl.poznan.put.structure.pseudoknots.elimination: Builds instances of type ImmutableMinGain.
ImmutableMultiLineDotBracket - Class in pl.poznan.put.structure.formats: Immutable implementation of MultiLineDotBracket.
ImmutableMultiLineDotBracket.Builder - Class in pl.poznan.put.structure.formats: Builds instances of type ImmutableMultiLineDotBracket.
ImmutableNucleotide - Class in pl.poznan.put.external.dssr: Immutable implementation of Nucleotide.
ImmutableNucleotide.Builder - Class in pl.poznan.put.external.dssr: Builds instances of type ImmutableNucleotide.
ImmutablePair - Class in pl.poznan.put.external.dssr: Immutable implementation of Pair.
ImmutablePair.Builder - Class in pl.poznan.put.external.dssr: Builds instances of type ImmutablePair.
ImmutablePdbAtomLine - Class in pl.poznan.put.pdb: Immutable implementation of PdbAtomLine.
ImmutablePdbAtomLine.Builder - Class in pl.poznan.put.pdb: Builds instances of type ImmutablePdbAtomLine.
ImmutablePdbChain - Class in pl.poznan.put.pdb.analysis: Immutable implementation of PdbChain.
ImmutablePdbChain.Builder - Class in pl.poznan.put.pdb.analysis: Builds instances of type ImmutablePdbChain.
ImmutablePdbCompactFragment - Class in pl.poznan.put.pdb.analysis: Immutable implementation of PdbCompactFragment.
ImmutablePdbCompactFragment.Builder - Class in pl.poznan.put.pdb.analysis: Builds instances of type ImmutablePdbCompactFragment.
ImmutablePdbExpdtaLine - Class in pl.poznan.put.pdb: Immutable implementation of PdbExpdtaLine.
ImmutablePdbExpdtaLine.Builder - Class in pl.poznan.put.pdb: Builds instances of type ImmutablePdbExpdtaLine.
ImmutablePdbHeaderLine - Class in pl.poznan.put.pdb: Immutable implementation of PdbHeaderLine.
ImmutablePdbHeaderLine.Builder - Class in pl.poznan.put.pdb: Builds instances of type ImmutablePdbHeaderLine.
ImmutablePdbModresLine - Class in pl.poznan.put.pdb: Immutable implementation of PdbModresLine.
ImmutablePdbModresLine.Builder - Class in pl.poznan.put.pdb: Builds instances of type ImmutablePdbModresLine.
ImmutablePdbNamedResidueIdentifier - Class in pl.poznan.put.pdb: Immutable implementation of PdbNamedResidueIdentifier.
ImmutablePdbNamedResidueIdentifier.Builder - Class in pl.poznan.put.pdb: Builds instances of type ImmutablePdbNamedResidueIdentifier.
ImmutablePdbRemark2Line - Class in pl.poznan.put.pdb: Immutable implementation of PdbRemark2Line.
ImmutablePdbRemark2Line.Builder - Class in pl.poznan.put.pdb: Builds instances of type ImmutablePdbRemark2Line.
ImmutablePdbRemark465Line - Class in pl.poznan.put.pdb: Immutable implementation of PdbRemark465Line.
ImmutablePdbRemark465Line.Builder - Class in pl.poznan.put.pdb: Builds instances of type ImmutablePdbRemark465Line.
ImmutablePdbResidueIdentifier - Class in pl.poznan.put.pdb: Immutable implementation of PdbResidueIdentifier.
ImmutablePdbResidueIdentifier.Builder - Class in pl.poznan.put.pdb: Builds instances of type ImmutablePdbResidueIdentifier.
ImmutablePdbTitleLine - Class in pl.poznan.put.pdb: Immutable implementation of PdbTitleLine.
ImmutablePdbTitleLine.Builder - Class in pl.poznan.put.pdb: Builds instances of type ImmutablePdbTitleLine.
ImmutablePhosphate - Class in pl.poznan.put.rna: Immutable implementation of Phosphate.
ImmutablePhosphate.Builder - Class in pl.poznan.put.rna: Builds instances of type ImmutablePhosphate.
ImmutablePseudophasePuckerType - Class in pl.poznan.put.rna: Immutable implementation of PseudophasePuckerType.
ImmutablePseudophasePuckerType.Builder - Class in pl.poznan.put.rna: Builds instances of type ImmutablePseudophasePuckerType.
ImmutableQuadruple<T> - Class in pl.poznan.put.types: Immutable implementation of Quadruple.
ImmutableQuadruple.Builder<T> - Class in pl.poznan.put.types: Builds instances of type ImmutableQuadruple.
ImmutableQuantifiedBasePair - Class in pl.poznan.put.structure: Immutable implementation of QuantifiedBasePair.
ImmutableQuantifiedBasePair.Builder - Class in pl.poznan.put.structure: Builds instances of type ImmutableQuantifiedBasePair.
ImmutableRegion - Class in pl.poznan.put.structure.pseudoknots: Immutable implementation of Region.
ImmutableRegion.Builder - Class in pl.poznan.put.structure.pseudoknots: Builds instances of type ImmutableRegion.
ImmutableResidueTorsionAngles - Class in pl.poznan.put.pdb.analysis: Immutable implementation of ResidueTorsionAngles.
ImmutableResidueTorsionAngles.Builder - Class in pl.poznan.put.pdb.analysis: Builds instances of type ImmutableResidueTorsionAngles.
ImmutableRibose - Class in pl.poznan.put.rna: Immutable implementation of Ribose.
ImmutableRibose.Builder - Class in pl.poznan.put.rna: Builds instances of type ImmutableRibose.
ImmutableStrandView - Class in pl.poznan.put.structure.formats: Immutable implementation of StrandView.
ImmutableStrandView.Builder - Class in pl.poznan.put.structure.formats: Builds instances of type ImmutableStrandView.
ImmutableTerminalMissing - Class in pl.poznan.put.structure.formats: Immutable implementation of TerminalMissing.
ImmutableTerminalMissing.Builder - Class in pl.poznan.put.structure.formats: Builds instances of type ImmutableTerminalMissing.
ImmutableTorsionAngleDelta - Class in pl.poznan.put.torsion: Immutable implementation of TorsionAngleDelta.
ImmutableTorsionAngleDelta.Builder - Class in pl.poznan.put.torsion: Builds instances of type ImmutableTorsionAngleDelta.
ImmutableTorsionAngleValue - Class in pl.poznan.put.torsion: Immutable implementation of TorsionAngleValue.
ImmutableTorsionAngleValue.Builder - Class in pl.poznan.put.torsion: Builds instances of type ImmutableTorsionAngleValue.
ImmutableTrigonometricMoment - Class in pl.poznan.put.circular.samples: Immutable implementation of TrigonometricMoment.
ImmutableTrigonometricMoment.Builder - Class in pl.poznan.put.circular.samples: Builds instances of type ImmutableTrigonometricMoment.
index() - Method in class pl.poznan.put.structure.DotBracketSymbol
index() - Method in class pl.poznan.put.structure.formats.BpSeq.Entry
index() - Method in class pl.poznan.put.structure.formats.Ct.ExtendedEntry
index() - Method in class pl.poznan.put.structure.formats.ImmutableEntry
index() - Method in class pl.poznan.put.structure.formats.ImmutableExtendedEntry
index() - Method in class pl.poznan.put.structure.ImmutableDotBracketSymbol
index(int) - Method in class pl.poznan.put.structure.formats.ImmutableEntry.Builder: Initializes the value for the index attribute.
index(int) - Method in class pl.poznan.put.structure.formats.ImmutableExtendedEntry.Builder: Initializes the value for the index attribute.
index(int) - Method in class pl.poznan.put.structure.ImmutableDotBracketSymbol.Builder: Initializes the value for the index attribute.
indexOf(ChainNumberICode) - Method in interface pl.poznan.put.pdb.analysis.ResidueCollection: Finds a residue by a triplet (chain, number, icode).
indexOfEndpoint(int) - Method in class pl.poznan.put.structure.pseudoknots.dp.ConflictClique: Finds the index of an endpoint in this conflict clique.
INFINITY - Static variable in class pl.poznan.put.constant.Unicode
INFRARED_SPECTROSCOPY - Enum constant in enum pl.poznan.put.pdb.ExperimentalTechnique
inputStrands() - Method in class pl.poznan.put.structure.formats.AbstractCombinedStrand
inputStrands() - Method in class pl.poznan.put.structure.formats.CombinedStrand
inputStrands() - Method in class pl.poznan.put.structure.formats.CombinedStrandFromPdb
inputStrands() - Method in class pl.poznan.put.structure.formats.ImmutableCombinedStrand
inputStrands() - Method in class pl.poznan.put.structure.formats.ImmutableCombinedStrandFromPdb
inputStrands(Iterable<? extends Strand>) - Method in class pl.poznan.put.structure.formats.ImmutableCombinedStrand.Builder: Sets or replaces all elements for inputStrands list.
inputStrands(Iterable<? extends Strand>) - Method in class pl.poznan.put.structure.formats.ImmutableCombinedStrandFromPdb.Builder: Sets or replaces all elements for inputStrands list.
inputSymbolToResidue() - Method in class pl.poznan.put.structure.formats.CombinedStrandFromPdb
inputSymbolToResidue() - Method in class pl.poznan.put.structure.formats.ImmutableCombinedStrandFromPdb
inputSymbolToResidue(Map<? extends DotBracketSymbol, ? extends PdbResidueIdentifier>) - Method in class pl.poznan.put.structure.formats.ImmutableCombinedStrandFromPdb.Builder: Sets or replaces all mappings from the specified map as entries for the inputSymbolToResidue map.
insertionCode() - Method in interface pl.poznan.put.pdb.analysis.PdbResidue
insertionCode() - Method in interface pl.poznan.put.pdb.ChainNumberICode
insertionCode() - Method in class pl.poznan.put.pdb.ImmutablePdbAtomLine
insertionCode() - Method in class pl.poznan.put.pdb.ImmutablePdbModresLine
insertionCode() - Method in class pl.poznan.put.pdb.ImmutablePdbNamedResidueIdentifier
insertionCode() - Method in class pl.poznan.put.pdb.ImmutablePdbRemark465Line
insertionCode() - Method in class pl.poznan.put.pdb.ImmutablePdbResidueIdentifier
insertionCode() - Method in class pl.poznan.put.pdb.PdbAtomLine
insertionCode() - Method in class pl.poznan.put.pdb.PdbModresLine
insertionCode() - Method in class pl.poznan.put.pdb.PdbNamedResidueIdentifier
insertionCode() - Method in class pl.poznan.put.pdb.PdbRemark465Line
insertionCode() - Method in class pl.poznan.put.pdb.PdbResidueIdentifier
insertionCode(String) - Method in class pl.poznan.put.pdb.ImmutablePdbAtomLine.Builder: Initializes the optional value insertionCode to insertionCode.
insertionCode(String) - Method in class pl.poznan.put.pdb.ImmutablePdbModresLine.Builder: Initializes the optional value insertionCode to insertionCode.
insertionCode(String) - Method in class pl.poznan.put.pdb.ImmutablePdbNamedResidueIdentifier.Builder: Initializes the optional value insertionCode to insertionCode.
insertionCode(String) - Method in class pl.poznan.put.pdb.ImmutablePdbRemark465Line.Builder: Initializes the optional value insertionCode to insertionCode.
insertionCode(String) - Method in class pl.poznan.put.pdb.ImmutablePdbResidueIdentifier.Builder: Initializes the optional value insertionCode to insertionCode.
insertionCode(Optional<String>) - Method in class pl.poznan.put.pdb.ImmutablePdbAtomLine.Builder: Initializes the optional value insertionCode to insertionCode.
insertionCode(Optional<String>) - Method in class pl.poznan.put.pdb.ImmutablePdbModresLine.Builder: Initializes the optional value insertionCode to insertionCode.
insertionCode(Optional<String>) - Method in class pl.poznan.put.pdb.ImmutablePdbNamedResidueIdentifier.Builder: Initializes the optional value insertionCode to insertionCode.
insertionCode(Optional<String>) - Method in class pl.poznan.put.pdb.ImmutablePdbRemark465Line.Builder: Initializes the optional value insertionCode to insertionCode.
insertionCode(Optional<String>) - Method in class pl.poznan.put.pdb.ImmutablePdbResidueIdentifier.Builder: Initializes the optional value insertionCode to insertionCode.
interactionType() - Method in class pl.poznan.put.structure.AnalyzedBasePair
interactionType() - Method in interface pl.poznan.put.structure.ClassifiedBasePair
interactionType() - Method in class pl.poznan.put.structure.ImmutableAnalyzedBasePair
interactionType() - Method in class pl.poznan.put.structure.ImmutableQuantifiedBasePair
interactionType() - Method in class pl.poznan.put.structure.QuantifiedBasePair
interactionType(InteractionType) - Method in class pl.poznan.put.structure.ImmutableAnalyzedBasePair.Builder: Initializes the value for the interactionType attribute.
interactionType(InteractionType) - Method in class pl.poznan.put.structure.ImmutableQuantifiedBasePair.Builder: Initializes the value for the interactionType attribute.
InteractionType - Class in pl.poznan.put.rna: A type of interaction between two nucleotides.
InteractionType() - Constructor for class pl.poznan.put.rna.InteractionType
interpolateColor(double, double, double) - Static method in class pl.poznan.put.constant.Colors: Interpolates a color in red-green spectrum from its value and a given range [min; max].
INVALID - Enum constant in enum pl.poznan.put.rna.ChiRange
INVALID - Enum constant in enum pl.poznan.put.rna.Pseudorotation
INVALID - Enum constant in enum pl.poznan.put.torsion.range.RangeDifference
INVALID - Enum constant in enum pl.poznan.put.torsion.range.TorsionRange
InvalidCircularOperationException - Exception in pl.poznan.put.circular.exception
InvalidCircularOperationException(String) - Constructor for exception pl.poznan.put.circular.exception.InvalidCircularOperationException
InvalidCircularOperationException(String, Throwable) - Constructor for exception pl.poznan.put.circular.exception.InvalidCircularOperationException
InvalidCircularValueException - Exception in pl.poznan.put.circular.exception
InvalidCircularValueException(String) - Constructor for exception pl.poznan.put.circular.exception.InvalidCircularValueException
InvalidCircularValueException(String, Throwable) - Constructor for exception pl.poznan.put.circular.exception.InvalidCircularValueException
InvalidVectorFormatException - Exception in pl.poznan.put.circular.exception
InvalidVectorFormatException(String) - Constructor for exception pl.poznan.put.circular.exception.InvalidVectorFormatException
InvalidVectorFormatException(String, Throwable) - Constructor for exception pl.poznan.put.circular.exception.InvalidVectorFormatException
invert() - Method in enum pl.poznan.put.notation.LeontisWesthof: Inverts the base edges e.g. cHS becomes cSH.
invert() - Method in enum pl.poznan.put.notation.StackingTopology
invert() - Method in class pl.poznan.put.rna.InteractionType
invert() - Method in class pl.poznan.put.structure.AnalyzedBasePair
invert() - Method in class pl.poznan.put.structure.BasePair
invert() - Method in interface pl.poznan.put.structure.ClassifiedBasePair
invert() - Method in class pl.poznan.put.structure.QuantifiedBasePair
INWARD - Enum constant in enum pl.poznan.put.notation.StackingTopology
is5to3() - Method in class pl.poznan.put.structure.BasePair
isBasePhosphate() - Method in interface pl.poznan.put.structure.ClassifiedBasePair
isBaseRibose() - Method in interface pl.poznan.put.structure.ClassifiedBasePair
isBetween(Angle, Angle) - Method in class pl.poznan.put.circular.Angle: Return strue if this instance is in range [begin; end).
isCanonical() - Method in enum pl.poznan.put.notation.Saenger
isCanonical() - Method in interface pl.poznan.put.structure.ClassifiedBasePair
isCanonical(Saenger) - Static method in enum pl.poznan.put.notation.Saenger: Checks if instance of Saenger represents a canonical base pair (XIX, XX and XXVIII).
isCanonicalPair(PdbResidue, PdbResidue) - Static method in class pl.poznan.put.structure.BasePair: Checks if two residues are canonical base pairs by means of (1) distance between atoms which form hydrogen bonds and (2) checking if two bases face each other.
isClosing() - Method in class pl.poznan.put.structure.DotBracketSymbol
isClosing(char) - Static method in class pl.poznan.put.structure.DotBracketSymbol: Checks if the given character is a closing character in dot-bracket format.
isCommentLine(String) - Static method in class pl.poznan.put.pdb.PdbRemark465Line: Checks if line is just a comment or a line with actual information.
isConflicting(Region, Region) - Static method in class pl.poznan.put.structure.pseudoknots.ConflictGraph: Checks if given regions are conflicting.
isConnectedTo(PdbResidue) - Method in interface pl.poznan.put.pdb.analysis.PdbResidue: Checks if this residue is connected with another one (see MoleculeType.areConnected(PdbResidue, PdbResidue)).
isHeavy() - Method in enum pl.poznan.put.atom.AtomName: Checks if atom is heavy (i.e. not a hydrogen).
isHeavy() - Method in enum pl.poznan.put.atom.AtomType: Checks if this atom is heavy i.e. not a hydrogen.
isIsolated(DotBracketSymbol) - Method in interface pl.poznan.put.structure.formats.DotBracket: Checks if a symbol is isolated, i.e., if it is a pairing symbol and both it and its pair are surrounded by unpaired residues.
isMissing() - Method in interface pl.poznan.put.pdb.analysis.PdbResidue
isMissing() - Method in class pl.poznan.put.structure.DotBracketSymbol
isModified() - Method in interface pl.poznan.put.pdb.analysis.PdbResidue
isModified(PdbResidueIdentifier) - Method in interface pl.poznan.put.pdb.analysis.PdbModel: Checks if a given residue is modified (as stated in the PDB or mmCIF headers).
isNonCanonical() - Method in interface pl.poznan.put.structure.ClassifiedBasePair
isolatedSymbols() - Method in interface pl.poznan.put.structure.formats.DotBracket
ISOLEUCINE - Enum constant in enum pl.poznan.put.protein.AminoAcid
isOpening() - Method in class pl.poznan.put.structure.DotBracketSymbol
isOpening(char) - Static method in class pl.poznan.put.structure.DotBracketSymbol: Checks if the given character is an opening character in dot-bracket format.
isPaired() - Method in class pl.poznan.put.structure.formats.BpSeq.Entry
isPaired() - Method in class pl.poznan.put.structure.formats.Ct.ExtendedEntry
isPairing() - Method in class pl.poznan.put.rna.ImmutableInteractionType: Checks if this interaction is a basis for base pairing.
isPairing() - Method in class pl.poznan.put.rna.InteractionType: Checks if this interaction is a basis for base pairing.
isPairing() - Method in interface pl.poznan.put.structure.ClassifiedBasePair
isPairing() - Method in class pl.poznan.put.structure.DotBracketSymbol
isPairing(boolean) - Method in class pl.poznan.put.rna.ImmutableInteractionType.Builder: Initializes the value for the isPairing attribute.
isPairing(char) - Static method in class pl.poznan.put.structure.DotBracketSymbol: Checks if the given character is a pairing character in dot-bracket format.
isPseudoTorsion() - Method in interface pl.poznan.put.torsion.AtomBasedTorsionAngleType
isPseudoTorsion() - Method in class pl.poznan.put.torsion.ImmutableAtomBasedTorsionAngleType
isPseudoTorsion(boolean) - Method in class pl.poznan.put.torsion.ImmutableAtomBasedTorsionAngleType.Builder: Initializes the value for the isPseudoTorsion attribute.
isRemoved() - Method in class pl.poznan.put.structure.pseudoknots.ImmutableRegion
isRemoved() - Method in class pl.poznan.put.structure.pseudoknots.Region
isRemoved(boolean) - Method in class pl.poznan.put.structure.pseudoknots.ImmutableRegion.Builder: Initializes the value for the isRemoved attribute.
isRepresented() - Method in class pl.poznan.put.structure.AnalyzedBasePair
isRepresented() - Method in interface pl.poznan.put.structure.ClassifiedBasePair
isRepresented() - Method in class pl.poznan.put.structure.ImmutableAnalyzedBasePair
isRepresented() - Method in class pl.poznan.put.structure.ImmutableQuantifiedBasePair
isRepresented() - Method in class pl.poznan.put.structure.QuantifiedBasePair
isRepresented(boolean) - Method in class pl.poznan.put.structure.ImmutableAnalyzedBasePair.Builder: Initializes the value for the isRepresented attribute.
isRepresented(boolean) - Method in class pl.poznan.put.structure.ImmutableQuantifiedBasePair.Builder: Initializes the value for the isRepresented attribute.
isSingleStrand() - Method in interface pl.poznan.put.structure.formats.Strand: Checks if this strand is "single strand" which means that neither of its base pairs starts and ends in this strand.
isStacking() - Method in interface pl.poznan.put.structure.ClassifiedBasePair
isValid() - Method in class pl.poznan.put.circular.Angle
IV - Enum constant in enum pl.poznan.put.notation.Saenger
IX - Enum constant in enum pl.poznan.put.notation.Saenger

K

K - Enum constant in enum pl.poznan.put.atom.AtomName
kurtosis() - Method in class pl.poznan.put.circular.samples.AngleSample
kurtosis() - Method in class pl.poznan.put.circular.samples.ImmutableAngleSample

L

largestBinSize() - Method in class pl.poznan.put.circular.Histogram: Finds the largest bin and calculate its relative size.
left() - Method in class pl.poznan.put.rna.ImmutableInteractionType
left() - Method in class pl.poznan.put.rna.InteractionType
left() - Method in class pl.poznan.put.structure.BasePair
left() - Method in class pl.poznan.put.structure.ImmutableBasePair
left(PdbNamedResidueIdentifier) - Method in class pl.poznan.put.structure.ImmutableBasePair.Builder: Initializes the value for the left attribute.
left(NucleotideComponentType) - Method in class pl.poznan.put.rna.ImmutableInteractionType.Builder: Initializes the value for the left attribute.
leftAtom(PdbAtomLine) - Method in class pl.poznan.put.torsion.ImmutableAtomPair.Builder: Initializes the value for the leftAtom attribute.
length() - Method in class pl.poznan.put.structure.formats.BpSeq.Entry
length() - Method in interface pl.poznan.put.structure.formats.DotBracket
length() - Method in class pl.poznan.put.structure.pseudoknots.Region
length(AtomType, AtomType) - Static method in class pl.poznan.put.atom.Bond: Returns bond length between two atoms.
leontisWesthof() - Method in class pl.poznan.put.structure.AnalyzedBasePair
leontisWesthof() - Method in interface pl.poznan.put.structure.ClassifiedBasePair
leontisWesthof() - Method in class pl.poznan.put.structure.ImmutableAnalyzedBasePair
leontisWesthof() - Method in class pl.poznan.put.structure.ImmutableQuantifiedBasePair
leontisWesthof() - Method in class pl.poznan.put.structure.QuantifiedBasePair
leontisWesthof(LeontisWesthof) - Method in class pl.poznan.put.structure.ImmutableAnalyzedBasePair.Builder: Initializes the value for the leontisWesthof attribute.
leontisWesthof(LeontisWesthof) - Method in class pl.poznan.put.structure.ImmutableQuantifiedBasePair.Builder: Initializes the value for the leontisWesthof attribute.
LeontisWesthof - Enum in pl.poznan.put.notation: A classification of RNA base pairs described in: Geometric Nomenclature and Classification of RNA Base Pairs.
LEUCINE - Enum constant in enum pl.poznan.put.protein.AminoAcid
loadResource(String) - Static method in class pl.poznan.put.utility.ResourcesHelper: Load contents of a resource file available in the JAR of running process.
loadResourceFile(String) - Static method in class pl.poznan.put.utility.ResourcesHelper: Translate resource address to a URI and then to File instance.
loadResourceUri(String) - Static method in class pl.poznan.put.utility.ResourcesHelper: Translate resource address to a URI.
longDisplayName() - Method in interface pl.poznan.put.interfaces.DisplayableExportable
longDisplayName() - Method in enum pl.poznan.put.protein.AminoAcidTorsionAngle
longDisplayName() - Method in enum pl.poznan.put.rna.NucleotideTorsionAngle
longDisplayName() - Method in class pl.poznan.put.rna.PseudophasePuckerType
longDisplayName() - Method in interface pl.poznan.put.torsion.AtomBasedTorsionAngleType
longDisplayName() - Method in class pl.poznan.put.torsion.AverageTorsionAngleType
longDisplayName() - Method in class pl.poznan.put.torsion.TorsionAngleDelta
longDisplayName() - Method in class pl.poznan.put.torsion.TorsionAngleValue
lw() - Method in class pl.poznan.put.external.dssr.ImmutablePair
lw() - Method in interface pl.poznan.put.external.dssr.Pair
lw(String) - Method in class pl.poznan.put.external.dssr.ImmutablePair.Builder: Initializes the value for the lw attribute.
LYSINE - Enum constant in enum pl.poznan.put.protein.AminoAcid

M

mainAngleTypes() - Method in enum pl.poznan.put.pdb.analysis.MoleculeType: Generates a list of main atom-based torsion angle types for this molecule type.
mapping() - Method in class pl.poznan.put.structure.formats.CombinedStrandFromPdb
mapping() - Method in class pl.poznan.put.structure.formats.ImmutableCombinedStrandFromPdb
MasterTorsionAngleType - Interface in pl.poznan.put.torsion: The main torsion angle type, which may consist of one or more basic angle types.
matchesName(String) - Method in enum pl.poznan.put.atom.AtomName: Checks if this constant matches a name found in PDB or mmCIF file.
matchingBracket(char) - Static method in class pl.poznan.put.structure.DotBracketSymbol: Finds a matching bracket (closing for opening and vice versa) of the same level.
MATH - Enum constant in enum pl.poznan.put.circular.enums.AngleTransformation: 0 degree is on the right, 90 degree is on top.
matrix() - Method in interface pl.poznan.put.types.DistanceMatrix
matrix() - Method in class pl.poznan.put.types.ImmutableDistanceMatrix
matrix(double[]...) - Method in class pl.poznan.put.types.ImmutableDistanceMatrix.Builder: Initializes the value for the matrix attribute.
max() - Method in interface pl.poznan.put.atom.BondLength
max() - Method in class pl.poznan.put.atom.ImmutableBondLength
max(double) - Method in class pl.poznan.put.atom.ImmutableBondLength.Builder: Initializes the value for the max attribute.
maxCliqueSize() - Method in class pl.poznan.put.structure.pseudoknots.dp.DynamicProgrammingAll
maxCliqueSize() - Method in class pl.poznan.put.structure.pseudoknots.dp.ImmutableDynamicProgrammingAll
maxCliqueSize(int) - Method in class pl.poznan.put.structure.pseudoknots.dp.ImmutableDynamicProgrammingAll.Builder: Initializes the value for the maxCliqueSize attribute.
MaxConflicts - Class in pl.poznan.put.structure.pseudoknots.elimination: Java implementation of Elimination Conflicts algorithm as presented in: Smit, S. et al., 2008.
MaxConflicts() - Constructor for class pl.poznan.put.structure.pseudoknots.elimination.MaxConflicts
maxSolutions() - Method in class pl.poznan.put.structure.formats.DefaultConverter
maxSolutions() - Method in class pl.poznan.put.structure.formats.ImmutableDefaultConverter
maxSolutions(int) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultConverter.Builder: Initializes the value for the maxSolutions attribute.
meanDeviation() - Method in class pl.poznan.put.circular.samples.AngleSample
meanDeviation() - Method in class pl.poznan.put.circular.samples.ImmutableAngleSample
meanDirection() - Method in class pl.poznan.put.circular.samples.AngleSample
meanDirection() - Method in class pl.poznan.put.circular.samples.ImmutableAngleSample
meanDirection() - Method in class pl.poznan.put.circular.samples.ImmutableTrigonometricMoment
meanDirection() - Method in class pl.poznan.put.circular.samples.TrigonometricMoment
meanDirection(Angle) - Method in class pl.poznan.put.circular.samples.ImmutableTrigonometricMoment.Builder: Initializes the value for the meanDirection attribute.
meanResultantLength() - Method in class pl.poznan.put.circular.samples.AngleSample
meanResultantLength() - Method in class pl.poznan.put.circular.samples.ImmutableAngleSample
meanResultantLength() - Method in class pl.poznan.put.circular.samples.ImmutableTrigonometricMoment
meanResultantLength() - Method in class pl.poznan.put.circular.samples.TrigonometricMoment
meanResultantLength(double) - Method in class pl.poznan.put.circular.samples.ImmutableTrigonometricMoment.Builder: Initializes the value for the meanResultantLength attribute.
medianAndMeanDeviation() - Method in class pl.poznan.put.circular.samples.AngleSample
medianAndMeanDeviation() - Method in class pl.poznan.put.circular.samples.ImmutableAngleSample
medianDirection() - Method in class pl.poznan.put.circular.samples.AngleSample
medianDirection() - Method in class pl.poznan.put.circular.samples.ImmutableAngleSample
merge(List<SVGDocument>) - Static method in class pl.poznan.put.utility.svg.SVGHelper: Merges several SVG images into one, by putting one next to another (from left to right).
merge(Region...) - Static method in class pl.poznan.put.structure.pseudoknots.Region: Merges many regions into a new one.
METHIONINE - Enum constant in enum pl.poznan.put.protein.AminoAcid
MG - Enum constant in enum pl.poznan.put.atom.AtomName
min() - Method in interface pl.poznan.put.atom.BondLength
min() - Method in class pl.poznan.put.atom.ImmutableBondLength
min(double) - Method in class pl.poznan.put.atom.ImmutableBondLength.Builder: Initializes the value for the min attribute.
MinGain - Class in pl.poznan.put.structure.pseudoknots.elimination: Java implementation of Elimination Gain algorithm as presented in: Smit, S. et al., 2008.
MinGain() - Constructor for class pl.poznan.put.structure.pseudoknots.elimination.MinGain
missingBegin() - Method in interface pl.poznan.put.structure.formats.Strand
missingEnd() - Method in interface pl.poznan.put.structure.formats.Strand
missingInternal() - Method in interface pl.poznan.put.structure.formats.DotBracket
missingResidues() - Method in class pl.poznan.put.pdb.analysis.DefaultCifModel
missingResidues() - Method in class pl.poznan.put.pdb.analysis.DefaultPdbModel
missingResidues() - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel
missingResidues() - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbModel
missingResidues() - Method in interface pl.poznan.put.pdb.analysis.PdbModel
missingResidues(Iterable<? extends PdbRemark465Line>) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel.Builder: Sets or replaces all elements for missingResidues list.
missingResidues(Iterable<? extends PdbRemark465Line>) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbModel.Builder: Sets or replaces all elements for missingResidues list.
missingTerminal() - Method in interface pl.poznan.put.structure.formats.DotBracket
MN - Enum constant in enum pl.poznan.put.atom.AtomName
model() - Method in class pl.poznan.put.structure.formats.DefaultDotBracketFromPdb
model() - Method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracketFromPdb
model(PdbModel) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracketFromPdb.Builder: Initializes the value for the model attribute.
MODEL_INVALID - Enum constant in enum pl.poznan.put.torsion.TorsionAngleDelta.State
ModelContainer - Interface in pl.poznan.put.pdb.analysis: A set of PDB files which all correspond to the same structure and also their chain names' mapping.
modelNumber() - Method in class pl.poznan.put.pdb.analysis.DefaultCifModel
modelNumber() - Method in class pl.poznan.put.pdb.analysis.DefaultPdbModel
modelNumber() - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel
modelNumber() - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbModel
modelNumber() - Method in interface pl.poznan.put.pdb.analysis.PdbModel
modelNumber() - Method in class pl.poznan.put.pdb.ImmutablePdbRemark465Line
modelNumber() - Method in class pl.poznan.put.pdb.PdbRemark465Line
modelNumber(int) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel.Builder: Initializes the value for the modelNumber attribute.
modelNumber(int) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbModel.Builder: Initializes the value for the modelNumber attribute.
modelNumber(int) - Method in class pl.poznan.put.pdb.ImmutablePdbRemark465Line.Builder: Initializes the value for the modelNumber attribute.
modificationDetails(PdbResidueIdentifier) - Method in interface pl.poznan.put.pdb.analysis.PdbModel: Provides details about modification of the residue.
modifiedResidueName() - Method in class pl.poznan.put.pdb.analysis.DefaultPdbResidue
modifiedResidueName() - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbResidue
modifiedResidueName() - Method in interface pl.poznan.put.pdb.analysis.PdbResidue
modifiedResidueName(String) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbResidue.Builder: Initializes the value for the modifiedResidueName attribute.
modifiedResidues() - Method in class pl.poznan.put.pdb.analysis.DefaultCifModel
modifiedResidues() - Method in class pl.poznan.put.pdb.analysis.DefaultPdbModel
modifiedResidues() - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel
modifiedResidues() - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbModel
modifiedResidues() - Method in interface pl.poznan.put.pdb.analysis.PdbModel
modifiedResidues(Iterable<? extends PdbModresLine>) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel.Builder: Sets or replaces all elements for modifiedResidues list.
modifiedResidues(Iterable<? extends PdbModresLine>) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbModel.Builder: Sets or replaces all elements for modifiedResidues list.
moleculeComponents() - Method in interface pl.poznan.put.pdb.analysis.ResidueInformationProvider
moleculeComponents() - Method in enum pl.poznan.put.protein.AminoAcid
moleculeComponents() - Method in enum pl.poznan.put.rna.Nucleotide
moleculeType() - Method in interface pl.poznan.put.pdb.analysis.ResidueInformationProvider
moleculeType() - Method in interface pl.poznan.put.pdb.analysis.SingleTypedResidueCollection
moleculeType() - Method in enum pl.poznan.put.protein.AminoAcid
moleculeType() - Method in interface pl.poznan.put.protein.Sidechain
moleculeType() - Method in interface pl.poznan.put.rna.Nucleobase
moleculeType() - Method in enum pl.poznan.put.rna.Nucleotide
moleculeType() - Method in class pl.poznan.put.rna.PseudophasePuckerType
moleculeType() - Method in interface pl.poznan.put.torsion.AtomBasedTorsionAngleType
moleculeType() - Method in class pl.poznan.put.torsion.AverageTorsionAngleType
moleculeType() - Method in class pl.poznan.put.torsion.ImmutableAtomBasedTorsionAngleType
moleculeType() - Method in class pl.poznan.put.torsion.ImmutableAverageTorsionAngleType
moleculeType() - Method in interface pl.poznan.put.torsion.TorsionAngleType
moleculeType(MoleculeType) - Method in class pl.poznan.put.torsion.ImmutableAtomBasedTorsionAngleType.Builder: Initializes the value for the moleculeType attribute.
moleculeType(MoleculeType) - Method in class pl.poznan.put.torsion.ImmutableAverageTorsionAngleType.Builder: Initializes the value for the moleculeType attribute.
MoleculeType - Enum in pl.poznan.put.pdb.analysis: A type of molecule (RNA or protein).
MultiLineDotBracket - Class in pl.poznan.put.structure.formats: An extended secondary structure, which contains also non-canonical base pairs.
MultiLineDotBracket() - Constructor for class pl.poznan.put.structure.formats.MultiLineDotBracket
multiply(double) - Method in class pl.poznan.put.circular.Angle: Multiplies the angular value by a constant.

N

N - Enum constant in enum pl.poznan.put.atom.AtomName
N - Enum constant in enum pl.poznan.put.atom.AtomType
N1 - Enum constant in enum pl.poznan.put.atom.AtomName
N2 - Enum constant in enum pl.poznan.put.atom.AtomName
N20 - Enum constant in enum pl.poznan.put.atom.AtomName
N3 - Enum constant in enum pl.poznan.put.atom.AtomName
N4 - Enum constant in enum pl.poznan.put.atom.AtomName
N6 - Enum constant in enum pl.poznan.put.atom.AtomName
N7 - Enum constant in enum pl.poznan.put.atom.AtomName
N9 - Enum constant in enum pl.poznan.put.atom.AtomName
name() - Method in class pl.poznan.put.pdb.analysis.ImmutablePdbCompactFragment
name() - Method in class pl.poznan.put.pdb.analysis.PdbCompactFragment
name() - Method in class pl.poznan.put.structure.formats.DefaultStrand
name() - Method in class pl.poznan.put.structure.formats.ImmutableDefaultStrand
name() - Method in class pl.poznan.put.structure.formats.ImmutableStrandView
name() - Method in interface pl.poznan.put.structure.formats.Strand
name() - Method in class pl.poznan.put.structure.formats.StrandView
name(String) - Method in class pl.poznan.put.pdb.analysis.ImmutablePdbCompactFragment.Builder: Initializes the value for the name attribute.
name(String) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultStrand.Builder: Initializes the value for the name attribute.
name(String) - Method in class pl.poznan.put.structure.formats.ImmutableStrandView.Builder: Initializes the value for the name attribute.
namedResidueIdentifier() - Method in interface pl.poznan.put.pdb.analysis.PdbResidue
namedResidueIdentifiers() - Method in interface pl.poznan.put.pdb.analysis.ResidueCollection
names() - Method in interface pl.poznan.put.types.DistanceMatrix
names() - Method in class pl.poznan.put.types.ImmutableDistanceMatrix
names(Iterable<String>) - Method in class pl.poznan.put.types.ImmutableDistanceMatrix.Builder: Sets or replaces all elements for names list.
ND1 - Enum constant in enum pl.poznan.put.atom.AtomName
ND2 - Enum constant in enum pl.poznan.put.atom.AtomName
NE - Enum constant in enum pl.poznan.put.atom.AtomName
NE1 - Enum constant in enum pl.poznan.put.atom.AtomName
NE2 - Enum constant in enum pl.poznan.put.atom.AtomName
NEUTRON_DIFFRACTION - Enum constant in enum pl.poznan.put.pdb.ExperimentalTechnique
nextPlacement(Vector3D, Vector3D, Vector3D, double, Angle, Angle) - Static method in class pl.poznan.put.circular.conversion.CartesianUtilities: Computes position of atom D, if you know positions of A, B and C, and the length of bond B-C, and the angle B-C-D and the torsion angle A-B-C-D.
NH1 - Enum constant in enum pl.poznan.put.atom.AtomName
NH2 - Enum constant in enum pl.poznan.put.atom.AtomName
NL - Enum constant in enum pl.poznan.put.atom.AtomName
normalize() - Method in class pl.poznan.put.circular.Angle
normalize() - Method in class pl.poznan.put.pdb.analysis.DefaultCifModel
normalize() - Method in class pl.poznan.put.pdb.analysis.DefaultPdbModel
NR - Enum constant in enum pl.poznan.put.atom.AtomName
NT - Enum constant in enum pl.poznan.put.atom.AtomName
nt1() - Method in class pl.poznan.put.external.dssr.ImmutablePair
nt1() - Method in interface pl.poznan.put.external.dssr.Pair
nt1(String) - Method in class pl.poznan.put.external.dssr.ImmutablePair.Builder: Initializes the value for the nt1 attribute.
nt2() - Method in class pl.poznan.put.external.dssr.ImmutablePair
nt2() - Method in interface pl.poznan.put.external.dssr.Pair
nt2(String) - Method in class pl.poznan.put.external.dssr.ImmutablePair.Builder: Initializes the value for the nt2 attribute.
NU0 - Enum constant in enum pl.poznan.put.rna.NucleotideTorsionAngle
NU0 - Static variable in class pl.poznan.put.constant.Unicode
NU1 - Enum constant in enum pl.poznan.put.rna.NucleotideTorsionAngle
NU1 - Static variable in class pl.poznan.put.constant.Unicode
NU2 - Enum constant in enum pl.poznan.put.rna.NucleotideTorsionAngle
NU2 - Static variable in class pl.poznan.put.constant.Unicode
NU3 - Enum constant in enum pl.poznan.put.rna.NucleotideTorsionAngle
NU3 - Static variable in class pl.poznan.put.constant.Unicode
NU4 - Enum constant in enum pl.poznan.put.rna.NucleotideTorsionAngle
NU4 - Static variable in class pl.poznan.put.constant.Unicode
NucleicAcidResidueComponent - Interface in pl.poznan.put.rna: A component of a nucleotide.
nucleobase() - Method in enum pl.poznan.put.rna.Nucleotide
Nucleobase - Interface in pl.poznan.put.rna: A nucleobase (adenine, cytosine, guanine, uracil or thymine).
NucleobaseEdge - Enum in pl.poznan.put.notation: An edge of the nucleobase.
nucleobasePlane() - Method in interface pl.poznan.put.pdb.analysis.PdbResidue: Calculates the plane equation of the nucleobase in this residue.
Nucleotide - Enum in pl.poznan.put.rna: A nucleotide (A, C, G, U or T) with all details regarding atoms, torsion angles, etc.
Nucleotide - Interface in pl.poznan.put.external.dssr
nucleotideComponentType() - Method in interface pl.poznan.put.rna.NucleicAcidResidueComponent
nucleotideComponentType() - Method in interface pl.poznan.put.rna.Nucleobase
nucleotideComponentType() - Method in class pl.poznan.put.rna.Phosphate
nucleotideComponentType() - Method in class pl.poznan.put.rna.Ribose
NucleotideComponentType - Enum in pl.poznan.put.rna: A type of the nucleotide component.
nucleotides() - Method in class pl.poznan.put.external.dssr.DssrJson
nucleotides() - Method in class pl.poznan.put.external.dssr.ImmutableDssrJson
nucleotides(Iterable<? extends Nucleotide>) - Method in class pl.poznan.put.external.dssr.ImmutableDssrJson.Builder: Sets or replaces all elements for nucleotides list.
NucleotideTorsionAngle - Enum in pl.poznan.put.rna: A torsion angle defined in a nucleotide.
NumberFormatUtils - Class in pl.poznan.put.utility: A class to provide useful NumberFormat instances.
NZ - Enum constant in enum pl.poznan.put.atom.AtomName

O

O - Enum constant in enum pl.poznan.put.atom.AtomName
O - Enum constant in enum pl.poznan.put.atom.AtomType
O1 - Enum constant in enum pl.poznan.put.atom.AtomName
O17 - Enum constant in enum pl.poznan.put.atom.AtomName
O18 - Enum constant in enum pl.poznan.put.atom.AtomName
O1A - Enum constant in enum pl.poznan.put.atom.AtomName
O1B - Enum constant in enum pl.poznan.put.atom.AtomName
O1C - Enum constant in enum pl.poznan.put.atom.AtomName
O1G - Enum constant in enum pl.poznan.put.atom.AtomName
O1P - Enum constant in enum pl.poznan.put.atom.AtomName
O1P3 - Enum constant in enum pl.poznan.put.atom.AtomName
O2 - Enum constant in enum pl.poznan.put.atom.AtomName
O22 - Enum constant in enum pl.poznan.put.atom.AtomName
O23 - Enum constant in enum pl.poznan.put.atom.AtomName
O2A - Enum constant in enum pl.poznan.put.atom.AtomName
O2B - Enum constant in enum pl.poznan.put.atom.AtomName
O2C - Enum constant in enum pl.poznan.put.atom.AtomName
O2G - Enum constant in enum pl.poznan.put.atom.AtomName
O2p - Enum constant in enum pl.poznan.put.atom.AtomName
O2P - Enum constant in enum pl.poznan.put.atom.AtomName
O2P3 - Enum constant in enum pl.poznan.put.atom.AtomName
O3 - Enum constant in enum pl.poznan.put.atom.AtomName
O3A - Enum constant in enum pl.poznan.put.atom.AtomName
O3B - Enum constant in enum pl.poznan.put.atom.AtomName
O3C - Enum constant in enum pl.poznan.put.atom.AtomName
O3G - Enum constant in enum pl.poznan.put.atom.AtomName
O3p - Enum constant in enum pl.poznan.put.atom.AtomName
O3P - Enum constant in enum pl.poznan.put.atom.AtomName
O3P3 - Enum constant in enum pl.poznan.put.atom.AtomName
O3T - Enum constant in enum pl.poznan.put.atom.AtomName
O4 - Enum constant in enum pl.poznan.put.atom.AtomName
O4p - Enum constant in enum pl.poznan.put.atom.AtomName
O5 - Enum constant in enum pl.poznan.put.atom.AtomName
O5p - Enum constant in enum pl.poznan.put.atom.AtomName
O5T - Enum constant in enum pl.poznan.put.atom.AtomName
O6 - Enum constant in enum pl.poznan.put.atom.AtomName
occupancy() - Method in class pl.poznan.put.pdb.ImmutablePdbAtomLine
occupancy() - Method in class pl.poznan.put.pdb.PdbAtomLine
occupancy(double) - Method in class pl.poznan.put.pdb.ImmutablePdbAtomLine.Builder: Initializes the value for the occupancy attribute.
OD1 - Enum constant in enum pl.poznan.put.atom.AtomName
OD2 - Enum constant in enum pl.poznan.put.atom.AtomName
OE1 - Enum constant in enum pl.poznan.put.atom.AtomName
OE2 - Enum constant in enum pl.poznan.put.atom.AtomName
of() - Static method in class pl.poznan.put.protein.ImmutableBackbone: Returns the default immutable singleton value of Backbone
of() - Static method in class pl.poznan.put.rna.ImmutablePhosphate: Returns the default immutable singleton value of Phosphate
of() - Static method in class pl.poznan.put.rna.ImmutablePseudophasePuckerType: Returns the default immutable singleton value of PseudophasePuckerType
of() - Static method in class pl.poznan.put.rna.ImmutableRibose: Returns the default immutable singleton value of Ribose
of() - Static method in class pl.poznan.put.structure.formats.ImmutableDefaultConverter: Returns the default immutable singleton value of DefaultConverter
of() - Static method in class pl.poznan.put.structure.pseudoknots.dp.ImmutableDynamicProgrammingAll: Returns the default immutable singleton value of DynamicProgrammingAll
of() - Static method in class pl.poznan.put.structure.pseudoknots.elimination.ImmutableMaxConflicts: Returns the default immutable singleton value of MaxConflicts
of() - Static method in class pl.poznan.put.structure.pseudoknots.elimination.ImmutableMinGain: Returns the default immutable singleton value of MinGain
of(char, char, int) - Static method in class pl.poznan.put.structure.ImmutableDotBracketSymbol: Construct a new immutable DotBracketSymbol instance.
of(double) - Static method in class pl.poznan.put.circular.ImmutableAngle: Construct a new immutable Angle instance.
of(double) - Static method in class pl.poznan.put.pdb.ImmutablePdbRemark2Line: Construct a new immutable PdbRemark2Line instance.
of(double, double, double) - Static method in class pl.poznan.put.atom.ImmutableBondLength: Construct a new immutable BondLength instance.
of(int, char, int) - Static method in class pl.poznan.put.structure.formats.ImmutableEntry: Construct a new immutable Entry instance.
of(int, char, int, int, int, int) - Static method in class pl.poznan.put.structure.formats.ImmutableExtendedEntry: Construct a new immutable ExtendedEntry instance.
of(int, String, String) - Static method in class pl.poznan.put.utility.ImmutableExecutionResult: Construct a new immutable ExecutionResult instance.
of(int, String, String, int, Optional<String>) - Static method in class pl.poznan.put.pdb.ImmutablePdbRemark465Line: Construct a new immutable PdbRemark465Line instance.
of(int, String, Optional<String>, String, String, int, Optional<String>, double, double, double, double, double, String, String) - Static method in class pl.poznan.put.pdb.ImmutablePdbAtomLine: Construct a new immutable PdbAtomLine instance.
of(File, Map<? extends File, ? extends BidiMap<String, String>>) - Static method in class pl.poznan.put.pdb.analysis.ImmutableCifContainer: Construct a new immutable CifContainer instance.
of(Iterable<? extends PdbResidue>) - Static method in class pl.poznan.put.pdb.analysis.ImmutableDefaultResidueCollection: Construct a new immutable DefaultResidueCollection instance.
of(Iterable<? extends PdbResidue>) - Static method in class pl.poznan.put.pdb.analysis.ImmutablePdbCompactFragment: Construct a new immutable PdbCompactFragment instance.
of(Iterable<? extends ExperimentalTechnique>) - Static method in class pl.poznan.put.pdb.ImmutablePdbExpdtaLine: Construct a new immutable PdbExpdtaLine instance.
of(Iterable<? extends DotBracketSymbol>) - Static method in class pl.poznan.put.structure.formats.ImmutableTerminalMissing: Construct a new immutable TerminalMissing instance.
of(Iterable<? extends BpSeq.Entry>) - Static method in class pl.poznan.put.structure.formats.ImmutableBpSeq: Construct a new immutable BpSeq instance.
of(Iterable<? extends BpSeq.Entry>) - Static method in class pl.poznan.put.structure.pseudoknots.ImmutableRegion: Construct a new immutable Region instance.
of(Iterable<? extends Ct.ExtendedEntry>) - Static method in class pl.poznan.put.structure.formats.ImmutableCt: Construct a new immutable Ct instance.
of(Iterable<? extends Strand>) - Static method in class pl.poznan.put.structure.formats.ImmutableCombinedStrand: Construct a new immutable CombinedStrand instance.
of(Iterable<? extends Strand>, Map<? extends DotBracketSymbol, ? extends PdbResidueIdentifier>) - Static method in class pl.poznan.put.structure.formats.ImmutableCombinedStrandFromPdb: Construct a new immutable CombinedStrandFromPdb instance.
of(Iterable<? extends Region>) - Static method in class pl.poznan.put.structure.pseudoknots.dp.ImmutableConflictClique: Construct a new immutable ConflictClique instance.
of(Iterable<? extends Region>) - Static method in class pl.poznan.put.structure.pseudoknots.ImmutableConflictGraph: Construct a new immutable ConflictGraph instance.
of(Iterable<String>, double[][]) - Static method in class pl.poznan.put.types.ImmutableDistanceMatrix: Construct a new immutable DistanceMatrix instance.
of(Iterable<PdbAtomLine>) - Static method in class pl.poznan.put.pdb.analysis.DefaultPdbModel: Creates an instance of this class with just a list of atoms and all other fields set to default values or empty.
of(String, int, Optional<String>) - Static method in class pl.poznan.put.pdb.ImmutablePdbResidueIdentifier: Construct a new immutable PdbResidueIdentifier instance.
of(String, int, Optional<String>, char) - Static method in class pl.poznan.put.pdb.ImmutablePdbNamedResidueIdentifier: Construct a new immutable PdbNamedResidueIdentifier instance.
of(String, Iterable<? extends PdbResidue>) - Static method in class pl.poznan.put.pdb.analysis.ImmutablePdbChain: Construct a new immutable PdbChain instance.
of(String, Iterable<? extends DotBracketSymbol>) - Static method in class pl.poznan.put.structure.formats.ImmutableDefaultStrand: Construct a new immutable DefaultStrand instance.
of(String, String) - Static method in class pl.poznan.put.pdb.ImmutablePdbTitleLine: Construct a new immutable PdbTitleLine instance.
of(String, String) - Static method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracket: Construct a new immutable DefaultDotBracket instance.
of(String, String, String, int, Optional<String>, String, String) - Static method in class pl.poznan.put.pdb.ImmutablePdbModresLine: Construct a new immutable PdbModresLine instance.
of(String, String, PdbModel) - Static method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracketFromPdb: Construct a new immutable DefaultDotBracketFromPdb instance.
of(String, Collection<? extends ClassifiedBasePair>) - Static method in class pl.poznan.put.structure.formats.ImmutableMultiLineDotBracket: Construct a new immutable MultiLineDotBracket instance.
of(String, Date, String) - Static method in class pl.poznan.put.pdb.ImmutablePdbHeaderLine: Construct a new immutable PdbHeaderLine instance.
of(String, List<PdbResidue>) - Static method in class pl.poznan.put.pdb.analysis.ImmutablePdbChain: Construct a new immutable PdbChain instance.
of(String, List<DotBracketSymbol>) - Static method in class pl.poznan.put.structure.formats.ImmutableDefaultStrand: Construct a new immutable DefaultStrand instance.
of(String, DotBracket, int, int) - Static method in class pl.poznan.put.structure.formats.ImmutableStrandView: Construct a new immutable StrandView instance.
of(Collection<Angle>) - Static method in class pl.poznan.put.circular.samples.ImmutableAngleSample: Construct a new immutable AngleSample instance.
of(Collection<Angle>, double) - Static method in class pl.poznan.put.circular.ImmutableHistogram: Construct a new immutable Histogram instance.
of(List<String>, double[][]) - Static method in class pl.poznan.put.types.ImmutableDistanceMatrix: Construct a new immutable DistanceMatrix instance.
of(List<PdbResidue>) - Static method in class pl.poznan.put.pdb.analysis.ImmutableDefaultResidueCollection: Construct a new immutable DefaultResidueCollection instance.
of(List<PdbResidue>) - Static method in class pl.poznan.put.pdb.analysis.ImmutablePdbCompactFragment: Construct a new immutable PdbCompactFragment instance.
of(List<ExperimentalTechnique>) - Static method in class pl.poznan.put.pdb.ImmutablePdbExpdtaLine: Construct a new immutable PdbExpdtaLine instance.
of(List<DotBracketSymbol>) - Static method in class pl.poznan.put.structure.formats.ImmutableTerminalMissing: Construct a new immutable TerminalMissing instance.
of(List<BpSeq.Entry>) - Static method in class pl.poznan.put.structure.pseudoknots.ImmutableRegion: Construct a new immutable Region instance.
of(List<Strand>) - Static method in class pl.poznan.put.structure.formats.ImmutableCombinedStrand: Construct a new immutable CombinedStrand instance.
of(List<Strand>, Map<DotBracketSymbol, PdbResidueIdentifier>) - Static method in class pl.poznan.put.structure.formats.ImmutableCombinedStrandFromPdb: Construct a new immutable CombinedStrandFromPdb instance.
of(List<Region>) - Static method in class pl.poznan.put.structure.pseudoknots.ImmutableConflictGraph: Construct a new immutable ConflictGraph instance.
of(Set<Region>) - Static method in class pl.poznan.put.structure.pseudoknots.dp.ImmutableConflictClique: Construct a new immutable ConflictClique instance.
of(SortedSet<BpSeq.Entry>) - Static method in class pl.poznan.put.structure.formats.ImmutableBpSeq: Construct a new immutable BpSeq instance.
of(SortedSet<Ct.ExtendedEntry>) - Static method in class pl.poznan.put.structure.formats.ImmutableCt: Construct a new immutable Ct instance.
of(Angle, double) - Static method in class pl.poznan.put.circular.samples.ImmutableTrigonometricMoment: Construct a new immutable TrigonometricMoment instance.
of(MoleculeType, Iterable<? extends MasterTorsionAngleType>) - Static method in class pl.poznan.put.torsion.ImmutableAverageTorsionAngleType: Construct a new immutable AverageTorsionAngleType instance.
of(MoleculeType, String, String, Quadruple<AtomName>, Quadruple<Integer>) - Static method in class pl.poznan.put.torsion.ImmutableAtomBasedTorsionAngleType: Construct a new immutable AtomBasedTorsionAngleType instance.
of(MoleculeType, List<MasterTorsionAngleType>) - Static method in class pl.poznan.put.torsion.ImmutableAverageTorsionAngleType: Construct a new immutable AverageTorsionAngleType instance.
of(PdbAtomLine, PdbAtomLine) - Static method in class pl.poznan.put.torsion.ImmutableAtomPair: Construct a new immutable AtomPair instance.
of(PdbHeaderLine, PdbExpdtaLine, PdbRemark2Line, int, Iterable<? extends PdbAtomLine>, Iterable<? extends PdbModresLine>, Iterable<? extends PdbRemark465Line>, String, Iterable<? extends PdbResidueIdentifier>) - Static method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbModel: Construct a new immutable DefaultPdbModel instance.
of(PdbHeaderLine, PdbExpdtaLine, PdbRemark2Line, int, Iterable<? extends PdbAtomLine>, Iterable<? extends PdbModresLine>, Iterable<? extends PdbRemark465Line>, String, Iterable<? extends PdbResidueIdentifier>, Iterable<? extends QuantifiedBasePair>) - Static method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel: Construct a new immutable DefaultCifModel instance.
of(PdbHeaderLine, PdbExpdtaLine, PdbRemark2Line, int, List<PdbAtomLine>, List<PdbModresLine>, List<PdbRemark465Line>, String, Set<PdbResidueIdentifier>) - Static method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbModel: Construct a new immutable DefaultPdbModel instance.
of(PdbHeaderLine, PdbExpdtaLine, PdbRemark2Line, int, List<PdbAtomLine>, List<PdbModresLine>, List<PdbRemark465Line>, String, Set<PdbResidueIdentifier>, List<QuantifiedBasePair>) - Static method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel: Construct a new immutable DefaultCifModel instance.
of(PdbNamedResidueIdentifier, PdbNamedResidueIdentifier) - Static method in class pl.poznan.put.structure.ImmutableBasePair: Construct a new immutable BasePair instance.
of(PdbResidueIdentifier, Iterable<? extends TorsionAngleValue>) - Static method in class pl.poznan.put.pdb.analysis.ImmutableResidueTorsionAngles: Construct a new immutable ResidueTorsionAngles instance.
of(PdbResidueIdentifier, String, String, Iterable<? extends PdbAtomLine>) - Static method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbResidue: Construct a new immutable DefaultPdbResidue instance.
of(PdbResidueIdentifier, String, String, List<PdbAtomLine>) - Static method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbResidue: Construct a new immutable DefaultPdbResidue instance.
of(PdbResidueIdentifier, List<TorsionAngleValue>) - Static method in class pl.poznan.put.pdb.analysis.ImmutableResidueTorsionAngles: Construct a new immutable ResidueTorsionAngles instance.
of(BasePair) - Static method in class pl.poznan.put.structure.ImmutableAnalyzedBasePair: Construct a new immutable AnalyzedBasePair instance.
of(BasePair, double, double, double, double, double, double) - Static method in class pl.poznan.put.structure.ImmutableQuantifiedBasePair: Construct a new immutable QuantifiedBasePair instance.
of(MasterTorsionAngleType, TorsionAngleDelta.State, Angle, RangeDifference) - Static method in class pl.poznan.put.torsion.ImmutableTorsionAngleDelta: Construct a new immutable TorsionAngleDelta instance.
of(TorsionAngleType, Angle) - Static method in class pl.poznan.put.torsion.ImmutableTorsionAngleValue: Construct a new immutable TorsionAngleValue instance.
of(T, T, T, T) - Static method in class pl.poznan.put.types.ImmutableQuadruple: Construct a new immutable Quadruple instance.
OG - Enum constant in enum pl.poznan.put.atom.AtomName
OG1 - Enum constant in enum pl.poznan.put.atom.AtomName
OH - Enum constant in enum pl.poznan.put.atom.AtomName
OL - Enum constant in enum pl.poznan.put.atom.AtomName
OMEGA - Enum constant in enum pl.poznan.put.protein.AminoAcidTorsionAngle
OMEGA - Static variable in class pl.poznan.put.constant.Unicode
oneLetterName() - Method in class pl.poznan.put.external.dssr.ImmutableNucleotide
oneLetterName() - Method in interface pl.poznan.put.external.dssr.Nucleotide
oneLetterName() - Method in interface pl.poznan.put.pdb.analysis.PdbResidue
oneLetterName() - Method in interface pl.poznan.put.pdb.analysis.ResidueInformationProvider
oneLetterName() - Method in class pl.poznan.put.pdb.ImmutablePdbNamedResidueIdentifier
oneLetterName() - Method in class pl.poznan.put.pdb.PdbNamedResidueIdentifier
oneLetterName() - Method in enum pl.poznan.put.protein.AminoAcid
oneLetterName() - Method in enum pl.poznan.put.rna.Nucleotide
oneLetterName(char) - Method in class pl.poznan.put.pdb.ImmutablePdbNamedResidueIdentifier.Builder: Initializes the value for the oneLetterName attribute.
oneLetterName(String) - Method in class pl.poznan.put.external.dssr.ImmutableNucleotide.Builder: Initializes the value for the oneLetterName attribute.
opening() - Method in class pl.poznan.put.structure.ImmutableQuantifiedBasePair
opening() - Method in class pl.poznan.put.structure.QuantifiedBasePair
opening(double) - Method in class pl.poznan.put.structure.ImmutableQuantifiedBasePair.Builder: Initializes the value for the opening attribute.
OPPOSITE - Enum constant in enum pl.poznan.put.torsion.range.RangeDifference
OR - Enum constant in enum pl.poznan.put.atom.AtomName
order() - Method in class pl.poznan.put.structure.DotBracketSymbol
orderedSubtract(Angle) - Method in class pl.poznan.put.circular.Angle: Returns an ordered difference between angles.
original() - Method in class pl.poznan.put.structure.formats.Ct.ExtendedEntry
original() - Method in class pl.poznan.put.structure.formats.ImmutableExtendedEntry
original(int) - Method in class pl.poznan.put.structure.formats.ImmutableExtendedEntry.Builder: Initializes the value for the original attribute.
originalCifChainName(File, String) - Method in class pl.poznan.put.pdb.analysis.CifContainer
originalCifChainName(File, String) - Method in interface pl.poznan.put.pdb.analysis.ModelContainer: Checks mapping of chains to get the original mmCIF chain name from the generated PDB chain name.
originalIndex(DotBracketSymbol) - Method in class pl.poznan.put.structure.formats.CombinedStrandFromPdb
originalIndex(DotBracketSymbol) - Method in class pl.poznan.put.structure.formats.DefaultDotBracketFromPdb
originalIndex(DotBracketSymbol) - Method in interface pl.poznan.put.structure.formats.DotBracket: Returns the index of a dot-bracket symbol according to some external source like PDB numbering.
OT1 - Enum constant in enum pl.poznan.put.atom.AtomName
OT2 - Enum constant in enum pl.poznan.put.atom.AtomName
OTHER - Enum constant in enum pl.poznan.put.atom.AtomType
OTHER - Static variable in class pl.poznan.put.rna.InteractionType: Another interaction type.
OUTWARD - Enum constant in enum pl.poznan.put.notation.StackingTopology
OY - Enum constant in enum pl.poznan.put.atom.AtomName

P

P - Enum constant in enum pl.poznan.put.atom.AtomName
P - Enum constant in enum pl.poznan.put.atom.AtomType
P3 - Enum constant in enum pl.poznan.put.atom.AtomName
PA - Enum constant in enum pl.poznan.put.atom.AtomName
pair() - Method in class pl.poznan.put.structure.formats.BpSeq.Entry
pair() - Method in class pl.poznan.put.structure.formats.Ct.ExtendedEntry
pair() - Method in class pl.poznan.put.structure.formats.ImmutableEntry
pair() - Method in class pl.poznan.put.structure.formats.ImmutableExtendedEntry
pair(int) - Method in class pl.poznan.put.structure.formats.ImmutableEntry.Builder: Initializes the value for the pair attribute.
pair(int) - Method in class pl.poznan.put.structure.formats.ImmutableExtendedEntry.Builder: Initializes the value for the pair attribute.
Pair - Interface in pl.poznan.put.external.dssr
paired() - Method in class pl.poznan.put.structure.formats.BpSeq
pairs() - Method in class pl.poznan.put.external.dssr.DssrJson
pairs() - Method in class pl.poznan.put.external.dssr.ImmutableDssrJson
pairs() - Method in class pl.poznan.put.structure.formats.CombinedStrand
pairs() - Method in class pl.poznan.put.structure.formats.CombinedStrandFromPdb
pairs() - Method in class pl.poznan.put.structure.formats.DefaultDotBracket
pairs() - Method in class pl.poznan.put.structure.formats.DefaultDotBracketFromPdb
pairs() - Method in interface pl.poznan.put.structure.formats.DotBracket
pairs() - Method in class pl.poznan.put.structure.formats.ImmutableCombinedStrand
pairs() - Method in class pl.poznan.put.structure.formats.ImmutableCombinedStrandFromPdb
pairs() - Method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracket
pairs() - Method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracketFromPdb
pairs(Iterable<? extends Pair>) - Method in class pl.poznan.put.external.dssr.ImmutableDssrJson.Builder: Sets or replaces all elements for pairs list.
parent() - Method in class pl.poznan.put.structure.formats.ImmutableStrandView
parent() - Method in class pl.poznan.put.structure.formats.StrandView
parent(DotBracket) - Method in class pl.poznan.put.structure.formats.ImmutableStrandView.Builder: Initializes the value for the parent attribute.
parse(String) - Method in class pl.poznan.put.pdb.analysis.CifParser: Parses content in mmCIF format.
parse(String) - Method in class pl.poznan.put.pdb.analysis.PdbParser: Parses a string in PDB format.
parse(String) - Static method in class pl.poznan.put.pdb.PdbAtomLine: Parses text as ATOM or HETATM line in strict mode (all 80 characters in the line are required).
parse(String) - Static method in class pl.poznan.put.pdb.PdbExpdtaLine: Parses text as an EXPDTA line in PDB format.
parse(String) - Static method in class pl.poznan.put.pdb.PdbHeaderLine: Parses text with HEADER line in PDB format.
parse(String) - Static method in class pl.poznan.put.pdb.PdbModresLine: Parses text with MODRES line in PDB format.
parse(String) - Static method in class pl.poznan.put.pdb.PdbRemark2Line: Parses the text in REMARK 2 of PDB format.
parse(String) - Static method in class pl.poznan.put.pdb.PdbRemark465Line: Parses a line of text to create an instance of this class.
parse(String) - Static method in class pl.poznan.put.pdb.PdbTitleLine: Parses a line of text as TITLE in PDB format.
parse(String, boolean) - Static method in class pl.poznan.put.pdb.PdbAtomLine: Parses text as ATOM or HETATM line in a strict or non-strict mode.
PB - Enum constant in enum pl.poznan.put.atom.AtomName
PC - Enum constant in enum pl.poznan.put.atom.AtomName
PdbAtomLine - Class in pl.poznan.put.pdb: Representation of ATOM and HETATM lines in both PDB and mmCIF files.
PdbAtomLine() - Constructor for class pl.poznan.put.pdb.PdbAtomLine
PdbBuilder() - Constructor for class pl.poznan.put.pdb.analysis.ResidueCollection.PdbBuilder
PdbChain - Class in pl.poznan.put.pdb.analysis: A chain in a structure.
PdbChain() - Constructor for class pl.poznan.put.pdb.analysis.PdbChain
PdbCompactFragment - Class in pl.poznan.put.pdb.analysis: A collection of residues such that (i, i+1) are connected.
PdbCompactFragment() - Constructor for class pl.poznan.put.pdb.analysis.PdbCompactFragment
PdbExpdtaLine - Class in pl.poznan.put.pdb: A representation of EXPDTA line in PDB files.
PdbExpdtaLine() - Constructor for class pl.poznan.put.pdb.PdbExpdtaLine
pdbFiles() - Method in class pl.poznan.put.pdb.analysis.CifContainer
pdbFiles() - Method in interface pl.poznan.put.pdb.analysis.ModelContainer
PdbHeaderLine - Class in pl.poznan.put.pdb: A representation of HEADER file in PDB format.
PdbHeaderLine() - Constructor for class pl.poznan.put.pdb.PdbHeaderLine
PdbModel - Interface in pl.poznan.put.pdb.analysis: A structure parsed from a PDB file.
PdbModresLine - Class in pl.poznan.put.pdb: A representation of MODRES line in PDB format.
PdbModresLine() - Constructor for class pl.poznan.put.pdb.PdbModresLine
PdbNamedResidueIdentifier - Class in pl.poznan.put.pdb: Class that represents a residue identifier with a known name.
PdbNamedResidueIdentifier() - Constructor for class pl.poznan.put.pdb.PdbNamedResidueIdentifier
PdbParser - Class in pl.poznan.put.pdb.analysis: A parser of PDB format.
PdbParser() - Constructor for class pl.poznan.put.pdb.analysis.PdbParser: Creates an instance with strictMode set to true.
PdbParser(boolean) - Constructor for class pl.poznan.put.pdb.analysis.PdbParser: Creates an instance with the possibility to set strictMode.
PdbParsingException - Exception in pl.poznan.put.pdb: When data in PDB files is inconsistent with the documented format.
PdbParsingException(String) - Constructor for exception pl.poznan.put.pdb.PdbParsingException
PdbParsingException(String, Throwable) - Constructor for exception pl.poznan.put.pdb.PdbParsingException
PdbRemark2Line - Class in pl.poznan.put.pdb: A representation of REMARK 2 line which describes experimental resolution.
PdbRemark2Line() - Constructor for class pl.poznan.put.pdb.PdbRemark2Line
PdbRemark465Line - Class in pl.poznan.put.pdb: A representation of REMARK 465 in PDB format which describes missing residues.
PdbRemark465Line() - Constructor for class pl.poznan.put.pdb.PdbRemark465Line
PdbResidue - Interface in pl.poznan.put.pdb.analysis: A residue (nucleotide or amino acid).
PdbResidueIdentifier - Class in pl.poznan.put.pdb: A residue identifier is used only to address a residue in the structure.
PdbResidueIdentifier() - Constructor for class pl.poznan.put.pdb.PdbResidueIdentifier
PdbTitleLine - Class in pl.poznan.put.pdb: A representation of TITLE line in PDB format.
PdbTitleLine() - Constructor for class pl.poznan.put.pdb.PdbTitleLine
PDF - Enum constant in enum pl.poznan.put.utility.svg.Format
PG - Enum constant in enum pl.poznan.put.atom.AtomName
PHENYLALANINE - Enum constant in enum pl.poznan.put.protein.AminoAcid
PHI - Enum constant in enum pl.poznan.put.protein.AminoAcidTorsionAngle
PHI - Static variable in class pl.poznan.put.constant.Unicode
Phosphate - Class in pl.poznan.put.rna: A phosphate, part of RNA backbone.
Phosphate() - Constructor for class pl.poznan.put.rna.Phosphate
PHOSPHATE - Enum constant in enum pl.poznan.put.rna.NucleotideComponentType
PI - Static variable in class pl.poznan.put.constant.Unicode
pl.poznan.put.atom - package pl.poznan.put.atom: Collection of utility classes to work with atom types, names and atomic bonds.
pl.poznan.put.circular - package pl.poznan.put.circular: Classes to deal with angular data and circular statistics.
pl.poznan.put.circular.conversion - package pl.poznan.put.circular.conversion: Contains classes useful in conversion between Cartesian and trigonometric representations.
pl.poznan.put.circular.enums - package pl.poznan.put.circular.enums: Package contains useful enums.
pl.poznan.put.circular.exception - package pl.poznan.put.circular.exception: Exceptions thrown when operations on circular values fail.
pl.poznan.put.circular.samples - package pl.poznan.put.circular.samples: Classes which deal with samples of data.
pl.poznan.put.constant - package pl.poznan.put.constant: Contains classes with useful constant values and static methods.
pl.poznan.put.external.dssr - package pl.poznan.put.external.dssr
pl.poznan.put.interfaces - package pl.poznan.put.interfaces: Interfaces useful in various contexts to clean up class design.
pl.poznan.put.notation - package pl.poznan.put.notation: A set of enums describing different notations used in structural biology.
pl.poznan.put.pdb - package pl.poznan.put.pdb: Contains classes responsible for PDB/mmCIF data modelling and analysis.
pl.poznan.put.pdb.analysis - package pl.poznan.put.pdb.analysis: Contains classes which work on data from PDB or mmCIF files.
pl.poznan.put.protein - package pl.poznan.put.protein
pl.poznan.put.rna - package pl.poznan.put.rna
pl.poznan.put.structure - package pl.poznan.put.structure: Package contains classes useful in describing secondary structure (base pairs, helices, etc.)
pl.poznan.put.structure.formats - package pl.poznan.put.structure.formats
pl.poznan.put.structure.pseudoknots - package pl.poznan.put.structure.pseudoknots: Package contains classes that handle pseudoknots in secondary structure.
pl.poznan.put.structure.pseudoknots.dp - package pl.poznan.put.structure.pseudoknots.dp: A set of dynamic programming solutions to pseudoknot detection.s
pl.poznan.put.structure.pseudoknots.elimination - package pl.poznan.put.structure.pseudoknots.elimination
pl.poznan.put.torsion - package pl.poznan.put.torsion: Contains classes dealing with torsion angles handling.
pl.poznan.put.torsion.range - package pl.poznan.put.torsion.range
pl.poznan.put.types - package pl.poznan.put.types
pl.poznan.put.utility - package pl.poznan.put.utility: Contains classes providing various useful functions.
pl.poznan.put.utility.svg - package pl.poznan.put.utility.svg: Contains classes useful for SVG processing.
PNG - Enum constant in enum pl.poznan.put.utility.svg.Format
POWDER_DIFFRACTION - Enum constant in enum pl.poznan.put.pdb.ExperimentalTechnique
PROLINE - Enum constant in enum pl.poznan.put.protein.AminoAcid
PROLOGUE - Static variable in class pl.poznan.put.pdb.PdbRemark2Line
PROLOGUE - Static variable in class pl.poznan.put.pdb.PdbRemark465Line
propeller() - Method in class pl.poznan.put.structure.ImmutableQuantifiedBasePair
propeller() - Method in class pl.poznan.put.structure.QuantifiedBasePair
propeller(double) - Method in class pl.poznan.put.structure.ImmutableQuantifiedBasePair.Builder: Initializes the value for the propeller attribute.
PROTEIN - Enum constant in enum pl.poznan.put.pdb.analysis.MoleculeType
pseudoknotFinder() - Method in class pl.poznan.put.structure.formats.DefaultConverter
pseudoknotFinder() - Method in class pl.poznan.put.structure.formats.ImmutableDefaultConverter
pseudoknotFinder(PseudoknotFinder) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultConverter.Builder: Initializes the value for the pseudoknotFinder attribute.
PseudoknotFinder - Interface in pl.poznan.put.structure.pseudoknots: A finder of pseudoknots in RNA secondary structure.
pseudoknotOrder() - Method in interface pl.poznan.put.structure.formats.DotBracket
PSEUDOPHASE_PUCKER - Enum constant in enum pl.poznan.put.rna.NucleotideTorsionAngle
PseudophasePuckerType - Class in pl.poznan.put.rna: An angle describing the pseudophase pucker.
PseudophasePuckerType() - Constructor for class pl.poznan.put.rna.PseudophasePuckerType
Pseudorotation - Enum in pl.poznan.put.rna: A range of pseudorotation values with their descriptions.
PSI - Enum constant in enum pl.poznan.put.protein.AminoAcidTorsionAngle
PSI - Static variable in class pl.poznan.put.constant.Unicode
Purine - Interface in pl.poznan.put.rna: A purine (adenine or guanine).
PURINE - Enum constant in enum pl.poznan.put.rna.Chi
putAllEnvironment(Map<String, ? extends String>) - Method in class pl.poznan.put.utility.ImmutableExecHelper.Builder: Put all mappings from the specified map as entries to environment map.
putAllFileChainMap(Map<? extends File, ? extends BidiMap<String, String>>) - Method in class pl.poznan.put.pdb.analysis.ImmutableCifContainer.Builder: Put all mappings from the specified map as entries to fileChainMap map.
putAllInputSymbolToResidue(Map<? extends DotBracketSymbol, ? extends PdbResidueIdentifier>) - Method in class pl.poznan.put.structure.formats.ImmutableCombinedStrandFromPdb.Builder: Put all mappings from the specified map as entries to inputSymbolToResidue map.
putEnvironment(String, String) - Method in class pl.poznan.put.utility.ImmutableExecHelper.Builder: Put one entry to the environment map.
putEnvironment(Map.Entry<String, ? extends String>) - Method in class pl.poznan.put.utility.ImmutableExecHelper.Builder: Put one entry to the environment map.
putFileChainMap(File, BidiMap<String, String>) - Method in class pl.poznan.put.pdb.analysis.ImmutableCifContainer.Builder: Put one entry to the fileChainMap map.
putFileChainMap(Map.Entry<? extends File, ? extends BidiMap<String, String>>) - Method in class pl.poznan.put.pdb.analysis.ImmutableCifContainer.Builder: Put one entry to the fileChainMap map.
putInputSymbolToResidue(Map.Entry<? extends DotBracketSymbol, ? extends PdbResidueIdentifier>) - Method in class pl.poznan.put.structure.formats.ImmutableCombinedStrandFromPdb.Builder: Put one entry to the inputSymbolToResidue map.
putInputSymbolToResidue(DotBracketSymbol, PdbResidueIdentifier) - Method in class pl.poznan.put.structure.formats.ImmutableCombinedStrandFromPdb.Builder: Put one entry to the inputSymbolToResidue map.
Pyrimidine - Interface in pl.poznan.put.rna: A pyrimidine (cytosine, uracil or thymine).
PYRIMIDINE - Enum constant in enum pl.poznan.put.rna.Chi

Q

Quadruple<T> - Interface in pl.poznan.put.types
QuantifiedBasePair - Class in pl.poznan.put.structure: A base pair which is classified and quantified with numerical parameters.
QuantifiedBasePair() - Constructor for class pl.poznan.put.structure.QuantifiedBasePair

R

radians() - Method in class pl.poznan.put.circular.Angle
radians() - Method in class pl.poznan.put.circular.ImmutableAngle
radians(double) - Method in class pl.poznan.put.circular.ImmutableAngle.Builder: Initializes the value for the radians attribute.
radians2PI() - Method in class pl.poznan.put.circular.Angle
range(Angle) - Method in enum pl.poznan.put.protein.AminoAcidTorsionAngle
range(Angle) - Method in enum pl.poznan.put.rna.NucleotideTorsionAngle
range(Angle) - Method in class pl.poznan.put.torsion.AverageTorsionAngleType
range(Angle) - Method in interface pl.poznan.put.torsion.MasterTorsionAngleType: Finds a matching range for the given angle value.
Range - Interface in pl.poznan.put.torsion.range: A named range of torsion angle values.
rangeDifference() - Method in class pl.poznan.put.torsion.ImmutableTorsionAngleDelta
rangeDifference() - Method in class pl.poznan.put.torsion.TorsionAngleDelta
rangeDifference(RangeDifference) - Method in class pl.poznan.put.torsion.ImmutableTorsionAngleDelta.Builder: Initializes the value for the rangeDifference attribute.
RangeDifference - Enum in pl.poznan.put.torsion.range: A distance between TorsionRange objects.
rangeProvider() - Static method in enum pl.poznan.put.torsion.range.TorsionRange
RangeProvider - Interface in pl.poznan.put.torsion.range: A provider of torsion angle ranges (different ranges are used for chi angle and for pseudophase pucker).
Region - Class in pl.poznan.put.structure.pseudoknots: A collection of pairs (BPSEQ entries) which are consecutive in sequence.
Region() - Constructor for class pl.poznan.put.structure.pseudoknots.Region
regionRemover() - Method in class pl.poznan.put.structure.pseudoknots.dp.DynamicProgrammingAll
regionRemover() - Method in class pl.poznan.put.structure.pseudoknots.dp.ImmutableDynamicProgrammingAll
regionRemover(Optional<? extends RegionRemover>) - Method in class pl.poznan.put.structure.pseudoknots.dp.ImmutableDynamicProgrammingAll.Builder: Initializes the optional value regionRemover to regionRemover.
regionRemover(RegionRemover) - Method in class pl.poznan.put.structure.pseudoknots.dp.ImmutableDynamicProgrammingAll.Builder: Initializes the optional value regionRemover to regionRemover.
RegionRemover - Interface in pl.poznan.put.structure.pseudoknots.elimination: A pseudoknot finder algorithm which works by selecting a region to remove in each iteration.
regions() - Method in class pl.poznan.put.structure.pseudoknots.ConflictGraph
regions() - Method in class pl.poznan.put.structure.pseudoknots.dp.ConflictClique
regions() - Method in class pl.poznan.put.structure.pseudoknots.dp.ImmutableConflictClique
regions() - Method in class pl.poznan.put.structure.pseudoknots.ImmutableConflictGraph
regions(Iterable<? extends Region>) - Method in class pl.poznan.put.structure.pseudoknots.dp.ImmutableConflictClique.Builder: Sets or replaces all elements for regions set.
regions(Iterable<? extends Region>) - Method in class pl.poznan.put.structure.pseudoknots.ImmutableConflictGraph.Builder: Sets or replaces all elements for regions list.
regionsWithConflicts() - Method in class pl.poznan.put.structure.pseudoknots.ConflictGraph: Returns all regions that are in conflict with at least one other region.
removeRegion(Region) - Method in class pl.poznan.put.structure.pseudoknots.ConflictGraph: Removes region and all associated conflicts with it from the graph.
reorderAtoms(PdbModel) - Static method in class pl.poznan.put.rna.ChainReorderer: Finds canonical base pairs (see CanonicalStructureExtractor.basePairs(ResidueCollection)) and reorders chains to keep connected ones together while minimizing the overall pseudoknot order.
reorderAtoms(PdbModel, Collection<? extends ClassifiedBasePair>) - Static method in class pl.poznan.put.rna.ChainReorderer: Reorders chains according to given canonical base pairs to keep connected chains together while minimizing the overall pseudoknot order.
requiredAtoms() - Method in interface pl.poznan.put.pdb.analysis.ResidueComponent
requiredAtoms() - Method in interface pl.poznan.put.protein.Backbone
requiredAtoms() - Method in class pl.poznan.put.rna.Phosphate
requiredAtoms() - Method in class pl.poznan.put.rna.Ribose
ResidueCollection - Interface in pl.poznan.put.pdb.analysis: A collection of residues.
ResidueCollection.CifBuilder - Class in pl.poznan.put.pdb.analysis: A builder that can merge many residue collections in one mmCIF file.
ResidueCollection.PdbBuilder - Class in pl.poznan.put.pdb.analysis: A builder that can merge many residue collections in one PDB file.
ResidueComponent - Interface in pl.poznan.put.pdb.analysis: A fragment of a residue with a set of expected atoms and a set of possible other atoms.
residueIdentifiers() - Method in interface pl.poznan.put.pdb.analysis.ResidueCollection
residueInformationProvider() - Method in class pl.poznan.put.pdb.analysis.DefaultPdbResidue
residueInformationProvider() - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbResidue: Detects the type of residue by its name and atom content.
residueInformationProvider() - Method in interface pl.poznan.put.pdb.analysis.PdbResidue: Detects the type of residue by its name and atom content.
ResidueInformationProvider - Interface in pl.poznan.put.pdb.analysis: A provider of detailed information about a residue (its type, expected atoms, torsion angles etc).
residueName() - Method in class pl.poznan.put.pdb.ImmutablePdbAtomLine
residueName() - Method in class pl.poznan.put.pdb.ImmutablePdbModresLine
residueName() - Method in class pl.poznan.put.pdb.ImmutablePdbRemark465Line
residueName() - Method in class pl.poznan.put.pdb.PdbAtomLine
residueName() - Method in class pl.poznan.put.pdb.PdbModresLine
residueName() - Method in class pl.poznan.put.pdb.PdbRemark465Line
residueName(String) - Method in class pl.poznan.put.pdb.ImmutablePdbAtomLine.Builder: Initializes the value for the residueName attribute.
residueName(String) - Method in class pl.poznan.put.pdb.ImmutablePdbModresLine.Builder: Initializes the value for the residueName attribute.
residueName(String) - Method in class pl.poznan.put.pdb.ImmutablePdbRemark465Line.Builder: Initializes the value for the residueName attribute.
residueNumber() - Method in class pl.poznan.put.external.dssr.ImmutableNucleotide
residueNumber() - Method in interface pl.poznan.put.external.dssr.Nucleotide
residueNumber() - Method in interface pl.poznan.put.pdb.analysis.PdbResidue
residueNumber() - Method in interface pl.poznan.put.pdb.ChainNumberICode
residueNumber() - Method in class pl.poznan.put.pdb.ImmutablePdbAtomLine
residueNumber() - Method in class pl.poznan.put.pdb.ImmutablePdbModresLine
residueNumber() - Method in class pl.poznan.put.pdb.ImmutablePdbNamedResidueIdentifier
residueNumber() - Method in class pl.poznan.put.pdb.ImmutablePdbRemark465Line
residueNumber() - Method in class pl.poznan.put.pdb.ImmutablePdbResidueIdentifier
residueNumber() - Method in class pl.poznan.put.pdb.PdbAtomLine
residueNumber() - Method in class pl.poznan.put.pdb.PdbModresLine
residueNumber() - Method in class pl.poznan.put.pdb.PdbNamedResidueIdentifier
residueNumber() - Method in class pl.poznan.put.pdb.PdbRemark465Line
residueNumber() - Method in class pl.poznan.put.pdb.PdbResidueIdentifier
residueNumber(int) - Method in class pl.poznan.put.external.dssr.ImmutableNucleotide.Builder: Initializes the value for the residueNumber attribute.
residueNumber(int) - Method in class pl.poznan.put.pdb.ImmutablePdbAtomLine.Builder: Initializes the value for the residueNumber attribute.
residueNumber(int) - Method in class pl.poznan.put.pdb.ImmutablePdbModresLine.Builder: Initializes the value for the residueNumber attribute.
residueNumber(int) - Method in class pl.poznan.put.pdb.ImmutablePdbNamedResidueIdentifier.Builder: Initializes the value for the residueNumber attribute.
residueNumber(int) - Method in class pl.poznan.put.pdb.ImmutablePdbRemark465Line.Builder: Initializes the value for the residueNumber attribute.
residueNumber(int) - Method in class pl.poznan.put.pdb.ImmutablePdbResidueIdentifier.Builder: Initializes the value for the residueNumber attribute.
residueRule() - Method in interface pl.poznan.put.torsion.AtomBasedTorsionAngleType
residueRule() - Method in class pl.poznan.put.torsion.ImmutableAtomBasedTorsionAngleType
residueRule(Quadruple<Integer>) - Method in class pl.poznan.put.torsion.ImmutableAtomBasedTorsionAngleType.Builder: Initializes the value for the residueRule attribute.
residues() - Method in class pl.poznan.put.pdb.analysis.AbstractPdbModel: Groups together atoms from the same residue and repeat that for every residue.
residues() - Method in class pl.poznan.put.pdb.analysis.DefaultCifModel
residues() - Method in class pl.poznan.put.pdb.analysis.DefaultPdbModel
residues() - Method in class pl.poznan.put.pdb.analysis.DefaultResidueCollection
residues() - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel: Groups together atoms from the same residue and repeat that for every residue.
residues() - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbModel: Groups together atoms from the same residue and repeat that for every residue.
residues() - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultResidueCollection
residues() - Method in class pl.poznan.put.pdb.analysis.ImmutablePdbChain
residues() - Method in class pl.poznan.put.pdb.analysis.ImmutablePdbCompactFragment
residues() - Method in class pl.poznan.put.pdb.analysis.PdbChain
residues() - Method in class pl.poznan.put.pdb.analysis.PdbCompactFragment
residues() - Method in interface pl.poznan.put.pdb.analysis.ResidueCollection
residues(Iterable<? extends PdbResidue>) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultResidueCollection.Builder: Sets or replaces all elements for residues list.
residues(Iterable<? extends PdbResidue>) - Method in class pl.poznan.put.pdb.analysis.ImmutablePdbChain.Builder: Sets or replaces all elements for residues list.
residues(Iterable<? extends PdbResidue>) - Method in class pl.poznan.put.pdb.analysis.ImmutablePdbCompactFragment.Builder: Sets or replaces all elements for residues list.
ResidueTorsionAngles - Class in pl.poznan.put.pdb.analysis: A collection of torsion angles values for a single residue.
ResidueTorsionAngles() - Constructor for class pl.poznan.put.pdb.analysis.ResidueTorsionAngles
residueToSymbol() - Method in class pl.poznan.put.structure.formats.DefaultDotBracketFromPdb
residueToSymbol() - Method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracketFromPdb
ResidueTypeDetector - Class in pl.poznan.put.pdb.analysis: A detector of residue type based on its name and atom content.
resolution() - Method in class pl.poznan.put.pdb.analysis.DefaultCifModel
resolution() - Method in class pl.poznan.put.pdb.analysis.DefaultPdbModel
resolution() - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel
resolution() - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbModel
resolution() - Method in interface pl.poznan.put.pdb.analysis.PdbModel
resolution() - Method in class pl.poznan.put.pdb.ImmutablePdbRemark2Line
resolution() - Method in class pl.poznan.put.pdb.PdbRemark2Line
resolution(double) - Method in class pl.poznan.put.pdb.ImmutablePdbRemark2Line.Builder: Initializes the value for the resolution attribute.
resolution(PdbRemark2Line) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel.Builder: Initializes the value for the resolution attribute.
resolution(PdbRemark2Line) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbModel.Builder: Initializes the value for the resolution attribute.
ResourcesHelper - Class in pl.poznan.put.utility: A collection of methods to work with resources (src/main/resources/).
Ribose - Class in pl.poznan.put.rna: A ribose, part of RNA backbone.
Ribose() - Constructor for class pl.poznan.put.rna.Ribose
RIBOSE - Enum constant in enum pl.poznan.put.rna.NucleotideComponentType
right() - Method in class pl.poznan.put.rna.ImmutableInteractionType
right() - Method in class pl.poznan.put.rna.InteractionType
right() - Method in class pl.poznan.put.structure.BasePair
right() - Method in class pl.poznan.put.structure.ImmutableBasePair
right(PdbNamedResidueIdentifier) - Method in class pl.poznan.put.structure.ImmutableBasePair.Builder: Initializes the value for the right attribute.
right(NucleotideComponentType) - Method in class pl.poznan.put.rna.ImmutableInteractionType.Builder: Initializes the value for the right attribute.
rightAtom(PdbAtomLine) - Method in class pl.poznan.put.torsion.ImmutableAtomPair.Builder: Initializes the value for the rightAtom attribute.
RNA - Enum constant in enum pl.poznan.put.pdb.analysis.MoleculeType

S

S - Enum constant in enum pl.poznan.put.atom.AtomType
saenger() - Method in class pl.poznan.put.external.dssr.ImmutablePair
saenger() - Method in interface pl.poznan.put.external.dssr.Pair
saenger() - Method in class pl.poznan.put.structure.AnalyzedBasePair
saenger() - Method in interface pl.poznan.put.structure.ClassifiedBasePair
saenger() - Method in class pl.poznan.put.structure.ImmutableAnalyzedBasePair
saenger() - Method in class pl.poznan.put.structure.ImmutableQuantifiedBasePair
saenger() - Method in class pl.poznan.put.structure.QuantifiedBasePair
saenger(String) - Method in class pl.poznan.put.external.dssr.ImmutablePair.Builder: Initializes the value for the saenger attribute.
saenger(Saenger) - Method in class pl.poznan.put.structure.ImmutableAnalyzedBasePair.Builder: Initializes the value for the saenger attribute.
saenger(Saenger) - Method in class pl.poznan.put.structure.ImmutableQuantifiedBasePair.Builder: Initializes the value for the saenger attribute.
Saenger - Enum in pl.poznan.put.notation: A classification of RNA base pairs described in Principles of Nucleic Acid Structure.
SD - Enum constant in enum pl.poznan.put.atom.AtomName
selectRegionToRemove(ConflictGraph) - Method in class pl.poznan.put.structure.pseudoknots.elimination.MaxConflicts: Selects a region which has the most conflicts with other regions.
selectRegionToRemove(ConflictGraph) - Method in class pl.poznan.put.structure.pseudoknots.elimination.MinGain: Selects a region which has the least gain (sum of length of all regions in conflict).
selectRegionToRemove(ConflictGraph) - Method in interface pl.poznan.put.structure.pseudoknots.elimination.RegionRemover: Uses data in the conflict graph to select one region to be removed.
seq() - Method in class pl.poznan.put.structure.formats.BpSeq.Entry
seq() - Method in class pl.poznan.put.structure.formats.Ct.ExtendedEntry
seq() - Method in class pl.poznan.put.structure.formats.ImmutableEntry
seq() - Method in class pl.poznan.put.structure.formats.ImmutableExtendedEntry
seq(char) - Method in class pl.poznan.put.structure.formats.ImmutableEntry.Builder: Initializes the value for the seq attribute.
seq(char) - Method in class pl.poznan.put.structure.formats.ImmutableExtendedEntry.Builder: Initializes the value for the seq attribute.
sequence() - Method in interface pl.poznan.put.pdb.analysis.ResidueCollection: Generates a sequence out of this residue collection.
sequence() - Method in class pl.poznan.put.structure.DotBracketSymbol
sequence() - Method in class pl.poznan.put.structure.formats.BpSeq
sequence() - Method in class pl.poznan.put.structure.formats.DefaultDotBracket
sequence() - Method in class pl.poznan.put.structure.formats.DefaultDotBracketFromPdb
sequence() - Method in interface pl.poznan.put.structure.formats.DotBracket
sequence() - Method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracket
sequence() - Method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracketFromPdb
sequence() - Method in class pl.poznan.put.structure.formats.ImmutableMultiLineDotBracket
sequence() - Method in class pl.poznan.put.structure.formats.MultiLineDotBracket
sequence() - Method in class pl.poznan.put.structure.ImmutableDotBracketSymbol
sequence(boolean) - Method in interface pl.poznan.put.structure.formats.DotBracket: Creates a string representation of nucleotide sequence, where strands may be separated with ampersand & or not.
sequence(char) - Method in class pl.poznan.put.structure.ImmutableDotBracketSymbol.Builder: Initializes the value for the sequence attribute.
sequence(String) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracket.Builder: Initializes the value for the sequence attribute.
sequence(String) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracketFromPdb.Builder: Initializes the value for the sequence attribute.
sequence(String) - Method in class pl.poznan.put.structure.formats.ImmutableMultiLineDotBracket.Builder: Initializes the value for the sequence attribute.
sequenceRY() - Method in interface pl.poznan.put.structure.formats.Strand
serialNumber() - Method in class pl.poznan.put.pdb.ImmutablePdbAtomLine
serialNumber() - Method in class pl.poznan.put.pdb.PdbAtomLine
serialNumber(int) - Method in class pl.poznan.put.pdb.ImmutablePdbAtomLine.Builder: Initializes the value for the serialNumber attribute.
SERINE - Enum constant in enum pl.poznan.put.protein.AminoAcid
SG - Enum constant in enum pl.poznan.put.atom.AtomName
SG1 - Enum constant in enum pl.poznan.put.atom.AtomName
SG2 - Enum constant in enum pl.poznan.put.atom.AtomName
shear() - Method in class pl.poznan.put.structure.ImmutableQuantifiedBasePair
shear() - Method in class pl.poznan.put.structure.QuantifiedBasePair
shear(double) - Method in class pl.poznan.put.structure.ImmutableQuantifiedBasePair.Builder: Initializes the value for the shear attribute.
shifted(int, int) - Method in class pl.poznan.put.pdb.analysis.PdbCompactFragment: Creates a new instance from this one which starts from a shifted position and has a limited size.
shortDisplayName() - Method in interface pl.poznan.put.interfaces.DisplayableExportable
shortDisplayName() - Method in enum pl.poznan.put.protein.AminoAcidTorsionAngle
shortDisplayName() - Method in enum pl.poznan.put.rna.NucleotideTorsionAngle
shortDisplayName() - Method in class pl.poznan.put.rna.PseudophasePuckerType
shortDisplayName() - Method in interface pl.poznan.put.torsion.AtomBasedTorsionAngleType
shortDisplayName() - Method in class pl.poznan.put.torsion.AverageTorsionAngleType
shortDisplayName() - Method in class pl.poznan.put.torsion.ImmutableAtomBasedTorsionAngleType
shortDisplayName() - Method in class pl.poznan.put.torsion.ImmutableAverageTorsionAngleType
shortDisplayName() - Method in class pl.poznan.put.torsion.TorsionAngleDelta
shortDisplayName() - Method in class pl.poznan.put.torsion.TorsionAngleValue
shortDisplayName(String) - Method in class pl.poznan.put.torsion.ImmutableAtomBasedTorsionAngleType.Builder: Initializes the value for the shortDisplayName attribute.
shortName() - Method in enum pl.poznan.put.notation.LeontisWesthof: Generates a three letter representation.
sidechain() - Method in enum pl.poznan.put.protein.AminoAcid
Sidechain - Interface in pl.poznan.put.protein: A sidechain in a protein.
SIMILAR - Enum constant in enum pl.poznan.put.torsion.range.RangeDifference
simplified() - Method in class pl.poznan.put.structure.pseudoknots.ConflictGraph: Creates a simplified copy of this instance.
SingleTypedResidueCollection - Interface in pl.poznan.put.pdb.analysis: A collection of residues with a common molecule type (RNA or protein).
size() - Method in class pl.poznan.put.structure.formats.BpSeq
size() - Method in class pl.poznan.put.structure.pseudoknots.dp.ConflictClique
skewness() - Method in class pl.poznan.put.circular.samples.AngleSample
skewness() - Method in class pl.poznan.put.circular.samples.ImmutableAngleSample
SOLID_STATE_NMR - Enum constant in enum pl.poznan.put.pdb.ExperimentalTechnique
SOLUTION_NMR - Enum constant in enum pl.poznan.put.pdb.ExperimentalTechnique
SOLUTION_SCATTERING - Enum constant in enum pl.poznan.put.pdb.ExperimentalTechnique
sortedData() - Method in class pl.poznan.put.circular.samples.AngleSample
sortedData() - Method in class pl.poznan.put.circular.samples.ImmutableAngleSample
sortedEndpoints() - Method in class pl.poznan.put.structure.pseudoknots.dp.ConflictClique
sortedEndpoints() - Method in class pl.poznan.put.structure.pseudoknots.dp.ImmutableConflictClique
STACKING - Static variable in class pl.poznan.put.rna.InteractionType: A stacking interaction.
stackingTopology() - Method in class pl.poznan.put.structure.AnalyzedBasePair
stackingTopology() - Method in interface pl.poznan.put.structure.ClassifiedBasePair
stackingTopology() - Method in class pl.poznan.put.structure.ImmutableAnalyzedBasePair
stackingTopology() - Method in class pl.poznan.put.structure.ImmutableQuantifiedBasePair
stackingTopology() - Method in class pl.poznan.put.structure.QuantifiedBasePair
stackingTopology(StackingTopology) - Method in class pl.poznan.put.structure.ImmutableAnalyzedBasePair.Builder: Initializes the value for the stackingTopology attribute.
stackingTopology(StackingTopology) - Method in class pl.poznan.put.structure.ImmutableQuantifiedBasePair.Builder: Initializes the value for the stackingTopology attribute.
StackingTopology - Enum in pl.poznan.put.notation: Stacking topologies are described in: New Metrics for Comparing and Assessing Discrepancies between RNA 3D Structures and Models.
stagger() - Method in class pl.poznan.put.structure.ImmutableQuantifiedBasePair
stagger() - Method in class pl.poznan.put.structure.QuantifiedBasePair
stagger(double) - Method in class pl.poznan.put.structure.ImmutableQuantifiedBasePair.Builder: Initializes the value for the stagger attribute.
standardError() - Method in interface pl.poznan.put.utility.ExecHelper.ExecutionResult
standardError() - Method in class pl.poznan.put.utility.ImmutableExecutionResult
standardError(String) - Method in class pl.poznan.put.utility.ImmutableExecutionResult.Builder: Initializes the value for the standardError attribute.
standardOutput() - Method in interface pl.poznan.put.utility.ExecHelper.ExecutionResult
standardOutput() - Method in class pl.poznan.put.utility.ImmutableExecutionResult
standardOutput(String) - Method in class pl.poznan.put.utility.ImmutableExecutionResult.Builder: Initializes the value for the standardOutput attribute.
standardReferenceFrame() - Method in interface pl.poznan.put.rna.Nucleobase
standardReferenceFrameString() - Method in interface pl.poznan.put.rna.Nucleobase
standardResidueName() - Method in class pl.poznan.put.pdb.analysis.DefaultPdbResidue
standardResidueName() - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbResidue
standardResidueName() - Method in interface pl.poznan.put.pdb.analysis.PdbResidue
standardResidueName() - Method in class pl.poznan.put.pdb.ImmutablePdbModresLine
standardResidueName() - Method in class pl.poznan.put.pdb.PdbModresLine
standardResidueName(String) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbResidue.Builder: Initializes the value for the standardResidueName attribute.
standardResidueName(String) - Method in class pl.poznan.put.pdb.ImmutablePdbModresLine.Builder: Initializes the value for the standardResidueName attribute.
state() - Method in class pl.poznan.put.torsion.ImmutableTorsionAngleDelta
state() - Method in class pl.poznan.put.torsion.TorsionAngleDelta
state(TorsionAngleDelta.State) - Method in class pl.poznan.put.torsion.ImmutableTorsionAngleDelta.Builder: Initializes the value for the state attribute.
stericity() - Method in enum pl.poznan.put.notation.LeontisWesthof
Stericity - Enum in pl.poznan.put.notation: A base pair stericity, either cis or trans.
Strand - Interface in pl.poznan.put.structure.formats: A continuous segment of residues.
strandCount() - Method in class pl.poznan.put.structure.formats.Ct
strands() - Method in class pl.poznan.put.structure.formats.AbstractCombinedStrand
strands() - Method in class pl.poznan.put.structure.formats.CombinedStrand
strands() - Method in class pl.poznan.put.structure.formats.CombinedStrandFromPdb
strands() - Method in class pl.poznan.put.structure.formats.DefaultDotBracket
strands() - Method in class pl.poznan.put.structure.formats.DefaultDotBracketFromPdb
strands() - Method in interface pl.poznan.put.structure.formats.DotBracket
strands() - Method in class pl.poznan.put.structure.formats.ImmutableCombinedStrand
strands() - Method in class pl.poznan.put.structure.formats.ImmutableCombinedStrandFromPdb
strands() - Method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracket
strands() - Method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracketFromPdb
strands(Iterable<? extends Strand>) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracket.Builder: Sets or replaces all elements for strands list.
strands(Iterable<? extends Strand>) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracketFromPdb.Builder: Sets or replaces all elements for strands list.
StrandView - Class in pl.poznan.put.structure.formats: A strand which is defined as a fragment of a dot-bracket structure.
StrandView() - Constructor for class pl.poznan.put.structure.formats.StrandView
stretch() - Method in class pl.poznan.put.structure.ImmutableQuantifiedBasePair
stretch() - Method in class pl.poznan.put.structure.QuantifiedBasePair
stretch(double) - Method in class pl.poznan.put.structure.ImmutableQuantifiedBasePair.Builder: Initializes the value for the stretch attribute.
structure() - Method in class pl.poznan.put.structure.DotBracketSymbol
structure() - Method in class pl.poznan.put.structure.formats.DefaultDotBracket
structure() - Method in class pl.poznan.put.structure.formats.DefaultDotBracketFromPdb
structure() - Method in interface pl.poznan.put.structure.formats.DotBracket
structure() - Method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracket
structure() - Method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracketFromPdb
structure() - Method in class pl.poznan.put.structure.ImmutableDotBracketSymbol
structure(boolean) - Method in interface pl.poznan.put.structure.formats.DotBracket: Creates a string of dots and brackets which represents base pairing, where strands may be separated with ampersand & or not.
structure(char) - Method in class pl.poznan.put.structure.ImmutableDotBracketSymbol.Builder: Initializes the value for the structure attribute.
structure(String) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracket.Builder: Initializes the value for the structure attribute.
structure(String) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracketFromPdb.Builder: Initializes the value for the structure attribute.
subtract(Angle) - Method in class pl.poznan.put.circular.Angle: Subtracts another angular value from this.
subtractAsVectors(double, double) - Static method in class pl.poznan.put.circular.Angle: Calculates angles' difference using formula acos(dot(left, right)).
subtractByAbsolutes(double, double) - Static method in class pl.poznan.put.circular.Angle: Calculates angles' difference using formula: pi - |pi - |left - right||.
subtractByMinimum(double, double) - Static method in class pl.poznan.put.circular.Angle: Calculates angles' difference using formula min(|left - right|, 360 - |left - right|).
subtractTorsionAngleValues(MasterTorsionAngleType, Angle, Angle) - Static method in class pl.poznan.put.torsion.TorsionAngleDelta: Subtracts torsion angle values and creates an instance of this class.
SUGAR - Enum constant in enum pl.poznan.put.notation.NucleobaseEdge
SUGAR_SUGAR - Static variable in class pl.poznan.put.rna.InteractionType: A ribose-ribose interaction.
suggestName() - Method in interface pl.poznan.put.interfaces.Exportable: Generates a useful file name for this kind of exported data.
SVG - Enum constant in enum pl.poznan.put.utility.svg.Format
SVGHelper - Class in pl.poznan.put.utility.svg: A collection of methods to work with SVG images.
svgNamespaceContext() - Static method in class pl.poznan.put.utility.svg.SVGHelper
symbol(PdbResidueIdentifier) - Method in class pl.poznan.put.structure.formats.CombinedStrandFromPdb
symbol(PdbResidueIdentifier) - Method in class pl.poznan.put.structure.formats.DefaultDotBracketFromPdb
symbol(PdbResidueIdentifier) - Method in interface pl.poznan.put.structure.formats.DotBracketFromPdb: Maps the given residue identifier to its corresponding dot-bracket symbol.
symbols() - Method in class pl.poznan.put.structure.formats.AbstractCombinedStrand
symbols() - Method in class pl.poznan.put.structure.formats.DefaultDotBracketFromPdb
symbols() - Method in class pl.poznan.put.structure.formats.CombinedStrand
symbols() - Method in class pl.poznan.put.structure.formats.CombinedStrandFromPdb
symbols() - Method in class pl.poznan.put.structure.formats.DefaultStrand
symbols() - Method in interface pl.poznan.put.structure.formats.DotBracket
symbols() - Method in class pl.poznan.put.structure.formats.ImmutableCombinedStrand
symbols() - Method in class pl.poznan.put.structure.formats.ImmutableCombinedStrandFromPdb
symbols() - Method in class pl.poznan.put.structure.formats.ImmutableDefaultStrand
symbols() - Method in class pl.poznan.put.structure.formats.ImmutableStrandView
symbols() - Method in class pl.poznan.put.structure.formats.ImmutableTerminalMissing
symbols() - Method in class pl.poznan.put.structure.formats.StrandView
symbols() - Method in class pl.poznan.put.structure.formats.TerminalMissing
symbols(Iterable<? extends DotBracketSymbol>) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultStrand.Builder: Sets or replaces all elements for symbols list.
symbols(Iterable<? extends DotBracketSymbol>) - Method in class pl.poznan.put.structure.formats.ImmutableTerminalMissing.Builder: Sets or replaces all elements for symbols list.
symbolToResidue() - Method in class pl.poznan.put.structure.formats.CombinedStrandFromPdb
symbolToResidue() - Method in class pl.poznan.put.structure.formats.DefaultDotBracketFromPdb
symbolToResidue() - Method in class pl.poznan.put.structure.formats.ImmutableCombinedStrandFromPdb
symbolToResidue() - Method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracketFromPdb
SYN - Enum constant in enum pl.poznan.put.rna.ChiRange
SYN_CIS - Enum constant in enum pl.poznan.put.torsion.range.TorsionRange
SYNCLINAL_GAUCHE_MINUS - Enum constant in enum pl.poznan.put.torsion.range.TorsionRange
SYNCLINAL_GAUCHE_PLUS - Enum constant in enum pl.poznan.put.torsion.range.TorsionRange

T

Tabular - Interface in pl.poznan.put.interfaces: A set of methods to be implemented by result objects with tabular form of data.
TabularExporter - Class in pl.poznan.put.utility: A collections of methods for easy export of tabular data to CSV files.
TARGET_INVALID - Enum constant in enum pl.poznan.put.torsion.TorsionAngleDelta.State
TAU - Static variable in class pl.poznan.put.constant.Unicode
temperatureFactor() - Method in class pl.poznan.put.pdb.ImmutablePdbAtomLine
temperatureFactor() - Method in class pl.poznan.put.pdb.PdbAtomLine
temperatureFactor(double) - Method in class pl.poznan.put.pdb.ImmutablePdbAtomLine.Builder: Initializes the value for the temperatureFactor attribute.
TerminalMissing - Class in pl.poznan.put.structure.formats: A colecction of missing dot-bracket symbols at 5' or 3' end.
TerminalMissing() - Constructor for class pl.poznan.put.structure.formats.TerminalMissing
THEORETICAL_MODEL - Enum constant in enum pl.poznan.put.pdb.ExperimentalTechnique
THETA - Enum constant in enum pl.poznan.put.rna.NucleotideTorsionAngle
THETA - Static variable in class pl.poznan.put.constant.Unicode
THETA_PRIM - Enum constant in enum pl.poznan.put.rna.NucleotideTorsionAngle
THETA_PRIM - Static variable in class pl.poznan.put.constant.Unicode
THH - Enum constant in enum pl.poznan.put.notation.LeontisWesthof
threeDecimalDigits() - Static method in class pl.poznan.put.utility.NumberFormatUtils
THREONINE - Enum constant in enum pl.poznan.put.protein.AminoAcid
THS - Enum constant in enum pl.poznan.put.notation.LeontisWesthof
THW - Enum constant in enum pl.poznan.put.notation.LeontisWesthof
THYMINE - Enum constant in enum pl.poznan.put.rna.Nucleotide
title() - Method in class pl.poznan.put.pdb.analysis.DefaultCifModel
title() - Method in class pl.poznan.put.pdb.analysis.DefaultPdbModel
title() - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel
title() - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbModel
title() - Method in interface pl.poznan.put.pdb.analysis.PdbModel
title() - Method in class pl.poznan.put.pdb.ImmutablePdbTitleLine
title() - Method in class pl.poznan.put.pdb.PdbTitleLine
title(String) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel.Builder: Initializes the value for the title attribute.
title(String) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbModel.Builder: Initializes the value for the title attribute.
title(String) - Method in class pl.poznan.put.pdb.ImmutablePdbTitleLine.Builder: Initializes the value for the title attribute.
toCif() - Method in interface pl.poznan.put.pdb.analysis.PdbResidue
toCif() - Method in interface pl.poznan.put.pdb.analysis.ResidueCollection: Generates a list of ATOM lines in mmCIF format from this instance.
toCif() - Method in class pl.poznan.put.pdb.PdbAtomLine: Creates an ATOM line in mmCIF format.
toHexString(Color) - Static method in class pl.poznan.put.constant.Colors: Converts a Color to hex String.
toNamedResidueIdentifer() - Method in interface pl.poznan.put.external.dssr.Nucleotide
toNumber() - Method in enum pl.poznan.put.notation.LeontisWesthof: Generates a value in range 1-12 (or Integer.MAX_VALUE) which corresponds to this instance.
toOneLetter() - Method in enum pl.poznan.put.structure.HelixOrigin
toPdb() - Method in interface pl.poznan.put.pdb.analysis.PdbResidue
toPdb() - Method in interface pl.poznan.put.pdb.analysis.ResidueCollection: Generates a list of ATOM lines in PDB format from this instance.
toPdb() - Method in class pl.poznan.put.pdb.PdbAtomLine: Creates an ATOM line in PDB format.
toPdb() - Method in class pl.poznan.put.pdb.PdbExpdtaLine
toPdb() - Method in class pl.poznan.put.pdb.PdbHeaderLine
toPdb() - Method in class pl.poznan.put.pdb.PdbModresLine
toPdb() - Method in class pl.poznan.put.pdb.PdbRemark2Line
toPdb() - Method in class pl.poznan.put.pdb.PdbRemark465Line
toPdb() - Method in class pl.poznan.put.pdb.PdbTitleLine
toResidue() - Method in class pl.poznan.put.pdb.PdbRemark465Line: Creates an instance of DefaultPdbResidue marked as missing and without atoms.
toResidueIdentifier() - Method in class pl.poznan.put.pdb.PdbNamedResidueIdentifier
torsionAngle(Vector3D, Vector3D, Vector3D) - Static method in class pl.poznan.put.circular.Angle: Calculates torsion angle given three vectors.
torsionAngle(Vector3D, Vector3D, Vector3D, Vector3D) - Static method in class pl.poznan.put.circular.Angle: Calculates torsion angle given four points.
torsionAngleByAcos(Vector3D, Vector3D, Vector3D, Vector3D) - Static method in class pl.poznan.put.circular.Angle: Calculates torsion angle given four points.
TorsionAngleDelta - Class in pl.poznan.put.torsion: A result of subtracting of two torsion angles.
TorsionAngleDelta() - Constructor for class pl.poznan.put.torsion.TorsionAngleDelta
TorsionAngleDelta.State - Enum in pl.poznan.put.torsion: A state of comparison of two torsion angle values.
torsionAngles(PdbResidueIdentifier) - Method in class pl.poznan.put.pdb.analysis.PdbCompactFragment: Computes torsion angles' values for a given residue.
TorsionAngleType - Interface in pl.poznan.put.torsion: A torsion angle.
torsionAngleTypes() - Method in interface pl.poznan.put.pdb.analysis.ResidueInformationProvider
torsionAngleTypes() - Method in enum pl.poznan.put.protein.AminoAcid
torsionAngleTypes() - Method in enum pl.poznan.put.rna.Nucleotide
torsionAngleTypes() - Method in interface pl.poznan.put.rna.Purine
torsionAngleTypes() - Method in interface pl.poznan.put.rna.Pyrimidine
TorsionAngleValue - Class in pl.poznan.put.torsion: A torsion angle with its value calculated.
TorsionAngleValue() - Constructor for class pl.poznan.put.torsion.TorsionAngleValue
TorsionRange - Enum in pl.poznan.put.torsion.range: A default torsion angle range as defined in Saenger's "Principles...".
toString() - Method in class pl.poznan.put.atom.ImmutableBondLength: Prints the immutable value BondLength with attribute values.
toString() - Method in class pl.poznan.put.circular.Angle
toString() - Method in class pl.poznan.put.circular.ImmutableHistogram: Prints the immutable value Histogram with attribute values.
toString() - Method in class pl.poznan.put.circular.samples.AngleSample
toString() - Method in class pl.poznan.put.circular.samples.ImmutableTrigonometricMoment: Prints the immutable value TrigonometricMoment with attribute values.
toString() - Method in class pl.poznan.put.external.dssr.ImmutableDssrJson: Prints the immutable value DssrJson with attribute values.
toString() - Method in class pl.poznan.put.external.dssr.ImmutableNucleotide: Prints the immutable value Nucleotide with attribute values.
toString() - Method in class pl.poznan.put.external.dssr.ImmutablePair: Prints the immutable value Pair with attribute values.
toString() - Method in enum pl.poznan.put.notation.LeontisWesthof
toString() - Method in enum pl.poznan.put.notation.Saenger
toString() - Method in class pl.poznan.put.pdb.analysis.DefaultPdbResidue
toString() - Method in class pl.poznan.put.pdb.analysis.ImmutableCifContainer: Prints the immutable value CifContainer with attribute values.
toString() - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel: Prints the immutable value DefaultCifModel with attribute values.
toString() - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbModel: Prints the immutable value DefaultPdbModel with attribute values.
toString() - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultResidueCollection: Prints the immutable value DefaultResidueCollection with attribute values.
toString() - Method in class pl.poznan.put.pdb.analysis.ImmutablePdbChain: Prints the immutable value PdbChain with attribute values.
toString() - Method in class pl.poznan.put.pdb.analysis.ImmutableResidueTorsionAngles: Prints the immutable value ResidueTorsionAngles with attribute values.
toString() - Method in class pl.poznan.put.pdb.analysis.PdbCompactFragment
toString() - Method in class pl.poznan.put.pdb.PdbAtomLine
toString() - Method in class pl.poznan.put.pdb.PdbExpdtaLine
toString() - Method in class pl.poznan.put.pdb.PdbHeaderLine
toString() - Method in class pl.poznan.put.pdb.PdbModresLine
toString() - Method in class pl.poznan.put.pdb.PdbNamedResidueIdentifier
toString() - Method in class pl.poznan.put.pdb.PdbRemark2Line
toString() - Method in class pl.poznan.put.pdb.PdbRemark465Line
toString() - Method in class pl.poznan.put.pdb.PdbResidueIdentifier
toString() - Method in class pl.poznan.put.pdb.PdbTitleLine
toString() - Method in class pl.poznan.put.protein.ImmutableBackbone: Prints the immutable value Backbone.
toString() - Method in class pl.poznan.put.rna.ImmutablePhosphate: Prints the immutable value Phosphate.
toString() - Method in class pl.poznan.put.rna.ImmutablePseudophasePuckerType: Prints the immutable value PseudophasePuckerType.
toString() - Method in class pl.poznan.put.rna.ImmutableRibose: Prints the immutable value Ribose.
toString() - Method in class pl.poznan.put.rna.InteractionType
toString() - Method in class pl.poznan.put.structure.BasePair
toString() - Method in class pl.poznan.put.structure.DotBracketSymbol
toString() - Method in class pl.poznan.put.structure.formats.BpSeq.Entry
toString() - Method in class pl.poznan.put.structure.formats.BpSeq
toString() - Method in class pl.poznan.put.structure.formats.CombinedStrand
toString() - Method in class pl.poznan.put.structure.formats.Ct.ExtendedEntry
toString() - Method in class pl.poznan.put.structure.formats.Ct
toString() - Method in class pl.poznan.put.structure.formats.DefaultDotBracket
toString() - Method in class pl.poznan.put.structure.formats.DefaultStrand
toString() - Method in class pl.poznan.put.structure.formats.ImmutableCombinedStrandFromPdb: Prints the immutable value CombinedStrandFromPdb with attribute values.
toString() - Method in class pl.poznan.put.structure.formats.ImmutableDefaultConverter: Prints the immutable value DefaultConverter with attribute values.
toString() - Method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracketFromPdb: Prints the immutable value DefaultDotBracketFromPdb with attribute values.
toString() - Method in class pl.poznan.put.structure.formats.ImmutableTerminalMissing: Prints the immutable value TerminalMissing with attribute values.
toString() - Method in class pl.poznan.put.structure.formats.MultiLineDotBracket
toString() - Method in class pl.poznan.put.structure.formats.StrandView
toString() - Method in enum pl.poznan.put.structure.HelixOrigin
toString() - Method in class pl.poznan.put.structure.ImmutableAnalyzedBasePair: Prints the immutable value AnalyzedBasePair with attribute values.
toString() - Method in class pl.poznan.put.structure.ImmutableQuantifiedBasePair: Prints the immutable value QuantifiedBasePair with attribute values.
toString() - Method in class pl.poznan.put.structure.pseudoknots.dp.ImmutableConflictClique: Prints the immutable value ConflictClique with attribute values.
toString() - Method in class pl.poznan.put.structure.pseudoknots.dp.ImmutableDynamicProgrammingAll: Prints the immutable value DynamicProgrammingAll with attribute values.
toString() - Method in class pl.poznan.put.structure.pseudoknots.elimination.ImmutableMaxConflicts: Prints the immutable value MaxConflicts.
toString() - Method in class pl.poznan.put.structure.pseudoknots.elimination.ImmutableMinGain: Prints the immutable value MinGain.
toString() - Method in class pl.poznan.put.structure.pseudoknots.ImmutableConflictGraph: Prints the immutable value ConflictGraph with attribute values.
toString() - Method in class pl.poznan.put.structure.pseudoknots.Region
toString() - Method in class pl.poznan.put.torsion.ImmutableAtomBasedTorsionAngleType: Prints the immutable value AtomBasedTorsionAngleType with attribute values.
toString() - Method in class pl.poznan.put.torsion.ImmutableAtomPair: Prints the immutable value AtomPair with attribute values.
toString() - Method in class pl.poznan.put.torsion.ImmutableAverageTorsionAngleType: Prints the immutable value AverageTorsionAngleType with attribute values.
toString() - Method in class pl.poznan.put.torsion.ImmutableTorsionAngleDelta: Prints the immutable value TorsionAngleDelta with attribute values.
toString() - Method in class pl.poznan.put.torsion.ImmutableTorsionAngleValue: Prints the immutable value TorsionAngleValue with attribute values.
toString() - Method in class pl.poznan.put.types.ImmutableDistanceMatrix: Prints the immutable value DistanceMatrix with attribute values.
toString() - Method in class pl.poznan.put.types.ImmutableQuadruple: Prints the immutable value Quadruple with attribute values.
toString() - Method in class pl.poznan.put.utility.ImmutableExecHelper: Prints the immutable value ExecHelper with attribute values.
toString() - Method in class pl.poznan.put.utility.ImmutableExecutionResult: Prints the immutable value ExecutionResult with attribute values.
toString(boolean) - Method in class pl.poznan.put.torsion.TorsionAngleDelta
toStringWithStrands() - Method in interface pl.poznan.put.structure.formats.DotBracket
toSvgString(Color) - Static method in class pl.poznan.put.constant.Colors: Converts a Color to SVG String.
toVector3D() - Method in class pl.poznan.put.pdb.PdbAtomLine
TRANS - Enum constant in enum pl.poznan.put.notation.Stericity
transform(double) - Method in enum pl.poznan.put.circular.enums.AngleTransformation: Transforms an angle value in radians to represent it on circle.
TrigonometricMoment - Class in pl.poznan.put.circular.samples: A quantitative measure of a trigonometric sample shape.
TrigonometricMoment() - Constructor for class pl.poznan.put.circular.samples.TrigonometricMoment
TRUE - Enum constant in enum pl.poznan.put.structure.HelixOrigin
TRYPTOPHAN - Enum constant in enum pl.poznan.put.protein.AminoAcid
TSH - Enum constant in enum pl.poznan.put.notation.LeontisWesthof
TSS - Enum constant in enum pl.poznan.put.notation.LeontisWesthof
TSW - Enum constant in enum pl.poznan.put.notation.LeontisWesthof
TWH - Enum constant in enum pl.poznan.put.notation.LeontisWesthof
TWIST_1_2 - Enum constant in enum pl.poznan.put.rna.Pseudorotation
TWIST_1_O - Enum constant in enum pl.poznan.put.rna.Pseudorotation
TWIST_2_1 - Enum constant in enum pl.poznan.put.rna.Pseudorotation
TWIST_2_3 - Enum constant in enum pl.poznan.put.rna.Pseudorotation
TWIST_3_2 - Enum constant in enum pl.poznan.put.rna.Pseudorotation
TWIST_3_4 - Enum constant in enum pl.poznan.put.rna.Pseudorotation
TWIST_4_3 - Enum constant in enum pl.poznan.put.rna.Pseudorotation
TWIST_4_O - Enum constant in enum pl.poznan.put.rna.Pseudorotation
TWIST_O_1 - Enum constant in enum pl.poznan.put.rna.Pseudorotation
TWIST_O_4 - Enum constant in enum pl.poznan.put.rna.Pseudorotation
TWS - Enum constant in enum pl.poznan.put.notation.LeontisWesthof
TWW - Enum constant in enum pl.poznan.put.notation.LeontisWesthof
TYROSINE - Enum constant in enum pl.poznan.put.protein.AminoAcid

U

um1() - Method in class pl.poznan.put.circular.samples.AngleSample
um1() - Method in class pl.poznan.put.circular.samples.ImmutableAngleSample
um2() - Method in class pl.poznan.put.circular.samples.AngleSample
um2() - Method in class pl.poznan.put.circular.samples.ImmutableAngleSample
Unicode - Class in pl.poznan.put.constant: A set of useful constants in structural bioinformatics e.g. greek letters, Angstrom, etc.
UNKNOWN - Enum constant in enum pl.poznan.put.atom.AtomName
UNKNOWN - Enum constant in enum pl.poznan.put.notation.BPh
UNKNOWN - Enum constant in enum pl.poznan.put.notation.BR
UNKNOWN - Enum constant in enum pl.poznan.put.notation.LeontisWesthof
UNKNOWN - Enum constant in enum pl.poznan.put.notation.NucleobaseEdge
UNKNOWN - Enum constant in enum pl.poznan.put.notation.Saenger
UNKNOWN - Enum constant in enum pl.poznan.put.notation.StackingTopology
UNKNOWN - Enum constant in enum pl.poznan.put.notation.Stericity
UNKNOWN - Enum constant in enum pl.poznan.put.pdb.analysis.MoleculeType
UNKNOWN - Enum constant in enum pl.poznan.put.pdb.ExperimentalTechnique
UNKNOWN - Enum constant in enum pl.poznan.put.rna.NucleotideComponentType
UNKNOWN - Enum constant in enum pl.poznan.put.structure.HelixOrigin
UPWARD - Enum constant in enum pl.poznan.put.notation.StackingTopology
URACIL - Enum constant in enum pl.poznan.put.rna.Nucleotide

V

V - Enum constant in enum pl.poznan.put.notation.Saenger
validate() - Method in class pl.poznan.put.structure.formats.BpSeq
validate() - Method in class pl.poznan.put.structure.formats.Ct
validate() - Method in class pl.poznan.put.structure.formats.DefaultDotBracket
validate() - Method in class pl.poznan.put.structure.formats.DefaultDotBracketFromPdb
VALINE - Enum constant in enum pl.poznan.put.protein.AminoAcid
value() - Method in class pl.poznan.put.torsion.ImmutableTorsionAngleValue
value() - Method in class pl.poznan.put.torsion.TorsionAngleValue
value(Angle) - Method in class pl.poznan.put.torsion.ImmutableTorsionAngleValue.Builder: Initializes the value for the value attribute.
value(MasterTorsionAngleType) - Method in class pl.poznan.put.pdb.analysis.ResidueTorsionAngles: Finds the value of a master torsion angle type in this collection.
value(TorsionAngleType) - Method in class pl.poznan.put.pdb.analysis.ResidueTorsionAngles: Finds the value of specific torsion angle type in this collection.
valueOf(String) - Static method in enum pl.poznan.put.atom.AtomName: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum pl.poznan.put.atom.AtomType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum pl.poznan.put.circular.enums.AngleTransformation: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum pl.poznan.put.notation.BPh: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum pl.poznan.put.notation.BR: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum pl.poznan.put.notation.LeontisWesthof: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum pl.poznan.put.notation.NucleobaseEdge: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum pl.poznan.put.notation.Saenger: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum pl.poznan.put.notation.StackingTopology: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum pl.poznan.put.notation.Stericity: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum pl.poznan.put.pdb.analysis.MoleculeType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum pl.poznan.put.pdb.ExperimentalTechnique: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum pl.poznan.put.protein.AminoAcid: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum pl.poznan.put.protein.AminoAcidTorsionAngle: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum pl.poznan.put.rna.Chi: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum pl.poznan.put.rna.ChiRange: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum pl.poznan.put.rna.Nucleotide: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum pl.poznan.put.rna.NucleotideComponentType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum pl.poznan.put.rna.NucleotideTorsionAngle: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum pl.poznan.put.rna.Pseudorotation: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum pl.poznan.put.structure.HelixOrigin: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum pl.poznan.put.torsion.range.RangeDifference: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum pl.poznan.put.torsion.range.TorsionRange: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum pl.poznan.put.torsion.TorsionAngleDelta.State: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum pl.poznan.put.utility.svg.Format: Returns the enum constant of this type with the specified name.
values() - Static method in enum pl.poznan.put.atom.AtomName: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum pl.poznan.put.atom.AtomType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum pl.poznan.put.circular.enums.AngleTransformation: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum pl.poznan.put.notation.BPh: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum pl.poznan.put.notation.BR: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum pl.poznan.put.notation.LeontisWesthof: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum pl.poznan.put.notation.NucleobaseEdge: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum pl.poznan.put.notation.Saenger: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum pl.poznan.put.notation.StackingTopology: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum pl.poznan.put.notation.Stericity: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Method in class pl.poznan.put.pdb.analysis.ImmutableResidueTorsionAngles
values() - Static method in enum pl.poznan.put.pdb.analysis.MoleculeType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Method in class pl.poznan.put.pdb.analysis.ResidueTorsionAngles
values() - Static method in enum pl.poznan.put.pdb.ExperimentalTechnique: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum pl.poznan.put.protein.AminoAcid: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum pl.poznan.put.protein.AminoAcidTorsionAngle: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum pl.poznan.put.rna.Chi: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum pl.poznan.put.rna.ChiRange: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum pl.poznan.put.rna.Nucleotide: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum pl.poznan.put.rna.NucleotideComponentType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum pl.poznan.put.rna.NucleotideTorsionAngle: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum pl.poznan.put.rna.Pseudorotation: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum pl.poznan.put.structure.HelixOrigin: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum pl.poznan.put.torsion.range.RangeDifference: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum pl.poznan.put.torsion.range.TorsionRange: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum pl.poznan.put.torsion.TorsionAngleDelta.State: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum pl.poznan.put.utility.svg.Format: Returns an array containing the constants of this enum type, in the order they are declared.
values(Iterable<? extends TorsionAngleValue>) - Method in class pl.poznan.put.pdb.analysis.ImmutableResidueTorsionAngles.Builder: Sets or replaces all elements for values list.
VI - Enum constant in enum pl.poznan.put.notation.Saenger
VII - Enum constant in enum pl.poznan.put.notation.Saenger
VIII - Enum constant in enum pl.poznan.put.notation.Saenger
Visualizable - Interface in pl.poznan.put.interfaces: A set of methods allowing to visualize the result.
visualize() - Method in interface pl.poznan.put.interfaces.Visualizable: Generates a visualization in SVG format.
visualize3D() - Method in interface pl.poznan.put.interfaces.Visualizable: Generates a visualization in 3D if possible.

W

WATSON_CRICK - Enum constant in enum pl.poznan.put.notation.NucleobaseEdge
withA(T) - Method in class pl.poznan.put.types.ImmutableQuadruple: Copy the current immutable object by setting a value for the a attribute.
withAfter(int) - Method in class pl.poznan.put.structure.formats.ImmutableExtendedEntry: Copy the current immutable object by setting a value for the after attribute.
withAlternateLocation(String) - Method in class pl.poznan.put.pdb.ImmutablePdbAtomLine: Copy the current immutable object by setting a present value for the optional alternateLocation attribute.
withAlternateLocation(Optional<String>) - Method in class pl.poznan.put.pdb.ImmutablePdbAtomLine: Copy the current immutable object by setting an optional value for the alternateLocation attribute.
withAngleType(MasterTorsionAngleType) - Method in class pl.poznan.put.torsion.ImmutableTorsionAngleDelta: Copy the current immutable object by setting a value for the angleType attribute.
withAngleType(TorsionAngleType) - Method in class pl.poznan.put.torsion.ImmutableTorsionAngleValue: Copy the current immutable object by setting a value for the angleType attribute.
withArguments(Iterable<String>) - Method in class pl.poznan.put.utility.ImmutableExecHelper: Copy the current immutable object with elements that replace the content of arguments.
withArguments(String...) - Method in class pl.poznan.put.utility.ImmutableExecHelper: Copy the current immutable object with elements that replace the content of arguments.
withAtomName(String) - Method in class pl.poznan.put.pdb.ImmutablePdbAtomLine: Copy the current immutable object by setting a value for the atomName attribute.
withAtoms(Iterable<? extends PdbAtomLine>) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel: Copy the current immutable object with elements that replace the content of atoms.
withAtoms(Iterable<? extends PdbAtomLine>) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbModel: Copy the current immutable object with elements that replace the content of atoms.
withAtoms(Iterable<? extends PdbAtomLine>) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbResidue: Copy the current immutable object with elements that replace the content of atoms.
withAtoms(PdbAtomLine...) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel: Copy the current immutable object with elements that replace the content of atoms.
withAtoms(PdbAtomLine...) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbModel: Copy the current immutable object with elements that replace the content of atoms.
withAtoms(PdbAtomLine...) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbResidue: Copy the current immutable object with elements that replace the content of atoms.
withAtoms(Quadruple<AtomName>) - Method in class pl.poznan.put.torsion.ImmutableAtomBasedTorsionAngleType: Copy the current immutable object by setting a value for the atoms attribute.
withAvg(double) - Method in class pl.poznan.put.atom.ImmutableBondLength: Copy the current immutable object by setting a value for the avg attribute.
withB(T) - Method in class pl.poznan.put.types.ImmutableQuadruple: Copy the current immutable object by setting a value for the b attribute.
withBasePair(BasePair) - Method in class pl.poznan.put.structure.ImmutableAnalyzedBasePair: Copy the current immutable object by setting a value for the basePair attribute.
withBasePair(BasePair) - Method in class pl.poznan.put.structure.ImmutableQuantifiedBasePair: Copy the current immutable object by setting a value for the basePair attribute.
withBasePairs(Iterable<? extends QuantifiedBasePair>) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel: Copy the current immutable object with elements that replace the content of basePairs.
withBasePairs(Collection<? extends ClassifiedBasePair>) - Method in class pl.poznan.put.structure.formats.ImmutableMultiLineDotBracket: Copy the current immutable object by setting a value for the basePairs attribute.
withBasePairs(QuantifiedBasePair...) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel: Copy the current immutable object with elements that replace the content of basePairs.
withBefore(int) - Method in class pl.poznan.put.structure.formats.ImmutableExtendedEntry: Copy the current immutable object by setting a value for the before attribute.
withBegin(int) - Method in class pl.poznan.put.structure.formats.ImmutableStrandView: Copy the current immutable object by setting a value for the begin attribute.
withBegin(int) - Method in class pl.poznan.put.structure.pseudoknots.ImmutableRegion: Copy the current immutable object by setting a value for the begin attribute.
withBinWidth(double) - Method in class pl.poznan.put.circular.ImmutableHistogram: Copy the current immutable object by setting a value for the binWidth attribute.
withBph(BPh) - Method in class pl.poznan.put.structure.ImmutableAnalyzedBasePair: Copy the current immutable object by setting a value for the bph attribute.
withBph(BPh) - Method in class pl.poznan.put.structure.ImmutableQuantifiedBasePair: Copy the current immutable object by setting a value for the bph attribute.
withBr(BR) - Method in class pl.poznan.put.structure.ImmutableAnalyzedBasePair: Copy the current immutable object by setting a value for the br attribute.
withBr(BR) - Method in class pl.poznan.put.structure.ImmutableQuantifiedBasePair: Copy the current immutable object by setting a value for the br attribute.
withBuckle(double) - Method in class pl.poznan.put.structure.ImmutableQuantifiedBasePair: Copy the current immutable object by setting a value for the buckle attribute.
withC(T) - Method in class pl.poznan.put.types.ImmutableQuadruple: Copy the current immutable object by setting a value for the c attribute.
withChainIdentifier(String) - Method in class pl.poznan.put.pdb.ImmutablePdbAtomLine: Copy the current immutable object by setting a value for the chainIdentifier attribute.
withChainIdentifier(String) - Method in class pl.poznan.put.pdb.ImmutablePdbModresLine: Copy the current immutable object by setting a value for the chainIdentifier attribute.
withChainIdentifier(String) - Method in class pl.poznan.put.pdb.ImmutablePdbNamedResidueIdentifier: Copy the current immutable object by setting a value for the chainIdentifier attribute.
withChainIdentifier(String) - Method in class pl.poznan.put.pdb.ImmutablePdbRemark465Line: Copy the current immutable object by setting a value for the chainIdentifier attribute.
withChainIdentifier(String) - Method in class pl.poznan.put.pdb.ImmutablePdbResidueIdentifier: Copy the current immutable object by setting a value for the chainIdentifier attribute.
withChainName(String) - Method in class pl.poznan.put.external.dssr.ImmutableNucleotide: Copy the current immutable object by setting a value for the chainName attribute.
withChainTerminatedAfter(Iterable<? extends PdbResidueIdentifier>) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel: Copy the current immutable object with elements that replace the content of chainTerminatedAfter.
withChainTerminatedAfter(Iterable<? extends PdbResidueIdentifier>) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbModel: Copy the current immutable object with elements that replace the content of chainTerminatedAfter.
withChainTerminatedAfter(PdbResidueIdentifier...) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel: Copy the current immutable object with elements that replace the content of chainTerminatedAfter.
withChainTerminatedAfter(PdbResidueIdentifier...) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbModel: Copy the current immutable object with elements that replace the content of chainTerminatedAfter.
withCharge(String) - Method in class pl.poznan.put.pdb.ImmutablePdbAtomLine: Copy the current immutable object by setting a value for the charge attribute.
withCifFile(File) - Method in class pl.poznan.put.pdb.analysis.ImmutableCifContainer: Copy the current immutable object by setting a value for the cifFile attribute.
withClassification(String) - Method in class pl.poznan.put.pdb.ImmutablePdbHeaderLine: Copy the current immutable object by setting a value for the classification attribute.
withCombineStrands(Iterable<? extends DotBracket>) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultStrand: Copy the current immutable object with elements that replace the content of combineStrands.
withCombineStrands(Iterable<? extends DotBracket>) - Method in class pl.poznan.put.structure.formats.ImmutableStrandView: Copy the current immutable object with elements that replace the content of combineStrands.
withCombineStrands(DotBracket...) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultStrand: Copy the current immutable object with elements that replace the content of combineStrands.
withCombineStrands(DotBracket...) - Method in class pl.poznan.put.structure.formats.ImmutableStrandView: Copy the current immutable object with elements that replace the content of combineStrands.
withCommand(String) - Method in class pl.poznan.put.utility.ImmutableExecHelper: Copy the current immutable object by setting a value for the command attribute.
withComment(String) - Method in class pl.poznan.put.pdb.ImmutablePdbModresLine: Copy the current immutable object by setting a value for the comment attribute.
withComment(String) - Method in class pl.poznan.put.structure.formats.ImmutableEntry: Copy the current immutable object by setting a value for the comment attribute.
withComment(String) - Method in class pl.poznan.put.structure.formats.ImmutableExtendedEntry: Copy the current immutable object by setting a value for the comment attribute.
withConsideredAngles(Iterable<? extends MasterTorsionAngleType>) - Method in class pl.poznan.put.torsion.ImmutableAverageTorsionAngleType: Copy the current immutable object with elements that replace the content of consideredAngles.
withConsideredAngles(MasterTorsionAngleType...) - Method in class pl.poznan.put.torsion.ImmutableAverageTorsionAngleType: Copy the current immutable object with elements that replace the content of consideredAngles.
withContinuation(String) - Method in class pl.poznan.put.pdb.ImmutablePdbTitleLine: Copy the current immutable object by setting a value for the continuation attribute.
withD(T) - Method in class pl.poznan.put.types.ImmutableQuadruple: Copy the current immutable object by setting a value for the d attribute.
withData(Collection<Angle>) - Method in class pl.poznan.put.circular.ImmutableHistogram: Copy the current immutable object by setting a value for the data attribute.
withData(Collection<Angle>) - Method in class pl.poznan.put.circular.samples.ImmutableAngleSample: Copy the current immutable object by setting a value for the data attribute.
withDelta(Angle) - Method in class pl.poznan.put.torsion.ImmutableTorsionAngleDelta: Copy the current immutable object by setting a value for the delta attribute.
withDepositionDate(Date) - Method in class pl.poznan.put.pdb.ImmutablePdbHeaderLine: Copy the current immutable object by setting a value for the depositionDate attribute.
withDescription(String) - Method in class pl.poznan.put.rna.ImmutableInteractionType: Copy the current immutable object by setting a value for the description attribute.
withElementSymbol(String) - Method in class pl.poznan.put.pdb.ImmutablePdbAtomLine: Copy the current immutable object by setting a value for the elementSymbol attribute.
withEnd(int) - Method in class pl.poznan.put.structure.formats.ImmutableStrandView: Copy the current immutable object by setting a value for the end attribute.
withEnd(int) - Method in class pl.poznan.put.structure.pseudoknots.ImmutableRegion: Copy the current immutable object by setting a value for the end attribute.
withEntries(Iterable<? extends BpSeq.Entry>) - Method in class pl.poznan.put.structure.formats.ImmutableBpSeq: Copy the current immutable object with elements that replace the content of entries.
withEntries(Iterable<? extends BpSeq.Entry>) - Method in class pl.poznan.put.structure.pseudoknots.ImmutableRegion: Copy the current immutable object with elements that replace the content of entries.
withEntries(Iterable<? extends Ct.ExtendedEntry>) - Method in class pl.poznan.put.structure.formats.ImmutableCt: Copy the current immutable object with elements that replace the content of entries.
withEntries(BpSeq.Entry...) - Method in class pl.poznan.put.structure.formats.ImmutableBpSeq: Copy the current immutable object with elements that replace the content of entries.
withEntries(BpSeq.Entry...) - Method in class pl.poznan.put.structure.pseudoknots.ImmutableRegion: Copy the current immutable object with elements that replace the content of entries.
withEntries(Ct.ExtendedEntry...) - Method in class pl.poznan.put.structure.formats.ImmutableCt: Copy the current immutable object with elements that replace the content of entries.
withEnvironment(Map<String, ? extends String>) - Method in class pl.poznan.put.utility.ImmutableExecHelper: Copy the current immutable object by replacing the environment map with the specified map.
withExitCode(int) - Method in class pl.poznan.put.utility.ImmutableExecutionResult: Copy the current immutable object by setting a value for the exitCode attribute.
withExperimentalData(PdbExpdtaLine) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel: Copy the current immutable object by setting a value for the experimentalData attribute.
withExperimentalData(PdbExpdtaLine) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbModel: Copy the current immutable object by setting a value for the experimentalData attribute.
withExperimentalTechniques(Iterable<? extends ExperimentalTechnique>) - Method in class pl.poznan.put.pdb.ImmutablePdbExpdtaLine: Copy the current immutable object with elements that replace the content of experimentalTechniques.
withExperimentalTechniques(ExperimentalTechnique...) - Method in class pl.poznan.put.pdb.ImmutablePdbExpdtaLine: Copy the current immutable object with elements that replace the content of experimentalTechniques.
withExportName(String) - Method in class pl.poznan.put.torsion.ImmutableAtomBasedTorsionAngleType: Copy the current immutable object by setting a value for the exportName attribute.
withFileChainMap(Map<? extends File, ? extends BidiMap<String, String>>) - Method in class pl.poznan.put.pdb.analysis.ImmutableCifContainer: Copy the current immutable object by replacing the fileChainMap map with the specified map.
withHeader(PdbHeaderLine) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel: Copy the current immutable object by setting a value for the header attribute.
withHeader(PdbHeaderLine) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbModel: Copy the current immutable object by setting a value for the header attribute.
withId(String) - Method in class pl.poznan.put.external.dssr.ImmutableNucleotide: Copy the current immutable object by setting a value for the id attribute.
withIdCode(String) - Method in class pl.poznan.put.pdb.ImmutablePdbHeaderLine: Copy the current immutable object by setting a value for the idCode attribute.
withIdCode(String) - Method in class pl.poznan.put.pdb.ImmutablePdbModresLine: Copy the current immutable object by setting a value for the idCode attribute.
withIdentifier(String) - Method in class pl.poznan.put.pdb.analysis.ImmutablePdbChain: Copy the current immutable object by setting a value for the identifier attribute.
withIdentifier(PdbResidueIdentifier) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbResidue: Copy the current immutable object by setting a value for the identifier attribute.
withIdentifier(PdbResidueIdentifier) - Method in class pl.poznan.put.pdb.analysis.ImmutableResidueTorsionAngles: Copy the current immutable object by setting a value for the identifier attribute.
withIdentifierSet(Iterable<? extends PdbResidueIdentifier>) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracketFromPdb: Copy the current immutable object with elements that replace the content of identifierSet.
withIdentifierSet(PdbResidueIdentifier...) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracketFromPdb: Copy the current immutable object with elements that replace the content of identifierSet.
withIndex(int) - Method in class pl.poznan.put.structure.formats.ImmutableEntry: Copy the current immutable object by setting a value for the index attribute.
withIndex(int) - Method in class pl.poznan.put.structure.formats.ImmutableExtendedEntry: Copy the current immutable object by setting a value for the index attribute.
withIndex(int) - Method in class pl.poznan.put.structure.ImmutableDotBracketSymbol: Copy the current immutable object by setting a value for the index attribute.
withInputStrands(Iterable<? extends Strand>) - Method in class pl.poznan.put.structure.formats.ImmutableCombinedStrand: Copy the current immutable object with elements that replace the content of inputStrands.
withInputStrands(Iterable<? extends Strand>) - Method in class pl.poznan.put.structure.formats.ImmutableCombinedStrandFromPdb: Copy the current immutable object with elements that replace the content of inputStrands.
withInputStrands(Strand...) - Method in class pl.poznan.put.structure.formats.ImmutableCombinedStrand: Copy the current immutable object with elements that replace the content of inputStrands.
withInputStrands(Strand...) - Method in class pl.poznan.put.structure.formats.ImmutableCombinedStrandFromPdb: Copy the current immutable object with elements that replace the content of inputStrands.
withInputSymbolToResidue(Map<? extends DotBracketSymbol, ? extends PdbResidueIdentifier>) - Method in class pl.poznan.put.structure.formats.ImmutableCombinedStrandFromPdb: Copy the current immutable object by replacing the inputSymbolToResidue map with the specified map.
withInsertionCode(String) - Method in class pl.poznan.put.pdb.ImmutablePdbAtomLine: Copy the current immutable object by setting a present value for the optional insertionCode attribute.
withInsertionCode(String) - Method in class pl.poznan.put.pdb.ImmutablePdbModresLine: Copy the current immutable object by setting a present value for the optional insertionCode attribute.
withInsertionCode(String) - Method in class pl.poznan.put.pdb.ImmutablePdbNamedResidueIdentifier: Copy the current immutable object by setting a present value for the optional insertionCode attribute.
withInsertionCode(String) - Method in class pl.poznan.put.pdb.ImmutablePdbRemark465Line: Copy the current immutable object by setting a present value for the optional insertionCode attribute.
withInsertionCode(String) - Method in class pl.poznan.put.pdb.ImmutablePdbResidueIdentifier: Copy the current immutable object by setting a present value for the optional insertionCode attribute.
withInsertionCode(Optional<String>) - Method in class pl.poznan.put.pdb.ImmutablePdbAtomLine: Copy the current immutable object by setting an optional value for the insertionCode attribute.
withInsertionCode(Optional<String>) - Method in class pl.poznan.put.pdb.ImmutablePdbModresLine: Copy the current immutable object by setting an optional value for the insertionCode attribute.
withInsertionCode(Optional<String>) - Method in class pl.poznan.put.pdb.ImmutablePdbNamedResidueIdentifier: Copy the current immutable object by setting an optional value for the insertionCode attribute.
withInsertionCode(Optional<String>) - Method in class pl.poznan.put.pdb.ImmutablePdbRemark465Line: Copy the current immutable object by setting an optional value for the insertionCode attribute.
withInsertionCode(Optional<String>) - Method in class pl.poznan.put.pdb.ImmutablePdbResidueIdentifier: Copy the current immutable object by setting an optional value for the insertionCode attribute.
withInteractionType(InteractionType) - Method in class pl.poznan.put.structure.ImmutableAnalyzedBasePair: Copy the current immutable object by setting a value for the interactionType attribute.
withInteractionType(InteractionType) - Method in class pl.poznan.put.structure.ImmutableQuantifiedBasePair: Copy the current immutable object by setting a value for the interactionType attribute.
withIsPairing(boolean) - Method in class pl.poznan.put.rna.ImmutableInteractionType: Copy the current immutable object by setting a value for the isPairing attribute.
withIsPseudoTorsion(boolean) - Method in class pl.poznan.put.torsion.ImmutableAtomBasedTorsionAngleType: Copy the current immutable object by setting a value for the isPseudoTorsion attribute.
withIsRemoved(boolean) - Method in class pl.poznan.put.structure.pseudoknots.ImmutableRegion: Copy the current immutable object by setting a value for the isRemoved attribute.
withIsRepresented(boolean) - Method in class pl.poznan.put.structure.ImmutableAnalyzedBasePair: Copy the current immutable object by setting a value for the isRepresented attribute.
withIsRepresented(boolean) - Method in class pl.poznan.put.structure.ImmutableQuantifiedBasePair: Copy the current immutable object by setting a value for the isRepresented attribute.
withLeft(PdbNamedResidueIdentifier) - Method in class pl.poznan.put.structure.ImmutableBasePair: Copy the current immutable object by setting a value for the left attribute.
withLeft(NucleotideComponentType) - Method in class pl.poznan.put.rna.ImmutableInteractionType: Copy the current immutable object by setting a value for the left attribute.
withLeftAtom(PdbAtomLine) - Method in class pl.poznan.put.torsion.ImmutableAtomPair: Copy the current immutable object by setting a value for the leftAtom attribute.
withLeontisWesthof(LeontisWesthof) - Method in class pl.poznan.put.structure.ImmutableAnalyzedBasePair: Copy the current immutable object by setting a value for the leontisWesthof attribute.
withLeontisWesthof(LeontisWesthof) - Method in class pl.poznan.put.structure.ImmutableQuantifiedBasePair: Copy the current immutable object by setting a value for the leontisWesthof attribute.
withLw(String) - Method in class pl.poznan.put.external.dssr.ImmutablePair: Copy the current immutable object by setting a value for the lw attribute.
withMatrix(double[]...) - Method in class pl.poznan.put.types.ImmutableDistanceMatrix: Copy the current immutable object with elements that replace the content of matrix.
withMax(double) - Method in class pl.poznan.put.atom.ImmutableBondLength: Copy the current immutable object by setting a value for the max attribute.
withMaxCliqueSize(int) - Method in class pl.poznan.put.structure.pseudoknots.dp.ImmutableDynamicProgrammingAll: Copy the current immutable object by setting a value for the maxCliqueSize attribute.
withMaxSolutions(int) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultConverter: Copy the current immutable object by setting a value for the maxSolutions attribute.
withMeanDirection(Angle) - Method in class pl.poznan.put.circular.samples.ImmutableTrigonometricMoment: Copy the current immutable object by setting a value for the meanDirection attribute.
withMeanResultantLength(double) - Method in class pl.poznan.put.circular.samples.ImmutableTrigonometricMoment: Copy the current immutable object by setting a value for the meanResultantLength attribute.
withMin(double) - Method in class pl.poznan.put.atom.ImmutableBondLength: Copy the current immutable object by setting a value for the min attribute.
withMissingResidues(Iterable<? extends PdbRemark465Line>) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel: Copy the current immutable object with elements that replace the content of missingResidues.
withMissingResidues(Iterable<? extends PdbRemark465Line>) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbModel: Copy the current immutable object with elements that replace the content of missingResidues.
withMissingResidues(PdbRemark465Line...) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel: Copy the current immutable object with elements that replace the content of missingResidues.
withMissingResidues(PdbRemark465Line...) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbModel: Copy the current immutable object with elements that replace the content of missingResidues.
withModel(PdbModel) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracketFromPdb: Copy the current immutable object by setting a value for the model attribute.
withModelNumber(int) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel: Copy the current immutable object by setting a value for the modelNumber attribute.
withModelNumber(int) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbModel: Copy the current immutable object by setting a value for the modelNumber attribute.
withModelNumber(int) - Method in class pl.poznan.put.pdb.ImmutablePdbRemark465Line: Copy the current immutable object by setting a value for the modelNumber attribute.
withModifiedResidueName(String) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbResidue: Copy the current immutable object by setting a value for the modifiedResidueName attribute.
withModifiedResidues(Iterable<? extends PdbModresLine>) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel: Copy the current immutable object with elements that replace the content of modifiedResidues.
withModifiedResidues(Iterable<? extends PdbModresLine>) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbModel: Copy the current immutable object with elements that replace the content of modifiedResidues.
withModifiedResidues(PdbModresLine...) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel: Copy the current immutable object with elements that replace the content of modifiedResidues.
withModifiedResidues(PdbModresLine...) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbModel: Copy the current immutable object with elements that replace the content of modifiedResidues.
withMoleculeType(MoleculeType) - Method in class pl.poznan.put.torsion.ImmutableAtomBasedTorsionAngleType: Copy the current immutable object by setting a value for the moleculeType attribute.
withMoleculeType(MoleculeType) - Method in class pl.poznan.put.torsion.ImmutableAverageTorsionAngleType: Copy the current immutable object by setting a value for the moleculeType attribute.
withName(String) - Method in class pl.poznan.put.pdb.analysis.ImmutablePdbCompactFragment: Copy the current immutable object by setting a value for the name attribute.
withName(String) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultStrand: Copy the current immutable object by setting a value for the name attribute.
withName(String) - Method in class pl.poznan.put.structure.formats.ImmutableStrandView: Copy the current immutable object by setting a value for the name attribute.
withNames(Iterable<String>) - Method in class pl.poznan.put.types.ImmutableDistanceMatrix: Copy the current immutable object with elements that replace the content of names.
withNames(String...) - Method in class pl.poznan.put.types.ImmutableDistanceMatrix: Copy the current immutable object with elements that replace the content of names.
withNt1(String) - Method in class pl.poznan.put.external.dssr.ImmutablePair: Copy the current immutable object by setting a value for the nt1 attribute.
withNt2(String) - Method in class pl.poznan.put.external.dssr.ImmutablePair: Copy the current immutable object by setting a value for the nt2 attribute.
withNucleotides(Iterable<? extends Nucleotide>) - Method in class pl.poznan.put.external.dssr.ImmutableDssrJson: Copy the current immutable object with elements that replace the content of nucleotides.
withNucleotides(Nucleotide...) - Method in class pl.poznan.put.external.dssr.ImmutableDssrJson: Copy the current immutable object with elements that replace the content of nucleotides.
withOccupancy(double) - Method in class pl.poznan.put.pdb.ImmutablePdbAtomLine: Copy the current immutable object by setting a value for the occupancy attribute.
withOneLetterName(char) - Method in class pl.poznan.put.pdb.ImmutablePdbNamedResidueIdentifier: Copy the current immutable object by setting a value for the oneLetterName attribute.
withOneLetterName(String) - Method in class pl.poznan.put.external.dssr.ImmutableNucleotide: Copy the current immutable object by setting a value for the oneLetterName attribute.
withOpening(double) - Method in class pl.poznan.put.structure.ImmutableQuantifiedBasePair: Copy the current immutable object by setting a value for the opening attribute.
withOriginal(int) - Method in class pl.poznan.put.structure.formats.ImmutableExtendedEntry: Copy the current immutable object by setting a value for the original attribute.
withoutAlternateLocations() - Method in interface pl.poznan.put.pdb.analysis.ResidueCollection: Creates a new instance of this class in which atoms with alternate locations are present only once.
withoutIsolatedPairs() - Method in class pl.poznan.put.structure.formats.BpSeq: Finds all isolated base pairs and creates a copy of this instance without them.
withoutIsolatedPairs() - Method in class pl.poznan.put.structure.formats.Ct: Finds all isolated base pairs and creates a copy of this instance without them.
withoutPair(BpSeq.Entry) - Method in class pl.poznan.put.structure.formats.BpSeq: Creates a copy of this instance, but with the given pair removed.
withoutPair(Ct.ExtendedEntry) - Method in class pl.poznan.put.structure.formats.Ct: Creates a copy of this instance, but with the given pair removed.
withPair(int) - Method in class pl.poznan.put.structure.formats.ImmutableEntry: Copy the current immutable object by setting a value for the pair attribute.
withPair(int) - Method in class pl.poznan.put.structure.formats.ImmutableExtendedEntry: Copy the current immutable object by setting a value for the pair attribute.
withPairs(Iterable<? extends Pair>) - Method in class pl.poznan.put.external.dssr.ImmutableDssrJson: Copy the current immutable object with elements that replace the content of pairs.
withPairs(Pair...) - Method in class pl.poznan.put.external.dssr.ImmutableDssrJson: Copy the current immutable object with elements that replace the content of pairs.
withParent(DotBracket) - Method in class pl.poznan.put.structure.formats.ImmutableStrandView: Copy the current immutable object by setting a value for the parent attribute.
withPropeller(double) - Method in class pl.poznan.put.structure.ImmutableQuantifiedBasePair: Copy the current immutable object by setting a value for the propeller attribute.
withPseudoknotFinder(PseudoknotFinder) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultConverter: Copy the current immutable object by setting a value for the pseudoknotFinder attribute.
withRadians(double) - Method in class pl.poznan.put.circular.ImmutableAngle: Copy the current immutable object by setting a value for the radians attribute.
withRangeDifference(RangeDifference) - Method in class pl.poznan.put.torsion.ImmutableTorsionAngleDelta: Copy the current immutable object by setting a value for the rangeDifference attribute.
withRegionRemover(Optional<? extends RegionRemover>) - Method in class pl.poznan.put.structure.pseudoknots.dp.ImmutableDynamicProgrammingAll: Copy the current immutable object by setting an optional value for the regionRemover attribute.
withRegionRemover(RegionRemover) - Method in class pl.poznan.put.structure.pseudoknots.dp.ImmutableDynamicProgrammingAll: Copy the current immutable object by setting a present value for the optional regionRemover attribute.
withRegions(Iterable<? extends Region>) - Method in class pl.poznan.put.structure.pseudoknots.dp.ImmutableConflictClique: Copy the current immutable object with elements that replace the content of regions.
withRegions(Iterable<? extends Region>) - Method in class pl.poznan.put.structure.pseudoknots.ImmutableConflictGraph: Copy the current immutable object with elements that replace the content of regions.
withRegions(Region...) - Method in class pl.poznan.put.structure.pseudoknots.dp.ImmutableConflictClique: Copy the current immutable object with elements that replace the content of regions.
withRegions(Region...) - Method in class pl.poznan.put.structure.pseudoknots.ImmutableConflictGraph: Copy the current immutable object with elements that replace the content of regions.
withResidueName(String) - Method in class pl.poznan.put.pdb.ImmutablePdbAtomLine: Copy the current immutable object by setting a value for the residueName attribute.
withResidueName(String) - Method in class pl.poznan.put.pdb.ImmutablePdbModresLine: Copy the current immutable object by setting a value for the residueName attribute.
withResidueName(String) - Method in class pl.poznan.put.pdb.ImmutablePdbRemark465Line: Copy the current immutable object by setting a value for the residueName attribute.
withResidueNumber(int) - Method in class pl.poznan.put.external.dssr.ImmutableNucleotide: Copy the current immutable object by setting a value for the residueNumber attribute.
withResidueNumber(int) - Method in class pl.poznan.put.pdb.ImmutablePdbAtomLine: Copy the current immutable object by setting a value for the residueNumber attribute.
withResidueNumber(int) - Method in class pl.poznan.put.pdb.ImmutablePdbModresLine: Copy the current immutable object by setting a value for the residueNumber attribute.
withResidueNumber(int) - Method in class pl.poznan.put.pdb.ImmutablePdbNamedResidueIdentifier: Copy the current immutable object by setting a value for the residueNumber attribute.
withResidueNumber(int) - Method in class pl.poznan.put.pdb.ImmutablePdbRemark465Line: Copy the current immutable object by setting a value for the residueNumber attribute.
withResidueNumber(int) - Method in class pl.poznan.put.pdb.ImmutablePdbResidueIdentifier: Copy the current immutable object by setting a value for the residueNumber attribute.
withResidueRule(Quadruple<Integer>) - Method in class pl.poznan.put.torsion.ImmutableAtomBasedTorsionAngleType: Copy the current immutable object by setting a value for the residueRule attribute.
withResidues(Iterable<? extends PdbResidue>) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultResidueCollection: Copy the current immutable object with elements that replace the content of residues.
withResidues(Iterable<? extends PdbResidue>) - Method in class pl.poznan.put.pdb.analysis.ImmutablePdbChain: Copy the current immutable object with elements that replace the content of residues.
withResidues(Iterable<? extends PdbResidue>) - Method in class pl.poznan.put.pdb.analysis.ImmutablePdbCompactFragment: Copy the current immutable object with elements that replace the content of residues.
withResidues(PdbResidue...) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultResidueCollection: Copy the current immutable object with elements that replace the content of residues.
withResidues(PdbResidue...) - Method in class pl.poznan.put.pdb.analysis.ImmutablePdbChain: Copy the current immutable object with elements that replace the content of residues.
withResidues(PdbResidue...) - Method in class pl.poznan.put.pdb.analysis.ImmutablePdbCompactFragment: Copy the current immutable object with elements that replace the content of residues.
withResolution(double) - Method in class pl.poznan.put.pdb.ImmutablePdbRemark2Line: Copy the current immutable object by setting a value for the resolution attribute.
withResolution(PdbRemark2Line) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel: Copy the current immutable object by setting a value for the resolution attribute.
withResolution(PdbRemark2Line) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbModel: Copy the current immutable object by setting a value for the resolution attribute.
withRight(PdbNamedResidueIdentifier) - Method in class pl.poznan.put.structure.ImmutableBasePair: Copy the current immutable object by setting a value for the right attribute.
withRight(NucleotideComponentType) - Method in class pl.poznan.put.rna.ImmutableInteractionType: Copy the current immutable object by setting a value for the right attribute.
withRightAtom(PdbAtomLine) - Method in class pl.poznan.put.torsion.ImmutableAtomPair: Copy the current immutable object by setting a value for the rightAtom attribute.
withSaenger(String) - Method in class pl.poznan.put.external.dssr.ImmutablePair: Copy the current immutable object by setting a value for the saenger attribute.
withSaenger(Saenger) - Method in class pl.poznan.put.structure.ImmutableAnalyzedBasePair: Copy the current immutable object by setting a value for the saenger attribute.
withSaenger(Saenger) - Method in class pl.poznan.put.structure.ImmutableQuantifiedBasePair: Copy the current immutable object by setting a value for the saenger attribute.
withSeq(char) - Method in class pl.poznan.put.structure.formats.ImmutableEntry: Copy the current immutable object by setting a value for the seq attribute.
withSeq(char) - Method in class pl.poznan.put.structure.formats.ImmutableExtendedEntry: Copy the current immutable object by setting a value for the seq attribute.
withSequence(char) - Method in class pl.poznan.put.structure.ImmutableDotBracketSymbol: Copy the current immutable object by setting a value for the sequence attribute.
withSequence(String) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracket: Copy the current immutable object by setting a value for the sequence attribute.
withSequence(String) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracketFromPdb: Copy the current immutable object by setting a value for the sequence attribute.
withSequence(String) - Method in class pl.poznan.put.structure.formats.ImmutableMultiLineDotBracket: Copy the current immutable object by setting a value for the sequence attribute.
withSerialNumber(int) - Method in class pl.poznan.put.pdb.ImmutablePdbAtomLine: Copy the current immutable object by setting a value for the serialNumber attribute.
withShear(double) - Method in class pl.poznan.put.structure.ImmutableQuantifiedBasePair: Copy the current immutable object by setting a value for the shear attribute.
withShortDisplayName(String) - Method in class pl.poznan.put.torsion.ImmutableAtomBasedTorsionAngleType: Copy the current immutable object by setting a value for the shortDisplayName attribute.
withStackingTopology(StackingTopology) - Method in class pl.poznan.put.structure.ImmutableAnalyzedBasePair: Copy the current immutable object by setting a value for the stackingTopology attribute.
withStackingTopology(StackingTopology) - Method in class pl.poznan.put.structure.ImmutableQuantifiedBasePair: Copy the current immutable object by setting a value for the stackingTopology attribute.
withStagger(double) - Method in class pl.poznan.put.structure.ImmutableQuantifiedBasePair: Copy the current immutable object by setting a value for the stagger attribute.
withStandardError(String) - Method in class pl.poznan.put.utility.ImmutableExecutionResult: Copy the current immutable object by setting a value for the standardError attribute.
withStandardOutput(String) - Method in class pl.poznan.put.utility.ImmutableExecutionResult: Copy the current immutable object by setting a value for the standardOutput attribute.
withStandardResidueName(String) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbResidue: Copy the current immutable object by setting a value for the standardResidueName attribute.
withStandardResidueName(String) - Method in class pl.poznan.put.pdb.ImmutablePdbModresLine: Copy the current immutable object by setting a value for the standardResidueName attribute.
withState(TorsionAngleDelta.State) - Method in class pl.poznan.put.torsion.ImmutableTorsionAngleDelta: Copy the current immutable object by setting a value for the state attribute.
withStrands(Iterable<? extends Strand>) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracket: Copy the current immutable object with elements that replace the content of strands.
withStrands(Iterable<? extends Strand>) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracketFromPdb: Copy the current immutable object with elements that replace the content of strands.
withStrands(Strand...) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracket: Copy the current immutable object with elements that replace the content of strands.
withStrands(Strand...) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracketFromPdb: Copy the current immutable object with elements that replace the content of strands.
withStretch(double) - Method in class pl.poznan.put.structure.ImmutableQuantifiedBasePair: Copy the current immutable object by setting a value for the stretch attribute.
withStructure(char) - Method in class pl.poznan.put.structure.ImmutableDotBracketSymbol: Copy the current immutable object by setting a value for the structure attribute.
withStructure(String) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracket: Copy the current immutable object by setting a value for the structure attribute.
withStructure(String) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultDotBracketFromPdb: Copy the current immutable object by setting a value for the structure attribute.
withSymbols(Iterable<? extends DotBracketSymbol>) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultStrand: Copy the current immutable object with elements that replace the content of symbols.
withSymbols(Iterable<? extends DotBracketSymbol>) - Method in class pl.poznan.put.structure.formats.ImmutableTerminalMissing: Copy the current immutable object with elements that replace the content of symbols.
withSymbols(DotBracketSymbol...) - Method in class pl.poznan.put.structure.formats.ImmutableDefaultStrand: Copy the current immutable object with elements that replace the content of symbols.
withSymbols(DotBracketSymbol...) - Method in class pl.poznan.put.structure.formats.ImmutableTerminalMissing: Copy the current immutable object with elements that replace the content of symbols.
withTemperatureFactor(double) - Method in class pl.poznan.put.pdb.ImmutablePdbAtomLine: Copy the current immutable object by setting a value for the temperatureFactor attribute.
withTitle(String) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultCifModel: Copy the current immutable object by setting a value for the title attribute.
withTitle(String) - Method in class pl.poznan.put.pdb.analysis.ImmutableDefaultPdbModel: Copy the current immutable object by setting a value for the title attribute.
withTitle(String) - Method in class pl.poznan.put.pdb.ImmutablePdbTitleLine: Copy the current immutable object by setting a value for the title attribute.
withValue(Angle) - Method in class pl.poznan.put.torsion.ImmutableTorsionAngleValue: Copy the current immutable object by setting a value for the value attribute.
withValues(Iterable<? extends TorsionAngleValue>) - Method in class pl.poznan.put.pdb.analysis.ImmutableResidueTorsionAngles: Copy the current immutable object with elements that replace the content of values.
withValues(TorsionAngleValue...) - Method in class pl.poznan.put.pdb.analysis.ImmutableResidueTorsionAngles: Copy the current immutable object with elements that replace the content of values.
withWorkingDirectory(File) - Method in class pl.poznan.put.utility.ImmutableExecHelper: Copy the current immutable object by setting a present value for the optional workingDirectory attribute.
withWorkingDirectory(Optional<? extends File>) - Method in class pl.poznan.put.utility.ImmutableExecHelper: Copy the current immutable object by setting an optional value for the workingDirectory attribute.
withX(double) - Method in class pl.poznan.put.pdb.ImmutablePdbAtomLine: Copy the current immutable object by setting a value for the x attribute.
withY(double) - Method in class pl.poznan.put.pdb.ImmutablePdbAtomLine: Copy the current immutable object by setting a value for the y attribute.
withZ(double) - Method in class pl.poznan.put.pdb.ImmutablePdbAtomLine: Copy the current immutable object by setting a value for the z attribute.
workingDirectory() - Method in class pl.poznan.put.utility.ExecHelper
workingDirectory() - Method in class pl.poznan.put.utility.ImmutableExecHelper
workingDirectory(File) - Method in class pl.poznan.put.utility.ImmutableExecHelper.Builder: Initializes the optional value workingDirectory to workingDirectory.
workingDirectory(Optional<? extends File>) - Method in class pl.poznan.put.utility.ImmutableExecHelper.Builder: Initializes the optional value workingDirectory to workingDirectory.

X

x() - Method in class pl.poznan.put.pdb.ImmutablePdbAtomLine
x() - Method in class pl.poznan.put.pdb.PdbAtomLine
x(double) - Method in class pl.poznan.put.pdb.ImmutablePdbAtomLine.Builder: Initializes the value for the x attribute.
X - Enum constant in enum pl.poznan.put.notation.Saenger
X_RAY_DIFFRACTION - Enum constant in enum pl.poznan.put.pdb.ExperimentalTechnique
XI - Enum constant in enum pl.poznan.put.notation.Saenger
XII - Enum constant in enum pl.poznan.put.notation.Saenger
XIII - Enum constant in enum pl.poznan.put.notation.Saenger
XIV - Enum constant in enum pl.poznan.put.notation.Saenger
XIX - Enum constant in enum pl.poznan.put.notation.Saenger
XV - Enum constant in enum pl.poznan.put.notation.Saenger
XVI - Enum constant in enum pl.poznan.put.notation.Saenger
XVII - Enum constant in enum pl.poznan.put.notation.Saenger
XVIII - Enum constant in enum pl.poznan.put.notation.Saenger
XX - Enum constant in enum pl.poznan.put.notation.Saenger
XXI - Enum constant in enum pl.poznan.put.notation.Saenger
XXII - Enum constant in enum pl.poznan.put.notation.Saenger
XXIII - Enum constant in enum pl.poznan.put.notation.Saenger
XXIV - Enum constant in enum pl.poznan.put.notation.Saenger
XXV - Enum constant in enum pl.poznan.put.notation.Saenger
XXVI - Enum constant in enum pl.poznan.put.notation.Saenger
XXVII - Enum constant in enum pl.poznan.put.notation.Saenger
XXVIII - Enum constant in enum pl.poznan.put.notation.Saenger

Y

y() - Method in class pl.poznan.put.pdb.ImmutablePdbAtomLine
y() - Method in class pl.poznan.put.pdb.PdbAtomLine
y(double) - Method in class pl.poznan.put.pdb.ImmutablePdbAtomLine.Builder: Initializes the value for the y attribute.

Z

z() - Method in class pl.poznan.put.pdb.ImmutablePdbAtomLine
z() - Method in class pl.poznan.put.pdb.PdbAtomLine
z(double) - Method in class pl.poznan.put.pdb.ImmutablePdbAtomLine.Builder: Initializes the value for the z attribute.
ZETA - Enum constant in enum pl.poznan.put.rna.NucleotideTorsionAngle
ZETA - Static variable in class pl.poznan.put.constant.Unicode

_

_0 - Enum constant in enum pl.poznan.put.notation.BPh
_0 - Enum constant in enum pl.poznan.put.notation.BR
_1 - Enum constant in enum pl.poznan.put.notation.BPh
_1 - Enum constant in enum pl.poznan.put.notation.BR
_2 - Enum constant in enum pl.poznan.put.notation.BPh
_2 - Enum constant in enum pl.poznan.put.notation.BR
_3 - Enum constant in enum pl.poznan.put.notation.BPh
_3 - Enum constant in enum pl.poznan.put.notation.BR
_4 - Enum constant in enum pl.poznan.put.notation.BPh
_4 - Enum constant in enum pl.poznan.put.notation.BR
_5 - Enum constant in enum pl.poznan.put.notation.BPh
_5 - Enum constant in enum pl.poznan.put.notation.BR
_6 - Enum constant in enum pl.poznan.put.notation.BPh
_6 - Enum constant in enum pl.poznan.put.notation.BR
_7 - Enum constant in enum pl.poznan.put.notation.BPh
_7 - Enum constant in enum pl.poznan.put.notation.BR
_8 - Enum constant in enum pl.poznan.put.notation.BPh
_8 - Enum constant in enum pl.poznan.put.notation.BR
_9 - Enum constant in enum pl.poznan.put.notation.BPh
_9 - Enum constant in enum pl.poznan.put.notation.BR

A B C D E F G H I K L M N O P Q R S T U V W X Y Z _
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form