All Classes

Class	Description
AbstractCombinedStrand
AbstractPdbModel	A structure which detects residues from atoms alone and then chains from residues.
AbstractRegionRemover	Java implementation of region removal algorithm as presented in: Smit, S. et al., 2008.
AminoAcid	An amino acid with all details regarding its atoms, torsion angles, etc.
AminoAcidTorsionAngle	A torsion angle defined for proteins.
AnalyzedBasePair	A pair of residues with metadata taken from analysis tool.
Angle	A measurement for which one can distinguish a direction (i.e. [0..360) degrees)
AngleFormat	A collection of formatting methods for angular values.
AngleSample	A sample of angular values and computed statistics.
AngleTransformation	A transformation used to display circular diagrams.
AtomBasedTorsionAngleType	A torsion angle which is defined upon four atomic coordinates.
AtomName	A unified atom name found in PDB and mmCIF files with a list of alternative names.
AtomPair	A pair of atoms.
AtomType	An atom type (carbon, hydrogen, etc.) to be found in PDB and mmCIF files.
AverageTorsionAngleType	An average of one or more basic angle types.
Backbone	A backbone in a protein.
BasePair	A pairing between two nucleotides' bases.
BasePairParameters
Bond	An atomic bond and corresponding length.
BondLength	An atomic bond length.
BPh	A base-phosphate notation described in: Classification and Energetics of the Base-Phosphate Interactions in RNA.
BpSeq	RNA secondary structure in BPSEQ format.
BpSeq.Entry	An entry of a BPSEQ data.
BR	A base-ribose notation described in: Classification and Energetics of the Base-Phosphate Interactions in RNA.
CanonicalStructureExtractor	A set of methods to analyze 3D data to extract the canonical 2D structure.
CartesianUtilities	A set of utility functions on the edge between cartesian and trigonometric representations.
ChainNumberICode	A set of methods that allow to address a residue by its chain name, residue number and insertion code.
ChainReorderer	A set of methods to reorder chains in an RNA structure.
Chi	A glycosidic bond torsion angle (chi), which is defined differently for purines and pyrimidines.
ChiRange	A range description for chi torsion angle type as defined in Saenger's "Principles...".
CifContainer	A container of one or more PDB files converted from a single mmCIF file.
CifConverter	A converter from mmCIF to one or more PDB files.
CifModel	A structure parsed from an mmCIF file.
CifParser	A parser of mmCIF format.
CifPdbIncompatibilityException	When it is impossible to convert from mmCIF to PDB.
ClassifiedBasePair	A pair of interacting nucleotides with classification info.
Clusterable	A set of methods that a data structure must implement to be clustered.
Colors	A set of utility functions to work with palettes and color interpolation.
CombinedStrand	A dot-bracket encoded structure made from combining one or more strands.
CombinedStrandFromPdb	A dot-bracket encoded structure made from combining one or more strands.
ConflictClique	A collection of regions conflicting with each other.
ConflictGraph	A graph of conflicts between regions.
Converter	A converter from BPSEQ to dot-bracket.
Ct	An RNA secondary structure encoded in CT (connect) format.
Ct.ExtendedEntry	A single entry in the CT formatted structure.
DefaultCifModel	A default implementation of a structure parsed from an mmCIF file.
DefaultConverter	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.
DefaultDotBracket	A default implementation of a dot-bracket.
DefaultDotBracketFromPdb	A default implementation of a dot-bracket structure which is mapped to data from 3D coordinates.
DefaultPdbModel	A default implementation of a structure parsed from a PDB file.
DefaultPdbResidue	A default implementation of a residue (nucleotide or amino acid).
DefaultResidueCollection	A container for a list of residues.
DefaultStrand	A default implementation of a strand.
DisplayableExportable	A set of methods that any kind of result has to implement to be displayable in UI or exportable to output file.
DistanceMatrix
DotBracket	An RNA structure encoded in dot-bracket format.
DotBracketFromPdb	A dot-bracket structure with correspondence to a 3D structure.
DotBracketSymbol	A single symbol in a dot-bracket structure.
DssrJson
DynamicProgrammingAll	Java implementation of OPT ALL algorithm as presented in: Smit, S. et al., 2008.
ExecHelper	An executor of external processes.
ExecHelper.ExecutionResult	A result of running external command.
ExperimentalTechnique	An experimental technique used to solve a structure (according to the PDB sources).
Exportable	A set of methods that any kind of result must implement to be exported to output file.
Format	An image format which can be used to export SVG images to.
HelixOrigin	An information whether a base pair originated from a helix.
Histogram	A collection of angular observations put into bins of specified width.
ImmutableAnalyzedBasePair	Immutable implementation of AnalyzedBasePair.
ImmutableAnalyzedBasePair.Builder	Builds instances of type ImmutableAnalyzedBasePair.
ImmutableAngle	Immutable implementation of Angle.
ImmutableAngle.Builder	Builds instances of type ImmutableAngle.
ImmutableAngleSample	Immutable implementation of AngleSample.
ImmutableAngleSample.Builder	Builds instances of type ImmutableAngleSample.
ImmutableAtomBasedTorsionAngleType	Immutable implementation of AtomBasedTorsionAngleType.
ImmutableAtomBasedTorsionAngleType.Builder	Builds instances of type ImmutableAtomBasedTorsionAngleType.
ImmutableAtomPair	Immutable implementation of AtomPair.
ImmutableAtomPair.Builder	Builds instances of type ImmutableAtomPair.
ImmutableAverageTorsionAngleType	Immutable implementation of AverageTorsionAngleType.
ImmutableAverageTorsionAngleType.Builder	Builds instances of type ImmutableAverageTorsionAngleType.
ImmutableBackbone	Immutable implementation of Backbone.
ImmutableBackbone.Builder	Builds instances of type ImmutableBackbone.
ImmutableBasePair	Immutable implementation of BasePair.
ImmutableBasePair.Builder	Builds instances of type ImmutableBasePair.
ImmutableBasePairParameters	Immutable implementation of BasePairParameters.
ImmutableBasePairParameters.Builder	Builds instances of type ImmutableBasePairParameters.
ImmutableBondLength	Immutable implementation of BondLength.
ImmutableBondLength.Builder	Builds instances of type ImmutableBondLength.
ImmutableBpSeq	Immutable implementation of BpSeq.
ImmutableBpSeq.Builder	Builds instances of type ImmutableBpSeq.
ImmutableCifContainer	Immutable implementation of CifContainer.
ImmutableCifContainer.Builder	Builds instances of type ImmutableCifContainer.
ImmutableCombinedStrand	Immutable implementation of CombinedStrand.
ImmutableCombinedStrand.Builder	Builds instances of type ImmutableCombinedStrand.
ImmutableCombinedStrandFromPdb	Immutable implementation of CombinedStrandFromPdb.
ImmutableCombinedStrandFromPdb.Builder	Builds instances of type ImmutableCombinedStrandFromPdb.
ImmutableConflictClique	Immutable implementation of ConflictClique.
ImmutableConflictClique.Builder	Builds instances of type ImmutableConflictClique.
ImmutableConflictGraph	Immutable implementation of ConflictGraph.
ImmutableConflictGraph.Builder	Builds instances of type ImmutableConflictGraph.
ImmutableCt	Immutable implementation of Ct.
ImmutableCt.Builder	Builds instances of type ImmutableCt.
ImmutableDefaultCifModel	Immutable implementation of DefaultCifModel.
ImmutableDefaultCifModel.Builder	Builds instances of type ImmutableDefaultCifModel.
ImmutableDefaultConverter	Immutable implementation of DefaultConverter.
ImmutableDefaultConverter.Builder	Builds instances of type ImmutableDefaultConverter.
ImmutableDefaultDotBracket	Immutable implementation of DefaultDotBracket.
ImmutableDefaultDotBracket.Builder	Builds instances of type ImmutableDefaultDotBracket.
ImmutableDefaultDotBracketFromPdb	Immutable implementation of DefaultDotBracketFromPdb.
ImmutableDefaultDotBracketFromPdb.Builder	Builds instances of type ImmutableDefaultDotBracketFromPdb.
ImmutableDefaultPdbModel	Immutable implementation of DefaultPdbModel.
ImmutableDefaultPdbModel.Builder	Builds instances of type ImmutableDefaultPdbModel.
ImmutableDefaultPdbResidue	Immutable implementation of DefaultPdbResidue.
ImmutableDefaultPdbResidue.Builder	Builds instances of type ImmutableDefaultPdbResidue.
ImmutableDefaultResidueCollection	Immutable implementation of DefaultResidueCollection.
ImmutableDefaultResidueCollection.Builder	Builds instances of type ImmutableDefaultResidueCollection.
ImmutableDefaultStrand	Immutable implementation of DefaultStrand.
ImmutableDefaultStrand.Builder	Builds instances of type ImmutableDefaultStrand.
ImmutableDistanceMatrix	Immutable implementation of DistanceMatrix.
ImmutableDistanceMatrix.Builder	Builds instances of type ImmutableDistanceMatrix.
ImmutableDotBracketSymbol	Immutable implementation of DotBracketSymbol.
ImmutableDotBracketSymbol.Builder	Builds instances of type ImmutableDotBracketSymbol.
ImmutableDssrJson	Immutable implementation of DssrJson.
ImmutableDssrJson.Builder	Builds instances of type ImmutableDssrJson.
ImmutableDynamicProgrammingAll	Immutable implementation of DynamicProgrammingAll.
ImmutableDynamicProgrammingAll.Builder	Builds instances of type ImmutableDynamicProgrammingAll.
ImmutableEntry	Immutable implementation of BpSeq.Entry.
ImmutableEntry.Builder	Builds instances of type ImmutableEntry.
ImmutableExecHelper	Immutable implementation of ExecHelper.
ImmutableExecHelper.Builder	Builds instances of type ImmutableExecHelper.
ImmutableExecutionResult	Immutable implementation of ExecHelper.ExecutionResult.
ImmutableExecutionResult.Builder	Builds instances of type ImmutableExecutionResult.
ImmutableExtendedEntry	Immutable implementation of Ct.ExtendedEntry.
ImmutableExtendedEntry.Builder	Builds instances of type ImmutableExtendedEntry.
ImmutableHistogram	Immutable implementation of Histogram.
ImmutableHistogram.Builder	Builds instances of type ImmutableHistogram.
ImmutableInteractionType	Immutable implementation of InteractionType.
ImmutableInteractionType.Builder	Builds instances of type ImmutableInteractionType.
ImmutableMaxConflicts	Immutable implementation of MaxConflicts.
ImmutableMaxConflicts.Builder	Builds instances of type ImmutableMaxConflicts.
ImmutableMinGain	Immutable implementation of MinGain.
ImmutableMinGain.Builder	Builds instances of type ImmutableMinGain.
ImmutableMultiLineDotBracket	Immutable implementation of MultiLineDotBracket.
ImmutableMultiLineDotBracket.Builder	Builds instances of type ImmutableMultiLineDotBracket.
ImmutableNucleotide	Immutable implementation of Nucleotide.
ImmutableNucleotide.Builder	Builds instances of type ImmutableNucleotide.
ImmutablePair	Immutable implementation of Pair.
ImmutablePair.Builder	Builds instances of type ImmutablePair.
ImmutablePdbAtomLine	Immutable implementation of PdbAtomLine.
ImmutablePdbAtomLine.Builder	Builds instances of type ImmutablePdbAtomLine.
ImmutablePdbChain	Immutable implementation of PdbChain.
ImmutablePdbChain.Builder	Builds instances of type ImmutablePdbChain.
ImmutablePdbCompactFragment	Immutable implementation of PdbCompactFragment.
ImmutablePdbCompactFragment.Builder	Builds instances of type ImmutablePdbCompactFragment.
ImmutablePdbExpdtaLine	Immutable implementation of PdbExpdtaLine.
ImmutablePdbExpdtaLine.Builder	Builds instances of type ImmutablePdbExpdtaLine.
ImmutablePdbHeaderLine	Immutable implementation of PdbHeaderLine.
ImmutablePdbHeaderLine.Builder	Builds instances of type ImmutablePdbHeaderLine.
ImmutablePdbModresLine	Immutable implementation of PdbModresLine.
ImmutablePdbModresLine.Builder	Builds instances of type ImmutablePdbModresLine.
ImmutablePdbNamedResidueIdentifier	Immutable implementation of PdbNamedResidueIdentifier.
ImmutablePdbNamedResidueIdentifier.Builder	Builds instances of type ImmutablePdbNamedResidueIdentifier.
ImmutablePdbRemark2Line	Immutable implementation of PdbRemark2Line.
ImmutablePdbRemark2Line.Builder	Builds instances of type ImmutablePdbRemark2Line.
ImmutablePdbRemark465Line	Immutable implementation of PdbRemark465Line.
ImmutablePdbRemark465Line.Builder	Builds instances of type ImmutablePdbRemark465Line.
ImmutablePdbResidueIdentifier	Immutable implementation of PdbResidueIdentifier.
ImmutablePdbResidueIdentifier.Builder	Builds instances of type ImmutablePdbResidueIdentifier.
ImmutablePdbTitleLine	Immutable implementation of PdbTitleLine.
ImmutablePdbTitleLine.Builder	Builds instances of type ImmutablePdbTitleLine.
ImmutablePhosphate	Immutable implementation of Phosphate.
ImmutablePhosphate.Builder	Builds instances of type ImmutablePhosphate.
ImmutablePseudophasePuckerType	Immutable implementation of PseudophasePuckerType.
ImmutablePseudophasePuckerType.Builder	Builds instances of type ImmutablePseudophasePuckerType.
ImmutableQuadruple<T>	Immutable implementation of Quadruple.
ImmutableQuadruple.Builder<T>	Builds instances of type ImmutableQuadruple.
ImmutableQuantifiedBasePair	Immutable implementation of QuantifiedBasePair.
ImmutableQuantifiedBasePair.Builder	Builds instances of type ImmutableQuantifiedBasePair.
ImmutableRegion	Immutable implementation of Region.
ImmutableRegion.Builder	Builds instances of type ImmutableRegion.
ImmutableResidueTorsionAngles	Immutable implementation of ResidueTorsionAngles.
ImmutableResidueTorsionAngles.Builder	Builds instances of type ImmutableResidueTorsionAngles.
ImmutableRibose	Immutable implementation of Ribose.
ImmutableRibose.Builder	Builds instances of type ImmutableRibose.
ImmutableStandardReferenceFrame	Immutable implementation of StandardReferenceFrame.
ImmutableStandardReferenceFrame.Builder	Builds instances of type ImmutableStandardReferenceFrame.
ImmutableStrandView	Immutable implementation of StrandView.
ImmutableStrandView.Builder	Builds instances of type ImmutableStrandView.
ImmutableTerminalMissing	Immutable implementation of TerminalMissing.
ImmutableTerminalMissing.Builder	Builds instances of type ImmutableTerminalMissing.
ImmutableTorsionAngleDelta	Immutable implementation of TorsionAngleDelta.
ImmutableTorsionAngleDelta.Builder	Builds instances of type ImmutableTorsionAngleDelta.
ImmutableTorsionAngleValue	Immutable implementation of TorsionAngleValue.
ImmutableTorsionAngleValue.Builder	Builds instances of type ImmutableTorsionAngleValue.
ImmutableTrigonometricMoment	Immutable implementation of TrigonometricMoment.
ImmutableTrigonometricMoment.Builder	Builds instances of type ImmutableTrigonometricMoment.
InteractionType	A type of interaction between two nucleotides.
InvalidCircularOperationException
InvalidCircularValueException
InvalidVectorFormatException
LeontisWesthof	A classification of RNA base pairs described in: Geometric Nomenclature and Classification of RNA Base Pairs.
MasterTorsionAngleType	The main torsion angle type, which may consist of one or more basic angle types.
MaxConflicts	Java implementation of Elimination Conflicts algorithm as presented in: Smit, S. et al., 2008.
MinGain	Java implementation of Elimination Gain algorithm as presented in: Smit, S. et al., 2008.
ModelContainer	A set of PDB files which all correspond to the same structure and also their chain names' mapping.
MoleculeType	A type of molecule (RNA or protein).
MultiLineDotBracket	An extended secondary structure, which contains also non-canonical base pairs.
NucleicAcidResidueComponent	A component of a nucleotide.
Nucleobase	A nucleobase (adenine, cytosine, guanine, uracil or thymine).
NucleobaseEdge	An edge of the nucleobase.
Nucleotide
Nucleotide	A nucleotide (A, C, G, U or T) with all details regarding atoms, torsion angles, etc.
NucleotideComponentType	A type of the nucleotide component.
NucleotideTorsionAngle	A torsion angle defined in a nucleotide.
NumberFormatUtils	A class to provide useful NumberFormat instances.
Pair
PdbAtomLine	Representation of ATOM and HETATM lines in both PDB and mmCIF files.
PdbChain	A chain in a structure.
PdbCompactFragment	A collection of residues such that (i, i+1) are connected.
PdbExpdtaLine	A representation of EXPDTA line in PDB files.
PdbHeaderLine	A representation of HEADER file in PDB format.
PdbModel	A structure parsed from a PDB file.
PdbModresLine	A representation of MODRES line in PDB format.
PdbNamedResidueIdentifier	Class that represents a residue identifier with a known name.
PdbParser	A parser of PDB format.
PdbParsingException	When data in PDB files is inconsistent with the documented format.
PdbRemark2Line	A representation of REMARK 2 line which describes experimental resolution.
PdbRemark465Line	A representation of REMARK 465 in PDB format which describes missing residues.
PdbResidue	A residue (nucleotide or amino acid).
PdbResidueIdentifier	A residue identifier is used only to address a residue in the structure.
PdbTitleLine	A representation of TITLE line in PDB format.
Phosphate	A phosphate, part of RNA backbone.
PseudoknotFinder	A finder of pseudoknots in RNA secondary structure.
PseudophasePuckerType	An angle describing the pseudophase pucker.
Pseudorotation	A range of pseudorotation values with their descriptions.
Purine	A purine (adenine or guanine).
Pyrimidine	A pyrimidine (cytosine, uracil or thymine).
Quadruple<T>
QuantifiedBasePair	A base pair which is classified and quantified with numerical parameters.
Range	A named range of torsion angle values.
RangeDifference	A distance between TorsionRange objects.
RangeProvider	A provider of torsion angle ranges (different ranges are used for chi angle and for pseudophase pucker).
Region	A collection of pairs (BPSEQ entries) which are consecutive in sequence.
RegionRemover	A pseudoknot finder algorithm which works by selecting a region to remove in each iteration.
ResidueCollection	A collection of residues.
ResidueComponent	A fragment of a residue with a set of expected atoms and a set of possible other atoms.
ResidueInformationProvider	A provider of detailed information about a residue (its type, expected atoms, torsion angles etc).
ResidueTorsionAngles	A collection of torsion angles values for a single residue.
ResidueTypeDetector	A detector of residue type based on its name and atom content.
ResourcesHelper	A collection of methods to work with resources (src/main/resources/).
Ribose	A ribose, part of RNA backbone.
Saenger	A classification of RNA base pairs described in Principles of Nucleic Acid Structure.
Sidechain	A sidechain in a protein.
SingleTypedResidueCollection	A collection of residues with a common molecule type (RNA or protein).
StandardReferenceFrame
Stericity	A base pair stericity, either cis or trans.
Strand	A continuous segment of residues.
StrandView	A strand which is defined as a fragment of a dot-bracket structure.
SVGHelper	A collection of methods to work with SVG images.
Tabular	A set of methods to be implemented by result objects with tabular form of data.
TabularExporter	A collections of methods for easy export of tabular data to CSV files.
TerminalMissing	A colecction of missing dot-bracket symbols at 5' or 3' end.
TorsionAngleDelta	A result of subtracting of two torsion angles.
TorsionAngleDelta.State	A state of comparison of two torsion angle values.
TorsionAngleType	A torsion angle.
TorsionAngleValue	A torsion angle with its value calculated.
TorsionRange	A default torsion angle range as defined in Saenger's "Principles...".
TrigonometricMoment	A quantitative measure of a trigonometric sample shape.
Unicode	A set of useful constants in structural bioinformatics e.g. greek letters, Angstrom, etc.
Visualizable	A set of methods allowing to visualize the result.