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