All Classes Interface Summary Class Summary Enum Summary Exception Summary
| Class |
Description |
| AbstractCifFileSupplier<S> |
Convert a BioJava object to a CifFile.
|
| AbstractCifFileSupplier.WrappedAtom |
Wrapped atoms represent individual atoms enriched with model- and chain-level information.
|
| AbstractScoresCache |
Abstact implementation of the ScoresCache with the shared code used
in all objects with a variables cache. |
| AbstractStructureAlignment |
|
| AbstractUserArgumentProcessor |
Base class for a new structure alignment CLI.
|
| AFP |
A class to represent a FATCAT aligned fragment pair (AFP)
|
| AFPAlignmentDisplay |
|
| AFPCalculator |
A class that performs calculations on AFPChains
|
| AFPChain |
A bean to contain the core of a structure alignment.
|
| AFPChainer |
a class to chain AFPs to an alignment
|
| AFPChainFlipper |
|
| AFPChainScorer |
|
| AfpChainWriter |
A class to convert the data in an AfpChain object to various String outputs.
|
| AFPChainXMLConverter |
|
| AFPChainXMLParser |
|
| AFPOptimizer |
|
| AFPPostProcessor |
does post processing after alignment chaingin
|
| AFPTwister |
|
| AligMatEl |
|
| Alignable |
|
| AlignmentProgressListener |
A class to listen to progress of the structure alignment calculations
|
| AlignmentResult |
A class to track the alignment results in a flat file
|
| AlignmentTools |
Methods for analyzing and manipulating AFPChains and for
other pairwise alignment utilities.
|
| AlignmentTools.IdentityMap<K> |
A Map can be viewed as a function from K to V.
|
| AligNPE |
|
| AlignUtils |
Low level helper methods for CE and FATCAT algorithms.
|
| AllChemCompProvider |
A ChemComp provider that downloads and caches the components.cif file from the wwPDB site.
|
| AltAligComparator |
A comparator to sort AlternativeAlignments based on their number of equivalent residues
and RMSD.
|
| AlternativeAlignment |
Implements a class which handles one possible (alternative) solution.
|
| AminoAcid |
A Group that represents an AminoAcid. |
| AminoAcidImpl |
AminoAcid inherits most from Hetatom.
|
| AngleOrderDetectorPlus |
Guesses an order of rotational symmetry from the angle.
|
| AsaCalculator |
Class to calculate Accessible Surface Areas based on
the rolling ball algorithm by Shrake and Rupley.
|
| Astral |
Provides programmatic access to ASTRAL representative sets.
|
| Astral.AstralSet |
An ASTRAL sequence-identity cutoff with an identifier such as:
|
| Atom |
A simple interface for an Atom.
|
| AtomCache |
A utility class that provides easy access to Structure objects.
|
| AtomContact |
A pair of atoms that are in contact
|
| AtomContactSet |
A set of atom-atom contacts to hold the results of intra and inter-chain contact calculations
|
| AtomIdentifier |
|
| AtomImpl |
Implementation of an Atom of a PDB file.
|
| AtomIterator |
an iterator over all atoms of a structure / group.
|
| AtomPositionMap |
|
| AtomPositionMap.GroupMatcher |
Used as a Predicate to indicate whether a particular Atom should be mapped
|
| AugmentedResidueRange |
Created by douglas on 1/23/15.
|
| Author |
Describes author attributes for author information in a PDB file.
|
| AxisAligner |
|
| BasePairParameters |
This module calculates the el Hassan-Calladine Base Pairing and Base-pair Step Parameters for any nucleic
acid containing structure that has the information about the core base-pair rings.
|
| BcifFileReader |
Parse binary Cif files and provide capabilities to store them locally.
|
| BerkeleyScopInstallation |
|
| BetaBridge |
Container that represents a beta Bridge between two residues.
|
| BioAssemblyIdentifier |
|
| BioAssemblyInfo |
Representation of a Biological Assembly annotation as provided by the PDB.
|
| BioAssemblyTools |
|
| BioJavaStructureAlignment |
Wrapper for the BioJava Structure Alignment Implementation
|
| BiologicalAssemblyBuilder |
Reconstructs the quaternary structure of a protein from an asymmetric unit
|
| BiologicalAssemblyTransformation |
The transformation needed for generation of biological assemblies
from the contents of a PDB/mmCIF file.
|
| BlastClustReader |
|
| Block |
A Block is a Data Structure that stores aligned positions of a
MultipleAlignment with the condition that residues are in a
sequential order. |
| BlockImpl |
General implementation of a Block that supports any type of
sequential alignment with gaps. |
| BlockSet |
A BlockSet is a Data Structure to store a flexible alignment part of a
multiple alignment.
|
| BlockSetImpl |
A general implementation of a BlockSet to store a flexible part of a multiple
alignment.
|
| Bond |
A simple bond -- it stores information about two atoms as well as information
about its bond order.
|
| BondImpl |
A simple bond -- it stores information about two atoms as well as information
about its bond order.
|
| BondMaker |
Adds polymer bonds for peptides and nucleotides based on distance cutoffs and
intra-group (residue) bonds based on data from the Chemical Component Dictionary
to the Structure object.
|
| BondType |
Work in progress - NOT final!
|
| BoundingBox |
A bounding box for short cutting some geometrical calculations.
|
| BravaisLattice |
An enum to represent the 7 Bravais lattices
|
| BridgeType |
A bridge is formed by two non-overlapping stretches of three residues each
(i-1,i,i+1) and (j-1,j,j+1), where i
|
| C2RotationSolver |
|
| CAConverter |
Converts full atom representations to Calpha only ones.
|
| Calc |
Utility operations on Atoms, AminoAcids, Matrices, Point3d, etc.
|
| CalcPoint |
Utility operations on Point3d.
|
| CallableStructureAlignment |
Simple Callable Class that calculates a pairwise alignment in a different
thread, so that multiple pairwise alignments can be run in parallel
(examples: all-to-all alignments, DB search alignments).
|
| CartesianProduct<T> |
A cartesian product between two lists A and B is the set of all ordered pairs
of the elements of both sets.
|
| CathCategory |
The categories found within CATH.
|
| CathDatabase |
General API for interacting with CATH.
|
| CathDomain |
A class which represents a single CATH domain.
|
| CathFactory |
|
| CathFragment |
|
| CathInstallation |
|
| CathNode |
Represents a node in the CATH hierarchy.
|
| CathSegment |
|
| CECalculator |
This is based on the original Combinatorial Extension (CE) source code from 2003 or 2004 (CE version 2.3),
as has been originally developed by I.
|
| CeCalculatorEnhanced |
This is based on the original Combinatorial Extension (CE) source code from 2003 or 2004 (CE version 2.3),
as has been originally developed by I.
|
| CeCPMain |
A wrapper for CeMain which sets default parameters to be appropriate for finding
circular permutations. |
| CeCPMain.CPRange |
Tiny wrapper for the disallowed regions of an alignment.
|
| CECPParameters |
|
| CECPParameters.DuplicationHint |
|
| CeCPUserArgumentProcessor |
|
| CeMain |
The main class of the Java implementation of the Combinatorial Extension Algorithm (CE),
as has been originally developed by I.
|
| CeParameters |
Contains the parameters that can be sent to CE
|
| CeParameters.ScoringStrategy |
|
| CeSideChainMain |
|
| CeSideChainUserArgumentProcessor |
|
| CeSymm |
Identify the symmetries in a structure by running an alignment of the
structure against itself disabling the diagonal of the identity alignment.
|
| CeSymmIterative |
Iterative version of CeSymm that aims at identifying all symmetry axis of a
structure.
|
| CESymmParameters |
Provides parameters to CeSymm. |
| CESymmParameters.OrderDetectorMethod |
|
| CESymmParameters.RefineMethod |
|
| CESymmParameters.SymmetryType |
The internal symmetry detection can be divided into two types: CLOSE:
includes the circular and dihedral symmetries, and OPEN: includes the
helical and protein repeats symmetries.
|
| CeSymmResult |
This Class stores all the relevant information of an internal symmetry result
obtained with CeSymm.
|
| CeUserArgumentProcessor |
process the arguments from command line
|
| CeUserArgumentProcessor.CeStartupParams |
|
| Chain |
Defines the interface for a Chain.
|
| ChainImpl |
A Chain in a PDB file.
|
| ChainSignature |
|
| ChargeAdder |
A class to add appropriate charge information to a structure.
|
| ChemComp |
Properties of a chemical component.
|
| ChemCompAtom |
Properties of an atom of a chemical component.
|
| ChemCompBond |
Properties of a bond in a chemical component.
|
| ChemCompConsumer |
|
| ChemCompConsumerImpl |
|
| ChemCompConverter |
Convert CifFiles to chem comps.
|
| ChemCompDescriptor |
Properties of the chemical component descriptor.
|
| ChemCompDistribution |
|
| ChemCompGroupFactory |
|
| ChemCompProvider |
Interface that is implemented by all classes that can provide ChemComp definitions. |
| ChemCompTools |
|
| ChemicalComponentDictionary |
A representation of the Chemical Component Dictionary.
|
| CholeskyDecomposition |
Cholesky Decomposition.
|
| CifBean |
Flag for BioJava beans that resemble categories defined by the mmCIF schema.
|
| CifChainSupplierImpl |
Convert a chain to a CifFile.
|
| CifFileConsumer<S> |
Defines a rather generic interface which allows to populate some data structure with data parsed from a CIF file.
|
| CifFileReader |
Parse text Cif files and provide capabilities to store them locally.
|
| CifFileSupplier<S> |
Create a CifFile instance for a given container of structure data.
|
| CifStructureConsumer |
Defines the categories to consume during CIF parsing.
|
| CifStructureConsumerImpl |
An implementation of a CifFileConsumer for BioJava.
|
| CifStructureConverter |
Convert BioJava structures to CifFiles and vice versa.
|
| CifStructureSupplierImpl |
Convert a structure to a CifFile.
|
| CliTools |
Utilities for autoconfiguring javabeans based on command line arguments.
|
| ClusterAltAligs |
A class that clusters alternative alignments according to their
similarity.
|
| ClusterDomains |
|
| CollectionTools |
Utilities for working with collections.
|
| ConfigStrucAligParams |
|
| ConfigurationException |
|
| Contact |
A simple class to store contacts in the form of pairs of indices and a distance associated to them.
|
| CoreSuperimposer |
Superimposes the core aligned residues of every structure in a
MultipleAlignment onto a reference structure. |
| CrystalBuilder |
A class containing methods to find interfaces in a given crystallographic Structure by
reconstructing the crystal lattice through application of symmetry operators
|
| CrystalCell |
A crystal cell's parameters.
|
| CrystalTransform |
Representation of a transformation in a crystal:
- a transformation id (each of the transformations in a space group, 0 to m)
- a crystal translation
The transformation matrix in crystal basis is stored, representing the basic
transformation together with the crystal translation.
|
| Cut |
|
| CutDomain |
|
| CutSites |
|
| CutValues |
|
| DatabasePDBRevRecord |
Represents revision records for use by PDBHeader. |
| DBRef |
A class to represent database cross references.
|
| DemoAsa |
|
| DemoAtomCache |
Example of how to load PDB files using the AtomCache class.
|
| DemoBerkeleyScop |
A demo for how to use the Berkeley version of SCOP instead of the default UK-SCOP
|
| DemoBioAssemblies |
|
| DemoCATH |
An example for how to access CATH data.
|
| DemoCE |
Example of how to run a structure alignment using the CE algorithm.
|
| DemoCeSymm |
Quick demo of how to call CE-Symm programmatically.
|
| DemoChangeChemCompProvider |
This demo shows how to use an alternative ChemCompProvider.
|
| DemoCommandLineStartup |
|
| DemoContacts |
|
| DemoCrystalInterfaces |
|
| DemoDomainsplit |
|
| DemoFATCAT |
|
| DemoLoadSecStruc |
Demonstration of how to load a Structure with the SS information, either from
the PDB file annotation (Author's assignment) or from the DSSP file in the
PDB servers (DSSP assignment).
|
| DemoLoadStructure |
Example for how to load protein structures (from PDB files).
|
| DemoMMCIFReader |
An example of how to read MMcif files
|
| DemoMmcifToPdbConverter |
An example of how to convert mmCIF file to PDB file
|
| DemoMmtfReader |
Class to show how to read a Biojava structure using MMTF
|
| DemoMmtfWriter |
|
| DemoMultipleMC |
Demo for running the MultipleMC Algorithm on a protein family.
|
| DemoQsAlign |
Demo on how to use programatically QsAlign for the alignment of
quaternary structures. |
| DemoSCOP |
A class demonstrating the use of the SCOP parsing tools
|
| DemoSecStrucCalc |
Demonstration on how to use the Secondary Structure Prediction (DSSP)
implementation in BioJava and obtain different SS representations and
outputs.
|
| DemoSymmetry |
A demo on how to use the quaternary symmetry detection algorithms.
|
| DistanceBox<T> |
|
| Domain |
|
| DomainProvider |
Decomposes a structure from the PDB into representative domains
|
| DownloadChemCompProvider |
This provider of chemical components can download and cache chemical component definition files from the RCSB PDB web
site.
|
| DSSPParser |
Class to parse a DSSP file (output of the DSSP program),
that contains the secondary structure assignment of a structure.
|
| EcodDatabase |
General API for interacting with ECOD.
|
| EcodDomain |
An EcodDomain contains all the information of the ECOD database: id,
classification groups (from higher to lower in the tree: X,H,T,F), PDB code,
chain, residue ranges and status (manual or automatic classification).
|
| EcodFactory |
|
| EcodInstallation |
Provides access to the Evolutionary Classification of Protein Domains (ECOD).
|
| EcodInstallation.EcodParser |
|
| EigenvalueDecomposition |
Eigenvalues and eigenvectors of a real matrix.
|
| Element |
Element is an enumeration of the elements of the periodic table.
|
| ElementType |
ElementType is an enumeration of the types of elements found in the periodic table.
|
| EntityFinder |
Heuristical finding of Entities (called Compounds in legacy PDB format)
in a given Structure.
|
| EntityInfo |
An object to contain the info from the PDB header for a Molecule.
|
| EntityType |
The type of entity (polymer, non-polymer, water, macrolide)
as defined in the mmCIF dictionary: |
| ExperimentalTechnique |
An enum to represent the experimental technique of a PDB structure
|
| FastaAFPChainConverter |
A collection of static utilities to convert between AFPChains and FastaSequences. |
| FastaStructureParser |
Reads a protein sequence from a fasta file and attempts to match it to a
3D structure.
|
| FatCat |
|
| FatCatAligner |
A class that does calculations on an AFPChain
|
| FatCatFlexible |
|
| FatCatParameters |
|
| FatCatRigid |
|
| FatCatUserArgumentProcessor |
|
| FCAlignHelper |
|
| FileConvert |
Methods to convert a structure object into different file formats.
|
| FileParsingParameters |
|
| FragmentJoiner |
Joins the initial Fragments together to larger Fragments
|
| FragmentPair |
a pair of fragments of two protein structures
|
| GapArray |
|
| GetDistanceMatrix |
|
| Gotoh |
a class to perform Gotoh algorithm
|
| GraphComponentOrderDetector |
The GraphOrderDetector transforms the self-alignment into a Graph and
extracts its maximally connected Components.
|
| GraphComponentRefiner |
The GraphRefiner transforms the self-alignment into a Graph and extracts its
maximally connected Components.
|
| Grid |
A grid to be used for calculating atom contacts through a spatial hashing algorithm.
|
| GridCell |
A grid cell to be used in contact calculation via spatial hashing algorithm.
|
| Group |
This is the data structure for a single Group of atoms.
|
| GroupAsa |
A class to store the results of ASA calculations, it can
hold ASA values per atom present in Group |
| GroupContact |
A pair of residues that are in contact
|
| GroupContactSet |
A set of residue-residue contacts.
|
| GroupIterator |
An iterator over all groups of a structure.
|
| GroupToSDF |
|
| GroupType |
This contains basic categories for Group types.
|
| GuiWrapper |
A class to wrap some of the strucutre.gui classes using Reflection
|
| HBond |
Container that represents a hidrogen bond.
|
| HelicalRepeatUnit |
|
| Helix |
|
| HelixAxisAligner |
|
| HelixExtender |
|
| HelixLayers |
|
| HelixSolver |
|
| HetatomImpl |
Generic Implementation of a Group interface.
|
| HetatomImpl.PerformanceBehavior |
Behaviors for how to balance memory vs.
|
| IcosahedralSampler |
Represents an even coverage of quaternion space by 60 points.
|
| Icosahedron |
|
| IdxComparator |
|
| IndexPair |
|
| InterfaceFinder |
A class containing methods to find interfaces in a given structure.
|
| JointFragments |
A utility class that defines which set of atoms are considered
to be on equivalent positions.
|
| JournalArticle |
PDB-specific
|
| Ladder |
A Ladder is a set of one or more consecutive bridges of identical type.
|
| LocalPDBDirectory |
|
| LocalPDBDirectory.FetchBehavior |
Controls when the class should fetch files from the ftp server
|
| LocalPDBDirectory.ObsoleteBehavior |
Behaviors for when an obsolete structure is requested.
|
| LocalProteinDomainParser |
Protein Domain Parser is a an algorithm that attempts at assigning domains for 3D protein structures.
|
| LocalScopDatabase |
Classes which implement ScopDatabase in a way which allows them to serve queries
without accessing the internet should implement this interface instead.
|
| LUDecomposition |
LU Decomposition.
|
| Maths |
|
| Matrices |
Matrices contains static methods to operate and transform matrices used in 3D
geometry (transformation matrices and rotation matrices).
|
| Matrix |
Jama = Java Matrix class.
|
| MatrixListener |
|
| MetalBondConsumer |
Consume metal bond data.
|
| MetalBondConsumerImpl |
Created by andreas on 6/9/16.
|
| MetalBondConverter |
Created by andreas on 6/6/16.
|
| MetalBondDistance |
A bean that contains cutoffs for correctly detecting metal bonds.
|
| MismatchedBasePairParameters |
This class allows for finding inter-strand base pairs that are not necessarily canonical Watson-Crick pairs.
|
| MmtfActions |
A class of functions for reading and writing Biojava structures using MMTF
|
| MMTFFileReader |
A class to read MMTF files and cache them locally.
|
| MmtfStructureReader |
A biojava specific structure inflator for MMTF.
|
| MmtfStructureWriter |
Class to take Biojava structure data and covert to the DataApi for encoding.
|
| MmtfSummaryDataBean |
Class to store the summary data for a given structure.
|
| MmtfUtils |
A utils class of functions needed for Biojava to read and write to mmtf.
|
| Model |
An internal utility class for StructureImpl to make it easier to manage poly and nonpoly chains.
|
| MomentsOfInertia |
The moment of inertia, otherwise known as the angular mass or rotational
inertia, of a rigid body determines the torque needed for a desired angular
acceleration about a rotational axis.
|
| MomentsOfInertia.SymmetryClass |
|
| MultipleAlignment |
A MultipleAlignment is a Data Structure to store the core information of a
multiple structure alignment, as a return type.
|
| MultipleAlignmentDisplay |
Utility functions to generalize the visualization of MultipleAlignments in
molecular viewers.
|
| MultipleAlignmentEnsemble |
A MultipleAlignmentEnsemble is a collection of MultipleAlignments
that share the same structures (Atoms) and creation properties (algorithm,
version, creation time, etc.). |
| MultipleAlignmentEnsembleImpl |
|
| MultipleAlignmentImpl |
|
| MultipleAlignmentScorer |
|
| MultipleAlignmentTools |
|
| MultipleAlignmentWriter |
This class contains functions for the conversion of MultipleAlignment
to various String outputs. |
| MultipleAlignmentXMLConverter |
Helper methods to convert all the hierarchy levels of a MultipleAlignment
into an XML format.
|
| MultipleAlignmentXMLParser |
|
| MultipleMcMain |
Main class of the Java implementation of the Combinatorial Extension -
Monte Carlo (CEMC) Algorithm,
as it was originally described by C.Guda, E.D.Scheeff, P.E.
|
| MultipleMcOptimizer |
This class takes a MultipleAlignment seed previously generated and runs a
Monte Carlo optimization in order to improve the overall score and highlight
common structural motifs.
|
| MultipleMcParameters |
Contains the parameters to be sent to the MC optimization.
|
| MultipleStructureAligner |
Interface for the Multiple Structure Alignment Algorithms.
|
| MultipleSuperimposer |
Interface for Multiple Alignment superposition algorithms.
|
| Mutator |
A class that can change one amino acid to another.
|
| NucleotideImpl |
A nucleotide group is almost the same as a Hetatm group.
|
| Octahedron |
|
| OperatorResolver |
A class to resolve the operators for transformations
|
| OptimalCECPMain |
A wrapper for CeMain which sets default parameters to be appropriate for finding
circular permutations. |
| OptimalCECPParameters |
Contains the parameters that can be sent to CE
|
| OrderDetector |
A method to decide the order of symmetry (number of subunits)
given a structure self-alignment, calculated by CE-Symm.
|
| OrderedPair<T> |
An ordered pair represents a component of a cartesian product.
|
| Pair<T> |
A Pair of objects.
|
| PassthroughIdentifier |
A stub StructureIdentifier, representing the full structure in all cases.
|
| PDBBioAssemblyParser |
Parses REMARK 350 records in a PDB file and creates transformations to
construct the quaternary structure of a protein from an asymmetric unit
|
| PDBCrystallographicInfo |
A class to hold crystallographic information about a PDB structure.
|
| PDBFileParser |
This class implements the actual PDB file parsing.
|
| PDBFileReader |
The wrapper class for parsing a PDB file.
|
| PDBHeader |
A class that contains PDB Header information.
|
| PdbId |
A wrapper class for the PDB identifier.
|
| PdbPair |
A pair for structure alignment.
|
| PdbPairsMessage |
|
| PdbPairXMLConverter |
|
| PDBParseException |
An exception during the parsing of a PDB file.
|
| PDBRecord |
An interface implemented by all classes that represent PDB records.
|
| PDBStatus |
Methods for getting the status of a PDB file (current, removed, unreleased)
and for accessing different versions of the structure.
|
| PDBStatus.Status |
Represents a simplified 3 state status of PDB IDs.
|
| PDBTemporaryStorageUtils |
Internal use only.
|
| PDBTemporaryStorageUtils.LinkRecord |
Temporary data storage for LINK records.
|
| PDPDistanceMatrix |
|
| PDPParameters |
|
| PermutationGenerator |
|
| PermutationGroup |
|
| Polyhedron |
|
| PolymerType |
Enumerates the classification of polymers.
|
| PowerSet<T> |
In mathematics, the power set (or powerset) of any set S, written P(S), is
the set of all subsets of S, including the empty set and S itself.
|
| Prism |
|
| ProteinComplexSignature |
|
| QRDecomposition |
QR Decomposition.
|
| QsAlign |
Quaternary Structure Alignment (QS-Align).
|
| QsAlignParameters |
The parameter bean for the QsAlign algorithm. |
| QsAlignResult |
Result of a Quaternary Structure Alignment QsAlign. |
| QsRelation |
The Quaternary Structure Relation describes the pairwise relation between two
quaternary structures.
|
| QuatSuperpositionScorer |
|
| QuatSymmetryDetector |
Detects the symmetry (global, pseudo, internal and local) of protein
structures.
|
| QuatSymmetryParameters |
The QuatSymmetryParameters specify the options used for the detection of
quaternary symmetry in structures using the QuatSymmetryDetector. |
| QuatSymmetryResults |
|
| QuatSymmetryScores |
|
| QuatSymmetrySolver |
|
| QuatSymmetrySubunits |
A bean to represent information about the set of Subunits being
considered for symmetry detection. |
| RectangularPrism |
|
| ReducedChemCompProvider |
|
| ReferenceSuperimposer |
|
| RefinerFailedException |
Refinement of the self-alignment failed.
|
| ResidueGroup |
A ResidueGroup is a set of residues that are part of a maximally connected
component of the self-Alignment Graph in symmetry analysis.
|
| ResidueNumber |
Everything that is needed to uniquely describe a residue position
|
| ResidueRange |
A chainName, a start residue, and an end residue.
|
| ResidueRangeAndLength |
A chain, a start residue, and an end residue.
|
| ResidueType |
Enumerates the possible classifications of residues.
|
| ResourceManager |
A class that manages the Strings that are defined in the spice.properties file.
|
| Rotation |
|
| RotationAxis |
Calculates the rotation axis for an alignment
|
| RotationAxisAligner |
|
| RotationGroup |
|
| RotationSolver |
|
| ScopCategory |
The various categories provided by SCOP.
|
| ScopDatabase |
General API how to interact with SCOP
|
| ScopDescription |
Contains data from
dir.des.scop.txt_1.75
|
| ScopDomain |
Container for the information for a domain.
|
| ScopFactory |
Controls the global ScopDatabase being used.
|
| ScopInstallation |
This class provides access to the SCOP protein structure classification.
|
| ScopIOException |
Indicates that an I/O error occurred with SCOP lazy initialization.
|
| ScopMirror |
Helper class to store paths to the four SCOP files
The string "%s" is replaced with the version number.
|
| ScopNode |
|
| ScoresCache |
Interface for classes which implement a temporary cache for various numeric
scores, e.g.
|
| SecStrucCalc |
Calculate and assign the secondary structure (SS) to the
Groups of a Structure object.
|
| SecStrucElement |
A secondary structure element (SSE) is an object representing a block of
sequential residues that share the same secondary structure type.
|
| SecStrucInfo |
Container for the secondary structure information of a single residue.
|
| SecStrucState |
This class extends the basic container for secondary structure annotation,
including all the information used in the DSSP algorithm.
|
| SecStrucTools |
This class contains methods for obtaining and converting secondary structure
information from BioJava Structures. |
| SecStrucType |
This enum contains all of the secondary structure types found in the DSSP
output.
|
| Segment |
|
| SegmentComparator |
|
| SeqMisMatch |
Created by andreas on 9/11/15.
|
| SeqMisMatchImpl |
Created by andreas on 9/11/15.
|
| SeqRes2AtomAligner |
Aligns the SEQRES residues to the ATOM residues.
|
| SequenceFunctionOrderDetector |
Calls Spencer's method for determining order.
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| SequenceFunctionRefiner |
Creates a refined alignment with the CE-Symm alternative self-alignment.
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| SerializableCache<K,V> |
A class that provides all that is necessary to create a Serializable Cache
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| ShortSegmentRemover |
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| SiftsChainEntry |
An entry in the chain-level SIFTS mapping between UniProt and the PDB.
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| SiftsChainToUniprotMapping |
A mapping between UniProt entries and PDB chains.
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| SiftsEntity |
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| SiftsMappingProvider |
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| SiftsResidue |
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| SiftsSegment |
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| SiftsXMLParser |
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| SigEva |
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| SingularValueDecomposition |
Singular Value Decomposition.
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| Site |
Holds the data of sites presented in PDB files.
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| SmithWaterman3Daligner |
Provides a 3D superimposition of two structures based on their sequence
alignment.
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| SmithWaterman3DParameters |
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| SmithWatermanUserArgumentProcessor |
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| SmithWatermanUserArgumentProcessor.SmithWatermanStartupParams |
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| SpaceGroup |
A crystallographic space group.
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| SpaceGroupMapElements |
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| SpaceGroupMapRoot |
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| SparseSquareMatrix |
A sparse, square matrix, implementing using two arrays of sparse
vectors, one representation for the rows and one for the columns.
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| SparseVector |
A sparse vector, implemented using a symbol table.
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| SphereSampler |
Sample possible orientations.
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| SSBondImpl |
A simple bean to store disulfide bridge information, the SSBOND records in the PDB files.
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| StandardAminoAcid |
A class that provides a set of standard amino acids.
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| StartupParameters |
A simple bean that contains the parameters that can get set at startup
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| Stoichiometry |
A utility object that describes Stoichiometry (composition of a protein assembly),
determined via clustering procedure SubunitClusterer,
and implements human-readable representation using various strategies. |
| Stoichiometry.StringOverflowStrategy |
What to do when the number of SubunitCluster exceeds the length of the alphabet. |
| StrCompAlignment |
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| StrucAligParameters |
A class that contains all the parameters of the structure alignment algorithm.
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| Structure |
Interface for a structure object.
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| StructureAlignment |
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| StructureAlignmentFactory |
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| StructureAlignmentOptimizer |
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| StructureException |
An exception during the parsing of a PDB file.
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| StructureFiletype |
An enum of supported file formats.
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| StructureIdentifier |
An identifier that uniquely identifies a whole Structure or
arbitrary substructure. |
| StructureImpl |
Implementation of a PDB Structure.
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| StructureInterface |
An interface between 2 molecules (2 sets of atoms).
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| StructureInterfaceCluster |
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| StructureInterfaceList |
A list of interfaces between 2 molecules (2 sets of atoms)
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| StructureIO |
A class that provides static access methods for easy lookup of protein structure related components
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| StructureIOFile |
StructureIOFile extends StructureProvider with methods specific to
parsing files from the filesystem.
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| StructureName |
A utility class that makes working with names of structures, domains and ranges easier.
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| StructureName.Source |
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| StructurePairAligner |
Perform a pairwise protein structure superimposition.
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| StructureProvider |
A class that can provide a protein structure object from somewhere.
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| StructureSequenceMatcher |
A utility class with methods for matching ProteinSequences with
Structures.
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| StructureTools |
A class that provides some tool methods.
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| SubstructureIdentifier |
This is the canonical way to identify a part of a structure.
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| Subunit |
A Subunit consists of a set of residues from a Structure, which may
correspond to an entire Chain, a Domain, or any subset or combination of
residues from them.
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| SubunitCluster |
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| SubunitClusterer |
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| SubunitClustererMethod |
The SubunitClustererMethod ennummerates all methods that can be used to
cluster Subunit in the SubunitCluster. |
| SubunitClustererParameters |
The SubunitClustererParameters specifies the options used for the clustering
of the subunits in structures using the SubunitClusterer. |
| SubunitExtractor |
The SubunitExtractor extracts the information of each protein Chain
in a Structure and converts them into a List of Subunit. |
| SuperPosition |
The SuperPosition interface defines and documents the required methods for
any superpostion algorithm implementation, so that the input and expected
output are uniform.
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| SuperPositionAbstract |
The SuperPositionAbstract contains common code shared by all SuperPosition
algorithm implementations.
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| SuperPositionQCP |
Implementation of the Quaternion-Based Characteristic Polynomial algorithm
for RMSD and Superposition calculations.
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| SuperPositionQuat |
The SuperPositionQuat implements a quaternion based algorithm to superpose
arrays of Points in 3D.
|
| SuperPositions |
SuperPositions is a Class that provides static helper methods and an easy
access to the whole family of SuperPosition algorithms. |
| SuperPositionSVD |
A class that calculates the superposition between two sets of points using an
SVD Matrix Decomposition.
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| SymbolTable<Key extends Comparable<Key>,Value> |
Sorted symbol table implementation using a java.util.TreeMap.
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| SymmetryAxes |
Data Structure that stores all the symmetry axis that describe
the symmetry of a structure.
|
| SymmetryAxes.Axis |
Represents an axis of symmetry
|
| SymmetryPerceptionMethod |
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| SymmetryRefiner |
Interface for all symmetry refinement implementations.
|
| SymmetryTools |
Utility methods for symmetry (quaternary and internal) detection and result
manipulation.
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| SymmOptimizer |
Optimizes a symmetry alignment by a Monte Carlo score optimization of the
repeat multiple alignment.
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| SymoplibParser |
A class containing static methods to parse the symop.lib file from the
CCP4 package.
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| SynchronizedOutFile |
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| SystematicSolver |
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| TertiaryBasePairParameters |
This class also finds the base pairing and base-pair step parameters but has a broader definition
of a base pair so that non-canonical-WC base pairs will be detected and reported.
|
| Tetrahedron |
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| TransfAlgebraicAdapter |
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| TransformType |
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| TreeMapSpaceGroupWrapper |
|
| UnitCellBoundingBox |
A class to contain the BoundingBoxes of all polymeric molecules in a full unit cell.
|
| UnitQuaternions |
UnitQuaternions is a static Class that contains methods for calculating and
using unit quaternions.
|
| URLConnectionTools |
A class that takes care about opening URLConnections and sets the proper timeouts
|
| URLIdentifier |
Represents a structure loaded from a URL (including a file URL)
A few custom query parameters are supported:
format=[pdb|cif] Specify the file format (will otherwise be
guessed from the extension)
pdbId=[String] Specify the PDB ID (also guessed from the filename)
chainID=[String] A single chain from the structure
residues=[String] Residue ranges, in a form understood by
SubstructureIdentifier
|
| UserArgumentProcessor |
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| UserConfiguration |
A container to persist config to the file system
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| ZipChemCompProvider |
This chemical component provider retrieves and caches chemical component definition files from a
zip archive specified in its construction.
|