Search Java Classes and Packages
#Org.biojava.nbio.structure Classes and Interfaces - 591 results found.
| Name | Description | Type | Package | Framework |
| AboutDialog | Class | org.biojava.nbio.structure.align.gui | BioJava | |
| AbstractAlignmentJmol | An Abstract Class to generalize the visualization of AFP and MultipleAlignment structure alignments in Jmol. | Class | org.biojava.nbio.structure.align.gui.jmol | BioJava |
| AbstractBean | a generic class that implements the toString method for a beanAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
| AbstractScoresCache | Abstact implementation of the ScoresCache with the shared code used in all objects with a variables cache. | Class | org.biojava.nbio.structure.align.multiple | BioJava |
| AbstractStructureAlignment | Class | org.biojava.nbio.structure.align | BioJava | |
| AbstractUserArgumentProcessor | Base class for a new structure alignment CLI. | Class | org.biojava.nbio.structure.align.ce | BioJava |
| AFP | A class to represent a FATCAT AFPAuthor:Andreas PrlicSee Also:Serialized Form | Class | org.biojava.nbio.structure.align.model | BioJava |
| AFPAlignmentDisplay | Class | org.biojava.nbio.structure.align.util | BioJava | |
| AFPCalculator | a class that performs calculations on AFPCHainsAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.align.fatcat.calc | BioJava |
| AFPChain | A bean to contain the core of a structure alignment. | Class | org.biojava.nbio.structure.align.model | BioJava |
| AFPChainCoordManager | Class | org.biojava.nbio.structure.align.gui.aligpanel | BioJava | |
| AFPChainer | a class to chain AFPs to an alignmentAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.align.fatcat.calc | BioJava |
| AFPChainFlipper | Class | org.biojava.nbio.structure.align.xml | BioJava | |
| AFPChainScorer | Class | org.biojava.nbio.structure.align.util | BioJava | |
| AfpChainWriter | A class to convert the data in an AfpChain object to various String outputs. | Class | org.biojava.nbio.structure.align.model | BioJava |
| AFPChainXMLConverter | Class | org.biojava.nbio.structure.align.xml | BioJava | |
| AFPChainXMLParser | Class | org.biojava.nbio.structure.align.xml | BioJava | |
| AFPOptimizer | Class | org.biojava.nbio.structure.align.fatcat.calc | BioJava | |
| AFPPostProcessor | does post processing after alignment chainginAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.align.fatcat.calc | BioJava |
| AFPTwister | Class | org.biojava.nbio.structure.align | BioJava | |
| AligMatEl | Class | org.biojava.nbio.structure.align.helper | BioJava | |
| Alignable | Interface | org.biojava.nbio.structure.align.pairwise | BioJava | |
| AlignedPosition | Class | org.biojava.nbio.structure.gui.util | BioJava | |
| AlignmentCalc | A class that obtains two structures via DAS and aligns them This is done in a separate thread. | Class | org.biojava.nbio.structure.align.gui | BioJava |
| AlignmentCalc | A class that obtains two structures via DAS and aligns them This is done in a separate thread. | Class | org.biojava.nbio.structure.gui.util | BioJava |
| AlignmentCalcDB | Class | org.biojava.nbio.structure.align.gui | BioJava | |
| AlignmentCalculationRunnable | Interface | org.biojava.nbio.structure.align.gui | BioJava | |
| AlignmentGui | A JFrame that allows to trigger a pairwise structure alignment, either from files in a directory, | Class | org.biojava.nbio.structure.align.gui | BioJava |
| AlignmentPositionListener | Interface | org.biojava.nbio.structure.gui.events | BioJava | |
| AlignmentProgressListener | Interface | org.biojava.nbio.structure.align.events | BioJava | |
| AlignmentProgressListener | Class | org.biojava.nbio.structure.align.pairwise | BioJava | |
| AlignmentResult | A class to track the alignment results in a flat fileAuthor:andreasSee Also:Serialized Form | Class | org.biojava.nbio.structure.align.pairwise | BioJava |
| AlignmentTextPanel | Class | org.biojava.nbio.structure.align.gui | BioJava | |
| AlignmentTools | Methods for analyzing and manipulating AFPChains and for other pairwise alignment utilities. | Class | org.biojava.nbio.structure.align.util | BioJava |
| AlignmentTools .IdentityMap | A Map can be viewed as a function from K to V. | Class | org.biojava.nbio.structure.align.util | BioJava |
| AligNPE | Class | org.biojava.nbio.structure.align.pairwise | BioJava | |
| AlignTools | Class | org.biojava.nbio.structure.align.helper | BioJava | |
| AligPanel | A JPanel that can display an AFPChain in a nice way and interact with Jmol. | Class | org.biojava.nbio.structure.align.gui.aligpanel | BioJava |
| AligPanelMouseMotionListener | Class | org.biojava.nbio.structure.align.gui.aligpanel | BioJava | |
| AligUIManager | Class | org.biojava.nbio.structure.align.webstart | BioJava | |
| AllChemCompProvider | A ChemComp provider that downloads and caches the components. | Class | org.biojava.nbio.structure.io.mmcif | BioJava |
| AltAligComparator | a comparator to sort AlternativeAlignments based on their number of equivalent residuesAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.align.pairwise | BioJava |
| AlternativeAlignment | Alternative alignments arise from different seed alignments or seed FPairs. | Class | org.biojava.nbio.structure.align.pairwise | BioJava |
| AlternativeAlignmentFrame | a frame showing the alternative alignments, which are the result of a structure superimpositionSince:1. | Class | org.biojava.nbio.structure.gui.util | BioJava |
| AminoAcid | A Group that represents an AminoAcid. | Interface | org.biojava.nbio.structure | BioJava |
| AminoAcidImpl | AminoAcid inherits most from Hetatom. | Class | org.biojava.nbio.structure | BioJava |
| AngleOrderDetectorPlus | Guesses an order of rotational symmetry from the angle. | Class | org.biojava.nbio.structure.symmetry.internal | BioJava |
| AngleOutlier | Java class for anonymous complex type. | Class | org.biojava.nbio.structure.validation | BioJava |
| AsaCalculator | Class to calculate Accessible Surface Areas based on the rolling ball algorithm by Shrake and Rupley. | Class | org.biojava.nbio.structure.asa | BioJava |
| AssignmentXMLSerializer | Class | org.biojava.nbio.structure.domain | BioJava | |
| Astral | Provides programmatic access to ASTRAL representative sets. | Class | org.biojava.nbio.structure.scop | BioJava |
| Astral .AstralSet | An ASTRAL sequence-identity cutoff with an identifier such as: Also contains a URL pointing to a FASTA file containing the representatives. | Class | org.biojava.nbio.structure.scop | BioJava |
| Atom | A simple interface for an Atom. | Interface | org.biojava.nbio.structure | BioJava |
| AtomCache | A utility class that provides easy access to Structure objects. | Class | org.biojava.nbio.structure.align.util | BioJava |
| AtomContact | A pair of atoms that are in contactAuthor:duarte_jSee Also:Serialized Form | Class | org.biojava.nbio.structure.contact | BioJava |
| AtomContactSet | A set of atom-atom contacts to hold the results of intra and inter-chain contact calculationsAuthor:duarte_jSee Also:Serialized Form | Class | org.biojava.nbio.structure.contact | BioJava |
| AtomIdentifier | Class | org.biojava.nbio.structure.contact | BioJava | |
| AtomImpl | currently the coordinates of an atom are represented by a double[3] array. | Class | org.biojava.nbio.structure | BioJava |
| AtomInfo | This class uniquely describes an atomAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.align.gui.jmol | BioJava |
| AtomInfoParser | Class | org.biojava.nbio.structure.align.gui.jmol | BioJava | |
| AtomIterator | an iterator over all atoms of a structure / group. | Class | org.biojava.nbio.structure | BioJava |
| AtomPositionMap | A map from ResidueNumbers to ATOM record positions in a PDB file. | Class | org.biojava.nbio.structure | BioJava |
| AtomPositionMap .GroupMatcher | Interface | org.biojava.nbio.structure | BioJava | |
| AtomSite | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| AuditAuthor | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| AugmentedResidueRange | Created by douglas on 1/23/15. | Class | org.biojava.nbio.structure | BioJava |
| Author | Describes author attributes for author information in a PDB file. | Class | org.biojava.nbio.structure | BioJava |
| AutoSuggestProvider | Interface | org.biojava.nbio.structure.align.gui.autosuggest | BioJava | |
| AxisAligner | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| BerkeleyScopInstallation | The Structural Classification of Proteins (extended) at Berkeley Lab and UC Berkeley (http://scop. | Class | org.biojava.nbio.structure.scop | BioJava |
| BetaBridge | Container that represents a beta Bridge between two residues. | Class | org.biojava.nbio.structure.secstruc | BioJava |
| BioAssemblyIdentifier | Class | org.biojava.nbio.structure | BioJava | |
| BioAssemblyInfo | Representation of a Biological Assembly annotation as provided by the PDB. | Class | org.biojava.nbio.structure.quaternary | BioJava |
| BioAssemblyTools | Class | org.biojava.nbio.structure.quaternary | BioJava | |
| BiojavaJmol | A class that provides a simple GUI for JmolSince:1. | Class | org.biojava.nbio.structure.gui | BioJava |
| BioJavaStructureAlignment | Wrapper for the BioJava Structure Alignment ImplementationAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.align | BioJava |
| BiologicalAssemblyBuilder | Reconstructs the quaternary structure of a protein from an asymmetric unitAuthor:Peter Rose, Andreas Prlic | Class | org.biojava.nbio.structure.quaternary | BioJava |
| BiologicalAssemblyTransformation | The transformation needed for generation of biological assemblies from the contents of a PDB/mmCIF file. | Class | org.biojava.nbio.structure.quaternary | BioJava |
| BioUnitDataProvider | Provides access to the data that is needed in order to rebuild the correct biological assembly of a protein. | Interface | org.biojava.nbio.structure.quaternary.io | BioJava |
| BioUnitDataProviderFactory | Factory to create BioUnitDataProvider instances. | Class | org.biojava.nbio.structure.quaternary.io | BioJava |
| BlastClustReader | Class | org.biojava.nbio.structure.symmetry.utils | BioJava | |
| Block | A Block is a Data Structure that stores aligned positions of a MultipleAlignment with the condition that residues are in a | Interface | org.biojava.nbio.structure.align.multiple | BioJava |
| BlockImpl | General implementation of a Block that supports any type of sequential alignment with gaps. | Class | org.biojava.nbio.structure.align.multiple | BioJava |
| BlockSet | A BlockSet is a Data Structure to store a flexible alignment part of a multiple alignment. | Interface | org.biojava.nbio.structure.align.multiple | BioJava |
| BlockSetImpl | A general implementation of a BlockSet to store a flexible part of a multiple alignment. | Class | org.biojava.nbio.structure.align.multiple | BioJava |
| Bond | A simple bond -- it stores information about two atoms as well as information about its bond order. | Interface | org.biojava.nbio.structure | BioJava |
| BondImpl | A simple bond -- it stores information about two atoms as well as information about its bond order. | Class | org.biojava.nbio.structure | BioJava |
| 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 | Class | org.biojava.nbio.structure.io | BioJava |
| BondOutlier | Java class for anonymous complex type. | Class | org.biojava.nbio.structure.validation | BioJava |
| BondType | Work in progress - NOT final!Author:Jules Jacobsen | Class | org.biojava.nbio.structure | BioJava |
| BoundingBox | A bounding box for short cutting some geometrical calculations. | Class | org.biojava.nbio.structure.contact | BioJava |
| BravaisLattice | An enum to represent the 7 Bravais latticesEnum Constant Summary | Class | org.biojava.nbio.structure.xtal | BioJava |
| 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 | Class | org.biojava.nbio.structure.secstruc | BioJava |
| BrowserOpener | Class | org.biojava.nbio.structure.align.webstart | BioJava | |
| C2RotationSolver | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| CachedRemoteScopInstallation | An extension of the RemoteScopInstallation that caches some of the data locally. | Class | org.biojava.nbio.structure.scop | BioJava |
| CacheFactory | provides a SoftHashMap singleton. | Class | org.biojava.nbio.structure.align.util | BioJava |
| CAConverter | Converts full atom representations to Calpha only ones. | Class | org.biojava.nbio.structure.io | BioJava |
| Calc | Utility operations on Atoms, AminoAcids, etc. | Class | org.biojava.nbio.structure | BioJava |
| CalcBioAssemblySymmetry | Class | org.biojava.nbio.structure.symmetry.analysis | BioJava | |
| CallableStructureAlignment | Class | org.biojava.nbio.structure.align | BioJava | |
| CartesianProduct | A cartesian product between two lists A and B is the set of all ordered pairs of the elements of both sets. | Class | org.biojava.nbio.structure.quaternary | BioJava |
| CathCategory | The categories found within CATH. | Class | org.biojava.nbio.structure.cath | BioJava |
| CathDatabase | General API for interacting with CATH. | Interface | org.biojava.nbio.structure.cath | BioJava |
| CathDomain | A class which represents a single CATH domain. | Class | org.biojava.nbio.structure.cath | BioJava |
| CathFactory | Controls global CathDatabases being used. | Class | org.biojava.nbio.structure.cath | BioJava |
| CathFragment | Class | org.biojava.nbio.structure.cath | BioJava | |
| CathInstallation | Class | org.biojava.nbio.structure.cath | BioJava | |
| CathNode | Represents a node in the CATH hierarchy. | Class | org.biojava.nbio.structure.cath | BioJava |
| CathSegment | Class | org.biojava.nbio.structure.cath | BioJava | |
| CECalculator | This is based on the original Combinatorial Extension (CE) source code from 2003 or 2004 (CE version 2. | Class | org.biojava.nbio.structure.align.ce | BioJava |
| CeCalculatorEnhanced | This is based on the original Combinatorial Extension (CE) source code from 2003 or 2004 (CE version 2. | Class | org.biojava.nbio.structure.align.ce | BioJava |
| CeCPMain | A wrapper for CeMain which sets default parameters to be appropriate for finding circular permutations. | Class | org.biojava.nbio.structure.align.ce | BioJava |
| CeCPMain .CPRange | Tiny wrapper for the disallowed regions of an alignment. | Class | org.biojava.nbio.structure.align.ce | BioJava |
| CECPParameters | Provides parameters to CeCPMainAuthor:Spencer Bliven | Class | org.biojava.nbio.structure.align.ce | BioJava |
| CECPParameters .DuplicationHint | Class | org.biojava.nbio.structure.align.ce | BioJava | |
| CeCPUserArgumentProcessor | Class | org.biojava.nbio.structure.align.ce | BioJava | |
| Cell | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| CeMain | The main class of the Java implementation of the Combinatorial Extension Algorithm (CE), as has been originally developed by I. | Class | org.biojava.nbio.structure.align.ce | BioJava |
| CeParameters | Contains the parameters that can be sent to CEAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.align.ce | BioJava |
| CeParameters .ScoringStrategy | Class | org.biojava.nbio.structure.align.ce | BioJava | |
| CeSideChainMain | Class | org.biojava.nbio.structure.align.ce | BioJava | |
| CeSideChainUserArgumentProcessor | Class | org.biojava.nbio.structure.align.ce | BioJava | |
| CeSymm | Identify the symmetries in a structure by running an alignment of the structure against itself disabling the diagonal of the identity alignment. | Class | org.biojava.nbio.structure.symmetry.internal | BioJava |
| CeSymmIterative | Iterative version of CeSymm that aims at identifying all symmetry axis (internal or quaternary) of a particular structure. | Class | org.biojava.nbio.structure.symmetry.internal | BioJava |
| CESymmParameters | Provides parameters to CeSymm. | Class | org.biojava.nbio.structure.symmetry.internal | BioJava |
| CESymmParameters .OrderDetectorMethod | Class | org.biojava.nbio.structure.symmetry.internal | BioJava | |
| CESymmParameters .RefineMethod | Class | org.biojava.nbio.structure.symmetry.internal | BioJava | |
| CESymmParameters .SymmetryType | The internal symmetry detection can be divided into two types: CLOSE: includes the circular and dihedral symmetries, and OPEN: includes the | Class | org.biojava.nbio.structure.symmetry.internal | BioJava |
| CeSymmResult | This Class stores all the relevant information of an internal symmetry result obtained with CeSymm. | Class | org.biojava.nbio.structure.symmetry.internal | BioJava |
| CeUserArgumentProcessor | process the arguments from command lineAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.align.ce | BioJava |
| CeUserArgumentProcessor .CeStartupParams | Class | org.biojava.nbio.structure.align.ce | BioJava | |
| Chain | Defines the interface for a Chain. | Interface | org.biojava.nbio.structure | BioJava |
| ChainClusterer | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| ChainImpl | A Chain in a PDB file. | Class | org.biojava.nbio.structure | BioJava |
| ChainSignature | Class | org.biojava.nbio.structure.symmetry.misc | BioJava | |
| ChargeAdder | Class | org.biojava.nbio.structure.io | BioJava | |
| ChemComp | A definition for a Chemical Component, as maintained by the wwPDB. | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
| ChemCompAtom | stores these fields: _chem_comp_atom. | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
| ChemCompBond | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| ChemCompConsumer | Class | org.biojava.nbio.structure.io.mmcif | BioJava | |
| ChemCompDescriptor | Container object for _pdbx_chem_comp_descriptorSince:3. | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
| ChemCompGroupFactory | Class | org.biojava.nbio.structure.io.mmcif | BioJava | |
| ChemCompProvider | Interface that is implemented by all classes that can provide ChemComp definitions. | Interface | org.biojava.nbio.structure.io.mmcif | BioJava |
| ChemCompTools | Some tools for working with chemical compounds. | Class | org.biojava.nbio.structure.io.mmcif.chem | BioJava |
| ChemicalComponentDictionary | A representation of the Chemical Component Dictionary. | Class | org.biojava.nbio.structure.io.mmcif | BioJava |
| CholeskyDecomposition | Cholesky Decomposition. | Class | org.biojava.nbio.structure.jama | BioJava |
| ChooseDirAction | Ask the user to provide a directory containting PDB files. | Class | org.biojava.nbio.structure.align.gui | BioJava |
| Clash | Java class for anonymous complex type. | Class | org.biojava.nbio.structure.validation | BioJava |
| CliTools | Utilities for autoconfiguring javabeans based on command line arguments. | Class | org.biojava.nbio.structure.align.util | BioJava |
| ClusterAltAligs | A class that clusters alternative alignments according to theirSince:1. | Class | org.biojava.nbio.structure.align | BioJava |
| ClusterDomains | Class | org.biojava.nbio.structure.domain.pdp | BioJava | |
| ClusterMerger | Merges clusters based on their sequence identity. | Class | org.biojava.nbio.structure.symmetry.core | BioJava |
| ClusterProteinChains | Clusters the chains of one or two structures by sequence. | Class | org.biojava.nbio.structure.symmetry.core | BioJava |
| CollectionTools | Utilities for working with collections. | Class | org.biojava.nbio.structure.align.util | BioJava |
| ColorConverter | Class | org.biojava.nbio.structure.symmetry.jmolScript | BioJava | |
| ColorInterpolator | Interface | org.biojava.nbio.structure.gui.util.color | BioJava | |
| ColorUtils | Class | org.biojava.nbio.structure.gui.util.color | BioJava | |
| CombinationGenerator | Class | org.biojava.nbio.structure.symmetry.utils | BioJava | |
| Compound | An object to contain the info from the PDB header for a Molecule. | Class | org.biojava.nbio.structure | BioJava |
| CompoundFinder | Heuristical finding of Compounds (called Entities in mmCIF dictionary) in a given Structure. | Class | org.biojava.nbio.structure.io | BioJava |
| ConfigPDBInstallPanel | Class | org.biojava.nbio.structure.align.gui | BioJava | |
| ConfigStrucAligParams | Interface | org.biojava.nbio.structure.align.ce | BioJava | |
| ConfigurationException | Class | org.biojava.nbio.structure.align.util | BioJava | |
| ConfigXMLHandler | Class | org.biojava.nbio.structure.align.webstart | BioJava | |
| ContinuousColorMapper | Provides a mapping between real numbers and Colors. | Interface | org.biojava.nbio.structure.gui.util.color | BioJava |
| ContinuousColorMapperTransform | Maps colors by performing a transform of the input data and then passing the transformed value to a ContinuousColorMapper for rendering. | Class | org.biojava.nbio.structure.gui.util.color | BioJava |
| CoordManager | a class that manages the conversion of sequence coordinate system to JPanel drawing coordinates | Class | org.biojava.nbio.structure.gui.util | BioJava |
| CoreSuperimposer | Superimposes the core aligned residues of every structure in a MultipleAlignment onto a reference structure. | Class | org.biojava.nbio.structure.align.multiple.util | BioJava |
| CountProgressListener | Class | org.biojava.nbio.structure.align.client | BioJava | |
| CrystalBuilder | A class containing methods to find interfaces in a given crystallographic Structure by reconstructing the crystal lattice through application of symmetry operators | Class | org.biojava.nbio.structure.xtal | BioJava |
| CrystalCell | A crystal cell's parameters. | Class | org.biojava.nbio.structure.xtal | BioJava |
| CrystalTransform | Representation of a transformation in a crystal: - a transformation id (each of the transformations in a space group, 0 to m) | Class | org.biojava.nbio.structure.xtal | BioJava |
| Cut | Class | org.biojava.nbio.structure.domain.pdp | BioJava | |
| CutDomain | Class | org.biojava.nbio.structure.domain.pdp | BioJava | |
| CutSites | Class | org.biojava.nbio.structure.domain.pdp | BioJava | |
| CutValues | Class | org.biojava.nbio.structure.domain.pdp | BioJava | |
| DatabasePDBremark | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| DatabasePDBrev | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| DatabasePdbrevRecord | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| DBRef | A class to represent database cross references. | Class | org.biojava.nbio.structure | BioJava |
| DBResultTable | Class | org.biojava.nbio.structure.align.gui | BioJava | |
| DBSearchGUI | Class | org.biojava.nbio.structure.align.gui | BioJava | |
| DefaultAutoSuggestProvider | Class | org.biojava.nbio.structure.align.gui.autosuggest | BioJava | |
| DefaultMatrixMapper | Color Mapper which mimics the default coloring of JMatrixPanel pixels. | Class | org.biojava.nbio.structure.gui.util.color | BioJava |
| DisplayAFP | A utility class for visualistion of structure alignmentsAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.align.gui | BioJava |
| DistanceBox | Class | org.biojava.nbio.structure.symmetry.geometry | BioJava | |
| Domain | Class | org.biojava.nbio.structure.domain.pdp | BioJava | |
| DomainProvider | Interface | org.biojava.nbio.structure.domain | BioJava | |
| DomainProviderFactory | Class | org.biojava.nbio.structure.domain | BioJava | |
| DotPlotPanel | Displays the dot plot trace for an alignment. | Class | org.biojava.nbio.structure.align.gui | BioJava |
| DownloadChemCompProvider | This provider of chemical components can download and cache chemical component definition files from the RCSB PDB web site. | Class | org.biojava.nbio.structure.io.mmcif | BioJava |
| DSSPParser | Class to parse a DSSP file (output of the DSSP program), that contains the secondary structure assignment of a structure. | Class | org.biojava.nbio.structure.secstruc | BioJava |
| EcodDatabase | General API for interacting with CATH. | Interface | org.biojava.nbio.structure.ecod | BioJava |
| EcodDomain | Class | org.biojava.nbio.structure.ecod | BioJava | |
| EcodFactory | Controls global CathDatabases being used. | Class | org.biojava.nbio.structure.ecod | BioJava |
| EcodInstallation | Provides access to the Evolutionary Classification of Protein Domains (ECOD). | Class | org.biojava.nbio.structure.ecod | BioJava |
| EcodInstallation .EcodParser | Class | org.biojava.nbio.structure.ecod | BioJava | |
| EigenvalueDecomposition | Eigenvalues and eigenvectors of a real matrix. | Class | org.biojava.nbio.structure.jama | BioJava |
| Element | Element is an enumeration of the elements of the periodic table. | Class | org.biojava.nbio.structure | BioJava |
| ElementType | ElementType is an enumeration of the types of elements found in the periodic table. | Class | org.biojava.nbio.structure | BioJava |
| Entity | A simple class to represent Entity records in mmCif filesAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
| EntityPolySeq | Container for _entity_poly_seq recordsField Name mmCIF Data Item | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
| EntitySrcGen | Data items in the ENTITY_SRC_GEN category record details of the source from which the entity was obtained in cases | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
| EntitySrcNat | Data items in the ENTITY_SRC_NAT category record details of the source from which the entity was obtained in cases | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
| EntitySrcSyn | PDBX_ENTITY_SRC_SYN records the details about each chemically synthesized molecule (entity) in the asymmetric unit. | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
| Entry | Java class for anonymous complex type. | Class | org.biojava.nbio.structure.validation | BioJava |
| ExperimentalTechnique | enum ExperimentalTechniqueAn enum to represent the experimental technique of a PDB structure | Class | org.biojava.nbio.structure | BioJava |
| Exptl | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| FarmJob | A job as it can be run on the farm. | Class | org.biojava.nbio.structure.align | BioJava |
| FarmJobParameters | Class | org.biojava.nbio.structure.align.client | BioJava | |
| FarmJobRunnable | Contains the single thread for a job that can run multiple alignments. | Class | org.biojava.nbio.structure.align.client | BioJava |
| FastaAFPChainConverter | A collection of static utilities to convert between AFPChains and FastaSequences. | Class | org.biojava.nbio.structure.io | BioJava |
| FastaStructureParser | Reads a protein sequence from a fasta file and attempts to match it to a 3D structure. | Class | org.biojava.nbio.structure.io | BioJava |
| FatCat | Class | org.biojava.nbio.structure.align.fatcat | BioJava | |
| FatCatAligner | A class that does calculations on an AFPChainAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.align.fatcat.calc | BioJava |
| FatCatFlexible | Class | org.biojava.nbio.structure.align.fatcat | BioJava | |
| FatCatParameters | Class | org.biojava.nbio.structure.align.fatcat.calc | BioJava | |
| FatCatRigid | Class | org.biojava.nbio.structure.align.fatcat | BioJava | |
| FatCatUserArgumentProcessor | Class | org.biojava.nbio.structure.align.fatcat | BioJava | |
| FCAlignHelper | Class | org.biojava.nbio.structure.align.fatcat.calc | BioJava | |
| FileConvert | Methods to convert a structure object into different file formats. | Class | org.biojava.nbio.structure.io | BioJava |
| FileDownloadUtils | Class | org.biojava.nbio.structure.io.util | BioJava | |
| FileParsingParameters | A class that configures parameters that can be sent to the PDB file parsers setParseCAOnly(boolean) - parse only the Atom records for C-alpha atoms setParseSecStruc(boolean) - a flag if the secondary structure information from the PDB file (author's assignment) should be parsed. | Class | org.biojava.nbio.structure.io | BioJava |
| FragmentJoiner | Joins the initial Fragments together to larger FragmentsSince:1. | Class | org.biojava.nbio.structure.align.pairwise | BioJava |
| FragmentPair | a pair of fragments of two protein structuresSince:1. | Class | org.biojava.nbio.structure.align.pairwise | BioJava |
| GapArray | Class | org.biojava.nbio.structure.align.helper | BioJava | |
| GetDistanceMatrix | Class | org.biojava.nbio.structure.domain.pdp | BioJava | |
| GetRepresentatives | TODO Move this to Representatives. | Class | org.biojava.nbio.structure.rcsb | BioJava |
| Gotoh | a class to perform Gotoh algorithmSince:10:56:53 AMVersion:%I% %G%Author:Andreas Prlic (Java), Peter Lackner (original C code) | Class | org.biojava.nbio.structure.align.pairwise | BioJava |
| GradientMapper | Maps a set of real values onto a gradient. | Class | org.biojava.nbio.structure.gui.util.color | BioJava |
| GradientPanel | Class | org.biojava.nbio.structure.gui.util.color | BioJava | |
| GraphComponentOrderDetector | The GraphOrderDetector transforms the self-alignment into a Graph and extracts its maximally connected Components. | Class | org.biojava.nbio.structure.symmetry.internal | BioJava |
| GraphComponentRefiner | The GraphRefiner transforms the self-alignment into a Graph and extracts its maximally connected Components. | Class | org.biojava.nbio.structure.symmetry.internal | BioJava |
| Grid | A grid to be used for calculating atom contacts through geometric hashing algorithm. | Class | org.biojava.nbio.structure.contact | BioJava |
| GridCell | A grid cell to be used in contact calculation via geometric hashing algorithm. | Class | org.biojava.nbio.structure.contact | BioJava |
| Group | This is the data structure for a single Group of atoms. | Interface | org.biojava.nbio.structure | BioJava |
| GroupAsa | A class to store the results of ASA calculations, it can hold ASA values per atom present in Group | Class | org.biojava.nbio.structure.asa | BioJava |
| GroupContact | A pair of residues that are in contactAuthor:duarte_jSee Also:Serialized Form | Class | org.biojava.nbio.structure.contact | BioJava |
| GroupContactSet | A set of residue-residue contacts. | Class | org.biojava.nbio.structure.contact | BioJava |
| GroupIterator | An iterator over all groups of a structure. | Class | org.biojava.nbio.structure | BioJava |
| GroupToSDF | Class | org.biojava.nbio.structure.io | BioJava | |
| GroupType | This contains basic categories for Group types. | Class | org.biojava.nbio.structure | BioJava |
| GUIAlignmentProgressListener | a GUI that allows to watch progress as multiple alignments are being processed. | Class | org.biojava.nbio.structure.align.gui | BioJava |
| GUIFarmJobRunnable | Class | org.biojava.nbio.structure.align.gui | BioJava | |
| GuiWrapper | A class to wrap some of the strucutre. | Class | org.biojava.nbio.structure.align.ce | BioJava |
| HasResultXMLConverter | Class | org.biojava.nbio.structure.align.xml | BioJava | |
| HBond | Container that represents a hidrogen bond. | Class | org.biojava.nbio.structure.secstruc | BioJava |
| HelicalRepeatUnit | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| Helix | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| HelixAxisAligner | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| HelixExtender | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| HelixLayers | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| HelixSolver | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| HelpDialog | Class | org.biojava.nbio.structure.align.gui | BioJava | |
| HetatomImpl | Generic Implementation of a Group interface. | Class | org.biojava.nbio.structure | BioJava |
| HetatomImpl .PerformanceBehavior | Behaviors for how to balance memory vs. | Class | org.biojava.nbio.structure | BioJava |
| HSVColorSpace | Class | org.biojava.nbio.structure.gui.util.color | BioJava | |
| HTTPConnectionTools | a class that takes care about opening HttpURLConnections and sets the proper timeoutsSince:9:58:25 AMVersion:%I% %G%Author:Andreas Prlic | Class | org.biojava.nbio.structure.align.util | BioJava |
| IcosahedralSampler | Class | org.biojava.nbio.structure.symmetry.geometry | BioJava | |
| Icosahedron | Class | org.biojava.nbio.structure.symmetry.geometry | BioJava | |
| Identifier | A collection of utilities to create StructureIdentifiers. | Class | org.biojava.nbio.structure | BioJava |
| IdxComparator | Class | org.biojava.nbio.structure.align.helper | BioJava | |
| IndexPair | Class | org.biojava.nbio.structure.align.helper | BioJava | |
| JAutoSuggest | A JTextField that can make suggestions for auto-complete. | Class | org.biojava.nbio.structure.align.gui.autosuggest | BioJava |
| JFatCatClient | Class | org.biojava.nbio.structure.align.client | BioJava | |
| JMatrixPanel | a JPanel that can display a difference of distance matrix and paths that have been taken for the alignment | Class | org.biojava.nbio.structure.gui | BioJava |
| JmolAlignedPositionListener | Class | org.biojava.nbio.structure.gui.events | BioJava | |
| JmolPanel | Class | org.biojava.nbio.structure.align.gui.jmol | BioJava | |
| JmolSymmetryScriptGenerator | Class | org.biojava.nbio.structure.symmetry.jmolScript | BioJava | |
| JmolSymmetryScriptGeneratorC1 | Class | org.biojava.nbio.structure.symmetry.jmolScript | BioJava | |
| JmolSymmetryScriptGeneratorCn | Class | org.biojava.nbio.structure.symmetry.jmolScript | BioJava | |
| JmolSymmetryScriptGeneratorDn | Class | org.biojava.nbio.structure.symmetry.jmolScript | BioJava | |
| JmolSymmetryScriptGeneratorH | Class | org.biojava.nbio.structure.symmetry.jmolScript | BioJava | |
| JmolSymmetryScriptGeneratorI | Class | org.biojava.nbio.structure.symmetry.jmolScript | BioJava | |
| JmolSymmetryScriptGeneratorO | Class | org.biojava.nbio.structure.symmetry.jmolScript | BioJava | |
| JmolSymmetryScriptGeneratorPointGroup | Class | org.biojava.nbio.structure.symmetry.jmolScript | BioJava | |
| JmolSymmetryScriptGeneratorT | Class | org.biojava.nbio.structure.symmetry.jmolScript | BioJava | |
| JmolTools | Class | org.biojava.nbio.structure.align.gui.jmol | BioJava | |
| JmolViewerImpl | Class | org.biojava.nbio.structure.gui | BioJava | |
| JNLPProxy | Class | org.biojava.nbio.structure.align.webstart | BioJava | |
| JobKillException | Class | org.biojava.nbio.structure.align.client | BioJava | |
| JointFragments | A utility class that defines which set of atoms are considered to be on equivalent positions. | Class | org.biojava.nbio.structure.align.helper | BioJava |
| JournalArticle | Class | org.biojava.nbio.structure | BioJava | |
| JPrintPanel | Class | org.biojava.nbio.structure.align.gui | BioJava | |
| Ladder | A Ladder is a set of one or more consecutive bridges of identical type. | Class | org.biojava.nbio.structure.secstruc | BioJava |
| LinearColorInterpolator | Class | org.biojava.nbio.structure.gui.util.color | BioJava | |
| LinearColorInterpolator .InterpolationDirection | Class | org.biojava.nbio.structure.gui.util.color | BioJava | |
| ListStringWrapper | Class | org.biojava.nbio.structure.scop.server | BioJava | |
| LocalPDBDirectory | Superclass for classes which download and interact with the PDB's FTP server, specifically PDBFileReader and MMCIFFileReader. | Class | org.biojava.nbio.structure.io | BioJava |
| LocalPDBDirectory .FetchBehavior | Controls when the class should fetch files from the ftp serverAuthor:Spencer Bliven | Class | org.biojava.nbio.structure.io | BioJava |
| LocalPDBDirectory .ObsoleteBehavior | Behaviors for when an obsolete structure is requested. | Class | org.biojava.nbio.structure.io | BioJava |
| LocalProteinDomainParser | Protein Domain Parser is a an algorithm that attempts at assigning domains for 3D protein structures. | Class | org.biojava.nbio.structure.domain | BioJava |
| LocalScopDatabase | Classes which implement ScopDatabase in a way which allows them to serve queries without accessing the internet should implement this interface instead. | Interface | org.biojava.nbio.structure.scop | BioJava |
| LogColorMapper | Performs a log10 transform on input before passing the values off to another For instance, to map [10^0, 10^10] to a rainbow gradient, use | Class | org.biojava.nbio.structure.gui.util.color | BioJava |
| LUDecomposition | For an m-by-n matrix A with m >= n, the LU decomposition is an m-by-n unit lower triangular matrix L, an n-by-n upper triangular matrix U, | Class | org.biojava.nbio.structure.jama | BioJava |
| Maths | Class | org.biojava.nbio.structure.jama | BioJava | |
| Matrix | Jama = Java Matrix class. | Class | org.biojava.nbio.structure.jama | BioJava |
| MatrixListener | Interface | org.biojava.nbio.structure.align.ce | BioJava | |
| MemoryMonitor | Tracks Memory allocated & used, displayed in graph form. | Class | org.biojava.nbio.structure.align.gui | BioJava |
| MenuCreator | Create the menus for structure alignment GUI windows (JFrames). | Class | org.biojava.nbio.structure.align.gui | BioJava |
| MenuCreator | Create the menu for BiojavaJmolSince:1. | Class | org.biojava.nbio.structure.gui.util | BioJava |
| MenuCreator .DotPlotListener | Creates a frame to display a DotPlotPanel. | Class | org.biojava.nbio.structure.align.gui | BioJava |
| MmCifBiolAssemblyProvider | Class | org.biojava.nbio.structure.quaternary.io | BioJava | |
| MMcifConsumer | An interface for the events triggered by a MMcifParser. | Interface | org.biojava.nbio.structure.io.mmcif | BioJava |
| MMCIFFileReader | How to parse an mmCif file:public static void main(String[] args) throws Exception { | Class | org.biojava.nbio.structure.io | BioJava |
| MMCIFFileTools | Some tools for mmCIF file writing. | Class | org.biojava.nbio.structure.io.mmcif | BioJava |
| MMcifParser | Interface that needs to be implemented by an MMcifParserSince:1. | Interface | org.biojava.nbio.structure.io.mmcif | BioJava |
| MmCifPDBBiolAssemblyProvider | A provider for information about biological units for PDB files that is based on reading local MMcif files. | Class | org.biojava.nbio.structure.quaternary.io | BioJava |
| ModelledSubgroup | Java class for anonymous complex type. | Class | org.biojava.nbio.structure.validation | BioJava |
| MogAngleOutlier | Java class for anonymous complex type. | Class | org.biojava.nbio.structure.validation | BioJava |
| MogBondOutlier | Java class for anonymous complex type. | Class | org.biojava.nbio.structure.validation | BioJava |
| MomentsOfInertia | Class | org.biojava.nbio.structure.symmetry.geometry | BioJava | |
| MomentsOfInertia .SymmetryClass | Class | org.biojava.nbio.structure.symmetry.geometry | BioJava | |
| MultipleAlignment | A MultipleAlignment is a Data Structure to store the core information of a multiple structure alignment, as a return type. | Interface | org.biojava.nbio.structure.align.multiple | BioJava |
| MultipleAlignmentCalc | A class that obtains structures via DAS and aligns them. | Class | org.biojava.nbio.structure.align.gui | BioJava |
| MultipleAlignmentCoordManager | Generalization of the Coodinate Manager to include an arbitrary number of sequences (lines) for MultipleAlignment visualization. | Class | org.biojava.nbio.structure.align.gui.aligpanel | BioJava |
| MultipleAlignmentDisplay | Utility functions to generalize the visualization of MultipleAlignments in molecular viewers. | Class | org.biojava.nbio.structure.align.multiple.util | BioJava |
| MultipleAlignmentEnsemble | A MultipleAlignmentEnsemble is a collection of MultipleAlignments that share the same structures (Atoms) and creation properties (algorithm, | Interface | org.biojava.nbio.structure.align.multiple | BioJava |
| MultipleAlignmentEnsembleImpl | A general implementation of a MultipleAlignmentEnsemble. | Class | org.biojava.nbio.structure.align.multiple | BioJava |
| MultipleAlignmentGUI | A JFrame that allows to trigger a multiple structure alignment, either from files in a directory or after manual upload. | Class | org.biojava.nbio.structure.align.gui | BioJava |
| MultipleAlignmentImpl | A general implementation of a MultipleAlignment. | Class | org.biojava.nbio.structure.align.multiple | BioJava |
| MultipleAlignmentJmol | A class that provides a 3D visualization Frame in Jmol for MultipleAlignments. | Class | org.biojava.nbio.structure.align.gui.jmol | BioJava |
| MultipleAlignmentJmolDisplay | Utility Class that provides helper methods for the visualization of MultipleAlignments. | Class | org.biojava.nbio.structure.align.gui | BioJava |
| MultipleAlignmentScorer | Utility class for calculating common scores of MultipleAlignments. | Class | org.biojava.nbio.structure.align.multiple.util | BioJava |
| MultipleAlignmentTools | Utility functions for working with MultipleAlignment. | Class | org.biojava.nbio.structure.align.multiple.util | BioJava |
| MultipleAlignmentWriter | This class contains functions for the conversion of MultipleAlignment to various String outputs. | Class | org.biojava.nbio.structure.align.multiple.util | BioJava |
| MultipleAlignmentXMLConverter | Helper methods to convert all the hierarchy levels of a MultipleAlignment into an XML format. | Class | org.biojava.nbio.structure.align.xml | BioJava |
| MultipleAlignmentXMLParser | Parse an XML file representing a MultipleAlignmentEnsemble, so that the original alignment can be recovered. | Class | org.biojava.nbio.structure.align.xml | BioJava |
| MultipleAligPanel | A JPanel that can display the sequence alignment of a MultipleAlignment in a nice way and interact with Jmol by | Class | org.biojava.nbio.structure.align.gui.aligpanel | BioJava |
| MultipleAligPanelMouseMotionListener | Mouse Motion Listener for the MultipleAligPanel, which provides methods to obtain positions of the mouse | Class | org.biojava.nbio.structure.align.gui.aligpanel | BioJava |
| MultipleMcMain | Main class of the Java implementation of the Combinatorial Extension - Monte Carlo (CEMC) Algorithm, | Class | org.biojava.nbio.structure.align.multiple.mc | BioJava |
| MultipleMcOptimizer | This class takes a MultipleAlignment seed previously generated and runs a Monte Carlo optimization in order to improve the overall score and highlight | Class | org.biojava.nbio.structure.align.multiple.mc | BioJava |
| MultipleMcParameters | Contains the parameters to be sent to the MC optimization. | Class | org.biojava.nbio.structure.align.multiple.mc | BioJava |
| MultipleStatusDisplay | This class provides information of the selected positions in the It has to be linked to a MultipleAligPanel in order to obtain | Class | org.biojava.nbio.structure.align.gui.aligpanel | BioJava |
| MultipleStructureAligner | Interface for the Multiple Structure Alignment Algorithms. | Interface | org.biojava.nbio.structure.align | BioJava |
| MultipleSuperimposer | Interface for Multiple Alignment superposition algorithms. | Interface | org.biojava.nbio.structure.align.multiple.util | BioJava |
| MultiThreadedDBSearch | Performs a multi threaded database search for an input protein structureAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.align | BioJava |
| Mutator | A class that can change one amino acid to another. | Class | org.biojava.nbio.structure | BioJava |
| MyAlignmentLoadListener | Loads an alignment in an XML format and displays its content in a new Jmol panel. | Class | org.biojava.nbio.structure.align.gui | BioJava |
| MyDistMaxListener | Shows the interatomic Distance Matrices of all the Structures aligned in different Frames. | Class | org.biojava.nbio.structure.align.gui | BioJava |
| MyExportListener | Class | org.biojava.nbio.structure.align.gui | BioJava | |
| MyJmolStatusListener | Class | org.biojava.nbio.structure.align.gui.jmol | BioJava | |
| MyOpenPdbFileListener | Class | org.biojava.nbio.structure.align.gui | BioJava | |
| MySaveFileListener | Save an alignment to a specified File by the user. | Class | org.biojava.nbio.structure.align.gui | BioJava |
| MyTableRowSorter | Class | org.biojava.nbio.structure.align.gui | BioJava | |
| NucleotideImpl | A nucleotide group is almost the same as a Hetatm group. | Class | org.biojava.nbio.structure | BioJava |
| ObjectFactory | This object contains factory methods for each Java content interface and Java element interface | Class | org.biojava.nbio.structure.validation | BioJava |
| Octahedron | Class | org.biojava.nbio.structure.symmetry.geometry | BioJava | |
| OperatorResolver | Class | org.biojava.nbio.structure.quaternary | BioJava | |
| OptimalCECPMain | A wrapper for CeMain which sets default parameters to be appropriate for finding circular permutations. | Class | org.biojava.nbio.structure.align.ce | BioJava |
| OptimalCECPParameters | Contains the parameters that can be sent to CEAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.align.ce | BioJava |
| OrderDetector | A method to decide the order of symmetry (number of subunits) given a structure self-alignment, calculated by CE-Symm. | Interface | org.biojava.nbio.structure.symmetry.internal | BioJava |
| OrderedPair | An ordered pair represents a component of a cartesian product. | Class | org.biojava.nbio.structure.quaternary | BioJava |
| Pair | A Pair of objects. | Class | org.biojava.nbio.structure.contact | BioJava |
| PairwiseAlignment | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| ParameterGUI | UI for ConfigStrucAligParams, for the AlignmentGUI. | Class | org.biojava.nbio.structure.align.gui | BioJava |
| PassthroughIdentifier | A stub StructureIdentifier, representing the full structure in all cases. | Class | org.biojava.nbio.structure | BioJava |
| PDBBioAssemblyParser | Parses REMARK 350 records in a PDB file and creates transformations to construct the quaternary structure of a protein from an asymmetric unit | Class | org.biojava.nbio.structure.io | BioJava |
| PDBBioUnitDataProvider | A BioUnitDataProvider that extracts the necessary info from PDB filesAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.quaternary.io | BioJava |
| PDBCrystallographicInfo | A class to hold crystallographic information about a PDB structure. | Class | org.biojava.nbio.structure | BioJava |
| PDBDirPanel | A class to define where a structure for the alignment is coming fromSince:1. | Class | org.biojava.nbio.structure.gui.util | BioJava |
| PDBDomainProvider | Class to fetch domains through the RCSB's REST API. | Class | org.biojava.nbio.structure.domain | BioJava |
| PDBFileParser | This class implements the actual PDB file parsing. | Class | org.biojava.nbio.structure.io | BioJava |
| PDBFileReader | The wrapper class for parsing a PDB file. | Class | org.biojava.nbio.structure.io | BioJava |
| PDBHeader | A class that contains PDB Header information. | Class | org.biojava.nbio.structure | BioJava |
| PdbIdLists | Utility classes for retrieving lists of PDB IDs. | Class | org.biojava.nbio.structure.rcsb | BioJava |
| PdbPair | A pair for structure alignmentAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.align.client | BioJava |
| PdbPairsMessage | Class | org.biojava.nbio.structure.align.xml | BioJava | |
| PdbPairXMLConverter | Class | org.biojava.nbio.structure.align.xml | BioJava | |
| PDBParseException | An exception during the parsing of a PDB file. | Class | org.biojava.nbio.structure.io | BioJava |
| PDBRecord | An interface implemented by all classes that represent PDB recordsSince:1. | Interface | org.biojava.nbio.structure | BioJava |
| PDBServerPanel | A class to define where a structure for the alignment is coming fromSince:1. | Class | org.biojava.nbio.structure.gui.util | BioJava |
| PDBStatus | Methods for getting the status of a PDB file (current, obsolete, etc) and for accessing different versions of the structure. | Class | org.biojava.nbio.structure | BioJava |
| PDBStatus .Status | Represents the status of PDB IDs. | Class | org.biojava.nbio.structure | BioJava |
| PDBTemporaryStorageUtils | Internal use only. | Class | org.biojava.nbio.structure.io.util | BioJava |
| PDBTemporaryStorageUtils .LinkRecord | Temporary data storage for LINK records. | Class | org.biojava.nbio.structure.io.util | BioJava |
| PDBUploadPanel | A JPanel to upload 2 custom PDB files. | Class | org.biojava.nbio.structure.gui.util | BioJava |
| PdbxChemCompDescriptor | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| PdbxChemCompIdentifier | _pdbx_chem_comp_identifier. | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
| PdbxEntityNonPoly | A bean for the Pdbx_entity_nonpoly category. | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
| PdbxNonPolyScheme | A bean for the PDBX_NONPOLY_SCHEME category, which provides residue level nomenclature mapping for non-polymer entities. | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
| PdbxPolySeqScheme | A bean for the PDBX_POLY_SEQ_SCHEME category, which provides residue level nomenclature mapping for polymer entities. | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
| PdbxStructAssembly | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| PdbxStructAssemblyGen | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| PdbxStructAssemblyGenXMLContainer | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| PdbxStructAssemblyXMLContainer | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| PdbxStructOperList | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| PdbxStructOperListXMLContainer | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| PDPDistanceMatrix | Class | org.biojava.nbio.structure.domain.pdp | BioJava | |
| PDPDomain | Class | org.biojava.nbio.structure.domain | BioJava | |
| PDPParameters | Class | org.biojava.nbio.structure.domain.pdp | BioJava | |
| PDPProvider | Decomposes a structure into representative PDP domains. | Interface | org.biojava.nbio.structure.domain | BioJava |
| PermutationGenerator | Class | org.biojava.nbio.structure.symmetry.utils | BioJava | |
| PermutationGroup | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| PersistentConfig | a class to store the config using the Java Web StartAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.align.webstart | BioJava |
| Polyhedron | Interface | org.biojava.nbio.structure.symmetry.geometry | BioJava | |
| PolymerType | Enumerates the classification of polymers. | Class | org.biojava.nbio.structure.io.mmcif.chem | BioJava |
| PositionInQueueXMLConverter | Class | org.biojava.nbio.structure.align.xml | BioJava | |
| Prism | Class | org.biojava.nbio.structure.symmetry.geometry | BioJava | |
| Program | Java class for anonymous complex type. | Class | org.biojava.nbio.structure.validation | BioJava |
| Programs | Java class for anonymous complex type. | Class | org.biojava.nbio.structure.validation | BioJava |
| ProteinChainExtractor | Extracts information about all the chains in a structure, including chain Ids, sequences, and atoms. | Class | org.biojava.nbio.structure.symmetry.core | BioJava |
| ProteinComplexSignature | Class | org.biojava.nbio.structure.symmetry.misc | BioJava | |
| ProteinSequenceClusterer | Represents a set of non-identical protein sequences. | Class | org.biojava.nbio.structure.symmetry.core | BioJava |
| QRDecomposition | For an m-by-n matrix A with m >= n, the QR decomposition is an m-by-n orthogonal matrix Q and an n-by-n upper triangular matrix R so that | Class | org.biojava.nbio.structure.jama | BioJava |
| QuatSuperpositionScorer | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| QuatSymmetryDetector | Detects global and local quaternary protein structure symmetry in a structure. | Class | org.biojava.nbio.structure.symmetry.core | BioJava |
| QuatSymmetryParameters | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| QuatSymmetryResults | Holds the results of quaternary symmetry perception. | Class | org.biojava.nbio.structure.symmetry.core | BioJava |
| QuatSymmetryScores | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| QuatSymmetrySolver | Interface | org.biojava.nbio.structure.symmetry.core | BioJava | |
| RasmolCommandListener | a utility class that listens to Ramsol script commands in the @link BiojavaJmol classAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.align.gui.jmol | BioJava |
| RasmolCommandListener | a utility class that listens to Ramsol script commands in the @link BiojavaJmol classAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.gui | BioJava |
| RawBioUnitDataProvider | Defines the methods that have to be implemented by a class that provides the data that is necessary to recreate the correct biological assembly of a protein. | Interface | org.biojava.nbio.structure.quaternary.io | BioJava |
| RCSBDescription | Corresponds to the wrapper element in an RCSB describeMol XML file. | Class | org.biojava.nbio.structure.rcsb | BioJava |
| RCSBDescriptionFactory | Fetches information from RCSB's RESTful Web Service Interface. | Class | org.biojava.nbio.structure.rcsb | BioJava |
| RCSBLigand | Corresponds to a ligand in a ligandInfo XML file. | Class | org.biojava.nbio.structure.rcsb | BioJava |
| RCSBLigands | Corresponds to the wrapper element "ligandInfo" in an RCSB ligandInfo XML file. | Class | org.biojava.nbio.structure.rcsb | BioJava |
| RCSBLigandsFactory | Fetches information from RCSB's RESTful Web Service Interface. | Class | org.biojava.nbio.structure.rcsb | BioJava |
| RCSBMacromolecule | Corresponds to a macromolecule in an RCSB describeMol XML file. | Class | org.biojava.nbio.structure.rcsb | BioJava |
| RCSBPolymer | Corresponds to a polymer in a describeMol XML file. | Class | org.biojava.nbio.structure.rcsb | BioJava |
| RCSBTaxonomy | Corresponds to a taxonomy in a describeMol XML file. | Class | org.biojava.nbio.structure.rcsb | BioJava |
| RCSBUpdates | Class | org.biojava.nbio.structure.rcsb | BioJava | |
| ReadUtils | Package-level static utilities for parsing XML. | Class | org.biojava.nbio.structure.rcsb | BioJava |
| RectangularPrism | Class | org.biojava.nbio.structure.symmetry.geometry | BioJava | |
| ReducedChemCompProvider | Unlike the DownloadChemCompProvider, this ChemCompProvider does not download any chem comp definitions. | Class | org.biojava.nbio.structure.io.mmcif | BioJava |
| ReferenceSuperimposer | Superimposes each structure in a MultipleAlignment onto a reference Performs a global superposition of the MultipleAlignment in case | Class | org.biojava.nbio.structure.align.multiple.util | BioJava |
| Refine | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| RefinerFailedException | Refinement of the self-alignment failed. | Class | org.biojava.nbio.structure.symmetry.internal | BioJava |
| RemoteBioUnitDataProvider | Class | org.biojava.nbio.structure.quaternary.io | BioJava | |
| RemoteDomainProvider | A DomainProvider that uses a mixture of SCOP and PDP domains. | Class | org.biojava.nbio.structure.domain | BioJava |
| RemotePDPProvider | A class that provided PDP assignments that are loaded from a remote web serverAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.domain | BioJava |
| RemoteRawBioUnitDataProvider | A BioUnitDataProvider that fetches the symmetry operations via remote calls to servers from RCSB PDBAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.quaternary.io | BioJava |
| RemoteScopInstallation | A class that fetches information about SCOP from a remote data-source. | Class | org.biojava.nbio.structure.scop | BioJava |
| RenderStyle | Class | org.biojava.nbio.structure.gui | BioJava | |
| RepresentativeXMLConverter | Class | org.biojava.nbio.structure.align.xml | BioJava | |
| ResidueGroup | A ResidueGroup is a set of residues that are part of a maximally connected component of the self-Alignment Graph in symmetry analysis. | Class | org.biojava.nbio.structure.symmetry.internal | BioJava |
| ResidueNumber | Everything that is needed to uniquely describe a residue positionAuthor:Andreas PrlicSee Also:Serialized Form | Class | org.biojava.nbio.structure | BioJava |
| ResidueRange | A chain, a start residue, and an end residue. | Class | org.biojava.nbio.structure | BioJava |
| ResidueRangeAndLength | A chain, a start residue, and an end residue. | Class | org.biojava.nbio.structure | BioJava |
| ResidueType | Enumerates the possible classifications of residues. | Class | org.biojava.nbio.structure.io.mmcif.chem | BioJava |
| ResourceManager | A class that manages the Strings that are defined in the spice. | Class | org.biojava.nbio.structure.align.util | BioJava |
| Rotation | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| RotationAxis | Calculates the rotation axis for an alignment A superposition of two structures is generally represented as a rotation | Class | org.biojava.nbio.structure.align.util | BioJava |
| RotationAxisAligner | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| RotationGroup | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| RotationSolver | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| SandboxStyleStructureProvider | The "Sandbox" style of organizing files is to have a directory structure like below, i. | Class | org.biojava.nbio.structure.io | BioJava |
| ScaleableMatrixPanel | A JPanel that can display the underlying distance matrix data of the protein structure alignment algorithm. | Class | org.biojava.nbio.structure.gui | BioJava |
| ScanSymmetry | Class | org.biojava.nbio.structure.symmetry.analysis | BioJava | |
| SCOPAutoSuggestProvider | Class | org.biojava.nbio.structure.align.gui.autosuggest | BioJava | |
| ScopCategory | The various categories provided by SCOP. | Class | org.biojava.nbio.structure.scop | BioJava |
| ScopDatabase | General API how to interact with SCOPSince:3. | Interface | org.biojava.nbio.structure.scop | BioJava |
| ScopDescription | dir. | Class | org.biojava.nbio.structure.scop | BioJava |
| ScopDescriptions | Class | org.biojava.nbio.structure.scop.server | BioJava | |
| ScopDomain | Container for the information for a domain. | Class | org.biojava.nbio.structure.scop | BioJava |
| ScopDomains | Class | org.biojava.nbio.structure.scop.server | BioJava | |
| ScopFactory | Controls the global ScopDatabase being used. | Class | org.biojava.nbio.structure.scop | BioJava |
| ScopInstallation | This class provides access to the SCOP protein structure classification. | Class | org.biojava.nbio.structure.scop | BioJava |
| ScopInstallationInstance | Class | org.biojava.nbio.structure.gui.util | BioJava | |
| ScopIOException | Indicates that an I/O error occurred with SCOP lazy initialization. | Class | org.biojava.nbio.structure.scop | BioJava |
| ScopMirror | Helper class to store paths to the four SCOP files The string "%s" is replaced with the version number. | Class | org.biojava.nbio.structure.scop | BioJava |
| ScopNode | Class | org.biojava.nbio.structure.scop | BioJava | |
| ScopNodes | Class | org.biojava.nbio.structure.scop.server | BioJava | |
| ScopSelectPanel | Class | org.biojava.nbio.structure.gui.util | BioJava | |
| ScoresCache | Interface for classes which implement a temporary cache for various numeric scores, e. | Interface | org.biojava.nbio.structure.align.multiple | BioJava |
| SecStrucCalc | Calculate and assign the secondary structure (SS) to the Groups of a Structure object. | Class | org.biojava.nbio.structure.secstruc | BioJava |
| SecStrucElement | A secondary structure element (SSE) is an object representing a block of sequential residues that share the same secondary structure type. | Class | org.biojava.nbio.structure.secstruc | BioJava |
| SecStrucInfo | Container for the secondary structure information of a single residue. | Class | org.biojava.nbio.structure.secstruc | BioJava |
| SecStrucState | This class extends the basic container for secondary structure annotation, including all the information used in the DSSP algorithm. | Class | org.biojava.nbio.structure.secstruc | BioJava |
| SecStrucTools | This class contains methods for obtaining and converting secondary structure information from BioJava Structures. | Class | org.biojava.nbio.structure.secstruc | BioJava |
| SecStrucType | This enum contains all of the secondary structure types found in the DSSP output. | Class | org.biojava.nbio.structure.secstruc | BioJava |
| Segment | Class | org.biojava.nbio.structure.domain.pdp | BioJava | |
| SegmentComparator | Class | org.biojava.nbio.structure.domain.pdp | BioJava | |
| Selection | Interface | org.biojava.nbio.structure.gui | BioJava | |
| SelectionImpl | Class | org.biojava.nbio.structure.gui | BioJava | |
| SelectMultiplePanel | A Text Panel that allows the user to specify multiple structure identifiers, space separated. | Class | org.biojava.nbio.structure.gui.util | BioJava |
| SelectPDBPanel | A Panel that allows user to specify PDB & chain ID, as well as sub-rangesAuthor:AndreasSee Also:Serialized Form | Class | org.biojava.nbio.structure.align.gui | BioJava |
| SeqMisMatch | Created by andreas on 9/11/15. | Interface | org.biojava.nbio.structure | BioJava |
| SeqMisMatchImpl | Created by andreas on 9/11/15. | Class | org.biojava.nbio.structure | BioJava |
| SeqRes2AtomAligner | Aligns the SEQRES residues to the ATOM residues. | Class | org.biojava.nbio.structure.io | BioJava |
| SequenceAlignmentCluster | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| SequenceDisplay | A sequence display that can show the results of a protein structure alignment. | Class | org.biojava.nbio.structure.gui | BioJava |
| SequenceFunctionOrderDetector | Calls Spencer's method for determining order. | Class | org.biojava.nbio.structure.symmetry.internal | BioJava |
| SequenceFunctionRefiner | Creates a refined alignment with the CE-Symm alternative self-alignment. | Class | org.biojava.nbio.structure.symmetry.internal | BioJava |
| SequenceMouseListener | a mouse listener for the AbstractChainRenderer class it listens to all mouse events and triggeres appropriate | Class | org.biojava.nbio.structure.gui.util | BioJava |
| SequenceScalePanel | A class that draws a Sequence as a rectangle, a scale display over it. | Class | org.biojava.nbio.structure.gui.util | BioJava |
| SerializableCache | A class that provides all that is necessary to create a Serializable CacheSince:3. | Class | org.biojava.nbio.structure.domain | BioJava |
| ShortSegmentRemover | Class | org.biojava.nbio.structure.domain.pdp | BioJava | |
| ShowPDBIDListener | Class | org.biojava.nbio.structure.align.gui | BioJava | |
| SiftsChainEntry | An entry in the chain-level SIFTS mapping between UniProt and the PDB. | Class | org.biojava.nbio.structure.io.sifts | BioJava |
| SiftsChainToUniprotMapping | A mapping between UniProt entries and PDB chains. | Class | org.biojava.nbio.structure.io.sifts | BioJava |
| SiftsEntity | Class | org.biojava.nbio.structure.io.sifts | BioJava | |
| SiftsMappingProvider | Class | org.biojava.nbio.structure.io.sifts | BioJava | |
| SiftsResidue | Class | org.biojava.nbio.structure.io.sifts | BioJava | |
| SiftsSegment | Class | org.biojava.nbio.structure.io.sifts | BioJava | |
| SiftsXMLParser | Class | org.biojava.nbio.structure.io.sifts | BioJava | |
| SigEva | Class | org.biojava.nbio.structure.align.fatcat.calc | BioJava | |
| SimpleMMcifConsumer | A MMcifConsumer implementation that builds an in-memory representation of the content of a mmcif file as a BioJava Structure object. | Class | org.biojava.nbio.structure.io.mmcif | BioJava |
| SimpleMMcifParser | A simple mmCif file parserString file = "path/to/mmcif/file"; | Class | org.biojava.nbio.structure.io.mmcif | BioJava |
| SingularValueDecomposition | Singular Value Decomposition. | Class | org.biojava.nbio.structure.jama | BioJava |
| Site | Holds the data of sites presented in PDB files. | Class | org.biojava.nbio.structure | BioJava |
| SmithWaterman3Daligner | provides a 3D superimposition based on the sequence alignmentAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.align.seq | BioJava |
| SmithWaterman3DParameters | Class | org.biojava.nbio.structure.align.seq | BioJava | |
| SmithWatermanUserArgumentProcessor | Class | org.biojava.nbio.structure.align.seq | BioJava | |
| SmithWatermanUserArgumentProcessor .SmithWatermanStartupParams | Class | org.biojava.nbio.structure.align.seq | BioJava | |
| SpaceGroup | A crystallographic space group. | Class | org.biojava.nbio.structure.xtal | BioJava |
| SpaceGroupMapElements | Class | org.biojava.nbio.structure.xtal.io | BioJava | |
| SpaceGroupMapRoot | Class | org.biojava.nbio.structure.xtal.io | BioJava | |
| SparseSquareMatrix | A sparse, square matrix, implementing using two arrays of sparse vectors, one representation for the rows and one for the columns. | Class | org.biojava.nbio.structure.math | BioJava |
| SparseVector | A sparse vector, implemented using a symbol table. | Class | org.biojava.nbio.structure.math | BioJava |
| SphereSampler | Class | org.biojava.nbio.structure.symmetry.geometry | BioJava | |
| SqrtColorMapper | Performs a sqrt transform on input before passing the values off to another For instance, to map [0^2, 10^2] to a rainbow gradient, use | Class | org.biojava.nbio.structure.gui.util.color | BioJava |
| SSBondImpl | A simple bean to store disulfide bridge information, the SSBOND records in the PDB files. | Class | org.biojava.nbio.structure.io | BioJava |
| StandardAminoAcid | A class that provides a set of standard amino acids. | Class | org.biojava.nbio.structure | BioJava |
| StartupParameters | a simple bean that contains the parameters that can get set at startupAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.align.ce | BioJava |
| StatusDisplay | Class | org.biojava.nbio.structure.align.gui.aligpanel | BioJava | |
| StrCompAlignment | Class | org.biojava.nbio.structure.align.pairwise | BioJava | |
| StrucAligParameters | A class that contains all the parameters of the structure alignment algorithm. | Class | org.biojava.nbio.structure.align | BioJava |
| Struct | a bean to contain the data of the _struct linesAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
| StructAsym | Contains the data for _struct_asymSince:1. | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
| StructConn | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| StructKeywords | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| StructNcsOper | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| StructRef | A class to containt the _struct_ref field dataAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
| StructRefSeq | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| StructRefSeqDif | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| StructSite | Created by Matt on 11/1/2015. | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
| StructSiteGen | Created by Matt on 10/31/2015. | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava |
| Structure | Interface for a structure object. | Interface | org.biojava.nbio.structure | BioJava |
| StructureAlignment | Interface | org.biojava.nbio.structure.align | BioJava | |
| StructureAlignmentDisplay | Class | org.biojava.nbio.structure.align.gui | BioJava | |
| StructureAlignmentFactory | Class | org.biojava.nbio.structure.align | BioJava | |
| StructureAlignmentJmol | A class that provides a simple GUI for JmolSince:1. | Class | org.biojava.nbio.structure.align.gui.jmol | BioJava |
| StructureAlignmentOptimizer | Class | org.biojava.nbio.structure.align.fatcat.calc | BioJava | |
| StructureException | An exception during the parsing of a PDB file. | Class | org.biojava.nbio.structure | BioJava |
| StructureIdentifier | An identifier that uniquely identifies a whole Structure or arbitrary substructure. | Interface | org.biojava.nbio.structure | BioJava |
| StructureImpl | provides the data contained in a PDB file. | Class | org.biojava.nbio.structure | BioJava |
| StructureInterface | An interface between 2 molecules (2 sets of atoms). | Class | org.biojava.nbio.structure.contact | BioJava |
| StructureInterfaceCluster | Class | org.biojava.nbio.structure.contact | BioJava | |
| StructureInterfaceList | A list of interfaces between 2 molecules (2 sets of atoms)Author:duarte_jSee Also:Serialized Form | Class | org.biojava.nbio.structure.contact | BioJava |
| StructureIO | A class that provides static access methods for easy lookup of protein structure related componentsSince:3. | Class | org.biojava.nbio.structure | BioJava |
| StructureIO .StructureFiletype | Class | org.biojava.nbio.structure | BioJava | |
| StructureIOFile | StructureIOFile extends StructureProvider with methods specific to parsing files from the filesystem. | Interface | org.biojava.nbio.structure.io | BioJava |
| StructureLoaderThread | Class | org.biojava.nbio.structure.align.gui | BioJava | |
| StructureName | A utility class that makes working with names of structures, domains and ranges easier. | Class | org.biojava.nbio.structure.align.client | BioJava |
| StructureName .Source | Class | org.biojava.nbio.structure.align.client | BioJava | |
| StructurePairAligner | Perform a pairwise protein structure superimposition. | Class | org.biojava.nbio.structure.align | BioJava |
| StructurePairSelector | To be implemented by JPanels that are part of the GUI to trigger structure aligmnents. | Interface | org.biojava.nbio.structure.gui.util | BioJava |
| StructureProvider | A class that can provide a protein structure object from somewhere. | Interface | org.biojava.nbio.structure.io | BioJava |
| StructureSequenceMatcher | A utility class with methods for matching ProteinSequences withAuthor:Spencer Bliven | Class | org.biojava.nbio.structure.io | BioJava |
| StructureTools | A class that provides some tool methods. | Class | org.biojava.nbio.structure | BioJava |
| StructureViewer | Interface | org.biojava.nbio.structure.gui | BioJava | |
| SubstructureIdentifier | This is the canonical way to identify a part of a structure. | Class | org.biojava.nbio.structure | BioJava |
| SubunitGraph | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| Subunits | A bean to represent info about the set of subunits being considered for a QuatSymmetryDetector alignment. | Class | org.biojava.nbio.structure.symmetry.core | BioJava |
| SuperPosition | Class | org.biojava.nbio.structure.symmetry.geometry | BioJava | |
| SuperPositionQCP | Class | org.biojava.nbio.structure.symmetry.geometry | BioJava | |
| SVDSuperimposer | A class that calculates the superimposition between two sets of atoms inspired by the biopython SVDSuperimposer class. | Class | org.biojava.nbio.structure | BioJava |
| SymbolTable | Sorted symbol table implementation using a java. | Class | org.biojava.nbio.structure.math | BioJava |
| SymmClash | Java class for anonymous complex type. | Class | org.biojava.nbio.structure.validation | BioJava |
| Symmetry | Class | org.biojava.nbio.structure.io.mmcif.model | BioJava | |
| SymmetryAxes | Data Structure that stores all the symmetry axis that describe the symmetry of a structure. | Class | org.biojava.nbio.structure.symmetry.internal | BioJava |
| SymmetryCalc | Calculates a symmetry analysis and displays the results. | Class | org.biojava.nbio.structure.symmetry.gui | BioJava |
| SymmetryDisplay | Class that provides visualizations methods for symmetry alignments. | Class | org.biojava.nbio.structure.symmetry.gui | BioJava |
| SymmetryGui | A JFrame that allows to trigger a symmetry analysis, either from files in a directory or after manual upload | Class | org.biojava.nbio.structure.symmetry.gui | BioJava |
| SymmetryListener | Action Listener for the symmetry menu. | Class | org.biojava.nbio.structure.symmetry.gui | BioJava |
| SymmetryRefiner | Interface for all symmetry refinement implementations. | Interface | org.biojava.nbio.structure.symmetry.internal | BioJava |
| SymmetryTools | Utility methods for the internal symmetry identification and manipulation. | Class | org.biojava.nbio.structure.symmetry.utils | BioJava |
| SymmOptimizer | Optimizes a symmetry alignment by a Monte Carlo score optimization of the repeat multiple alignment. | Class | org.biojava.nbio.structure.symmetry.internal | BioJava |
| SymoplibParser | A class containing static methods to parse the symop. | Class | org.biojava.nbio.structure.xtal | BioJava |
| SynchronizedOutFile | Class | org.biojava.nbio.structure.align.util | BioJava | |
| SystematicSolver | Class | org.biojava.nbio.structure.symmetry.core | BioJava | |
| SystemInfo | Class | org.biojava.nbio.structure.align.gui | BioJava | |
| Tetrahedron | Class | org.biojava.nbio.structure.symmetry.geometry | BioJava | |
| TransfAlgebraicAdapter | Class | org.biojava.nbio.structure.xtal.io | BioJava | |
| TransformType | Class | org.biojava.nbio.structure.xtal | BioJava | |
| TreeMapSpaceGroupWrapper | Class | org.biojava.nbio.structure.xtal.io | BioJava | |
| TreeSetStringWrapper | Class | org.biojava.nbio.structure.scop.server | BioJava | |
| UniqueSequenceList | Bean for a single sequence. | Class | org.biojava.nbio.structure.symmetry.core | BioJava |
| UnitCellBoundingBox | Class | org.biojava.nbio.structure.xtal | BioJava | |
| URLIdentifier | Represents a structure loaded from a URL (including a file URL) A few custom query parameters are supported: | Class | org.biojava.nbio.structure | BioJava |
| UserArgumentProcessor | Interface | org.biojava.nbio.structure.align.ce | BioJava | |
| UserConfiguration | A container to persist config to the file systemAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.align.util | BioJava |
| WebStartDBSearch | A Web Start wrapper for a FarmJobRunnable. | Class | org.biojava.nbio.structure.align.webstart | BioJava |
| WebStartDBSearchResults | Class | org.biojava.nbio.structure.align.webstart | BioJava | |
| WebStartMain | Class | org.biojava.nbio.structure.align.webstart | BioJava | |
| WwPDBValidationInformation | Java class for anonymous complex type. | Class | org.biojava.nbio.structure.validation | BioJava |
| XMLUtil | Utility classes for the XML serialization and de-serialization of SCOP. | Class | org.biojava.nbio.structure.scop.server | BioJava |
| ZipChemCompProvider | This chemical component provider retrieves and caches chemical component definition files from a zip archive specified in its construction. | Class | org.biojava.nbio.structure.io.mmcif | BioJava |