Uses of Package
org.biojava.nbio.structure
-
Classes in org.biojava.nbio.structure used by demo Class Description Structure Interface for a structure object.StructureException An exception during the parsing of a PDB file. -
Classes in org.biojava.nbio.structure used by org.biojava.nbio.protmod.structure Class Description Atom A simple interface for an Atom.Chain Defines the interface for a Chain.Group This is the data structure for a single Group of atoms.ResidueNumber Everything that is needed to uniquely describe a residue positionStructure Interface for a structure object. -
Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure Class Description AminoAcid AGroup
that represents an AminoAcid.Atom A simple interface for an Atom.AtomPositionMap A map fromResidueNumbers
to ATOM record positions in a PDB file.AtomPositionMap.GroupMatcher Used as a Predicate to indicate whether a particular Atom should be mappedAuthor Describes author attributes for author information in a PDB file.Bond A simple bond -- it stores information about two atoms as well as information about its bond order.BondType Work in progress - NOT final!Chain Defines the interface for a Chain.DBRef A class to represent database cross references.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.EntityInfo An object to contain the info from the PDB header for a Molecule.EntityType ExperimentalTechnique An enum to represent the experimental technique of a PDB structureGroup This is the data structure for a single Group of atoms.GroupType This contains basic categories for Group types.HetatomImpl Generic Implementation of a Group interface.HetatomImpl.PerformanceBehavior Behaviors for how to balance memory vs. performance.JournalArticle PDB-specificPDBCrystallographicInfo A class to hold crystallographic information about a PDB structure.PDBHeader A class that contains PDB Header information.PDBRecord An interface implemented by all classes that represent PDB records.PDBStatus.Status Represents the status of PDB IDs.ResidueNumber Everything that is needed to uniquely describe a residue positionResidueRange A chainName, a start residue, and an end residue.ResidueRangeAndLength A chain, a start residue, and an end residue.SeqMisMatch Created by andreas on 9/11/15.Site Holds the data of sites presented in PDB files.Structure Interface for a structure object.StructureException An exception during the parsing of a PDB file.StructureIdentifier An identifier that uniquely identifies a wholeStructure
or arbitrary substructure.StructureIO.StructureFiletype SubstructureIdentifier This is the canonical way to identify a part of a structure. -
Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.align Class Description Atom A simple interface for an Atom.Group This is the data structure for a single Group of atoms.Structure Interface for a structure object.StructureException An exception during the parsing of a PDB file. -
Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.align.ce Class Description Atom A simple interface for an Atom.Group This is the data structure for a single Group of atoms.Structure Interface for a structure object.StructureException An exception during the parsing of a PDB file. -
Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.align.client Class Description Atom A simple interface for an Atom.Structure Interface for a structure object.StructureException An exception during the parsing of a PDB file.StructureIdentifier An identifier that uniquely identifies a wholeStructure
or arbitrary substructure.SubstructureIdentifier This is the canonical way to identify a part of a structure. -
Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.align.fatcat Class Description Atom A simple interface for an Atom.StructureException An exception during the parsing of a PDB file. -
Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.align.fatcat.calc Class Description Atom A simple interface for an Atom.Group This is the data structure for a single Group of atoms.StructureException An exception during the parsing of a PDB file. -
Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.align.gui Class Description Atom A simple interface for an Atom.Group This is the data structure for a single Group of atoms.Structure Interface for a structure object.StructureException An exception during the parsing of a PDB file.StructureIdentifier An identifier that uniquely identifies a wholeStructure
or arbitrary substructure. -
Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.align.gui.aligpanel Class Description Atom A simple interface for an Atom.StructureException An exception during the parsing of a PDB file. -
Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.align.gui.jmol Class Description Atom A simple interface for an Atom.Structure Interface for a structure object. -
Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.align.helper Class Description Atom A simple interface for an Atom. -
Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.align.model Class Description Atom A simple interface for an Atom. -
Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.align.multiple Class Description Atom A simple interface for an Atom.StructureException An exception during the parsing of a PDB file.StructureIdentifier An identifier that uniquely identifies a wholeStructure
or arbitrary substructure. -
Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.align.multiple.mc Class Description StructureException An exception during the parsing of a PDB file. -
Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.align.multiple.util Class Description Atom A simple interface for an Atom.Structure Interface for a structure object.StructureException An exception during the parsing of a PDB file. -
Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.align.pairwise Class Description Atom A simple interface for an Atom.Structure Interface for a structure object.StructureException An exception during the parsing of a PDB file. -
Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.align.quaternary Class Description Atom A simple interface for an Atom.Structure Interface for a structure object.StructureException An exception during the parsing of a PDB file. -
Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.align.seq Class Description Atom A simple interface for an Atom.StructureException An exception during the parsing of a PDB file. -
Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.align.util Class Description Atom A simple interface for an Atom.Chain Defines the interface for a Chain.Group This is the data structure for a single Group of atoms.ResidueNumber Everything that is needed to uniquely describe a residue positionStructure Interface for a structure object.StructureException An exception during the parsing of a PDB file.StructureIdentifier An identifier that uniquely identifies a wholeStructure
or arbitrary substructure. -
Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.align.xml Class Description Atom A simple interface for an Atom.StructureException An exception during the parsing of a PDB file. -
Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.asa Class Description Atom A simple interface for an Atom.Group This is the data structure for a single Group of atoms.Structure Interface for a structure object. -
Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.basepairs Class Description Chain Defines the interface for a Chain.Group This is the data structure for a single Group of atoms.Structure Interface for a structure object. -
Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.cath Class Description Structure Interface for a structure object.StructureException An exception during the parsing of a PDB file.StructureIdentifier An identifier that uniquely identifies a wholeStructure
or arbitrary substructure.SubstructureIdentifier This is the canonical way to identify a part of a structure. -
Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.cluster Class Description Atom A simple interface for an Atom.Structure Interface for a structure object.StructureException An exception during the parsing of a PDB file.StructureIdentifier An identifier that uniquely identifies a wholeStructure
or arbitrary substructure. -
Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.contact Class Description Atom A simple interface for an Atom.Chain Defines the interface for a Chain.EntityInfo An object to contain the info from the PDB header for a Molecule.Group This is the data structure for a single Group of atoms.ResidueNumber Everything that is needed to uniquely describe a residue positionStructure Interface for a structure object. -
Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.domain Class Description Atom A simple interface for an Atom.ResidueRange A chainName, a start residue, and an end residue.Structure Interface for a structure object.StructureException An exception during the parsing of a PDB file.StructureIdentifier An identifier that uniquely identifies a wholeStructure
or arbitrary substructure.SubstructureIdentifier This is the canonical way to identify a part of a structure. -
Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.domain.pdp Class Description Atom A simple interface for an Atom.StructureException An exception during the parsing of a PDB file. -
Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.ecod Class Description ResidueRange A chainName, a start residue, and an end residue.Structure Interface for a structure object.StructureException An exception during the parsing of a PDB file.StructureIdentifier An identifier that uniquely identifies a wholeStructure
or arbitrary substructure.SubstructureIdentifier This is the canonical way to identify a part of a structure. -
Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.gui Class Description Structure Interface for a structure object. -
Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.gui.events Class Description Structure Interface for a structure object. -
Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.gui.util Class Description Chain Defines the interface for a Chain.Structure Interface for a structure object.StructureException An exception during the parsing of a PDB file.StructureIdentifier An identifier that uniquely identifies a wholeStructure
or arbitrary substructure. -
Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.io Class Description Atom A simple interface for an Atom.Bond A simple bond -- it stores information about two atoms as well as information about its bond order.Chain Defines the interface for a Chain.EntityInfo An object to contain the info from the PDB header for a Molecule.Group This is the data structure for a single Group of atoms.PDBRecord An interface implemented by all classes that represent PDB records.ResidueNumber Everything that is needed to uniquely describe a residue positionStructure Interface for a structure object.StructureException An exception during the parsing of a PDB file. -
Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.io.mmcif Class Description Atom A simple interface for an Atom.Chain Defines the interface for a Chain.Group This is the data structure for a single Group of atoms.Structure Interface for a structure object. -
Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.io.mmtf Class Description Atom A simple interface for an Atom.Chain Defines the interface for a Chain.ExperimentalTechnique An enum to represent the experimental technique of a PDB structureGroup This is the data structure for a single Group of atoms.PDBCrystallographicInfo A class to hold crystallographic information about a PDB structure.Structure Interface for a structure object. -
Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.quaternary Class Description Structure Interface for a structure object. -
Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.scop Class Description ResidueRange A chainName, a start residue, and an end residue.Structure Interface for a structure object.StructureException An exception during the parsing of a PDB file.StructureIdentifier An identifier that uniquely identifies a wholeStructure
or arbitrary substructure.SubstructureIdentifier This is the canonical way to identify a part of a structure. -
Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.secstruc Class Description Group This is the data structure for a single Group of atoms.ResidueNumber Everything that is needed to uniquely describe a residue positionResidueRangeAndLength A chain, a start residue, and an end residue.Structure Interface for a structure object.StructureException An exception during the parsing of a PDB file. -
Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.symmetry.core Class Description Structure Interface for a structure object. -
Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.symmetry.gui Class Description Structure Interface for a structure object.StructureException An exception during the parsing of a PDB file. -
Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.symmetry.internal Class Description Atom A simple interface for an Atom.StructureException An exception during the parsing of a PDB file.StructureIdentifier An identifier that uniquely identifies a wholeStructure
or arbitrary substructure. -
Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.symmetry.utils Class Description Atom A simple interface for an Atom.Group This is the data structure for a single Group of atoms.Structure Interface for a structure object.StructureException An exception during the parsing of a PDB file. -
Classes in org.biojava.nbio.structure used by org.biojava.nbio.structure.xtal Class Description Structure Interface for a structure object.