Interfaces and classes for protein structure (PDB).
See also the BioJava 3 tutorial for more information on the protein structure modules.
Parse PDB filesTo load a PDB file see the PDBFileReader class in the IO subpackage.
Parse mmCif filesTo laod a mmCif file see the MMCIFFileReader class.
The Structure objectThe Structure object allows to access the PDB header information as well as to the data from the ATOM records. The header information is currently available through the following objects: how to work with groups.
- Calculate protein structure alignments with CE and FATCAT.
- Serialize PDB files to databases using Hibernate
- Tools for performing calculations
- Display structures in Jmol
For more documentation on how to work with the Structure API please see http://biojava.org/wiki/BioJava:CookBook#Protein_Structure
Interface Summary Interface Description AminoAcidA
Groupthat represents an AminoAcid.
AtomA simple interface for an Atom. AtomPositionMap.GroupMatcherUsed as a Predicate to indicate whether a particular Atom should be mapped BondA simple bond -- it stores information about two atoms as well as information about its bond order. ChainDefines the interface for a Chain. GroupThis is the data structure for a single Group of atoms. PDBRecordAn interface implemented by all classes that represent PDB records. SeqMisMatchCreated by andreas on 9/11/15. StructureInterface for a structure object. StructureIdentifierAn identifier that uniquely identifies a whole
Structureor arbitrary substructure.
Class Summary Class Description AminoAcidImplAminoAcid inherits most from Hetatom. AtomImplImplementation of an Atom of a PDB file. AtomIteratoran iterator over all atoms of a structure / group. AtomPositionMapA map from
ResidueNumbersto ATOM record positions in a PDB file.
AugmentedResidueRangeCreated by douglas on 1/23/15. AuthorDescribes author attributes for author information in a PDB file. BioAssemblyIdentifier BondImplA simple bond -- it stores information about two atoms as well as information about its bond order. CalcUtility operations on Atoms, AminoAcids, Matrices, Point3d, etc. ChainImplA Chain in a PDB file. DatabasePDBRevRecordRepresents revision records for use by
DBRefA class to represent database cross references. EntityInfoAn object to contain the info from the PDB header for a Molecule. GroupIteratorAn iterator over all groups of a structure. HetatomImplGeneric Implementation of a Group interface. JournalArticlePDB-specific ModelAn internal utility class for StructureImpl to make it easier to manage poly and nonpoly chains. MutatorA class that can change one amino acid to another. NucleotideImplA nucleotide group is almost the same as a Hetatm group. PassthroughIdentifierA stub StructureIdentifier, representing the full structure in all cases. PDBCrystallographicInfoA class to hold crystallographic information about a PDB structure. PDBHeaderA class that contains PDB Header information. PdbIdA wrapper class for the PDB identifier. PDBStatusMethods for getting the status of a PDB file (current, removed, unreleased) and for accessing different versions of the structure. ResidueNumberEverything that is needed to uniquely describe a residue position ResidueRangeA chainName, a start residue, and an end residue. ResidueRangeAndLengthA chain, a start residue, and an end residue. SeqMisMatchImplCreated by andreas on 9/11/15. SiteHolds the data of sites presented in PDB files. StandardAminoAcidA class that provides a set of standard amino acids. StructureImplImplementation of a PDB Structure. StructureIOA class that provides static access methods for easy lookup of protein structure related components StructureToolsA class that provides some tool methods. SubstructureIdentifierThis is the canonical way to identify a part of a structure. URLIdentifierRepresents 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
Enum Summary Enum Description BondTypeWork in progress - NOT final! ElementElement is an enumeration of the elements of the periodic table. ElementTypeElementType is an enumeration of the types of elements found in the periodic table. EntityType ExperimentalTechniqueAn enum to represent the experimental technique of a PDB structure GroupTypeThis contains basic categories for Group types. HetatomImpl.PerformanceBehaviorBehaviors for how to balance memory vs. performance. PDBStatus.StatusRepresents a simplified 3 state status of PDB IDs.
Exception Summary Exception Description StructureExceptionAn exception during the parsing of a PDB file.