Uses of Package
org.biojava.nbio.structure.io

Packages that use org.biojava.nbio.structure.io

Package	Description
demo
org.biojava.nbio.structure	Interfaces and classes for protein structure (PDB).
org.biojava.nbio.structure.align.util
org.biojava.nbio.structure.io	Input and Output of Structures
org.biojava.nbio.structure.io.cif

Classes in org.biojava.nbio.structure.io used by demo

Class	Description
PDBFileReader	The wrapper class for parsing a PDB file.

Classes in org.biojava.nbio.structure.io used by org.biojava.nbio.structure

Class	Description
PDBFileParser	This class implements the actual PDB file parsing.
PDBParseException	An exception during the parsing of a PDB file.
StructureFiletype	An enum of supported file formats.

Classes in org.biojava.nbio.structure.io used by org.biojava.nbio.structure.align.util

Class	Description
FileParsingParameters	A class that configures parameters that can be sent to the PDB file parsers FileParsingParameters.setParseCAOnly(boolean) - parse only the Atom records for C-alpha atoms FileParsingParameters.setParseSecStruc(boolean) - a flag if the secondary structure information from the PDB file (author's assignment) should be parsed.
LocalPDBDirectory.FetchBehavior	Controls when the class should fetch files from the ftp server
LocalPDBDirectory.ObsoleteBehavior	Behaviors for when an obsolete structure is requested.
StructureFiletype	An enum of supported file formats.

Classes in org.biojava.nbio.structure.io used by org.biojava.nbio.structure.io

Class	Description
FileParsingParameters	A class that configures parameters that can be sent to the PDB file parsers FileParsingParameters.setParseCAOnly(boolean) - parse only the Atom records for C-alpha atoms FileParsingParameters.setParseSecStruc(boolean) - a flag if the secondary structure information from the PDB file (author's assignment) should be parsed.
LocalPDBDirectory	Superclass for classes which download and interact with the PDB's FTP server, specifically PDBFileReader and CifFileReader.
LocalPDBDirectory.FetchBehavior	Controls when the class should fetch files from the ftp server
LocalPDBDirectory.ObsoleteBehavior	Behaviors for when an obsolete structure is requested.
SSBondImpl	A simple bean to store disulfide bridge information, the SSBOND records in the PDB files.
StructureFiletype	An enum of supported file formats.
StructureIOFile	StructureIOFile extends StructureProvider with methods specific to parsing files from the filesystem.
StructureProvider	A class that can provide a protein structure object from somewhere.

Classes in org.biojava.nbio.structure.io used by org.biojava.nbio.structure.io.cif

Class	Description
FileParsingParameters	A class that configures parameters that can be sent to the PDB file parsers FileParsingParameters.setParseCAOnly(boolean) - parse only the Atom records for C-alpha atoms FileParsingParameters.setParseSecStruc(boolean) - a flag if the secondary structure information from the PDB file (author's assignment) should be parsed.