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
org.biojava.nbio.structure.io.mmcif	Input and Output of mmcif files.

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

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

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

Class and Description
PDBFileParser This class implements the actual PDB file parsing.
PDBParseException An exception during the parsing of a PDB file.

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

Class and 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.

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

Class and 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 MMCIFFileReader.
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.
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 and 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.

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

Class and 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.