Uses of Package org.biojava.nbio.structure.io (biojava 5.2.0 API)

Packages that use org.biojava.nbio.structure.io
Package	Description
demo
org.biojava.nbio.structure
org.biojava.nbio.structure.align.util
org.biojava.nbio.structure.io	Input and Output of Structures
org.biojava.nbio.structure.io.mmcif	Input and Output of mmcif files.

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.

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.

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 `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.mmcif
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.