Package org.biojava.bio.structure.io

Input and Output of Structures

See:
Description

Interface Summary

StructureIO	Defines the interface how to access Structure (- PDB file) input,output readers, writers.
StructureIOFile	interface StructureIOFile extends the StructureIO interface and adds a few File specific methods.
StructureProvider	A class that can provide a protein structure object from somewhere.

Class Summary

CAConverter	Converts full atom representations to Calpha only ones.
FastaStructureParser	Reads a protein sequence from a fasta file and attempts to match it to a 3D structure.
FileConvert	Methods to convert a structure object into different file formats.
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.
LocalCacheStructureProvider	Provides structures based on locally cached PDB files.
MMCIFFileReader	How to parse an mmCif file:
PDBFileParser	This class implements the actual PDB file parsing.
PDBFileReader	The wrapper class for parsing a PDB file.
PDBSRSReader	reads a PDB file from a local SRS installation using getz Actually is the same as PDBFileReader, but instead of reading from a file stream, reads from a buffered stream.
SandboxStyleStructureProvider	The "Sandbox" style of organizing files is to have a directory structure like below, i.e.
SeqRes2AtomAligner	Aligns the SEQRES residues to the ATOM residues.
StructureSequenceMatcher	A utility class with methods for matching ProteinSequences with Structures.

Exception Summary

PDBParseException

An exception during the parsing of a PDB file.

Package org.biojava.bio.structure.io Description

Input and Output of Structures