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.
 

Class Summary
CAConverter Converts full atom representations to Calpha only ones.
DASStructureClient A DAS client that connects to a DAS structure service and returns a Biojava structure class.
FileConvert Methods to convert a structure object into different file formats.
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.
PDBMSDReader retreive a structure from an installation of the MSD - search database ( http://www.ebi.ac.uk/msd/index.html , http://www.ebi.ac.uk/msd-srv/docs/dbdoc/ )
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.
SeqRes2AtomAligner Aligns the SEQRES residues to the ATOM residues.
 

Exception Summary
PDBParseException An exception during the parsing of a PDB file.
 

Package org.biojava.bio.structure.io Description

Input and Output of Structures