Package org.biojava.nbio.structure.io

Input and Output of Structures

Interface Summary

Interface	Description
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.

Class Summary

Class	Description
BondMaker	Adds polymer bonds for peptides and nucleotides based on distance cutoffs and intra-group (residue) bonds based on data from the Chemical Component Dictionary to the Structure object.
CAConverter	Converts full atom representations to Calpha only ones.
ChargeAdder	A class to add appropriate charge information to a structure.
EntityFinder	Heuristical finding of Entities (called Compounds in legacy PDB format) in a given Structure.
FastaAFPChainConverter	A collection of static utilities to convert between AFPChains and FastaSequences.
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.
GroupToSDF
LocalPDBDirectory	Superclass for classes which download and interact with the PDB's FTP server, specifically PDBFileReader and MMCIFFileReader.
MMCIFFileReader	How to parse an mmCif file:
MMTFFileReader	A class to read MMTF files and cache them locally.
PDBBioAssemblyParser	Parses REMARK 350 records in a PDB file and creates transformations to construct the quaternary structure of a protein from an asymmetric unit
PDBFileParser	This class implements the actual PDB file parsing.
PDBFileReader	The wrapper class for parsing a PDB file.
SandboxStyleStructureProvider	The "Sandbox" style of organizing files is to have a directory structure like below, i.e. the files are organized into directory with two characters, based on the two middle characters of a PDB ID directory of PDB ID several files that are available for this PDB ID
SeqRes2AtomAligner	Aligns the SEQRES residues to the ATOM residues.
SSBondImpl	A simple bean to store disulfide bridge information, the SSBOND records in the PDB files.
StructureSequenceMatcher	A utility class with methods for matching ProteinSequences with Structures.

Enum Summary

Enum	Description
LocalPDBDirectory.FetchBehavior	Controls when the class should fetch files from the ftp server
LocalPDBDirectory.ObsoleteBehavior	Behaviors for when an obsolete structure is requested.

Exception Summary

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