Interface | Description |
---|---|
StructureIO | Deprecated
Do no use any longer, StructureIO is now a static utility calss on the org.biojava3.structure level..
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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 | Description |
---|---|
CAConverter |
Converts full atom representations to Calpha only ones.
|
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.
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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:
|
PDBBioAssemblyParser | |
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.
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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 | Description |
---|---|
PDBParseException |
An exception during the parsing of a PDB file.
|