Interface | Description |
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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 |
StructureIOFile defines a few methods that are useful when parsing PDB files from file system.
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StructureProvider |
A class that can provide a protein structure object from somewhere.
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Class | Description |
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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.
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CAConverter |
Converts full atom representations to Calpha only ones.
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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.
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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.
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MMCIFFileReader |
How to parse an mmCif file:
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PDBBioAssemblyParser |
Parses REMARK 350 records in a PDB file and creates transformations to
construct the quaternary structure of a protein from an asymmetric unit
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PDBFileParser |
This class implements the actual PDB file parsing.
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PDBFileReader |
The wrapper class for parsing a PDB file.
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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.
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SeqRes2AtomAligner |
Aligns the SEQRES residues to the ATOM residues.
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StructureSequenceMatcher |
A utility class with methods for matching ProteinSequences with
Structures.
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Exception | Description |
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PDBParseException |
An exception during the parsing of a PDB file.
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