|
|||||||||
PREV PACKAGE NEXT PACKAGE | FRAMES NO FRAMES |
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. |
Input and Output of Structures
|
|||||||||
PREV PACKAGE NEXT PACKAGE | FRAMES NO FRAMES |