| Interface | Description |
|---|---|
| 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 | Description |
|---|---|
| CAConverter |
Converts full atom representations to Calpha only ones.
|
| 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:
public static void main(String[] args){
String filename = "/path/to/something.cif.gz" ;
StructureIOFile reader = new MMCIFFileReader();
try{
Structure struc = reader.getStructure(filename);
System.out.println(struc);
} catch (Exception e) {
e.printStackTrace();
}
}
|
| 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. 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
a1/2a1v/2a1v.cif.gz
a1/2a1v/2a1v.dssp.gz
a1/2a1v/2a1v.pdb-250.jpg.gz
a1/2a1v/2a1v.pdb-500.jpg.gz
a1/2a1v/2a1v.pdb-65.jpg.gz
a1/2a1v/2a1v.pdb-80.jpg.gz
a1/2a1v/2a1v.pdb1-250.jpg.gz
a1/2a1v/2a1v.pdb1-500.jpg.gz
a1/2a1v/2a1v.pdb1-65.jpg.gz
a1/2a1v/2a1v.pdb1-80.jpg.gz
a1/2a1v/2a1v.pdb1.gz
a1/2a1v/2a1v.stride.gz
a1/2a1v/2a1v.xml.gz
a1/2a1v/pdb2a1v.ent.gz
a1/2a1v/r2a1vsf.ent.gz
a1/2a1w/2a1w-deriv.cif.gz
a1/2a1w/2a1w-extatom.xml.gz
a1/2a1w/2a1w-noatom.xml.gz
a1/2a1w/2a1w.cif.gz
a1/2a1w/2a1w.dssp.gz
a1/2a1w/2a1w.pdb-250.jpg.gz
a1/2a1w/2a1w.pdb-500.jpg.gz
a1/2a1w/2a1w.pdb-65.jpg.gz
a1/2a1w/2a1w.pdb-80.jpg.gz
a1/2a1w/2a1w.pdb1-250.jpg.gz
a1/2a1w/2a1w.pdb1-500.jpg.gz
a1/2a1w/2a1w.pdb1-65.jpg.gz
a1/2a1w/2a1w.pdb1-80.jpg.gz
a1/2a1w/2a1w.pdb1.gz
a1/2a1w/2a1w.pdb2-250.jpg.gz
a1/2a1w/2a1w.pdb2-500.jpg.gz
a1/2a1w/2a1w.pdb2-65.jpg.gz
a1/2a1w/2a1w.pdb2-80.jpg.gz
a1/2a1w/2a1w.pdb2.gz
a1/2a1w/2a1w.pdb3-250.jpg.gz
a1/2a1w/2a1w.pdb3-500.jpg.gz
a1/2a1w/2a1w.pdb3-65.jpg.gz
a1/2a1w/2a1w.pdb3-80.jpg.gz
a1/2a1w/2a1w.pdb3.gz
a1/2a1w/2a1w.pdb4-250.jpg.gz
a1/2a1w/2a1w.pdb4-500.jpg.gz
a1/2a1w/2a1w.pdb4-65.jpg.gz
a1/2a1w/2a1w.pdb4-80.jpg.gz
a1/2a1w/2a1w.pdb4.gz
a1/2a1w/2a1w.pdb5-250.jpg.gz
a1/2a1w/2a1w.pdb5-500.jpg.gz
a1/2a1w/2a1w.pdb5-65.jpg.gz
a1/2a1w/2a1w.pdb5-80.jpg.gz
a1/2a1w/2a1w.pdb5.gz
a1/2a1w/2a1w.pdb6-250.jpg.gz
a1/2a1w/2a1w.pdb6-500.jpg.gz
a1/2a1w/2a1w.pdb6-65.jpg.gz
a1/2a1w/2a1w.pdb6-80.jpg.gz
a1/2a1w/2a1w.pdb6.gz
a1/2a1w/2a1w.stride.gz
a1/2a1w/2a1w.xml.gz
a1/2a1w/pdb2a1w.ent.gz
a1/2a1w/r2a1wsf.ent.gz
a1/2a1x/2a1x-deriv.cif.gz
a1/2a1x/2a1x-extatom.xml.gz
a1/2a1x/2a1x-noatom.xml.gz
|
| SeqRes2AtomAligner |
Aligns the SEQRES residues to the ATOM residues.
|
| Exception | Description |
|---|---|
| PDBParseException |
An exception during the parsing of a PDB file.
|
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