org.biojava.bio.structure.io
Class SandboxStyleStructureProvider

java.lang.Object
  org.biojava.bio.structure.io.SandboxStyleStructureProvider

All Implemented Interfaces:

StructureProvider

public class SandboxStyleStructureProvider
extends Object
implements StructureProvider

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

Author:

Andreas Prlic

Field Summary

static String

fileSeparator

Constructor Summary

SandboxStyleStructureProvider()

Method Summary

List<String>	getAllPDBIDs() Returns a list of all PDB IDs that are available in this installation
Structure	getBiologicalUnit(String pdbId) get the biological unit for a file
FileParsingParameters	getFileParsingParameters() Get the parameters that should be used for file parsing
Structure	getStructureById(String pdbId) get the structure for a PDB ID
void	setFileParsingParameters(FileParsingParameters params) Set the parameters that should be used for file parsing
void	setPath(String p) directory where to find PDB files

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

fileSeparator

public static final String fileSeparator

Constructor Detail

SandboxStyleStructureProvider

public SandboxStyleStructureProvider()

Method Detail

setPath

public void setPath(String p)

directory where to find PDB files

getStructureById

public Structure getStructureById(String pdbId)
                           throws IOException,
                                  StructureException

Description copied from interface: StructureProvider

get the structure for a PDB ID

Specified by:

getStructureById in interface StructureProvider

Returns:

Throws:

IOException

StructureException

getBiologicalUnit

public Structure getBiologicalUnit(String pdbId)
                            throws StructureException,
                                   IOException

Description copied from interface: StructureProvider

get the biological unit for a file

Specified by:

getBiologicalUnit in interface StructureProvider

Returns:

Throws:

StructureException

IOException

setFileParsingParameters

public void setFileParsingParameters(FileParsingParameters params)

Description copied from interface: StructureProvider

Set the parameters that should be used for file parsing

Specified by:

setFileParsingParameters in interface StructureProvider

Parameters:

params - FileParsingParameters

getFileParsingParameters

public FileParsingParameters getFileParsingParameters()

Description copied from interface: StructureProvider

Get the parameters that should be used for file parsing

Specified by:

getFileParsingParameters in interface StructureProvider

Returns:

the FileParsingParameters that are configuring the behavior of the parser

getAllPDBIDs

public List<String> getAllPDBIDs()
                          throws IOException

Returns a list of all PDB IDs that are available in this installation

Returns:

a list of PDB IDs

Throws:

IOException