java.lang.Object

org.biojava.nbio.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

Fields

Modifier and Type

Field

Description

static final String

fileSeparator
Constructor Summary

Constructors

Constructor

Description

SandboxStyleStructureProvider()
Method Summary

Modifier and Type

Method

Description

List<String>

getAllPDBIDs()

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

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 Details
- fileSeparator
  
  public static final String fileSeparator
Constructor Details
- SandboxStyleStructureProvider
  
  public SandboxStyleStructureProvider()
Method Details
- 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
- 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

Class SandboxStyleStructureProvider

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Details

fileSeparator

Constructor Details

SandboxStyleStructureProvider

Method Details

setPath

getStructureById

setFileParsingParameters

getFileParsingParameters

getAllPDBIDs