Package org.biojava.nbio.structure.io
Class SandboxStyleStructureProvider
- java.lang.Object
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- org.biojava.nbio.structure.io.SandboxStyleStructureProvider
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- 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
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Field Summary
Fields Modifier and Type Field Description static String
fileSeparator
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Constructor Summary
Constructors Constructor Description SandboxStyleStructureProvider()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description List<String>
getAllPDBIDs()
Returns a list of all PDB IDs that are available in this installationFileParsingParameters
getFileParsingParameters()
Get the parameters that should be used for file parsingStructure
getStructureById(String pdbId)
Get the structure for a PDB IDvoid
setFileParsingParameters(FileParsingParameters params)
Set the parameters that should be used for file parsingvoid
setPath(String p)
directory where to find PDB files
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Field Detail
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fileSeparator
public static final String fileSeparator
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Constructor Detail
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SandboxStyleStructureProvider
public SandboxStyleStructureProvider()
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Method Detail
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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 interfaceStructureProvider
- Returns:
- Throws:
IOException
StructureException
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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 interfaceStructureProvider
- Parameters:
params
- FileParsingParameters
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getFileParsingParameters
public FileParsingParameters getFileParsingParameters()
Description copied from interface:StructureProvider
Get the parameters that should be used for file parsing- Specified by:
getFileParsingParameters
in interfaceStructureProvider
- Returns:
- the FileParsingParameters that are configuring the behavior of the parser
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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
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