org.biojava.bio.structure.io
Class LocalCacheStructureProvider

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

All Implemented Interfaces:

StructureProvider

public class LocalCacheStructureProvider
extends java.lang.Object
implements StructureProvider

Provides structures based on locally cached PDB files. The path where to cache this can be configured in FileParsingParameters

Author:

Andreas Prlic

Field Summary

static java.lang.String

lineSplit

Constructor Summary

LocalCacheStructureProvider()

Method Summary

Structure	getBiologicalUnit(java.lang.String pdbId) Returns the first available biological unit for the PDB ID.
FileParsingParameters	getFileParsingParameters() Get the parameters that should be used for file parsing
java.lang.String	getPath() Returns the path value.
Structure	getStructureById(java.lang.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(java.lang.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

lineSplit

public static final java.lang.String lineSplit

Constructor Detail

LocalCacheStructureProvider

public LocalCacheStructureProvider()

Method Detail

setPath

public void setPath(java.lang.String p)

directory where to find PDB files

getPath

public java.lang.String getPath()

Returns the path value.

Returns:

a String representing the path value

See Also:

setPath(java.lang.String)

getStructureById

public Structure getStructureById(java.lang.String pdbId)
                           throws java.io.IOException

Description copied from interface: StructureProvider

get the structure for a PDB ID

Specified by:

getStructureById in interface StructureProvider

Returns:

Throws:

java.io.IOException

getBiologicalUnit

public Structure getBiologicalUnit(java.lang.String pdbId)
                            throws StructureException,
                                   java.io.IOException

Returns the first available biological unit for the PDB ID. Note: the biological units are represented using multiple models. You need to work with all models to get the full set of atoms.

Specified by:

getBiologicalUnit in interface StructureProvider

Returns:

Throws:

java.io.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