Package org.biojava.nbio.structure.io
Class PDBFileReader
- java.lang.Object
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- org.biojava.nbio.structure.io.LocalPDBDirectory
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- org.biojava.nbio.structure.io.PDBFileReader
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- All Implemented Interfaces:
StructureIOFile
,StructureProvider
public class PDBFileReader extends LocalPDBDirectory
The wrapper class for parsing a PDB file.
Several flags can be set for this class
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#setAutoFetch(boolean)
- if the PDB file can not be found locally, should it be fetched from the PDB ftp servers? (default:false) - Other parameters can be set using the
LocalPDBDirectory.setFileParsingParameters(FileParsingParameters)
Example
Q: How can I get a Structure object from a PDB file?
A:
public
Access PDB files from a directory, take care of compressed PDB filesStructure
loadStructure(String pathToPDBFile){PDBFileReader
pdbreader = newPDBFileReader
();Structure
structure = null; try{ structure = pdbreader.getStructure(pathToPDBFile); System.out.println(structure); } catch (IOException e) { e.printStackTrace(); } return structure; }public
Structure
loadStructureById() { String path = "/path/to/PDB/directory/";PDBFileReader
pdbreader = newPDBFileReader
(); pdbreader.setPath(path);Structure
structure = null; try { structure = pdbreader.getStructureById("5pti"); } catch (IOException e){ e.printStackTrace(); } return structure; }- Author:
- Andreas Prlic
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Nested Class Summary
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Nested classes/interfaces inherited from class org.biojava.nbio.structure.io.LocalPDBDirectory
LocalPDBDirectory.FetchBehavior, LocalPDBDirectory.ObsoleteBehavior
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Field Summary
Fields Modifier and Type Field Description static String[]
PDB_OBSOLETE_DIR
static String[]
PDB_SPLIT_DIR
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Fields inherited from class org.biojava.nbio.structure.io.LocalPDBDirectory
DEFAULT_PDB_FILE_SERVER, LAST_REMEDIATION_DATE, lineSplit, MIN_PDB_FILE_SIZE, PDB_FILE_SERVER_PROPERTY
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Constructor Summary
Constructors Constructor Description PDBFileReader()
Constructs a new PDBFileReader, initializing the extensions member variable.PDBFileReader(String path)
Constructs a new PDBFileReader, initializing the extensions member variable.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected String
getFilename(String pdbId)
Converts a PDB ID into a filename with the proper extensionprotected String[]
getObsoleteDirPath()
Location of obsolete files within the directory, as an array of paths.protected String[]
getSplitDirPath()
Location of split files within the directory, as an array of paths.Structure
getStructure(InputStream inStream)
Handles the actual parsing of the file into a Structure object.-
Methods inherited from class org.biojava.nbio.structure.io.LocalPDBDirectory
addExtension, checkFileExists, clearExtensions, deleteStructure, downloadStructure, getDir, getExtensions, getFetchBehavior, getFileParsingParameters, getInputStream, getLocalFile, getObsoleteBehavior, getPath, getServerName, getStructure, getStructure, getStructure, getStructureById, initPaths, prefetchStructure, setFetchBehavior, setFileParsingParameters, setObsoleteBehavior, setPath
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Field Detail
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PDB_SPLIT_DIR
public static final String[] PDB_SPLIT_DIR
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PDB_OBSOLETE_DIR
public static final String[] PDB_OBSOLETE_DIR
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Constructor Detail
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PDBFileReader
public PDBFileReader()
Constructs a new PDBFileReader, initializing the extensions member variable. The path is initialized in the same way asUserConfiguration
, i.e. to system property/environment variableUserConfiguration.PDB_DIR
. Both autoFetch and splitDir are initialized to false
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PDBFileReader
public PDBFileReader(String path)
Constructs a new PDBFileReader, initializing the extensions member variable. The path is initialized to the given path, both autoFetch and splitDir are initialized to false.If path is null, initialize using the system property/environment variable
UserConfiguration.PDB_DIR
.- Parameters:
path
- Path to the PDB file directory
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Method Detail
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getFilename
protected String getFilename(String pdbId)
Description copied from class:LocalPDBDirectory
Converts a PDB ID into a filename with the proper extension- Specified by:
getFilename
in classLocalPDBDirectory
- Returns:
- The filename, e.g. "4hhb.pdb.gz"
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getStructure
public Structure getStructure(InputStream inStream) throws IOException
Description copied from class:LocalPDBDirectory
Handles the actual parsing of the file into a Structure object.- Specified by:
getStructure
in classLocalPDBDirectory
- Returns:
- Throws:
IOException
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getSplitDirPath
protected String[] getSplitDirPath()
Description copied from class:LocalPDBDirectory
Location of split files within the directory, as an array of paths. These will be joined with either slashes (for the URL) or the file separator (for directories). The returned results should be constant, to allow for caching.- Specified by:
getSplitDirPath
in classLocalPDBDirectory
- Returns:
- A list of directories, relative to the /pub/pdb directory on the server
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getObsoleteDirPath
protected String[] getObsoleteDirPath()
Description copied from class:LocalPDBDirectory
Location of obsolete files within the directory, as an array of paths. These will be joined with either slashes (for the URL) or the file separator (for directories). The returned results should be constant, to allow for caching.- Specified by:
getObsoleteDirPath
in classLocalPDBDirectory
- Returns:
- A list of directories, relative to the /pub/pdb directory on the server
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