org.biojava.nbio.structure.io

Class PDBFileReader

java.lang.Object

org.biojava.nbio.structure.io.LocalPDBDirectory

org.biojava.nbio.structure.io.PDBFileReader

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

• LocalPDBDirectory.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 setFileParsingParameters(FileParsingParameters)

Example

Q: How can I get a Structure object from a PDB file?

A:

 public Structure loadStructure(String pathToPDBFile){
                PDBFileReader pdbreader = new PDBFileReader();

                Structure structure = null;
                try{
                        structure = pdbreader.getStructure(pathToPDBFile);
                        System.out.println(structure);
                } catch (IOException e) {
                        e.printStackTrace();
                }
                return structure;
        }
 

Access PDB files from a directory, take care of compressed PDB files

 public Structure loadStructureById() {
                String path = "/path/to/PDB/directory/";

                PDBFileReader pdbreader = new PDBFileReader();
                pdbreader.setPath(path);
                Structure structure = null;
                try {
                        structure = pdbreader.getStructureById("5pti");
                } catch (IOException e){
                        e.printStackTrace();
                }
                return structure;

        }
        

Author:

Andreas Prlic

Nested Class Summary

Nested classes/interfaces inherited from class org.biojava.nbio.structure.io.LocalPDBDirectory

LocalPDBDirectory.FetchBehavior, LocalPDBDirectory.ObsoleteBehavior

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	LOAD_CHEM_COMP_PROPERTY
static java.lang.String[]	PDB_OBSOLETE_DIR
static java.lang.String[]	PDB_SPLIT_DIR

Fields inherited from class org.biojava.nbio.structure.io.LocalPDBDirectory

DEFAULT_PDB_FILE_SERVER, LAST_REMEDIATION_DATE, lineSplit, PDB_FILE_SERVER_PROPERTY

Constructor Summary

Constructors

Constructor and Description
PDBFileReader() Constructs a new PDBFileReader, initializing the extensions member variable.
PDBFileReader(java.lang.String path) Constructs a new PDBFileReader, initializing the extensions member variable.

Method Summary

Methods

Modifier and Type	Method and Description
void	downloadPDB(java.lang.String pdbId) Deprecated.
protected java.lang.String	getFilename(java.lang.String pdbId) Converts a PDB ID into a filename with the proper extension
protected java.lang.String[]	getObsoleteDirPath() Location of obsolete files within the directory, as an array of paths.
protected java.lang.String[]	getSplitDirPath() Location of split files within the directory, as an array of paths.
Structure	getStructure(java.io.InputStream inStream) Handles the actual parsing of the file into a Structure object.
boolean	isFetchCurrent() Deprecated. Use FileParsingParameters#getObsoleteBehavior()
boolean	isFetchFileEvenIfObsolete() Deprecated. Use FileParsingParameters#getObsoleteBehavior()
static void	main(java.lang.String[] args)
void	setFetchCurrent(boolean fetchNewestCurrent) Deprecated. Use FileParsingParameters#setObsoleteBehavior(ObsoleteBehavior)
void	setFetchFileEvenIfObsolete(boolean fetchFileEvenIfObsolete) Deprecated. Use FileParsingParameters#setObsoleteBehavior(ObsoleteBehavior)
void	setFileParsingParameters(FileParsingParameters params) Set the parameters that should be used for file parsing

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, isAutoFetch, prefetchStructure, setAutoFetch, setFetchBehavior, setObsoleteBehavior, setPath

Methods inherited from class java.lang.Object

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

Field Detail

LOAD_CHEM_COMP_PROPERTY

public static final java.lang.String LOAD_CHEM_COMP_PROPERTY

See Also:

Constant Field Values

PDB_SPLIT_DIR

public static final java.lang.String[] PDB_SPLIT_DIR

PDB_OBSOLETE_DIR

public static final java.lang.String[] PDB_OBSOLETE_DIR

Constructor Detail

PDBFileReader

public PDBFileReader()

Constructs a new PDBFileReader, initializing the extensions member variable. The path is initialized in the same way as UserConfiguration, i.e. to system property/environment variable UserConfiguration.PDB_DIR. Both autoFetch and splitDir are initialized to false

PDBFileReader

public PDBFileReader(java.lang.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

Method Detail

main

public static void main(java.lang.String[] args)

downloadPDB

@Deprecated
public void downloadPDB(java.lang.String pdbId)
                 throws java.io.IOException

Deprecated.

Throws:

java.io.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

Overrides:

setFileParsingParameters in class LocalPDBDirectory

Parameters:

params - FileParsingParameters

setFetchFileEvenIfObsolete

@Deprecated
public void setFetchFileEvenIfObsolete(boolean fetchFileEvenIfObsolete)

Deprecated. Use FileParsingParameters#setObsoleteBehavior(ObsoleteBehavior)

N.B. This feature won't work unless the structure wasn't found & autoFetch is set to true.

Parameters:

fetchFileEvenIfObsolete - the fetchFileEvenIfObsolete to set

isFetchFileEvenIfObsolete

@Deprecated
public boolean isFetchFileEvenIfObsolete()

Deprecated. Use FileParsingParameters#getObsoleteBehavior()

forces the reader to fetch the file if its status is OBSOLETE. This feature has a higher priority than setFetchCurrent(boolean).
N.B. This feature won't work unless the structure wasn't found & autoFetch is set to true.

Returns:

the fetchFileEvenIfObsolete

Since:

3.0.2

See Also:

#fetchCurrent

setFetchCurrent

@Deprecated
public void setFetchCurrent(boolean fetchNewestCurrent)

Deprecated. Use FileParsingParameters#setObsoleteBehavior(ObsoleteBehavior)

if enabled, the reader searches for the newest possible PDB ID, if not present in he local installation. The setFetchFileEvenIfObsolete(boolean) function has a higher priority than this function.
N.B. This feature won't work unless the structure wasn't found & autoFetch is set to true.

Parameters:

fetchCurrent - the fetchCurrent to set

Since:

3.0.2

See Also:

setFetchFileEvenIfObsolete(boolean)

isFetchCurrent

@Deprecated
public boolean isFetchCurrent()

Deprecated. Use FileParsingParameters#getObsoleteBehavior()

N.B. This feature won't work unless the structure wasn't found & autoFetch is set to true.

Returns:

the fetchCurrent

getFilename

protected java.lang.String getFilename(java.lang.String pdbId)

Description copied from class: LocalPDBDirectory

Converts a PDB ID into a filename with the proper extension

Specified by:

getFilename in class LocalPDBDirectory

Returns:

The filename, e.g. "4hhb.pdb.gz"

getStructure

public Structure getStructure(java.io.InputStream inStream)
                       throws java.io.IOException

Description copied from class: LocalPDBDirectory

Handles the actual parsing of the file into a Structure object.

Specified by:

getStructure in class LocalPDBDirectory

Returns:

Throws:

java.io.IOException

getSplitDirPath

protected java.lang.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 class LocalPDBDirectory

Returns:

A list of directories, relative to the /pub/pdb directory on the server

getObsoleteDirPath

protected java.lang.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 class LocalPDBDirectory

Returns:

A list of directories, relative to the /pub/pdb directory on the server