org.biojava.bio.structure.io

Class PDBFileReader

java.lang.Object

org.biojava.bio.structure.io.PDBFileReader

All Implemented Interfaces:

StructureIO, StructureIOFile

public class PDBFileReader
extends java.lang.Object
implements StructureIOFile

The wrapper class for parsing a PDB file.

Several flags can be set for this class

• 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

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	DEFAULT_PDB_FILE_SERVER
static long	lastRemediationDate
static java.lang.String	lineSplit
static java.lang.String	LOAD_CHEM_COMP_PROPERTY
static java.lang.String	PDB_FILE_SERVER_PROPERTY

Constructor Summary

Constructors

Constructor and Description
PDBFileReader()

Method Summary

Methods

Modifier and Type	Method and Description
void	addExtension(java.lang.String s) define supported file extensions compressed extensions .Z,.gz do not need to be specified they are dealt with automatically.
boolean	checkFileExists(java.lang.String pdbId)
void	clearExtensions() clear the supported file extensions
void	downloadPDB(java.lang.String pdbId)
FileParsingParameters	getFileParsingParameters() Get the parameters that should be used for file parsing
java.io.InputStream	getInputStream(java.lang.String pdbId) try to find the file in the filesystem and return a filestream in order to parse it rules how to find file - first check: if file is in path specified by PDBpath - second check: if not found check in PDBpath/xy/ where xy is second and third char of PDBcode.
java.io.InputStream	getInputStreamBioAssembly(java.lang.String pdbId) Returns an input stream for a biological assembly file based on the passed in pdbId and the biological assembly id setBioAssemblyId(int).
java.lang.String	getPath() Returns the path value.
Structure	getStructure(java.io.File filename) opens filename, parses it and returns a Structure object
Structure	getStructure(java.lang.String filename) opens filename, parses it and returns aStructure object .
Structure	getStructure(java.net.URL u)
Structure	getStructureById(java.lang.String pdbId) load a structure from local file system and return a PDBStructure object
boolean	isAutoFetch() Fetch files automatically from FTP server.
boolean	isFetchCurrent() N.B. This feature won't work unless the structure wasn't found & autoFetch is set to true.
boolean	isFetchFileEvenIfObsolete() forces the reader to fetch the file if its status is OBSOLETE.
boolean	isPdbDirectorySplit() Flag that defines if the PDB directory is containing all PDB files or is split into sub dirs (like the FTP site).
static void	main(java.lang.String[] args)
void	setAutoFetch(boolean autoFetch) Tell the parser to fetch missing PDB files from the FTP server automatically.
void	setBioAssemblyFallback(boolean bioAssemblyFallback) Set bioAssemblyFallback to true, to download the original PDB file in cases that a biological assembly file is not available.
void	setBioAssemblyId(int bioAssemblyId) Sets the ID of the biological assembly to be loaded.
void	setFetchCurrent(boolean fetchNewestCurrent) if enabled, the reader searches for the newest possible PDB ID, if not present in he local installation.
void	setFetchFileEvenIfObsolete(boolean fetchFileEvenIfObsolete) N.B. This feature won't work unless the structure wasn't found & autoFetch is set to true.
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
void	setPdbDirectorySplit(boolean pdbDirectorySplit) Flag that defines if the PDB directory is containing all PDB files or is split into sub dirs (like the FTP site).

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

lineSplit

public static final java.lang.String lineSplit

DEFAULT_PDB_FILE_SERVER

public static final java.lang.String DEFAULT_PDB_FILE_SERVER

See Also:

Constant Field Values

PDB_FILE_SERVER_PROPERTY

public static final java.lang.String PDB_FILE_SERVER_PROPERTY

See Also:

Constant Field Values

lastRemediationDate

public static final long lastRemediationDate

Constructor Detail

PDBFileReader

public PDBFileReader()

Method Detail

main

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

setPath

public void setPath(java.lang.String p)

directory where to find PDB files

Specified by:

setPath in interface StructureIOFile

Parameters:

p - a String specifying the path value

getPath

public java.lang.String getPath()

Returns the path value.

Specified by:

getPath in interface StructureIOFile

Returns:

a String representing the path value

See Also:

setPath(java.lang.String)

addExtension

public void addExtension(java.lang.String s)

define supported file extensions compressed extensions .Z,.gz do not need to be specified they are dealt with automatically.

Specified by:

addExtension in interface StructureIOFile

Parameters:

s - a String ...

clearExtensions

public void clearExtensions()

clear the supported file extensions

Specified by:

clearExtensions in interface StructureIOFile

isPdbDirectorySplit

public boolean isPdbDirectorySplit()

Flag that defines if the PDB directory is containing all PDB files or is split into sub dirs (like the FTP site).

Specified by:

isPdbDirectorySplit in interface StructureIOFile

Returns:

boolean. default is false (all files in one directory)

setPdbDirectorySplit

public void setPdbDirectorySplit(boolean pdbDirectorySplit)

Flag that defines if the PDB directory is containing all PDB files or is split into sub dirs (like the FTP site).

Specified by:

setPdbDirectorySplit in interface StructureIOFile

Parameters:

pdbDirectorySplit - boolean. If set to false all files are in one directory.

setBioAssemblyId

public void setBioAssemblyId(int bioAssemblyId)

Sets the ID of the biological assembly to be loaded. By default, the bioAssemblyId=0, which corresponds to the original PDB file. If an ID > 0 is specified, the corresponding biological assembly file will be loaded. Note, the number of available biological unit files varies. Many entries don't have a biological unit specified (i.e. NMR structures), many entries have only one biological unit (bioAssemblyId=1), and a few structures have multiple biological assemblies.

Parameters:

bioAssemblyId - ID of the biological assembly to be loaded

Since:

3.2

setBioAssemblyFallback

public void setBioAssemblyFallback(boolean bioAssemblyFallback)

Set bioAssemblyFallback to true, to download the original PDB file in cases that a biological assembly file is not available.

Parameters:

bioAssemblyFallback - if true, tries reading original PDB file in case the biological assembly file is not available

Since:

3.2

getInputStream

public java.io.InputStream getInputStream(java.lang.String pdbId)
                                   throws java.io.IOException

try to find the file in the filesystem and return a filestream in order to parse it rules how to find file - first check: if file is in path specified by PDBpath - second check: if not found check in PDBpath/xy/ where xy is second and third char of PDBcode. if autoFetch is set it will try to download missing PDB files automatically.

Throws:

java.io.IOException

getInputStreamBioAssembly

public java.io.InputStream getInputStreamBioAssembly(java.lang.String pdbId)
                                              throws java.io.IOException

Returns an input stream for a biological assembly file based on the passed in pdbId and the biological assembly id setBioAssemblyId(int). Files are cached in a local directory.

Parameters:

pdbId -

Returns:

InputStream

Throws:

java.io.IOException

Since:

3.2

checkFileExists

public boolean checkFileExists(java.lang.String pdbId)

downloadPDB

public void downloadPDB(java.lang.String pdbId)

getStructureById

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

load a structure from local file system and return a PDBStructure object

Specified by:

getStructureById in interface StructureIO

Specified by:

getStructureById in interface StructureIOFile

Parameters:

pdbId - a String specifying the id value (PDB code)

Returns:

the Structure object

Throws:

java.io.IOException - ...

getStructure

public Structure getStructure(java.lang.String filename)
                       throws java.io.IOException

opens filename, parses it and returns aStructure object .

Specified by:

getStructure in interface StructureIOFile

Parameters:

filename - a String

Returns:

the Structure object

Throws:

java.io.IOException - ...

getStructure

public Structure getStructure(java.io.File filename)
                       throws java.io.IOException

opens filename, parses it and returns a Structure object

Specified by:

getStructure in interface StructureIOFile

Parameters:

filename - a File object

Returns:

the Structure object

Throws:

java.io.IOException - ...

getStructure

public Structure getStructure(java.net.URL u)
                       throws java.io.IOException

Throws:

java.io.IOException

setFileParsingParameters

public void setFileParsingParameters(FileParsingParameters params)

Description copied from interface: StructureIOFile

Set the parameters that should be used for file parsing

Specified by:

setFileParsingParameters in interface StructureIOFile

Parameters:

params - FileParsingParameters

getFileParsingParameters

public FileParsingParameters getFileParsingParameters()

Description copied from interface: StructureIOFile

Get the parameters that should be used for file parsing

Specified by:

getFileParsingParameters in interface StructureIOFile

Returns:

the FileParsingParameters that are configuring the behavior of the parser

isAutoFetch

public boolean isAutoFetch()

Description copied from interface: StructureIOFile

Fetch files automatically from FTP server. Default: false

Specified by:

isAutoFetch in interface StructureIOFile

Returns:

flag is true or false.

setAutoFetch

public void setAutoFetch(boolean autoFetch)

Description copied from interface: StructureIOFile

Tell the parser to fetch missing PDB files from the FTP server automatically. default is false. If true, new PDB files will be automatically stored in the Path and gzip compressed.

Specified by:

setAutoFetch in interface StructureIOFile

Parameters:

autoFetch - flag.

setFetchFileEvenIfObsolete

public void setFetchFileEvenIfObsolete(boolean fetchFileEvenIfObsolete)

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

public boolean isFetchFileEvenIfObsolete()

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

public void setFetchCurrent(boolean fetchNewestCurrent)

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

public boolean isFetchCurrent()

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

Returns:

the fetchCurrent