PDBFileReader (biojava 3.0.3 API)

java.lang.Object
- org.biojava.bio.structure.io.PDBFileReader

All Implemented Interfaces:: StructureIO, StructureIOFile

public class PDBFileReader
extends 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?

 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 String`	`DEFAULT_PDB_FILE_SERVER`
`static String`	`lineSplit`
`static String`	`LOAD_CHEM_COMP_PROPERTY`
`static String`	`PDB_FILE_SERVER_PROPERTY`

Constructor Summary

Constructors
Constructor and Description

PDBFileReader()

Constructors
Constructor and Description
`PDBFileReader()`

Method Summary

Methods
Modifier and Type	Method and Description
`void`	`addExtension(String s)` define supported file extensions compressed extensions .Z,.gz do not need to be specified they are dealt with automatically.
`void`	`clearExtensions()` clear the supported file extensions
`FileParsingParameters`	`getFileParsingParameters()` Get the parameters that should be used for file parsing
`String`	`getPath()` Returns the path value.
`Structure`	`getStructure(File filename)` opens filename, parses it and returns a Structure object
`Structure`	`getStructure(String filename)` opens filename, parses it and returns aStructure object .
`Structure`	`getStructure(URL u)`
`Structure`	`getStructureById(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.
`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(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.
`void`	`setFileParsingParameters(FileParsingParameters params)` Set the parameters that should be used for file parsing
`void`	`setPath(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 String LOAD_CHEM_COMP_PROPERTY
```
    See Also:
    Constant Field Values
  - lineSplit
```
public static final String lineSplit
```
  - DEFAULT_PDB_FILE_SERVER
```
public static final String DEFAULT_PDB_FILE_SERVER
```
    See Also:
    Constant Field Values
  - PDB_FILE_SERVER_PROPERTY
```
public static final String PDB_FILE_SERVER_PROPERTY
```
    See Also:
    Constant Field Values
- Constructor Detail
  - PDBFileReader
```
public PDBFileReader()
```
- Method Detail
  - main
```
public static void main(String[] args)
```
  - setPath
```
public void setPath(String p)
```
    directory where to find PDB files
    
    Specified by:
    
    setPath in interface StructureIOFile
    
    Parameters:
    p - a String specifying the path value
  - getPath
```
public 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(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
  - getStructureById
```
public Structure getStructureById(String pdbId)
                           throws 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:
    
    IOException - ...
  - getStructure
```
public Structure getStructure(String filename)
                       throws IOException
```
    opens filename, parses it and returns aStructure object .
    
    Specified by:
    
    getStructure in interface StructureIOFile
    
    Parameters:
    filename - a String
    
    Returns:
    the Structure object
    
    Throws:
    
    IOException - ...
  - getStructure
```
public Structure getStructure(File filename)
                       throws 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:
    
    IOException - ...
  - getStructure
```
public Structure getStructure(URL u)
                       throws IOException
```
    Throws:
    
    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

Class PDBFileReader

Example

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

LOAD_CHEM_COMP_PROPERTY

lineSplit

DEFAULT_PDB_FILE_SERVER

PDB_FILE_SERVER_PROPERTY

Constructor Detail

PDBFileReader

Method Detail

main

setPath

getPath

addExtension

clearExtensions

isPdbDirectorySplit

setPdbDirectorySplit

setBioAssemblyId

setBioAssemblyFallback

getStructureById

getStructure

getStructure

getStructure

setFileParsingParameters

getFileParsingParameters

isAutoFetch

setAutoFetch

setFetchFileEvenIfObsolete

isFetchFileEvenIfObsolete

setFetchCurrent

isFetchCurrent