org.biojava.bio.structure.io
Class PDBFileReader

java.lang.Object
  extended by 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

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

Constructor Summary
PDBFileReader()
           
 
Method Summary
 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
 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 getStructureById(String pdbId)
          load a structure from local file system and return a PDBStructure object
 boolean isAlignSeqRes()
          get the flag if the SEQRES and ATOM amino acids are going to be aligned
 boolean isAutoFetch()
          should the parser to fetch missing PDB files from the EBI FTP server automatically? default is false
 boolean isParseCAOnly()
          return the flag if only the CA atoms should be parsed
 boolean isParseSecStruc()
           
static void main(String[] args)
           
 void setAlignSeqRes(boolean alignSeqRes)
          set the flag if the SEQRES and ATOM amino acids should be aligned and linked
 void setAutoFetch(boolean autoFetch)
          tell the parser to fetch missing PDB files from the EBI FTP server automatically.
 void setParseCAOnly(boolean parseCAOnly)
          only the CA atoms should be parsed from the PDB file
 void setParseSecStruc(boolean parseSecStruc)
           
 void setPath(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
 

Constructor Detail

PDBFileReader

public PDBFileReader()
Method Detail

main

public static void main(String[] args)

isParseCAOnly

public boolean isParseCAOnly()
return the flag if only the CA atoms should be parsed

Returns:
flag if CA only should be read

setParseCAOnly

public void setParseCAOnly(boolean parseCAOnly)
only the CA atoms should be parsed from the PDB file

Parameters:
parseCAOnly -

isAlignSeqRes

public boolean isAlignSeqRes()
get the flag if the SEQRES and ATOM amino acids are going to be aligned

Returns:
flag

setAlignSeqRes

public void setAlignSeqRes(boolean alignSeqRes)
set the flag if the SEQRES and ATOM amino acids should be aligned and linked

Parameters:
alignSeqRes -

isAutoFetch

public boolean isAutoFetch()
should the parser to fetch missing PDB files from the EBI FTP server automatically? default is false

Specified by:
isAutoFetch in interface StructureIOFile
Returns:
flag

setAutoFetch

public void setAutoFetch(boolean autoFetch)
tell the parser to fetch missing PDB files from the EBI 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 -

isParseSecStruc

public boolean isParseSecStruc()

setParseSecStruc

public void setParseSecStruc(boolean parseSecStruc)

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

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
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 - ...