Package org.biojava.nbio.structure.io

Class PDBFileParser

java.lang.Object
org.biojava.nbio.structure.io.PDBFileParser
public class PDBFileParser extends Object
This class implements the actual PDB file parsing. Do not access it directly, but via the PDBFileReader class.

Parsing

During the PDBfile parsing several Flags can be set. See the setFileParsingParameters(FileParsingParameters) methods.

To provide excessive memory usage for large PDB files, there is the ATOM_CA_THRESHOLD. If more Atoms than this threshold are being parsed in a PDB file, the parser will automatically switch to a C-alpha only representation.

The result of the parsing of the PDB file is a new Structure object.

For more documentation on how to work with the Structure API please see http://biojava.org/wiki/BioJava:CookBook#Protein_Structure

Example

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

A: 

 public Structure loadStructure(String pathToPDBFile){
        // The PDBFileParser is wrapped by the PDBFileReader
        PDBFileReader pdbreader = new PDBFileReader();

        Structure structure = null;
        try{
                structure = pdbreader.getStructure(pathToPDBFile);
                System.out.println(structure);
        } catch (IOException e) {
                e.printStackTrace();
        }
        return structure;
 }
Since:
1.4
Author:
Andreas Prlic, Jules Jacobsen, Jose Duarte

  • Constructor Details

    • PDBFileParser

      public PDBFileParser()

  • Method Details

    • parsePDBFile

      public Structure parsePDBFile(InputStream inStream) throws IOException
      Parse a PDB file and return a datastructure implementing PDBStructure interface.
      Parameters:
      inStream - an InputStream object
      Returns:
      a Structure object
      Throws:
      IOException

    • parsePDBFile

      public Structure parsePDBFile(BufferedReader buf) throws IOException
      Parse a PDB file and return a datastructure implementing PDBStructure interface.
      Parameters:
      buf - a BufferedReader object
      Returns:
      the Structure object
      Throws:
      IOException - ...

    • linkChains2Compound

      public void linkChains2Compound(Structure s)
      After the parsing of a PDB file the Chain and Compound objects need to be linked to each other.
      Parameters:
      s - the structure

    • setFileParsingParameters

      public void setFileParsingParameters(FileParsingParameters params)

    • getFileParsingParameters

      public FileParsingParameters getFileParsingParameters()