Class PDBFileParser


  • public class PDBFileParser
    extends java.lang.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 Detail

      • PDBFileParser

        public PDBFileParser()
    • Method Detail

      • parsePDBFile

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

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