Package org.biojava.bio.structure.io

Class 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

    • setParseCAOnly(boolean) - parse only the Atom records for C-alpha atoms (default:false)
    • setParseSecStruc(boolean) - a flag if the secondary structure information from the PDB file (author's assignment) should be parsed. If true the assignment can be accessed through AminoAcid.getSecStruc(); (default:false)
    • setAlignSeqRes(boolean) - should the AminoAcid sequences from the SEQRES and ATOM records of a PDB file be aligned? (default:true)
    • setAutoFetch(boolean) - if the PDB file can not be found locally, should it be fetched from the EBI - ftp server? (default:false)

    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

      Constructors 
      Constructor Description
      PDBFileReader()  

    • Method Summary

      All Methods Static Methods Instance Methods Concrete Methods 
      Modifier and Type Method 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.
      void clearExtensions()
      clear the supported file extensions
      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 getStructureById​(java.lang.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​(java.lang.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​(java.lang.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​(java.lang.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​(java.lang.String p)
        directory where to find PDB files
        Specified by:
        setPath in interface StructureIOFile
        Parameters:
        p - a String specifying the path value

      • 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 ...

      • 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
        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 - ...