Package org.openscience.cdk.io

Class PDBReader

java.lang.Object
org.openscience.cdk.io.ChemObjectIO
org.openscience.cdk.io.DefaultChemObjectReader
org.openscience.cdk.io.PDBReader
All Implemented Interfaces:
Closeable, AutoCloseable, IChemObjectIO, IChemObjectReader, ISimpleChemObjectReader
public class PDBReader extends DefaultChemObjectReader
Reads the contents of a PDBFile.

A description can be found at http://www.rcsb.org/pdb/static.do?p=file_formats/pdb/index.html.

Author:
Edgar Luttmann, Bradley Smith <bradley@baysmith.com>, Martin Eklund <martin.eklund@farmbio.uu.se>, Ola Spjuth <ola.spjuth@farmbio.uu.se>, Gilleain Torrance <gilleain.torrance@gmail.com>
This class is affected by these bug(s):
1714141 1794439
Source code:
main
Belongs to CDK module:
pdb
Keywords:
file format, PDB
Created on:
2001-08-06

  • Constructor Details

    • PDBReader

      public PDBReader(InputStream oIn)
      Constructs a new PDBReader that can read Molecules from a given InputStream.
      Parameters:
      oIn - The InputStream to read from

    • PDBReader

      public PDBReader(Reader oIn)
      Constructs a new PDBReader that can read Molecules from a given Reader.
      Parameters:
      oIn - The Reader to read from

    • PDBReader

      public PDBReader()

  • Method Details

    • getFormat

      public IResourceFormat getFormat()
      Description copied from interface: IChemObjectIO
      Returns the IResourceFormat class for this IO class.

    • setReader

      public void setReader(Reader input) throws CDKException
      Description copied from interface: IChemObjectReader
      Sets the Reader from which this ChemObjectReader should read the contents.
      Throws:
      CDKException

    • setReader

      public void setReader(InputStream input) throws CDKException
      Description copied from interface: IChemObjectReader
      Sets the InputStream from which this ChemObjectReader should read the contents.
      Throws:
      CDKException

    • accepts

      public boolean accepts(Class<? extends IChemObject> classObject)
      Description copied from interface: IChemObjectIO
      Returns whether the given IChemObject can be read or written.
      Parameters:
      classObject - IChemObject of which is tested if it can be handled.
      Returns:
      true, if the IChemObject can be handled.

    • read

      public <T extends IChemObject> T read(T oObj) throws CDKException
      Takes an object which subclasses IChemObject, e.g. Molecule, and will read this (from file, database, internet etc). If the specific implementation does not support a specific IChemObject it will throw an Exception.
      Parameters:
      oObj - The object that subclasses IChemObject
      Returns:
      The IChemObject read
      Throws:
      CDKException

    • close

      public void close() throws IOException
      Description copied from interface: IChemObjectIO
      Closes this IChemObjectIO's resources.
      Throws:
      IOException - when the wrapper IO class cannot be closed.

    • customizeJob

      public void customizeJob()