Class PCSubstanceXMLReader

All Implemented Interfaces:
Closeable, AutoCloseable, IChemObjectIO, IChemObjectReader, ISimpleChemObjectReader

public class PCSubstanceXMLReader extends DefaultChemObjectReader
Reads an object from ASN formated input for PubChem Compound entries. The following bits are supported: atoms.aid, atoms.element, bonds.aid1, bonds.aid2. Additionally, it extracts the InChI and canonical SMILES properties.
Source code:
main
Belongs to CDK module:
io
Keywords:
file format, PubChem Compound ASN
  • Constructor Details

    • PCSubstanceXMLReader

      public PCSubstanceXMLReader(Reader input) throws Exception
      Construct a new reader from a Reader type object.
      Parameters:
      input - reader from which input is read
      Throws:
      Exception
    • PCSubstanceXMLReader

      public PCSubstanceXMLReader(InputStream input) throws Exception
      Throws:
      Exception
    • PCSubstanceXMLReader

      public PCSubstanceXMLReader() throws Exception
      Throws:
      Exception
  • 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 object) throws CDKException
      Description copied from interface: ISimpleChemObjectReader
      Reads an IChemObject of type "object" from input. The constructor of the actual implementation may take a Reader as input to get a very flexible reader that can read from string, files, etc.
      Parameters:
      object - the type of object to return
      Returns:
      returns an object of that contains the content (or part) of the input content
      Throws:
      CDKException - it is thrown if the type of information is not available from the input
    • 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.