Class MolInputStream

All Implemented Interfaces:
Closeable, AutoCloseable

@PublicApi public class MolInputStream extends PositionedInputStream
Molecule input stream that has the ability to determine the input file format.
  • Constructor Details

    • MolInputStream

      public MolInputStream(InputStream is) throws IOException
      Create a molecule input stream from an ordinary one, and determine the format.
      Parameters:
      is - the original input stream
      Throws:
      IOException - error occurred while trying to guess the file format
    • MolInputStream

      public MolInputStream(InputStream is, String fmt) throws IOException
      Create a molecule input stream from an ordinary one, If null is specified as the fmt argument, then the file format is determined automatically. If "mol" or "csmol" is specified, then the file format is determined from the first line as "mol", "csmol", "rxn", "csrxn", "rgf" or "csrgf".
      Parameters:
      is - the original input stream
      fmt - the input file format or null
      Throws:
      IOException - error occurred while trying to guess the file format
    • MolInputStream

      public MolInputStream(InputStream is, String fmt, String enc) throws IOException
      Create a molecule input stream from an ordinary one, If null is specified as the fmt argument, then the file format is determined automatically. If "mol" or "csmol" is specified, then the file format is determined from the first line as "mol", "csmol", "rxn", "csrxn", "rgf" or "csrgf".
      Parameters:
      is - the original input stream
      fmt - the input file format or null
      enc - the input encoding or null
      Throws:
      IOException - error occurred while trying to guess the file format
      Since:
      Marvin 3.5.5
    • MolInputStream

      public MolInputStream(InputStream is, String fmt, String enc, String path) throws IOException
      Create a molecule input stream from an ordinary one, If null is specified as the fmt argument, then the file format is determined automatically. If "mol" or "csmol" is specified, then the file format is determined from the first line as "mol", "csmol", "rxn", "csrxn", "rgf" or "csrgf". If the file format cannot be determined from the contents and the file name is not null, then the file extension is used to guess the format.
      Parameters:
      is - the original input stream
      fmt - the input file format or null
      enc - the input encoding or null
      path - the file path (it can also be an URL) or null
      Throws:
      IOException - error occurred while trying to guess the file format
      Since:
      Marvin 4.1, 01/03/2006
  • Method Details

    • getFormat

      public String getFormat()
      Get the molecule file format.
      Returns:
      "mrv", "mol", "mol:V3", "csmol", "sdf", "cssdf", "rdf", "csrdf", "smiles", "sybyl", "mol2", "pdb", "xyz" or "cube" or "inchi", "gzip" or "chemaxon.struc.Molecule" if imported from ObjectInputStream (serialized molecule)
    • setFormat

      public void setFormat(String fmt)
      Sets the molecule file format.
      Parameters:
      fmt - the format
      Since:
      Marvin 5.0, 05/25/2007
    • getPath

      public String getPath()
      Gets the path or URL of the file.
      Returns:
      the path or null if unknown
      Since:
      Marvin 5.3, 09/17/2009