Class MolInputStream

    • Constructor Detail

      • 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 Detail

      • 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