4.1 Using OEChem oemolstreams

The previous example demonstrated reading and writing SMILES strings from the command line. This requires the programmer to perform the I/O explicitly. While this may be reasonable for SMILES strings that can be read on a single line, it is unsuitable for more complex file formats. To ease this task, OEChem provides the ``molstream'' abstraction. The classes oemolistream and oemolostream allow input and output of molecules from files or strings.

The first interface to stream I/O uses functions to read and write molecules. This is provided by the functions OEReadMolecule and OEWriteMolecule that both take a molstream and a OEMolBase as arguments. As a high-level function OEReadMolecule calls mol.Clear() automatically for each incoming molecule.

#!/usr/bin/env python
# ch4-1.py
from openeye.oechem import *

ifs = oemolistream()
ofs = oemolostream()

mol = OEGraphMol()

while (OEReadMolecule(ifs, mol) == 1):
    OEWriteMolecule(ofs, mol)

In this example, the script will read molecules from stdin in SMILES format and write them to stdout in (absolute) SMILES format. Notice that in this example, there's no need to call the Clear method to reset the molecule, or OEAssignAromaticFlags to normalize aromaticity. This is done automatically by the OEReadMolecule method.

				OEChem - Python Theory Manual Version 1.3.1

				OEChem - Python Theory Manual Version 1.3.1