3.1 Using OEChem oemolstreams

The previous example demonstrated reading and writing SMILES strings from a file. This required the programmer to perform the file I/O explicitly. Whilst this may be reasonable for SMILES strings that may be read via STL's getline, it isn't suitable for more complex file formats. To ease this task, OEChem provides the oemolstream abstraction. The classes oemolistream and oemolostream allow input and output of molecules using C++'s « and » operators respectively.

#include "oechem.h"

using namespace OEChem;

int main()
{
  oemolistream ims;
  oemolostream oms;
  OEMol mol;

  while (ims >> mol)
    oms << mol;
  return 0;
}

In this example, the program will read molecules from cin (or stdin) in SMILES format and write them to cout (or stdout) in (absolute) SMILES format. Notice that in this example, there's no need to call the mol.Clear() method to reset the molecule, OEAssignAromaticFlags() to normalize aromaticity, or if(mol) to test the validity of the molecule. This is done automatically for you by the » operator.

Some C++ programmers prefer--and C, Python and Java programmers need to use--a functional interface rather than use the « and » operators for file I/O. These are provided by the functions OEReadMolecule and OEWriteMolecule that both take a oemolstream and OEMolBase& as arguments. Identically, OEReadMolecule calls mol.Clear() and perceives appropriate properties for each connection table, and skips any invalid molecules automatically.

#include "oechem.h"

using namespace OEChem;

int main()
{
  oemolistream ims;
  oemolostream oms;
  OEMol mol;

  while (OEReadMolecule(ims,mol))
    OEWriteMolecule(oms,mol);
  return 0;
}

				OEChem - C++ Theory Manual Version 1.3.1

				OEChem - C++ Theory Manual Version 1.3.1