3.3 Molecular File Formats

In addition to SMILES strings, OEChem is able to read numerous other molecular file formats, including MDL SD files, Tripos Mol2 files and PDB files. The format of an input file or stream may be associated with an oemolistream using the SetFormat method, and may be retrieved with GetFormat. These take an unsigned integer representing the file format, which should be one of the constants defined in the OEFormat namespace. A value of OEFormat::UNDEFINED (zero) means that there is no file format associated with the oemolstream.

The following example demonstrates how to use oemolstreams to convert MDL SD files into Tripos Mol2 files using oemolstream iterators.

#include "oechem.h"

using namespace OEChem;
using namespace OESystem;

int main()
{
  OEIter<OEMolBase> mol;
  oemolistream ims;
  oemolostream oms;

  ims.SetFormat(OEFormat::SDF);
  oms.SetFormat(OEFormat::MOL2);
  for (mol=ims.GetMolBases(); mol; ++mol)
    oms << mol;
  return 0;
}

The following file formats are supported by OEChem.

The default format for input oemolstreams is OEFormat::SMI. In most cases, the SetFormat method should only be called on an input oemolstream before the first connection table is read.

				OEChem - C++ Theory Manual Version 1.3.1

				OEChem - C++ Theory Manual Version 1.3.1