OEChem - C++ Theory Manual

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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.

 1 #include "openeye.h"
 2 #include "oechem.h"
 3
 4 using namespace OEChem;
 5 using namespace OESystem;
 6
 7 int main()
 8 {
 9   OEIter<OEMolBase> mol;
10   oemolistream ims;
11   oemolostream oms;
12
13   ims.SetFormat(OEFormat::SDF);
14   oms.SetFormat(OEFormat::MOL2);
15   for (mol=ims.GetMolBases(); mol; ++mol)
16     oms << mol;
17   return 0;
18 }

The file formats supported by OEChem are listed in Table 3.1. 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.

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				OEChem - C++ Theory Manual

Previous: 3.2 Reading Molecules with Up: 3. Reading and Writing Next: 3.4 Molecule Input and

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Documentation released on June 4, 2008.