OEChem - Python Theory Manual Version 1.3.1

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4.3 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 a oemolstream using the SetFormat method, and may be retrieved with GetFormat. These take (or return) and integer constant defined in C++. The following table shows the constants and the corresponding file formats supported by OEChem. A value of OEFormat_UNDEFINED (zero) means that there is no file format associated with the molstream. Note that the default format associated with an oemolstream is OEFormat_SMI.

The following example shows how to use oemolstreams to convert MDL SD files into Tripos Mol2 files.

#!/usr/bin/env python
# ch4-4.py
from openeye.oechem import *

ifs = oemolistream()
ifs.open()
ofs = oemolostream()
ofs.open()

ifs.SetFormat(OEFormat_SDF)
ofs.SetFormat(OEFormat_MOL2)

for mol in ifs.GetOEMols():
    OEWriteMolecule(ofs, mol)

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In general, the SetFormat method should only be called on an oemolistream before the first connection table is read.

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				OEChem - Python Theory Manual Version 1.3.1

Previous: 4.2 Reading Molecules with Up: 4. Reading and Writing Next: 4.4 Molecule Input and

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Documentation released on July 30, 2004.