4.2 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.

File Format	Description	Read?	Write?
`OEFormat.OEB`	New Style OpenEye OEBinary	Yes	Yes
`OEFormat.BIN`	Old Style OEBinary	Yes	Yes
`OEFormat.CAN`	Canonical SMILES	Yes	Yes
`OEFormat.FASTA`	FASTA protein sequence	Yes	Yes
`OEFormat.ISM`	Isomeric SMILES	Yes	Yes
`OEFormat.MDL`	MDL Mol File	Yes	Yes
`OEFormat.MF`	Molecular Formula (Hill order)	No	Yes
`OEFormat.MOL2`	Tripos Sybyl mol2 file	Yes	Yes
`OEFormat.MOL2H`	Sybyl mol2 with explicit hydrogens	Yes	Yes
`OEFormat.MOPAC`	MOPAC file format(s)	Yes	Yes
`OEFormat.PDB`	Protein Databank PDB file	Yes	Yes
`OEFormat.SDF`	MDL SD File	Yes	Yes
`OEFormat.SMI`	Absolute SMILES	Yes	Yes
`OEFormat.XYZ`	XMol XYZ format	Yes	Yes

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

 1 /**************************************************************
 2  * Copyright 2005, OpenEye Scientific Software, Inc.
 3  *************************************************************/
 4 import openeye.oechem.*;
 5
 6 public class Sdf2Mol2 {
 7   public static void main(String argv[]) {
 8     oemolistream ifs = new oemolistream();
 9     oemolostream ofs = new oemolostream();
10
11     ifs.SetFormat(OEFormat.SDF);
12     ofs.SetFormat(OEFormat.MOL2);
13
14     OEGraphMol mol = new OEGraphMol();
15     while (oechem.OEReadMolecule(ifs, mol)) {
16       oechem.OEWriteMolecule(ofs, mol);
17     }
18   }
19 }
20

Listing:4.3 Converting SDF to MOL2 using stdin/stdout

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

				OEChem - Java Theory Manual

				OEChem - Java Theory Manual