Importing and Exporting molecule properties

Molecule objects can contain general properties (property value - property key pairs). The formats mrv, sdf, rdf are able to store the molecule properties.

Reading properties after import

    String value = molecule.getProperty(LOGP_FIELD); //LOGP_FIELD is the name of the property

Otherwise we need to go through the property names. An example is below:

    for (int i=0; i<molecule.getPropertyCount(); i++) {
        String key = molecule.getPropertyKey(i); // name of the property
        String value = molecule.getProperty(key); // the property value
    }

For a complete source code, please see ImportProperties.java.

Collecting property keys

	MolFileHandler.collectFileInfo(inputStream, 0, collectedFields);
	java.util.Iterator iterator = collectedFields.iterator();
	while (iterator.hasNext()) {
	    System.out.println(iterator.next());
	}	

For a complete source code, please see CollectProperties.java.

Adding and exporting properties

The following example shows how to add properties via API:

	Molecule mol = MolImporter.importMol("ccccc");
	MHashProp hashProp = new MHashProp();
	mol.setPropertyObject("ROOT", hashProp);
	hashProp.put("CdId", new MStringProp("1"));
	hashProp.put("Formula", new MStringProp("C5H10"));
	MMoleculeProp secondaryStruc = new MMoleculeProp(MolImporter.importMol("cc"));
	hashProp.put("secondStruct", secondaryStruc);
	mol.setProperty("$REGNO", "MI24");
	System.out.println(MolExporter.exportToFormat(mol, "rdf"));

For a complete source code, please see ExportProperties.java.

External or internal registry number of a molecule can be added to the molecule or reaction via API. The mrv, mol (sdf, rdf) format exports and imports these registry numbers after specifying them:

	...
	int regno = 218;
	while ((mol=imp.read())!=null){
	    //add the internal registry number (sequence number in the database) of the reaction
	    mol.setProperty("$REGNO", "RI" + regno);
	    regno++;
	    exp.write(mol);  
	}
	...

For a complete source code, please see ExportingReactions.java.