Iterate over SDFile, calculates properties, and stores in new SDF.

calcPropsSdf.js

//***************************************************************
// Script that iterates over a file, calculates properties
// and stores all in a new SDFile. Requires Sample Data installed.
//
// Author: Ola Spjuth
//****************************************************************

it = cdk.createMoleculeIterator("/Sample Data/SDF/Fragments2.sdf");
list=cdk.createMoleculeList();

while (it.hasNext()){
	mol=it.next();
	i=inchi.generate(mol);
	ikey=inchi.generateKey(mol);	
	fp=mol.getFingerprint(true);

	//Store properties for the mol
	cdk.setProperty(mol, "inchi", i)
	cdk.setProperty(mol, "inchikey", ikey)
	cdk.setProperty(mol, "cdk:fingerprint", fp)
	list.add(mol);
}

cdk.saveSDFile("Virtual/Fragment2_with_props.sdf", list);