public class MaccsBenchmark
extends Object
This class runs several benchmark computations using the implementation of MDL's
MACCS fingerprint.
The Molecule sets for the benchmark are collected into separate directories (called DIR here),
each containing three files, all in SDF format, one containing the original "lead"
ligand, one with the molecules appeared to be ligands and the decoys.
The names of the files are:
DIR/DIR_orig.sdf Original "lead" ligand
DIR/DIR_ligands.sdf Ligands
DIR/DIR_decoys.sdf Decoys
The program computes the fingerprints for each molecule and then the Tanimoto
dissimilarity. Sorts the dissimilarities, and analyzes the ligand content of a
number of closest sets. These are 1%, 5% and 10% of the total number of molecules.
Also the first 10 is used to provide
The output is written to standard output, progress report to standard error.