This manual is to familiarize the user with the GraphSim TK functionalities. It does not provide explanations of basic OEChem TK classes and functions. Therefore reading the OEChem TK manual beforehand is highly recommended.
The GraphSim TK library provides a facility for encoding 2D molecular graph information into fingerprints. The following basic fingerprint functionalities are available:
Emphasis has been placed on speed, with attention to rapid in-memory fingerprint search (see Fingerprint Database chapter).
Molecule similarity based on fingerprints is visualized by the following method: (See example in Figure: Example of depiction of molecule similarity based on fingerprints)
Visualizing similarity of two molecules based on their fingerprints provides insight into molecule similarity beyond a single numerical score and reveals information about the underlying fingerprint methods.
The Python script that visualizes molecule similarity based on fingerprints can be downloaded from the OpenEye Python Cookbook