Field-based similarity search system and method

A field-based similarity search system, comprising:

• a feature database for storing data pertaining to candidate molecule, said database comprising a hash table having entries which are generated based on:
• a set of descriptors generated from conformations of fragment graphs of said candidate molecule, said fragment graphs including plural fragment nodes connected by rotatable bond edges, a specific conformation of said fragment node comprising a fragment of said candidate molecule, and two neighboring fragments connected by a rotatable bond at a specific dihedral angle comprising a fragment pair;
• and
• a context-adapted descriptor-to-key mapping which maps said set of descriptors to a set of feature keys comprising indices that label grid cells in discriminant space;
• an input device for inputting data pertaining to a query molecule;
• a processor which identifies a candidate molecule which is similar to said query molecule by:
• generating scoops, descriptors and keys for said query molecule;
• identifying features of a candidate molecule fragment pair which correspond to features of a query molecule fragment pair, by comparing said keys of said query molecule to said keys in said feature database, a correspondence comprising a scoop for said candidate molecule stored in said feature database having a same key as a scoop for said query molecule,
• wherein the candidate molecule fragment pair is within a set of candidate molecule fragment pairs describing the candidate molecule wherein the number of candidate molecule fragment pairs in the set, Cfp, is given by Cfp=(n−1)·(Cfrag)2·Crbe, where n is a number of fragments in said candidate molecule and n−1 is a number of rotatable bond edges connecting said n fragments, Cfrag is a number of conformations in a fragment of said fragments, and Crbe is a number of steps in which said rotatable bond edges are sampled;
• and
• aligning said candidate molecule fragment pair to said query molecule by overlaying internal coordinate axes of said scoops for said candidate and query molecules, said correspondence implying an alignment of said candidate molecule and query molecule fragment pairs;
• and
• a display device for displaying an output of said processor,
• wherein said processor aligns retrieved fragment pairs using a pose clustering method,
• wherein said features of said candidate molecule fragment pair and query molecule fragment pair comprise generalizations of comparative molecular moment analysis (CoMMA) descriptors, and
• wherein an entry of said hash table refers to a fragment pair of said candidate molecule and describes an internal frame associated with a descriptor.