Conformational analysis using a simplified tms implemented with object-oriented and logic programming
Timothy D. Koschmann · 1987
This thesis describes ROTAMER, a program written to assist chemists in identifying the likely three-dimensional shapes (conformations) that a given organic molecule might assume. This problem is geometric in nature, unlike the more topological problems addressed by earlier AI programs in chemistry. The search of the space of all possible conformations is approached as a constraint-satisfaction problem. The structure generator in ROTAMER uses a simplified Truth Maintenance System (TMS), inspired by de Kleer's Assumption-based Truth Maintenance System, to cache information acquired in the course of exploring the conformation space. ROTAMER was implemented using a combination of object-centered and logic programming on a Xerox Lisp Machine. Objects were used for a variety of purposes in ROTAMER. They were used to represent structural information about molecules and to implement both the simplified TMS and the chemist's interface. Logic programming was used to derive inferences within the TMS environments. A general purpose interface was developed between the LOOPS object-oriented programming environment and Prolog in order to be able to combine the two programming styles. The simplified TMS works under certain restrictions but could be applied to other constraint resolution problems. It is observed that the computational benefits of using this TMS increase with the size of the problem. Directions for future research are discussed.