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1 INDEX 251 Subject Index Downloaded via on November 14, 2018 at 22:58:10 (UTC). See for options on how to legitimately share published articles. A Academia, goals of expert systems, 11 ACanalysis, function, 218 ACanalyst, function, 216 ACassurance, function, 216 ACcontrol description, 226 function, instrument control, 226,227/ user and instrument interface development, ACdiagnosis conditions, 223 description, function, 217 generation of rule base, ACexpert AAS application, 228,229f ACcontrol, 226 ACdiagnosis, ,225/ ACmethods, 220r, f ACteach, analyst's role, assignment of tube elements, 228,23Qf calibration curve, 231,233/ components of modules, 218 design specifications, design using shells, development, 211 future research, 231 incorporation into automated control program of any instrument, 231 instrument control, 226,227/ manager's role, modules, phototube response, 231,232/" rule analysis strategies, 218 Sampler application, 228, schematic representation, 215/ software simulation, front panel of atomic absorption spectrometer, 228,229f stages of prototyping, 217 Acid, definition, 24,26-27 Acid cleaning, procedure, 155 ACmethods example of ambiguous response, 221,222/" example of conditions and case conclusions, 225/ final screen output, 221/ function, 216,217,220 strategy and conditions, 220r ACteach, description, AICHE meeting AI papers, list, Automated metal analysis by atomic absorption spectrometry, design of expert system, Automation in analytical laboratory applications of expert systems, 211 development, evolution of expert systems, use of expert systems, 211 Backward-chaining rule analysis, description, 218 Bases, definition, 27 Brooks data structure, description, 94 Chemical language editor, KNODE, 54-55,5^ Chemical language interpreter, KNODE, 54-55,5^ Chemical process control, expert system, Chemistry-based expert system shell (CHESS) architecture, 45,4^f components, 34 general chemical knowledge, GUESS, 45 implementation, 45,46/47 knowledge extraction utility, molecular structure representation and recognition, 44 parameter estimation and calculation, 44 purpose, reaction libraries, 44 CHESS, Complex solids characterization, use of CACSS, Computational language interface, KNODE, 53 Computer-aided characterization of solids and surfaces (CACSS) case study, choice of optimal starting set of analytical techniques, criterion for rejection, crystallographic modeling, 198 description of project, 191 implementation of project, 196,197/ interpretation of experimental results, matrix discussion group, outline of project, role of expert systems, schematic outline, 196,197/ structure elucidation from crystal powders, 196,198 use of artificial intelligence technology, 192

252 EXPERT SYSTEM APPLICATIONS IN CHEMISTRY Computer-assisted instruction development, 20 intelligent tutoring systems, 21 Corrosimeter, evolution, 150 Corrosion direct measurement, 149 indirect

2 252 EXPERT SYSTEM APPLICATIONS IN CHEMISTRY Computer-assisted instruction development, 20 intelligent tutoring systems, 21 Corrosimeter, evolution, 150 Corrosion direct measurement, 149 indirect measurement, 149 Corrosion of metallic materials classes, 148 damage of resources, 147 evolution of corrosion-monitoring systems, objectives of prevention efforts, problems induced, 148 Corrosion-monitoring systems design of model emulating expert reasoning behavior, development of probes, 150 evolution, improvement in corrosimeters, 150 Corrosion rate measurements, reliability, 149 D Data-directed expert system description, 4 example, 4 5 Descriptive inorganic chemistry database, 24,25; expert system design, 24 expert system development, groups of reactant classes, 24,26* PIRExS, 22 reactant classes, 24,26r,27 reaction classes, reactions with one reactant, 28 reactions with two reactants, 28-29,31* rules for reactivity prediction, DOCENT caricature of macromolecule by model matching, 94,95/ deducing atomic-scale geometry from generalized cylinders, features, 93 function, 93 manipulation of generalized cylinder representation, 99 ribbon as set of generalized cylinders, use of acronym-style modeler in molecular displays, use of generalized cylinders in interpretation of scene, 94-95,96f,97 Drug design disadvantages of linear methods, method of receptor fit, 82 use of protein pseudoreceptor, E Environmental test plan conditions and requirements, procedures, 200 use of ES-EPA, Expert reasoning instrument for corrosive environments (ERICE) advantages, 150 applications, 154,155/,156 corrosion rate behavior during different plant conditions, 155/,156 examples of hypothesizing production rules, 153/ future developments, 156 knowledge base system, knowledge base tree structure, 152f outcomes, 156 plant data base multiwindow updating system, 152,153/ system functionalities, use of Personal Consultant Plus shell, 152 Expert system(s) advantages, 7 application selection, 6 applications in chemistry, 2-9 computer platform selection, 6 7 description, 2,21 design using shells, development, 6-7,21-22 disadvantages, 7 future impact in chemistry, 7 glossary, 7-9 inference engine, 3 knowledge base, 2-3,244 pieces,2 prediction of inorganic reactions, sharing of knowledge bases, 10 software selection, 6-7 user interface, 3 Expert system for environmental pollutant analysis (ES-EPA) abstraction level plans, 201 architecture, 203,205/ characteristics of planning methods used by human experts, 201 control module, 203 development, 201 future directions, 209 hardware environment, knowledge base module, 203 multiple template, 204,207/ plan templates, 202 planning mechanism, 204, / schematic representation of hierarchical planning, 204,205/ single template, 204,206f software environment, user interface, 208f,209

3 INDEX 253 Expert system for environmental pollutant analysis (ES-EPA) Continued user interface module, 203 Expert system for instrumental analysis, criteria for development, 212 F Forward-chaining rule analysis, description, 218 FORWARD program generalized plan, 76,78,8Qf procedure, refunctionalization reactions, 76,78-79,8Qf sample output, 79,8Qf Inorganic reactions, system for predicting, Intelligent scientific computing systems description, 49 design of KNODE, Intelligent tutoring systems description, 21 expert system, Implementation of knowledge-based system difficulty of rule modification, 240 ease of understanding rationale for determinations, 240 expertise required, 240 programming language selection, tool selection, 244 use of shell programs, 245 G G2 real-time expert system application example, applications, 169 critical path planning, 172,175/ description, knowledge base management, 176,177/ knowledge representation, managing knowledge on workspaces, 176,177/ reasoning about knowledge, 176,178 robot navigation example, 176,174/ use of high-level interfaces, 169 Generalized cylinders applications, 100 components of ribbon, deduction of atomic-scale geometry, 98 examples, 94,95/ manipulation of representation, 99 use in interpretation of scene, 94-95,9^,97 General-purpose expert system shell (GUESS) description, 45 use in CHESS, 45 Glossary, expert systems, 7-9 Goal-directed expert system description, 4 example, 4 GUESS, 45 Indole, substitution patterns, 111,114/115 Industry, goals of expert systems, 11 Inference engine data-directed approach, 4-5 description, 3 goal-directed approach, 4 structure, 3-4 use of meta-knowledge, 5 Job control, KNODE, Job packer-controller, KNODE, 55,57-60 K KDS3 expert system shell description, development of expert systems, 219 example of analytical methods selection expert, 219,220r standard screen interface, ,221/ KNODE chemical language editor, 54-55,56f chemical language interpreter, 54-55,5^" comparison to procedure by human experts, 50 computational language interface, 53 control flow of job-control module, 57,5 f file hierarchy as viewed from job control module, 57,5Sjf job control, job packer-controller, 55,57-60 mathematical language interface, overview, phase implementation, principal modules and data pathways, 50,51/ scientific language interface, 50,52,54 56 scientific visualization module, 54 syntactic and semantic analyzer function of scientific language interface, 55,56/" system supervisor, 50 Knowledge base description, 2-3 encoding of knowledge, 3 frames for encoding, 3 production rules for encoding, 3 scope, 3 sharing, 10-16

254 EXPERT SYSTEM APPLICATIONS IN CHEMISTRY Knowledge base management for G2 expert system, examples for workspaces, 176,177/ Knowledge base module of expert system for environmental pollutant

4 254 EXPERT SYSTEM APPLICATIONS IN CHEMISTRY Knowledge base management for G2 expert system, examples for workspaces, 176,177/ Knowledge base module of expert system for environmental pollutant analysis analysis item KB, 203 analysis task KB, 203 customer KB, 203 sample type and purpose KB, 203 Knowledge-based systems, development, Knowledge extraction utility for chemistry-based expert system shell cluster analysis results, 3839T complete grid, 40,41/ example, example grid, 3637/38 procedure, questions asked by inference engine, 40,43/ reported results, 40,43/ typical rules generated, 40,42/* Knowledge for G2 expert system, truth maintenance, 176,178 Knowledge representation for G2 expert system concurrent use of analytic and heuristic models, 170 critical path planning, 172,175/ defining heuristic knowledge, 170,171/,172 dynamic behavior and live data, 170 generic knowledge for classes of objects, 172,173/ interaction between objects, 170 robot navigation example, 172,174/ Kuhn statistical segment picture of chain dynamics, use in molecular displays, L Laboratory information management system, development, 34 Life cycle, definition, 127 Meta-knowledge, definition, 5 Metal analysis manual incorporation of expert system, 214 model, 212,213/214 procedure, role of laboratory information management system, 214 use of ACexpert, 215/216 Metallic materials, corrosion, Molecular modeling Brooks data structure, 93 caricature of macromolecule by model matching, 94,95/ deducing atomic-scale geometry from generalized cylinders, examples of generalized cylinders, 94,95/ manipulation of generalized cylinder representation, 98 ribbon as set of generalized cylinders, use of acronym-style modeler in molecular displays, use of generalized cylinders in interpretation of scene, 94-95,9^,97 Molecular modeling software caricaturization of macromolecules, 93 disadvantages, Multilayered design approach, SYNLMA, 104,105/,106,107/ N NUT crystallographic modeling, 198 framework, schematic outline, 196,197/ structure elucidation from crystal powders, 196,198 M Maintenance of knowledge-based system design specifications, practical importance, 246 proper programming techniques, 246 scientific importance, Material hazard classification ASTM, FM-NFPA, 135 UN-TNO, 135,13^,137 Mathematical language interface, KNODE, Matrix discussion group establishment, 190 strengths and weaknesses, O Optimization of combustion in multiple-burner installations development of simple learning system, 186 related work, 181 rule base, 181,182^,183 rule-based optimization of 12-burner zone of furnace, 185 rule-based optimization of simulation, 183,184/185 statement of problem, 180 system that learns its own rules, Organic synthesis, designing an expert system,

5 INDEX 255 Personal construct theory applications, 40 description, PIRExS description, 22 explanation facility, 32 pedagogical uses, types of predicted reactions, 22,23* Plant safety, example of G2 expert system, Polyalanine polypeptide, ribbon structure, 84,85/ Principle of minimum chemical distance, description, Program for analysis of IR spectra (PAIRS) availability and modifiability of knowledge base, description, 236 example of results, 241,242/* expectations for system, 236 implementation, 241, information required to answer query, 241, / intended audience, 237 maintenance, partial interpreter trace, 241,243/ publishability, 247 schematic representation, 237,23 f significant advances during development, 237,238f source of expertise, 239 system magnitude, 237,239 Pseudoreceptor calculation of energy and conformational features, 83 creation, 83 definition, 83 methodology, 83 structure and reaction determination, 83 Pseudoreceptor method of drug design configuration of side chains of muted pseudoreceptor, 88,8Sjf enthalpic and entropy contributions to binding and stability, 88,90 learning cycle, 90 low-energy structures of substrates, 84,86/" materials, 84 packing around substrate, 88 peptide structure after substrate insertion into pocket, 84,87/88 Receptor fit method of drug design, description, 82 Rule-based optimization of simulation of multiple-burner installations optimization of simulation, 184/ randomly generated model, 184,185/ simulation, 183,184/" simulator, 183 Rule-based optimization of 12-burner zone of furnace hardware, 185 optimization of furnace, 185 Rule base for optimization of combustion in multiple-burner installations classification of situations, 181,182/",183 composition of actions and examples of rules, 181 origin of rules, 181 type of rule, 181 S Scientific and engineering computation, Scientific language interface, KNODE, 50,52,54-56 Scientific visualization module, KNODE, 54 Shape, representation, 92 Sharing of knowledge bases ability for customization and improvement, 13 accessibility, 13 advancement of science, 13 advantages, applications, 16 dangers, 15 development costs, 11,12/",13 different goals for different users, 11 economic obstacles, ll,12f,13 modular expert systems, 16 need for numerical data-sharing mechanisms, 15 problems, 11 rule examples, 13,14/ technical obstacles, 11,13 trade secret vs. public domain information, SYNGEN program bond-set selection from screen, 72,73/ characterization of structures and reactions, 64,66,67/ construction refunctionalization reactions, 69 description, example of reaction generation, 66,68/" examples of operator selection choices, 74,75/ generalized form of construction reactions, 66,68/"

6 256 EXPERT SYSTEM APPLICATIONS IN CHEMISTRY SYNGEN program Continued generalized plan, 78,8Qf generation of synthetic sequences from bond sets, 66,69 match of SYNGEN to SYNLIB, 76 mechanism tests for chemical solidity, 69,71-72 operator selections from output, 72,73/,74,75/ output summary from screen, 72,73/ procedure, 62,64 protocol, 62 refunctionalization reactions, 76,78-79,8Qf removal of equivalent reactions, 74 sample match of SYNGEN to REACCS, 76,77/ sample page of reactions from screen, 72,74/*,75 samples of half-reactions, 69,7Qf searching for literature precedents, 74,76,77/ selection criteria for synthesis routes, 64 skeletal bondsets and assembly plans, 64,65/ SYNLMA advantages of separate reasoning component, applications, 103 chemical islands, 111 components, 102 description of present system, implementation of tree-building stage, ,12Qf implementation of tree-definition stage, implementation of tree-verification stage, 119,121 indole substitution patterns, 111,114/115 initial retrosynthetic paths of cocaine, 111,112/" interfacing with commerical data base, 121 layer structure, 104,105/ methodology-driven ibogamine synthesis, 111,114^,115 modeling strategic planning for synthesis process, multilayered design approach, 104,105/106,107/ network of environment pairs, 104,106,107/ nonselective carbene insertion, 108,10Sjf pruned synthesis of ibuprofen, 108,109/" reaction rule constraints, 108,1lQf,l 11 reaction taxonomy, 119,12Qf scope of system, 106, sophistication, 108 substructure-driven ibogamine synthesis, 111,113/ system implementation, tree-building stage, 115 tree-definition stage, 111, tree-verification stage, 116 Synthesis tree, schematic diagram, 62,63/ System supervisor, KNODE, 50 T Target functionality, definition, 69 Titanium-vanadium denoting catalyst conclusions from case study, 193 function, 192 surface characterization by CACSS, Tree-building stage, SYNLMA, 115,116, Tree-definition stage, SYNLMA, 111, /115 Tree-verification stage, SYNLMA, 116,119,121 U Unit reaction, definition, 66 User interface description, 3 expert interaction, 5-6, novice interaction, 6 parts, 5-6 V Validation, definition, 127 Vendors, goals of expert systems, 11 Verification, definition, 127 Verification and validation of expert systems for chemical process risk management background, by and for expert systems, 131,132/",133 case study for prototype development, computer-aided software engineering, current AI activities in chemical engineering, definitions, 127 early recognition of needs, example for expert system, 131,132/" future of software systems safety, future research, 139 international factors, 129 prototype hazard classification system, purpose, software systems safety, status of research, 138 tools, 126

7 INDEX 257 W Wool dyeing experience required, 159 procedure, WOOLY characteristics, 164 data retrieval, 167 default values, 167 development, 158 evaluation of class of dyestuffs for given fastness requirements, 159,163/,164 expertise required of user, explanation facility, inference mechanism, 167 knowledge types, 164, main screen output, 159,161/ WOOLY Continued perspiration alkaline fastness for recipe, 164,165/ quantitative model, 167 rules, 167 schematic representation of wool dyeing process, 159,16Qf standard end-use fastness requirements for hand knitting yarn, 159,162/* temperature time diagram for dyeing process, 164,166/ X XTSYN, description, 103

Preparing a PDB File

Preparing a PDB File Figure 1: Schematic view of the ligand-binding domain from the vitamin D receptor (PDB file 1IE9). The crystallographic waters are shown as small spheres and the bound ligand is shown as a CPK model. HO