Coot is a molecular-graphics application for model building and validation of biological macromolecules. The program displays electron-density maps and atomic models and allows model manipulations such as idealization, real-space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers and Ramachandran idealization. Furthermore, tools are provided for model validation as well as interfaces to external programs for refinement, validation and graphics. The software is designed to be easy to learn for novice users, which is achieved by ensuring that tools for common tasks are `discoverable' through familiar user-interface elements (menus and toolbars) or by intuitive behaviour (mouse controls). Recent developments have focused on providing tools for expert users, with customisable key bindings, extensions and an extensive scripting interface. The software is under rapid development, but has already achieved very widespread use within the crystallographic community. The current state of the software is presented, with a description of the facilities available and of some of the underlying methods employed.

/pdf/features-and-development-of-coot-5al5bhwkg1.pdf

Features and development of Coot.

: A partial theory is presented of thinking, combining a number of classical and modern concepts from psychology, linguistics, and AI. In a new situation one selects from memory a structure called a frame: a remembered framework to be adapted to fit reality by changing details as necessary, and a data-structure for representing a stereotyped situation. Attached to each frame are several kinds of information -- how to use the frame, what one can expect to happen next, and what to do if these expectations are not confirmed. The report discusses collections of related frames that are linked together into frame-systems.

/pdf/a-framework-for-representing-knowledge-4ptb6mi5zb.pdf

A framework for representing knowledge

This paper describes a computer system for understanding English. The system answers questions, executes commands, and accepts information in an interactive English dialog. It is based on the belief that in modeling language understanding, we must deal in an integrated way with all of the aspects of language—syntax, semantics, and inference. The system contains a parser, a recognition grammar of English, programs for semantic analysis, and a general problem solving system. We assume that a computer cannot deal reasonably with language unless it can understand the subject it is discussing. Therefore, the program is given a detailed model of a particular domain. In addition, the system has a simple model of its own mentality. It can remember and discuss its plans and actions as well as carrying them out. It enters into a dialog with a person, responding to English sentences with actions and English replies, asking for clarification when its heuristic programs cannot understand a sentence through the use of syntactic, semantic, contextual, and physical knowledge. Knowledge in the system is represented in the form of procedures, rather than tables of rules or lists of patterns. By developing special procedural representations for syntax, semantics, and inference, we gain flexibility and power. Since each piece of knowledge can be a procedure, it can call directly on any other piece of knowledge in the system.

Understanding Natural Language

A type system is a syntactic method for automatically checking the absence of certain erroneous behaviors by classifying program phrases according to the kinds of values they compute. The study of type systems -- and of programming languages from a type-theoretic perspective -- has important applications in software engineering, language design, high-performance compilers, and security.This text provides a comprehensive introduction both to type systems in computer science and to the basic theory of programming languages. The approach is pragmatic and operational; each new concept is motivated by programming examples and the more theoretical sections are driven by the needs of implementations. Each chapter is accompanied by numerous exercises and solutions, as well as a running implementation, available via the Web. Dependencies between chapters are explicitly identified, allowing readers to choose a variety of paths through the material.The core topics include the untyped lambda-calculus, simple type systems, type reconstruction, universal and existential polymorphism, subtyping, bounded quantification, recursive types, kinds, and type operators. Extended case studies develop a variety of approaches to modeling the features of object-oriented languages.

https://www.seas.upenn.edu/~bcpierce/tapl/contents.pdf

Types and Programming Languages

The Connection Machine describes a fundamentally different kind of computer. It offers a preview of a parallel processing computer that Daniel Hillis and others are now developing to perform tasks that no conventional, sequential machine can solve in a reasonable time.

The Connection Machine

The report gives a defining description of the programming language Scheme. Scheme is a statically scoped and properly tail-recursive dialect of the Lisp programming language invented by Guy Lewis Steele, Jr. and Gerald Jay Sussman. It was designed to have an exceptionally clear and simple semantics and few different ways to form expressions. A wide variety of programming paradigms, including imperative, functional, and message passing styles, find convenient expression in Scheme.

The introduction offers a brief history of the language and of the report.

The first three chapters present the fundamental ideas of the language and describe the notational conventions used for describing the language and for writing programs in the language.

Sections 5 and 6 describe the syntax and semantics of expressions, programs, and definitions.

Section 7 describes Scheme‘s built-in procedures, which include all of the language‘s data manipulation and input/output primitives.

Section 8 provides a formal syntax for Scheme written in extended BNF, along with a formal denotational semantics. An example of the use of the language follows the formal syntax and semantics.

The report concludes with a list of references and an alphabetic index and is followed by a short list of clarifications and corrections.

Revised Report on the Algorithmic Language Scheme

The report gives a defining description of the programming language Scheme. Scheme is a statically scoped and properly tail-recursive dialect of the Lisp programming language invented by Guy Lewis Steele Jr. and Gerald Jay Sussman. It was designed to have an exceptionally clear and simple semantics and few different ways to form expressions. A wide variety of programming paradigms, including imperative, functional, and message passing styles, find convenient expression in Scheme.

Revised4 report on the algorithmic language scheme

/pdf/revised-5-report-on-the-algorithmic-language-26r0nsx5sp.pdf

Revised 5 Report on the Algorithmic Language

: The manual is an introduction and reference to the latest version of the Conniver programming language, an artificial intelligence language with general control and data-base structures. (Author)

Gerald Jay Sussman

Papers

Revised Report on the Algorithmic Language Scheme

Revised4 report on the algorithmic language scheme

Revised 5 Report on the Algorithmic Language

The Conniver Reference Manual

An Interpreter for Extended Lambda Calculus