A Perturbation Scheme for Spherical Arrangements with Application to Molecular Modeling

We describe a software package for computing and manipulating the subdivision of a sphere by a collection of (not necessarily great) circles and for computing the boundary surface of the union of spheres. We present problems that arise in the implementation of the software and the solutions that we have found for them. At the core of the paper is a novel perturbation scheme to overcome degeneracies and precision problems in computing spherical arrangements while using floating point arithmetic. The scheme is relatively simple, it balances between the efficiency of computation and the magnitude of the perturbation, and it performs well in practice. In one O(n) time pass through the data, it perturbs the inputs necessary to insure no potential degeneracies and then passes the perturbed inputs on to the geometric algorithm. We report and discuss experimental results. Our package is a major component in a larger package aimed to support geometric queries on molecular models; it is currently employed by chemists working in "rational drug design." The spherical subdivisions are used to construct a geometric model of a molecule where each sphere represents an atom. We also give an overview of the molecular modeling package and detail additional features and implementation issues.

Revised Report on the Algorithmic Language Scheme

Data and procedures and the values they amass, Higher-order functions to combine and mix and match, Objects with their local state, the message they pass, A property, a package, the control of point for a catch- In the Lambda Order they are all first-class. One thing to name them all, one things to define them, one thing to place them in environments and bind them, in the Lambda Order they are all first-class. Keywords: Scheme, Lisp, functional programming, computer languages.

MIT Scheme Reference Manual

MIT Scheme is an implementation of the Scheme programming language that runs on many popular workstations. The MIT Scheme Reference Manual describes the special forms, procedures, and datatypes provided by the implementation for use by application programmers.

RABBIT: A Compiler for SCHEME

We have developed a compiler for the lexically-scoped dialect of LISP known as SCHEME. The compiler knows relatively little about specific data manipulation primitives such as arithmetic operators, but concentrates on general issues of environment and control. Rather than having specialized knowledge about a large variety of control and environment constructs, the compiler handles only a small basis set which reflects the semantics of lambda-calculus. All of the traditional imperative constructs, such as sequencing, assignment, looping, GOTO, as well as many standard LISP constructs such as AND, OR, and COND, are expressed in macros in terms of the applicative basis set. A small number of optimization techniques, coupled with the treatment of function calls as GOTO statements, serve to produce code as good as that produced by more traditional compilers. The macro approach enables speedy implementation of new constructs as desired without sacrificing efficiency in the generated code. A fair amount of analysis is devoted to determining whether environments may be stack-allocated or must be heap-allocated. Heap-allocated environments are necessary in general because SCHEME (unlike Algol 60 and Algol 68, for example) allows procedures with free lexically scoped variables to be returned as the values of other procedures; the Algol stack-allocation environment strategy does not suffice. The methods used here indicate that a heap-allocating generalization of the "display" technique leads to an efficient implementation of such "upward funargs". Moreover, compile-time optimization and analysis can eliminate many "funargs" entirely, and so far fewer environment structures need be allocated at run time than might be expected. A subset of SCHEME (rather than triples, for example) serves as the representation intermediate between the optimized SCHEME code and the final output code; code is expressed in this subset in the so-called continuation-passing style. As a subset of SCHEME, it enjoys the same theoretical properties; one could even apply the same optimizer used on the input code to the intermediate code. However, the subset is so chosen that all temporary quantities are made manifest as variables, and no control stack is needed to evaluate it. As a result, this apparently applicative representation admits an imperative interpretation which permits easy transcription to final imperative machine code. These qualities suggest that an applicative language like SCHEME is a better candidate for an UNCOL than the more imperative candidates proposed to date.