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.

Coot is a molecular-graphics program designed to assist in the building of protein and other macromolecular models. The current state of development and available features are presented.

Features and development of Coot

We present an interprocedural flow-insensitive points-to analysis based on type inference methods with an almost linear time cost complexity To our knowledge, this is the asymptotically fastest non-trivial interprocedural points-to analysis algorithm yet described The algorithm is based on a non-standard type system. The type inferred for any variable represents a set of locations and includes a type which in turn represents a set of locations possibly pointed to by the variable. The type inferred for a function variable represents a set of functions It may point to and includes a type signature for these functions The results are equivalent to those of a flow-insensitive alias analysis (and control flow analysis) that assumes alias relations are reflexive and transitive.This work makes three contributions. The first is a type system for describing a universally valid storage shape graph for a program in linear space. The second is a constraint system which often leads to better results than the "obvious" constraint system for the given type system The third is an almost linear time algorithm for points-to analysis by solving a constraint system.

/pdf/points-to-analysis-in-almost-linear-time-ziolc34o27.pdf

Points-to analysis in almost linear time

In the last three decades a large number of compiler transformations for optimizing programs have been implemented. Most optimizations for uniprocessors reduce the number of instructions executed by the program using transformations based on the analysis of scalar quantities and data-flow techniques. In contrast, optimizations for high-performance superscalar, vector, and parallel processors maximize parallelism and memory locality with transformations that rely on tracking the properties of arrays using loop dependence analysis.This survey is a comprehensive overview of the important high-level program restructuring techniques for imperative languages, such as C and Fortran. Transformations for both sequential and various types of parallel architectures are covered in depth. We describe the purpose of each transformation, explain how to determine if it is legal, and give an example of its application.Programmers wishing to enhance the performance of their code can use this survey to improve their understanding of the optimizations that compilers can perform, or as a reference for techniques to be applied manually. Students can obtain an overview of optimizing compiler technology. Compiler writers can use this survey as a reference for most of the important optimizations developed to date, and as bibliographic reference for the details of each optimization. Readers are expected to be familiar with modern computer architecture and basic program compilation techniques.

Compiler transformations for high-performance computing

Category theorists invented monads in the 1960's to concisely express certain aspects of universal algebra. Functional programmers invented list comprehensions in the 1970's to concisely express certain programs involving lists. This paper shows how list comprehensions may be generalised to an arbitrary monad, and how the resulting programming feature can concisely express in a pure functional language some programs that manipulate state, handle exceptions, parse text, or invoke continuations. A new solution to the old problem of destructive array update is also presented. No knowledge of category theory is assumed.

Comprehending monads

Programming languages should be designed not by piling feature on top of feature, but by removing the weaknesses and restrictions that make additional features appear necessary. Scheme demonstrates that a very small number of rules for forming expressions, with no restrictions on how they are composed, are enough to form a practical and efficient programming language that is flexible enough to support most of the major programming paradigms in use today. This book contains the three parts comprising 'R6RS', the sixth revision of a series of reports describing the programming language Scheme. The book is divided into parts: a description of the language itself, a description of the standard libraries and non-normative appendices. Early chapters introduce Scheme and later chapters act as a reference manual. This is an important report for programmers that work with or want to learn about the Scheme language.

/pdf/revised-6-report-on-the-algorithmic-language-scheme-28yop7oyoj.pdf

Revised [6] 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.

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

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Revised [6] Report on the Algorithmic Language Scheme

Revised Report on the Algorithmic Language Scheme

Revised4 report on the algorithmic language scheme