The MOLSCRIPT program produces plots of protein structures using several different kinds of representations. Schematic drawings, simple wire models, ball-and-stick models, CPK models and text labels can be mixed freely. The schematic drawings are shaded to improve the illusion of three dimensionality. A number of parameters affecting various aspects of the objects drawn can be changed by the user. The output from the program is in PostScript format.

https://journals.iucr.org/j/issues/1991/05/00/gl0206/gl0206.pdf

MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures

1 Graphical modeling using L-systems.- 1.1 Rewriting systems.- 1.2 DOL-systems.- 1.3 Turtle interpretation of strings.- 1.4 Synthesis of DOL-systems.- 1.4.1 Edge rewriting.- 1.4.2 Node rewriting.- 1.4.3 Relationship between edge and node rewriting.- 1.5 Modeling in three dimensions.- 1.6 Branching structures.- 1.6.1 Axial trees.- 1.6.2 Tree OL-systems.- 1.6.3 Bracketed OL-systems.- 1.7 Stochastic L-systems.- 1.8 Context-sensitive L-systems.- 1.9 Growth functions.- 1.10 Parametric L-systems.- 1.10.1 Parametric OL-systems.- 1.10.2 Parametric 2L-systems.- 1.10.3 Turtle interpretation of parametric words.- 2 Modeling of trees.- 3 Developmental models of herbaceous plants.- 3.1 Levels of model specification.- 3.1.1 Partial L-systems.- 3.1.2 Control mechanisms in plants.- 3.1.3 Complete models.- 3.2 Branching patterns.- 3.3 Models of inflorescences.- 3.3.1 Monopodial inflorescences.- 3.3.2 Sympodial inflorescences.- 3.3.3 Polypodial inflorescences.- 3.3.4 Modified racemes.- 4 Phyllotaxis.- 4.1 The planar model.- 4.2 The cylindrical model.- 5 Models of plant organs.- 5.1 Predefined surfaces.- 5.2 Developmental surface models.- 5.3 Models of compound leaves.- 6 Animation of plant development.- 6.1 Timed DOL-systems.- 6.2 Selection of growth functions.- 6.2.1 Development of nonbranching filaments.- 6.2.2 Development of branching structures.- 7 Modeling of cellular layers.- 7.1 Map L-systems.- 7.2 Graphical interpretation of maps.- 7.3 Microsorium linguaeforme.- 7.4 Dryopteris thelypteris.- 7.5 Modeling spherical cell layers.- 7.6 Modeling 3D cellular structures.- 8 Fractal properties of plants.- 8.1 Symmetry and self-similarity.- 8.2 Plant models and iterated function systems.- Epilogue.- Appendix A Software environment for plant modeling.- A.1 A virtual laboratory in botany.- A.2 List of laboratory programs.- Appendix B About the figures.- Turtle interpretation of symbols.

/pdf/the-algorithmic-beauty-of-plants-4f9yunhil9.pdf

The Algorithmic Beauty of Plants

A method is presented for analytically calculating a smooth, three-dimensional contour about a molecule. The molecular surface envelope may be drawn on either color raster computer displays or real-time vector computer graphics systems. Molecular areas and volumes may be computed analytically from this surface representation. Unlike most previous computer graphics representations of molecules, which imitate wire models or space-filling plastic spheres, this surface shows only the atoms that are accessible to solvent. This analytical method extends the earlier dot surface numerical algorithm, which has been applied in enzymology, rational drug design, immunology, and understanding DNA base sequence recognition.

/pdf/solvent-accessible-surfaces-of-proteins-and-nucleic-acids-3euqtz86k0.pdf

Solvent-Accessible Surfaces of Proteins and Nucleic Acids

This ebook is the first authorized digital version of Kernighan and Ritchie's 1988 classic, The C Programming Language (2nd Ed.). One of the best-selling programming books published in the last fifty years, "K&R" has been called everything from the "bible" to "a landmark in computer science" and it has influenced generations of programmers. Available now for all leading ebook platforms, this concise and beautifully written text is a "must-have" reference for every serious programmers digital library.

As modestly described by the authors in the Preface to the First Edition, this "is not an introductory programming manual; it assumes some familiarity with basic programming concepts like variables, assignment statements, loops, and functions. Nonetheless, a novice programmer should be able to read along and pick up the language, although access to a more knowledgeable colleague will help."

The C programming language

A technique for rendering images of volumes containing mixtures of materials is presented. The shading model allows both the interior of a material and the boundary between materials to be colored. Image projection is performed by simulating the absorption of light along the ray path to the eye. The algorithms used are designed to avoid artifacts caused by aliasing and quantization and can be efficiently implemented on an image computer. Images from a variety of applications are shown.

Volume rendering

Fundamentals of interactive computer graphics , Fundamentals of interactive computer graphics , مرکز فناوری اطلاعات و اطلاع رسانی کشاورزی

Fundamentals of interactive computer graphics

Computer graphics: principles and practice (2nd ed.)

From the Publisher:
This new introductory text to computer graphics is an adaptation of Computer Graphics: Principles and Practice, Second Edition, which remains the most comprehensive and authoritative work in the field. While retaining the currency and accuracy of the larger book, this abbreviated version focuses on topics essential for all beginners in computer graphics and provides expanded explanations for readers with little or no technical background. Worked examples have been added to illustrate important concepts and techniques, and program code has been written in the C language to enhance the book's usefulness. In addition, the book contains an extensive illustration program, with more than 50 full-color images.

Topic coverage includes basic graphics programming, hardware, and applications. Important algorithms are included to facilitate implementation of both 2D and 3D graphics. A separate chapter covers SPHIGSa simplified dialect of the PHIGS 3D standardand coincides with the availability of an updated version of the software. Chapter 9 and presents a concise overview of interaction issues and techniques. Advanced material from the larger book has been condensed, and the mathematics needed for it has been explained carefully . 

The result is an accessible introduction to computer graphics, crafted to provide a solid foundation for further work in this exciting field.
Features
Adaptation of the definitive computer graphics book in the fieldhalf the length.
Presents key concepts geared toward students with minimal technical background.
Provides worked examples in C.
Retains the highlevel of teaching standards of the parent graphics text.

Introduction to Computer Graphics

characterized by four distinguishable interface styles, each lasting for many years and optimized to the hardware available at the time. In the first period, the early 1950s and 1960s, computers were used in batch mode with punched-card input and line-printer output; there were essentially no user interfaces because there were no interactive users (although some of us were privileged to be able to do console debugging using switches and lights as our “user interface”). The second period in the evolution of interfaces (early 1960s through early 1980s) was the era of timesharing on mainframes and minicomputers using mechanical or “glass” teletypes (alphanumeric displays), when for the first time users could interact with the computer by typing in commands with parameters. Note that this era persisted even through the age of personal microcomputers with such operating systems as DOS and Unix with their command line shells. During the 1970s, timesharing and manual command lines remained deeply entrenched, but at Xerox PARC the third age of user interfaces dawned. Raster graphics-based networked workstations and “pointand-click” WIMP GUIs (graphical user interfaces based on windows, icons, menus, and a pointing device, typically a mouse) are the legacy of Xerox PARC that we’re still using today. WIMP GUIs were popularized by the Macintosh in 1984 and later copied by Windows on the PC and Motif on Unix workstations. Applications today have much the same look and feel as the early desktop applications (except for the increased “realism” achieved through the use of drop shadows for buttons and other UI widgets); the main advance lies in the shift from monochrome displays to color and in a large set of software-engineering tools for building WIMP interfaces. I find it rather surprising that the third generation of WIMP user interfaces has been so dominant for more than two decades; they are apparently sufficiently good for conventional desktop tasks that the field is stuck comfortably in a rut. I argue in this essay that the status quo does not suffice—that the newer forms of computing and computing devices available today necessitate new thinking t h e h u m a n c o n n e c t i o n Andries van Dam

Post-WIMP user interfaces

The 3D components of today’s user interfaces are still underdeveloped. Direct interaction with 3D objects has been limited thus far to gestural picking, manipulation with linear transformations, and simple camera motion. Further, there are no toolkits for building 3D user interfaces. We present a system which allows experimentation with 3D widgets, encapsulated 3D geometry and behavior. Our widgets are first-class objects in the same 3D environment used to develop the application. This integration of widgets and application objects provides a higher bandwidth between interface and application than exists in more traditional UI toolkit-based interfaces. We hope to allow user-interface designers to build highly interactive 3D environments more easily than is possible with today’s tools.

/pdf/three-dimensional-widgets-43gak7c4yg.pdf

Andries van Dam

Papers

Fundamentals of interactive computer graphics

Computer graphics: principles and practice (2nd ed.)

Introduction to Computer Graphics

Post-WIMP user interfaces

Three-dimensional widgets