VEGA: a versatile program to convert,handle and visualize molecular structure on Windows-based PCs

We here propose the program VEGA, that was developed to create a bridge between the most popular molecular software packages. In this tool some features are implemented some features to analyze, display and manage the three dimensional (3D) structure of the molecules. The most important features are (1) file format conversion (with assignment of the atom types and atomic charges), (2) surface calculation and (3) trajectory analysis. The executable and the source code can be free downloaded from [URL: see text].     

A template for real-time image processing development: Windows-based PCs and webcams for computer vision research and education

A free and open-source software package called TRIPOD: Template for Real-time Image Processing Development, is described. TRIPOD was designed for classroom implementation or self-instruction. USB Logitech, Windows PC, Microsoft Visual C++ 6.0 compiler, and ANSI C/C++ are used in TRIPOD. The motivation for TRIPOD stemmed from observations that affordable, widely available, and portable components have made a strong impact on robotics. The article showcased applications like laser rangefinding and visual servoing.     

Recent developments in molecular graphics: visualization of chemical structures and properties

As three-dimensional models of chemical objects are essential tools for understanding their intimate structure and function, nowadays molecular graphics techniques allow building, visualizing, and manipulating, of complex molecular structures and their related properties. This paper presents several developments recently achieved in this field, namely: the representation of macromolecular structures such as proteins; the modelization of molecular envelopes as dot surfaces, mesh surfaces, and solid models; the evaluation and visualization of color-coded reactivity indices based on intermolecular interaction energies. The last application is shown to be particularly useful in several applications, such as molecular recognition and drug design.     

Transferring a macro program to a micro machine

A powerful graphical PASCAL extension has transferred from a large computer to a microcomputer. The graphical extension, called M1RA-2D, allows the user to program computer graphics applications in a modern, structured and efficient language. The problems encountered were mainly due to the limits of a microcomputer-based system and to the size of the project. Problems involved memory space, documentation, low-power peripherals, PASCAL restrictions and hardware robustness and quality. Finally, M1RA-2D is compared with two other graphics software packages implemented on microcomputers: Applegraphics and an implementation of a 2D, level 2 Core System.     

Knowledge visualization: A new framework for interactive graphic interface design

Diagrams communicate massive amounts of information at a glance. Complex domains can be simplified and extended with diagrammatic notations. Computational systems can certainly benefit from the use of diagrams. However, graphic interfaces are difficult and time consuming to write. We need a way of shortening the graphic-interface building cycle so that it is relatively easy and fast to add a graphic interface to any application that may benefit from it.A general-purpose, graphic-interface-building tool kit that a designer or user, not a programmer, can use to design and attach graphic interfaces to applications can greatly speed up and lower the costs of adding graphics to systems. In this paper, I describe a new framework for interactive graphic interface design. The framework will enable graphic-interface-building tools which are general purpose, inter-active, and application-specific.The framework consists of a taxonomy (ontology) of visual properties that span sub-object properties, full objects, and the relationships between objects. The taxonomy forms a skeleton on which to hang methods for manipulating these visual properties, objects, relations, and composites. The methods consist of the generation of prototypes, the recognition of properties in objects, and mouse manipulation functions for modifying properties in an object. Further characteristics of the framework are that the properties are composable, that objects can be explicitly, incrementally described through repeated composition and application of recognition methods, and that the composition of properties to form more fully described and more complex objects is recursive. This makes the framework and the objects within it quite flexible, incremental, uniform, and modular.     

Working with occam: a program for generating display images

It is assumed that a host processor computes the corner coordinates of surfaces and outputs these sequentially, in ranked order, to the components described in an OCCAM program. The data is precomputed and stored in a sequential file. A scheduler controls the activity of a number of zone management processors (ZMPs), all running in parallel, and a special memory buffer. Each ZMP handles only one surface at a time. A processor can pick up a new surface for display when the previous surface has been completed. Only one ZMP can write into a given raster scanline at one time. Others may be writing into the same column of other lines at the same time. Hidden surface elimination is achieved by processing the surfaces in an order ranked on distance from the viewing point. This ranking is done in the host processor. The ranked data is held on a file, which is read sequentially in 512 byte blocks. This data has been previously computed and stored as a sequence of double-byte integers in the required order for a series of picture frames, one frame per 512 byte block. The occam implementation on the Apple II europlus running under UCSD version 4 is very slow. It is postulated that an implementation using separate occam professor hardware units for each appropriate process would run in real time. There is considerable communication between the processors. The activity of each processor is generally sequential and all the processors run in parallel. Comments are made about some of the problems and advantages of programming in occam in an appendix.     

Are autostereograms useful for computer graphics and scientific visualization

Autostereograms are images that can be observed as “flat” 2D pictures or as a display of 3D objects without any extra apparatus. More than one million copies of books on this subject have been sold recently, but are autostereograms useful for computer graphics and scientific visualization? This short note provides some assistance for easily designing still and animated autostereograms, and tries to encourage reader involvement in finding new scientific applications.     

LANDISVIEW: A visualization tool for landscape modelling

A major challenge in landscape and environmental modelling is to effectively visualize large amounts of time-series simulation output, often in various Geographic Information System (GIS) formats. We developed a software tool (LANDISVIEW), to easily visualize and animate time-series of ERDAS *.gis maps. The open source tool can also be used to generate batch files for FRAGSTATS, a widely used spatial analysis program.     

A priori molecular descriptors in QSAR: a case of HIV-1 protease inhibitors. II. Molecular graphics and modeling

Molecular graphics and modeling methods illustrated the chemical background of the a priori approach from part I, and visualized steric and electronic enzyme-inhibitor relationships at qualitative and quantitative level for 34 and its derivatives. The enzyme-inhibitor electron density overlap occurs at 1.5–5.5 Å cut-off distance, beyond van der Waals radii. Derivatives of 34 exhibit linear relationships between biological activity, molecular size and number of intermolecular interactions.     

tPSODock:基于化学得分函数和两层粒子群算法的计算机分子对接程序

药物分子对接是计算机辅助药物设计的主要方法之一。利用化学得分函数(Chemscor)作为能量函数,以及将一种新的优化算法一两层粒子群算法作为搜索算法,得到了一种新的计算机分子对接程序：tPSODock。利用tPSODock计算了100个蛋白质一配体的复合物,并且与Consdock和Autodock3．0计算结果进行了对比,结果显示88％的计算结果RMSD小于2．0A,优于Consdock以及Autodock的计算结果。说明tPSODock在是一种高效的分子对接软件,可以用于大规模数据库的筛选工作,适合新药的开发和研制。     

MolSpace: a computer desktop tool for visualization of massive molecular data

The authors have developed a software tool, MolSpace, to visualize massive molecular datasets. MolSpace can project a set of massive multivariate data onto a visual space (two- or three-dimensional space) by means of principal component analysis. MolSpace allows users not only to draw a scatter diagram of the data but also to display their two- or three-dimensional molecular structures as the objects in that space. With a probe (a molecular object) the user can navigate vast data spaces, thus facilitating understanding of the data structure. In addition, partial space searching is also available that is based on similarity searching techniques. It is possible to interrogate a three-dimensional structure of a chemical compound that corresponds to each object on the space in real time. The detail of the system is discussed with an illustrative example.     

MOLVIE: an interactive visualization environment for molecular structures

A Molecular visualization interactive environment (MOLVIE), is designed to display three-dimensional (3D) structures of molecules and support the structural analysis and research on proteins. The paper presents the features, design considerations and applications of MOLVIE, especially the new functions used to compare the structures of two molecules and view the partial fragment of a molecule. Being developed in JAVA, MOLVIE is platform-independent. Moreover, it may run on a webpage as an applet for remote users. MOLVIE is available at http://www.cs.ucsb.edu/~mli/Bioinf/software/index.html.     

三维分子结构的制作、显示和格式转换

本文总结了各种三维分子结构在计算机和网络上显示与制作的方法,包括三维动画如3D Studio MAX、VRML、化学结构插件如MDL Chime Plugin、CS ChemOffice Plugin和HyperChem Plugin等、CML、Flash 3D动画、JAVA动画等,比较了他们制作和显示三维分子的优缺点,同时总结了各种三维分子结构格式的相互关系及转换方法,认为以通用的“mol”格式可以作中介可以较好地实现格式转换。     

用Java 3D技术开发基于网络的分子模拟可视化系统

分子模拟的可视化在分子模拟系统中具有重要的现实意义,本文在分析了网络环境下Java3D的图形处理优势之后,就开发基于网络环境的分子模拟可视化系统中的三维图形的结构表示、生成、显示、控制以及模拟结果的动态显示等问题进行了探讨,这些方法已成功地用于基于网络环境的分子模拟可视化系统。     

Discrim: a computer program using an interactive approach to dissect a mixture of normal or lognormal distributions

DISCRIM is an interactive computer graphics program that dissects mixtures of normal or lognormal distributions. The program was written in an effort to obtain a more satisfactory solution to the dissection problem than that offered by a graphical or numerical approach alone. It combines graphic and analytic techniques using a Tektronix¹ terminal in a time-share computing environment. The main program and subroutines were written in the FORTRAN language.     

Script visualization (ScriptViz): a smart system that makes writing fun

We have built the first version of ScriptViz v.1.0 that allows users to visualize their screenplays in real time via animated graphics. Our system consists of a text understanding module, a high-level planning module and a scene generator. The user can input a screenplay as a set of well-formed english sentences via a graphic user interface. The text understanding module interprets the input sentences and triggers the high-level planner to construct a plan of actions for the appropriate agents. Then the agents execute the plans, and the scene generator renders the scene as the story evolves. Our system provides the user with a powerful tool to visualize his screenplays (stories) in the form of computer graphics, which makes writing story fun for students as well as for screenplay writers.

An interactive tool for the visualization of cathode-ray tube monitor gamuts

The aim of this work was the development of an interactive tool for the visualization and the comparison of cathode-ray tube monitor gamuts.     

Chemical ideograms and molecular computer graphics

Molecular computer graphics (MCG) has become the indispensable complement of experimental chemical and biological tools and, in a way, will shape the evolution of these fields. This accelerated and popularized evolution takes root in the visual, even scenic, grasping of fundamental chemical concepts, perceived as veritable ideograms, which condense a vast amount of information with a few two- or threedimensional graphic symbols. With MCG one can carry out real computerized syntheses of chemical images. MCG is also an ideal tool through which to visualize the changes of a system as a function of time. This review article describes the potentials and advantages of structural MCG for visualizing the basic steps of important modelization concepts, particularly for handling on-line structures in information networks and in computer-assisted drug design (CADD) applications.