Structure software

In order to obtain detailed structure, a knowledge of diffraction intensities is essential, the intensities being related to the structure factor. Computer-controlled single-crystal X-ray diffractometers with structure (software) packages have made structure elucidation a routine matter. The availability of synchrotron X-radiation of continuously variable wavelength has made X-ray diffraction a still more powerful structural tool for the study of solids. A technique of great utility to solid state chemists is the Rietveld treatment of powder X-ray diffraction profiles (Rietveld, 1969 Manohar, 1983). Automated structure packages for the determination of unknown structures by this method are now commercially available (see section 2.2.3). In Fig. 2.1, we show a typical set of profile data. 

Daniel E. Meyer, Wendy A. Warr, and Richard A. Love, Chemical Structure Software for Personal Computers, American Chemical Society, Washington, DC,... 

Figure 3.6 shows 12 structures that may correspond to the abbreviation DPA. Six of them can be output by the ACD/Name to Structure software package, and six more were found by browsing the Internet. Note that even a specific context cannot guarantee an exact meaning. For example, both structures 3 and 8 were found in publications about coordination compounds. In general, chemical abbreviations are not unique and can rarely be distinguished from other trivial names except for the rather weak criterion that all letters are capitalized. We can conclude that conversion of any trivial name shorter than about five or six characters is not safe. A few rarer exceptions do exist, but this is a very short list. Examples include reserved abbreviations such as those for dimethyl sulfoxide (DMSO) and ethylenediaminetetraacetic acid, EDTA. 

Bio-Rad Laboratories includes programs for predicting 13C spectra hum data based on more than 40,000 compounds in its Sadder Suite (on CD-ROM), which also covers infrared spectra and chemical structure software. 

Directory structure Software construction File header and commenting Version control File naming conventions... 

Stepwise Rehnement FDA (1995) A structured software design technique data and processing steps are dehned broadly at hrst, and then further dehned with increasing detail. 

Other important and interesting aspects of the Atoms, Bonding and Structure software include ... 

Acknowledgments The authors kindly acknowledge and thank Ray Le Couteur, the designer of the Atoms, Bonding and Structure software used. Abdoolatiff also thanks Ray Le Couteur for allowing her to use the software for classroom teaching. 

Due to the realization effort of the challenging approach of IMPROVE this can only mean that we do not aim at case-dependent solutions. Instead, we are looking for a framework of reusable components (dark grey parts of Fig. 1.8) and a carefully structured software development process to get a distributed overall environment by making use of the framework. 

RNA genes are ubiquitous in the cell and are involved in a number of biochemical processes. Because there is a close relationship between function and structure, software tools that predict the secondary structure of noncoding RNAs from the base sequence are very helpful. In this article, we focus our attention on the inference of conserved secondary structure for a group of homologous RNA sequences. We present the caRNAc software, which enables the analysis of families of homologous sequences without prior alignment. The method relies both on comparative analysis and thermodynamic information. 

MOLCAS, Electronic Structure Software, Almlof J, Blomberg M, Karlstrom G, Malmqvist P-A, Roos BO, Sadlej AJ, Siegbahn PEM, Widmark P-O... 

Many databases used in drug discovery are ISIS/Oracle-based using MDL structural software and a variety of data entry and analysis systems, some are PC/Mac-based, and some are on a server. The ability to capture data and, then reassess its value through in silico approaches (148) has the potential to be a vast improvement over the "individual memory" systems that many drug companies used for the better part of the last century. Thus, with the retirement of a key scientist, the whole history of a project or even a department disappeared, and whatever folklore existed regarding unexplained findings with compounds 10 or 20 years before was lost with the individual. 

Fig. 1.2 Directory structure - Software, data and documentation subdirectories installed according Check its 1.2.11 and 1.2.1.3.

Because the protein structure record IBNl has three barnase molecules in the crystallographic unit, the PDB file has been hand-edited using a text editor to delete the superfluous chains. Editing data files is an accepted and widespread practice in three-dimensional molecular structure software, forcing the three-dimensional structure viewer to show what the user wants. In this case, the crystallographic data... 

Biomolecular three-dimensional structure database records are cmrently not compatible with macroscopic software tools such as those based on CAD software. Computer-aided design software represents a mature, robust technology, generally superior to the available molecular structure software. However, CAD software and file formats in general are ill-suited to examine the molecular world, owing to the lack of certain specialty views and analytical functions built in for the examination of details of protein structures. 

By 1986, when we were ready to buy chemical structure software, there was a number of systems on offer. A year earlier the position might have been very different. The main contenders were MACCS, DARC and OSAC, a program derived from the reaction storage and searching program, ORAC. In addition, HTSS and SABRE were of interest although we had doubts about their state of development at the time. 

Jackson, M. (2001). Problem Frames Analyzing and Structuring Software Development Problems, Addison-Wesley, Reading, MA. 

A further step in the direction of a DMU was taken when companies like ComputerVision with CAMU, Dassault Systemes with CATIA Session and VPM, understood that representing the product as an assembly was the step beyond to represent a complete product. They used the bill of material principle, already valid (and stiU) in all industry, to adapt their product structure software to the need. In the 90s, some industrial companies added their configuration management system into the DMU to manage the evolution of their products. 

This training should include data structures, software design, and graphics. Because data and its use comprise such important aspects of chemistry and chemical engineering, and because appropriate use of IT resources can empower unprecedented advances in the chemical arena, it is crucial that the appropriate training, at all levels, be a part of chemical education. 

Jackson, M. Problem Frames. Analyzing and structuring software development problems. 

This paper derives from experience gained in using the Hull Chemical Nomenclature Translator as a front-end to various structure-based software packages. The benefits of nomenclature input facilities for chemical structure software present a need to link stand-alone packages into multiprocess systems running on PCs under MS-DOS, using connection tables for data exchange. 

Littlewood 1975] B. Littlewood. A Reliability Model for Markov Structured Software, in Proc. 1975 Int. Conf. on Reliable Software, Los Angeles, IEEE. New York, 1975. 

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