Input Graphics

To recognize which programs can be used for graphical input and visualization of molecular structures... 

The compact textual coding requires no graphical input and additionally permits a fast transmission. These are important advantages of using SMILES in chemical applications via the Internet and in online services. SMILES is also used for the input of structures in the Daylight Toolkit [22]. 

The CACTVS molecule editor is a graphical input tool for molecular structures and is free of charge for non-profit use. It can be used as a stand-alone or as a dependent remote program of the CACTVS computation workbench. The software is available for aU platforms (excluding Macintosh systems). 

The TcIcSpcc system offens two ways of reading in a query structure. The structure can be input cither directly as a SMILES string (cf. Section 2,3.3) or via a molecule editor which converts the graphical input into the SMILES string. Figure 10.2-10 gives the input form of TeleSpec. 

To date, EROS development has concentrated very much on the system itself and its chemistry. Far less attention has been paid to the interface between EROS and user. To rectify this situation, work has begun on implementing procedures for graphical input and output of molecular structures. 

Select Add Trendline. .. to get the graphical input selection menu for the trendline as shown in Figure 4-8. 

In essence, IGOR is a TRG II and a set of service modules. Besides a user-friendly graphic input-output system, the most important service modules enable the user to avoid the processing of excessively large amounts of data by imposing as many further boundary conditions as are needed. For instance, any constitutional features and substructures of the participating reactants can be demanded, or be forbidden. 

There are three Tektronix terminals that are emulated, the 4010, 4014 and 4027. The 4010 is a high resolution terminal with cross hair cursors for graphics input, the 4014 adds a hardware line patterns, choice of character sizes and user definable character sets with local storage for commonly used structures. The 4027 is a color raster terminal with 64 colors, 16 character fonts, as well as polygon and vector commands. 

The constitution of a molecule is usually specified by a constitutional formula, i.e., a graph whose nodes are atoms and whose edges are bonds. It seems therefore attractive to put man-machine communication on a graphical basis, too. However, to make EROS independent of special hardware requirements, no use of graphical input devices was projected in the initial phase. 

The user-friendly main menu driver, which allows the graphic input of educt and/or product structures, management of the (retro)synthetic tree (traversal through and display of nodes), display of structures generated by the SPS generator, selection of acceptable reactions and reaction paths, and similar interactive tasks. 

The importance of the graphic capabilities of computers is rapidly increasing. More and more computer applications in chemistry rely on graphic input/output systems, and the popularity of so-called modelling systems is growing at an astounding rate. 

Free patent information is provided by the website http //www.freepatentsonline.com/, covering U.S., EP, and PCT patents/applications and Japanese patent abstracts. In addition to the usual text-based searches in various search fields, this site also enables graphically input chemical structure searches to be performed on over 9 million compounds (including prophetic compounds) using exact structure, substructure, or chemical similarity searches. Chemistry searches using SMILES strings or chemical names are also possible. Full patent documents may be viewed in text or PDF format. 

There are disadvantages too. Some databases do not include all of the material available in conventional form for example, much of the early Chemical Abstracts is not available on-line. Another problem is that the software for on-line searching is relatively complex, so it is more difficult to learn and, as a result, on-line searches by inexperienced users can be unreliable. The increasing use of personal computers and graphical input and output have made database searching much easier but a good understanding of the software is stUl essential. Finally the cost of hardware, software, consumables, and the searches themselves, can be considerable. 

The molecular mechanics routine is highly interactive and relies on graphical input and output. A molecule being modelled can be displayed in any desired orientation for inspection by the user. If such inspection shows that the model is trapped in a local minimum of the strain energy, then interactive routines allow the user to alter the model to bring it out of the minimum. 

CAMSEQ/M was developed around a Tektronix 4051 Microcomputer Graphics System. The hardware required includes the basic 4051 microcomputer with a minimum of 16k bytes of memory (32k is recommended), a "joystick" graphical input device, and a matrix function package (in a read-only memory firmware pack). A vastly more versatile system requires the addition of a file manager/ disk system. In order to communicate with the NIH-EPA-CIS or another "host" computer, a communications interface is necessary. The total hardware cost is approximately 17,000. Table II outlines the required hardware. The 4051 utilizes a direct view storage display which does not employ a selective erase feature. Therefore, it is necessary to replot the screen frequently in order to remove unwanted information. This handicap is the price one must pay for low cost, but quite sophisticated computer graphics features, and does not pose any major problems in CAMSEQ/M. 

Graphical input and output is essential to any chemical Web application. One common method to provide this is using Marvin or another sketching tool. Rather than have each application generate the javascript needed to present the sketcher or viewer, consider storing this code in the database and selecting it when needed. The marvin sketch function returns javascript that will cause a marvin sketch applet to appear on a Web page. 

The internal representation of molecules is accomplished using the technique developed by Wipke and Dyott (3), and later used by Molecular Design Limited (MDL) in several of their commercial programs. An MDL program, MACCS, is used to graphically input the molecular structure of the compound of interest, then save that structure into a file (molfile). The importation of this file provides CHESS with information such as the number and type of atoms and bonds, as well as stereochemical information. 

Spartan SGI Version 4.0.4 Spartan is a comprehensive computational chemistry program with MM, ab initio, density functional and SE capabiUty, combined with powerful graphical input and output. 

However, the introduction of online methods of retrieving informal tion, such as CAS ONLINE [9,10] and DARC [27] (which provide convenient and rapid searching of large files with the aid of graphic input and output), will reduce the future need for nomenclatures and notations by an extent that is difficult to predict. 

Tel. 212-460-1622, e-mail griepke spint.compuserve.com Structure building. Stick and dot surface display. Geometry optimization dynamics by AMBER parameters. MNDO and AMI semiempirical calculations. AUTONOM for computerized assignment of chemical nomenclature to structures from graphical input. Beilstein and Brookhaven chemical databases in CD-ROM format. PC. 

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