ASCII

The ROSDAL (Representation of Organic Structures Description Arranged Linearly) syntax was developed by S. Welford, J. Barnard, and M.F. Lynch in 1985 for the Beilstein Institute. This line notation was intended to transmit structural information between the user and the Beilstein DIALOG system (Beilstein-Ohlme) during database retrieval queries and structure displays. This exchange of structure information by the ROSDAL ASCII character string is very fast. 

The most important feature of editing software is the option to save the structure in standard file formats which contain information about the structure (e,g., Mol-filc. PDB-filc). Most of these file formats arc ASCII text files (which can be viewed in simple text editors) and cover international standardized and normalized specifications of the molecule, such as atom and bond types or connectivities (CT) (see Section 2,4). Thus, with these files, the structure can be exchanged between different programs. Furthermore, they can seiwe as input files to other chemical software, e.g, to calculate 3D structures or molecular properties. 

This format was developed in our group and is used fruitfully in SONNIA, software for producing Kohonen Self Organizing Maps (KSOM) and Coimter-Propaga-tion (CPG) neural networks for chemical application [6]. This file format is ASCII-based, contains the entire information about patterns and usually comes with the extension "dat . 

Atom types represen t the chemical environment of an atom. The atom types associated with a given force field could be hard-wired to have specific vahiesand meaning. llyperChem also allows flexible definitions of the atom types and the associated chemical en vironmen Is. Th e ch em ical en viron men t of an atom (a set of rules for defining a type) and the default rules are in a standard ASCII text file, chem.nil. included with llyperChem. You can modify this file and compile it m a binary form that llyperChem... 

HypcrCliem provides two form s of param eter sets an. ASCII text form and the Td/ / database form eonsistent with dB.ASH IV and a large n iini her of other database packages. Since the prin cipal diffi-ctilty with using molecular mechan ics is having or obtaining appropriate pa ram eters, you may wan t to explore parameter sets as a database in the Tc// /form. 

We shall find the equation that best fits the points in columns 1 and 3 of Table 1-3 with TableCurve. On opening TableCurve, one is presented with a blank desktop with several commands at the top. The command to enter data is not Enter but Edit. Two formats are available, the TableCurve editor and the ASCII editor. The TableCurve format is probably a little simpler than the ASCII format, but they are both fairly self-evident and either should yield a data file resembling the data... 

In most programs, it is still possible to input a geometry manually in an ASCII input file. If the geometry is already in a file but of the wrong format, there are several utilities for converting molecular structure files. The most popular of these is the Babel program, which is described in Appendix A. 

NWChem uses ASCII input and output files. The input format allows geometry to be input as Cartesian coordinates or a Z-matrix. If symmetry is specified, only the Cartesian coordinates of the symmetry-unique atoms are included. Some sections of the code require additional input files. 

The program uses two ASCII input files for the SCF and properties stages of the calculation. There is a text output file as well as a number of binary or ASCII data files that can be created. The geometry is entered in fractional coordinates for periodic dimensions and Cartesian coordinates for nonperiodic dimensions. The user must specify the symmetry of the system. The input geometry must be oriented according to the symmetry axes and only the symmetry-unique atoms are listed. Some aspects of the input are cumbersome, such as the basis set specification. However, the input format is documented in detail. 

GAMESS stands for general atomic and molecular electronic structure system (we reviewed a version dated Dec. 2, 1998). It is an ah initio and semiempirical program, and has seen the most widespread use for ah initio calculations. The ASCII input hie format is usable but somewhat more lengthy than some other programs. The fact that GAMESS is a free, high-quality software makes it a favorite of many academic researchers. 

Alternatively, the user can construct ASCII input files manually. The file format includes many numerical flags to control the type of calculation. The researcher should plan on investing some time in learning to use the program in this way. Jaguar can be executed from the command line, making it possible to use batch processing or job queue systems. 

The ASCII input file includes elements of a scripting language. Thus, the input can contain variables, loops, and procedures. This is one of the aspects of the program that makes it possible to do very complex calculations. The documentation describes the input options, but does not discuss when and why they should be used. The user must have a solid understanding of ah initio theory in order to correctly utilize many of the functions in this program. It is very powerful, but not for beginners. 

Q-Chem (we tested Version 1.2) is an ah intio program designed for efficient calculations on large molecules. Q-Chem uses ASCII input and output files. 

Gaussian users will find that Q-Chem feels familiar. The ASCII input format is a bit more wordy than Gaussian it is more similar to GAMESS input. The output is very similar to Gaussian output, but a bit cleaner. The code can easily be used with a job-queueing system. 

AMPAC can also be run from a shell or queue system using an ASCII input file. The input file format is easy to use. It consists of a molecular structure defined either with Cartesian coordinates or a Z-matrix and keywords for the type of calculation. The program has a very versatile set of options for including molecular geometry and symmetry constraints. 

MacroModel (we tested Version 6.5) is a powerful molecular mechanics program. The program can be run from either its graphic interface or an ASCII command file. The command file structure allows very complex simulations to be performed. The XCluster utility permits the analysis and filtering of a large number of structures, such as Monte Carlo or dynamics trajectories. The documentation is very thorough. 

The molecular structure input requires atom types to be assigned, which are not the same from one force field to the next. The input also includes a list of bonds in the molecule. There is not a module to automatically assign atom types. Most of the modules use a Cartesian coordinate molecular structure, except for a few that work with torsional space. The same keyword file is read by all the executables. A little bit of input is obtained by the program either interactively or from an ASCII file piped to standard input, which makes for a somewhat cryptic input file. This system of common input files and the user choosing which executables to run give TINKER the ability to run very sophisticated simulations while keeping the input required for simple calculations fairly minimal within the limitations mentioned here. 

The input to POLYRATE is a free-format ASCII hie. There are a large... 

Cursors of different shapes and sizes can be designed easily by the microcomputer user through simple programming, such as using the BASIC commands GET and PUT. The movement of the user-created cursor is controlled through the use of the INKEY function and by testing the ASCII codes of the keyboard keys. 

Using a Terminal. Dial-up terminals may also be used to access a vendor s databases however, the terminal, personal computer, word processor, or microcomputer must all be compatible with specific functionaHties. Eor example in order to access the DIALOG service these must all be TTY compatible have ASCII coding and be compatible for asynchronous transmission in full-duplex mode for communication through DIALNET,... 

Script files A seript file is an ASCII text file of MATLAB eommands, that ean be ereated using... 

Alternatively, the SCREEN.DAT file may be edited as an ASCII file using a text or line editor, and selected input parameters changed before rerunning the model. Since the original SCREEN.DAT file will be overwritten each time the model is run, it is advisable to save the modified inputs under a different file name. 

System can communicate with other systems (e.g., Lotus, dBASE, ASCII, and DIF data formats Macintosh and IBM equipment). 

A,-i-,DG-A,DG-A-M B,-t-,DG-B,DG-B-M C,-i-,DG-C,DG-C-M where the semicolon designates enter. Notice these equations are linked with BLACKOUT being the top event. This completes the preparation of FTAP input selection 6 exits FTAPlus to return to the FTAPSUn menu (Figure 6.4-3). Figure 6.4-2 shows file FN.Fl was created. This is an ASCII file which can be edited, if needed, with a text editor. 

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