Command line

One significant characteristic of the program is the Command Line. Hereby, the visualization of the molecules is directed in the viewer with commands from a script language. The scripts, such as loop or batch files, can be saved, lutp //openrasmoi.org... 

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. 

Babel (we tested Version 1.6) is a utility for converting computational chemistry input hies from one format to another. It is able to interconvert about 50 different hie formats, including conversions between SMILES, Cartesian coordinate, and Z-matrix input. The algorithm that generates a Z-matrix from Cartesian coordinates is fairly simplistic, so the Z-matrix will correctly represent the geometry, but will not include symmetry, dummy atoms, and the like. Babel can be run with command line options or in a menu-driven mode. There have been some third-party graphic interfaces created for Babel. 

Step 2. For MS Windows users, start the CASim software by double clicking CASim.BAT in the CAProgram directory. If you wish, you can bring CASim.BAT to the desktop so that you can start from there. For other platforms, first set CAProgram as the default directory, then you may start the software by entering java CASim at the command line. 

File Transfer Protocol. A protocol used to move files over the Internet. Typically, you use a command line command, browser capability, or program on your computer called an FTP client to connect to an FTP server found on the Internet. Once connected to the FTP server, you can move files back and forth between your computer and the FTP server. SFTP, Secure FTP, is a more secure protocol for moving data over the Internet in which both your login information and data are encrypted during communications. 

There are three CRT graphic displays which the operator may select. They are a picture of the reactor labeled with current process variable values, a trend plot of key variables, and the command file itself, highlighted to show active command lines. 

Now using the MATLAB command line software, we can easily demonstrate this solution (for the multivariate problem we have identified) using a series of simple matrix operations as shown in Table 21-1 below ... 

Several software packages contain simple command lines for performing matrix computations directly and thus are conveniently capable of computing the correlation coefficient, for example as in r2 (Equation 59-8). 

Command-line parser, a component to read commands and parse them against a command grammar... 

Hence, you should implement the technical architecture as early as possible. Have all communication paths working—from user input and command-line parsing to the data... 

Figure 2-3 shows an example spreadsheet. Cells A3 C4 contain the elements of the 2x3 matrix A. In order to perform the matrix transposition cells E3 F5, which will contain the result, A1, have to be pre-selected. Next =TRANSPOSE(A3 C4) is typed on the Excel command line followed by the SHIFT+CTRL+ENTERl key combination. 

Note the curly braces that have appeared in the command line and indicate a matrix operation applied to a block of cells. The curly braces must not be typed in explicitly. 

Note the difference in the command line between Figure 2-5 and Figure 2-6. 

The computer program used in this chapter has been made publicly available under an Open Source Initiative BSD License at http //glare.sourceforge.net. This program is written in C++ and has been successfully compiled on diverse platforms such as Mac OS 10.X, Linux, IBM AIX, and Windows XR Under its current form, GLARE is mainly a command line application that is invoked identically on any of the platforms. Details of the parameters and options can be found at the aforementioned web site. 

Start ProSa - enter at the system command line proea2003... 

Lines starting with a within a literal text block are commands. You should type the text following the into your terminal window, finishing by hitting the re turn-key. (The signifies the command line prompt, which may be different on your system). 

If a few simple structure predictions is all you want to do, if you are baffled by the command line, and compiling programs just seems too technical, then web services are for you. 

Several useful sites for doing RNA structure analysis are available on the web. Most of the tasks described below can be performed with the Vienna RNA web server [3] at http / / rna. tbi. uni vie. ac. at /. Currently, it offers web access to the RNAfold, RNAalif old, and RNAinverse programs whose command line usage is shown below. 

Web servers are not ideal for analyzing many or very long sequences. Command line tools, on the other hand, are ideally suited for automating repetitive tasks. They can even be combined in pipes to process the results of one program with another. 

You can also design many sequences in one run by adding a -R num option to the command line. 

Note further that the entries of one row of a matrix (or of a row vector) can be entered into MATLAB s workspace either separated by a blank space or by a comma, while a semicolon indicates the start of a new row. A comma or a blank at the end of a command line will cause screen display of the object that has just been defined, while a semicolon after a command will not. 

The commas after our MATLAB commands above are necessary as delimiters to be able to place several commands onto one line of code. They create screen output, whereas semicolons would have suppressed it. The final entry result = [size(A ), length(A )] on the command line creates the vector (4, 3, 4), called result by us. It contains the number of rows (4) of AT, followed by AT,s number of columns (3) and its length or maximal dimension (4). 

Our two command lines below first generate the coefficient matrix A and the right hand side vector b for (1.1), followed by the MATLAB backslash linear equations solver that computes the solution vector x. This is followed by a simple verification of the error inherent in the residual vector A-x — b for our numerical solution x. This error is nearly zero since in MATLAB the number -1.3323e-15 describes the real number —1.3323 10-15. 

Here A is suppressed on screen and only the right hand side b is displayed since it was followed by a comma, on the command line instead of the suppressing . Next MATLAB issues a warning that our chosen 3 by 4 matrix A has deficient rank two instead of three, and then it gives the least squares solution... 

We advise our students to follow our text and to always copy our MATLAB command lines onto their MATLAB desktop as they read through this chapter. Our students and readers should observe the execution of these commands, and we encourage them to alter these commands slightly to learn more about MATLAB.]... 

In order to call newtonpoly (start, n) implicitly on a command line with success, the two implicit inputs start and n must have been declared previously and must be available in the current workspace. Of course, one can also call newtonpoly9 explicitly by entering newtonpoly (21,42), for example, on the command line if one wants to see the list of 41 Newton iterates for the same polynomial-root problem, starting from start = xo = 21. 

In the previous sections we have used MATLAB commands that were typed in on the desktop command line, as well as MATLAB commands that invoke special stored MATLAB files, called m files. When starting to work with MATLAB, we advise our users to create a special folder for their personal MATLAB m files once and to continue to use this folder to store personal m files. To access the stored m files from the MATLAB desktop, the user has to point the small desktop window called Current Directory to the personal m file folder. Then all stored m files, as well as all built in MATLAB functions can be accessed, called upon, and used from the command line. All stored personal... 

In our first call above, we have not named an output and we have omitted the no screen output colon so that the first (unnamed) output variable y is displayed only as ans. In the second call of funct we have preceded the call of funct by assigning names to both outputs and have followed the command funct(x,y,k) with a blank space. This creates the screen output of both variables, called yy and sign by us. In the last call the command names the output why and ka and it is followed by a colon . Therefore, we have no output to the screen initially. Only after the pause command is ended by hitting the return key does the output called why appear on screen. After another return stroke to overcome the second pause command, the second output ka is displayed. Note that in the second command the computed values for yy and sign are both available in the workspace whether we use a blank, a comma, or a colon following the call of funct since the output is explicitly defined on the command line. Likewise for the third call of funct and why and ka. If on the first command line, however, we had finished the command funct(3,5,17) with a colon instead, then there would have been no output at all, not onto the screen, nor onto the workspace. 

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