UNIX system

Platforms PC, many UNIX systems Contact information Schrodinger, Inc. 

If an optimization tuns out of steps, do not blindly assume that increasing the number of steps will fix the problem. Examine the output and determine whether the optimization was making progress or not. For example this command will provide a quick summary of an optimization s progress on a UNIX system (blank lines ate added for readability) ... 

System Type UNIX systems VMS systems Windows systems... 

Hardware supported includes IBM-PC, SUN, Silicon Graphics, HP, IBM RS/6000, and DEC Unix workstations VAX workstations, Encore Unix systems. 

Volume 2 of "Exploring QSAR" by Hansch and Leo (1995) contains the most extensive hard-copy database of log Poct values — about 18,000 values for over 16,500 structures. Sangster (1989) has published log P measurements and offers a comparable computer database on diskettes. Several of the computerized calculation programs access a similar log Poct database. If values in other solvent/ water systems are needed, the MASTERFILE database can accompany the CLOGP program on VAX and UNIX systems and contains about 40,000 measured log P values in over 300 solvent systems in addition to about 10,000 measured values of pKa. 

Accelrys provides data management and sequence analysis tools through the DS SeqStore and GCG Wisconsin Package products, running on UNIX systems. DS Gene provides PC access for visualization and analysis capabilities within the Discovery Studio product family. 

Tables 9.18, 9.19, and 9.20 list the equivalent commands for several systems (all commands are followed by CRLF, "carriage return + line feed", or by pressing "RETURN" or "CR" on the terminal keyboard) these three tables deal with running the FORTRAN program INVERT discussed above. Finally, Table 9.21 gives some file management instructions on a UNIX system.

K. Haviland and B. Salama, UNIX System Programming, Addison-Wesley, New York, 1987. 

It would be pure speculation to estimate the impact of changes in hardware and operating systems on chemical information management. Presently, Sun Microsystems is probably the dominant Unix system in chemical database management, largely because of their network presence and their support of Java. Microsoft has released their Windows XP operating system, which merges the Win-... 

ADAPT II is supplied as FORTRAN code for VAX VMS, MS DOS, and SUN UNIX systems. It performs simulations, fitting, and optimal sampling and includes extended least-squares and Bayesian optimization. Models can be... 

GenomeViz has been tested to run successfully on Linux and Solaris operating systems (see Note 7). Unix systems that have ActiveTcl installed may also run GenomeViz but we have not tested this. 

The user will also need Perl to run the scripts that are distributed with GenomeViz (see Note 8 ). Perl is usually installed by default on Linux/Unix systems in the path/usr/bin/perl. The user can easily check this by typing the following command on the terminal, which perl The user may get /usr/bin/perl... 

Operating system. If available, we recommend to use a Linux/UNIX system for the analysis. Also Mac OS X, in principle a full-featured UNIX system, is an adaequate platform. Alternatively, RNAz can also be run on Microsoft Windows. Most of the methods described in this chapter can be carried out on Windows without any modification. 

Another important point is that the Perl programs expect that the path of the Perl executable is /usr/bin/perl. This is the standard location on almost all Linux/UNIX systems and OS X. If the Perl installation is different, the user has to customize the first line of all the Perl programs according to the location of the perl executable. 

J. Erlebacher and H. L. Carrell, ICRVIEW, Program for UNIX systems for the Silicon Graphics System, The Institute for Cancer Research, Philadelphia, PA, 1992. 

The process of writing and rimning a Perl script is similar on Windows and UNIX systems but slightly different for Macintosh users. The basic steps are described below. 

On a Windows or UNIX system, create a text-only file containing the following lines ... 

If Perl is installed in the standard way on the computer, the perl command does not have to be explicitly typed. On UNIX systems, the script file can be marked as being directly executable using the chmod command ... 

The topmost line is also a Perl comment, but on UNIX systems it serves doubleduty as a directive to the UNIX shell to tell it to execute the command /usr/bin/ perl when the script file is executed. On Macintosh and Windows systems, this line is extraneous, but it is better to include it to maintain portability with UNIX machines and as a matter of good form. 

The open fimction expects exactly two arguments. The first is a name for the filehandle (MYFILE). This is an arbitrary name that the user chooses, with the convention being to use all uppercase letters. The second argument is the name of the file to open. If just the file name is provided, as shown in the example, Perl will attempt to open a file by that name in the ciurent directory (on Windows and UNIX systems, the directory in which the command to run the script was given on Macintoshes, the folder that the script is located in). The full path, explicitly giving the location of the file, can also be given. 

Unfortunately, the way one specifies a file path is different on the three different operating systems. On UNIX systems, a path begins with a forward slash and each directory is separated by additional slashes. On Windows systems, a path begins with the drive letter (e.g., c ) and uses backslashes to separate directories. On Macintoshes, the path begins with the name of the hard disk, and colons separate the name of each successive folder. Examples of fully qualified path names on UNIX, Windows, and Macintosh systems are shown below. 

The names STDIN and STDOUT are derived from standard input and standard output, an idea popularized by the UNIX operating system. Standard input and standard output are abstract files from which a script can accept input and send output, respectively. When a script is first launched, standard input corresponds to the keyboard and standard output corresponds to the computer screen. On Windows and UNIX systems, standard output appears in the command interpreter window. On Macs, the output appears in a small scrolling window that MacPerl creates specifically for this pmpose. When a Perl script is laimched, the user has the option of changing where standard input and output come from and go to. The user can also arrange for the standard output of one script to be sent to the standard input of another script in assembly-line fashion. This is actually a very powerful facility, but one that is beyond the scope of this chapter. 

To redirect standard input from a file in either Microsoft Windows or UNIX systems, use the less-than (<) symbol to indicate the file ... 

Choice of Operating Systems It is also important to be familiar with operating systems like Windows, Linux, and Mac OS. Students and faculties of chemoin-formatics and bioinformatics should be able to execute commands in Linux/UNIX systems for computationally intensive tasks. Some of the most frequently used... 

Introduction to basics of programming Here, we will print the name of a small molecule of caffeine using the simplest code snippet in Fortran on a UNIX system. Caffeine is a stimulant and dmg molecule from the alkaloid family (Fig. 1.1). 

Available for Windows, MacOS X, Linux and UNIX systems, this program is freeware and is developed at the Cambridge Crystallography Data Centre, CCDC [3J. 

UNIX is a registered trademark of UNIX System Laboratories, Inc. 

As with OS/2, certain PC-based UNIX systems allow users to run MS-DOS applications by use of a special MS-DOS window. By using the virtual 8086 mode of the 80386, it will be possible with some UNIX systems to run simultaneously several MS-DOS programs as well as UNIX ones. Whatever operating system is used for providing structure-based systems with nomenclature interfaces, the use of this facility would be beneficial. 

Octave is a programming language with syntax very similar to that in MATLAB. It is used in academia and industry for numerical analysis. The software is available for free under the terms of the GNU General Public License and runs on both Windows and Unix systems. 

Remote logins (rlogin) and remote shells (rsh) of UNIX systems share many characteristics of Telnet, but the.se services are far less portable and there are some differences concerning the transport of environment variables, escapes to the local machine, etc. 

The PDB has introduced substantial enhancements to data deposition and management and user access in the past four years. The PDB Browser, first introduced on PC and UNIX systems, and later via the Internet s World Wide Web, lets researchers search and retrieve information from the PDB faster and far more flexibly than the older printed indices. This browser is being upgraded and enhanced constantly to meet the increasing needs of its user community worldwide. Further, PDB s new AutoDep facility lets researchers deposit their data quickly and accurately over the Internet directly to the PDB, where it is then processed by the PDB staff. 

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