Catalyst UNIX Commands

The advantage of running a program in a UNIX shell is that you can still use Catalyst to do other things at the same time, although more slowly, on the same machine. Or you can run the background UNIX session on another machine on the network so that you have the full power of your machine for your interactive session.

Note: some familiarity with UNIX directory structure and file operations is required for the command line procedures. See your operating system manuals or other UNIX user documentation. Also see "To use a UNIX window and command line".

Background processes for both conformer generation and hypothesis generation can be set up, started, monitored, and the results imported back into your session, using the Catalyst interface and without using a UNIX shell window.

Go to the next topic to see the information available on Catalyst background operations.

Select the UNIX command line operation you want information about:

Tasks you can do in a UNIX window

Set up and start a background conformer generation process

Set up and start a background hypothesis generation process

Use catSearch to do a database search

Use the catDB database utilities to build, modify, or analyze databases

To Use a UNIX Window and Command Line

1. Create a UNIX window using the toolchest in the corner of your screen. In the new window you will see the command "prompt" character, which is at the left end of the command line.

   

2. Change the size of the window by grabbing one of its corners or sides with the mouse cursor (the cursor changes into an arrow pointing to the corner, or an arrow pointing to the side, when placed over one of them, as shown in the diagram) and dragging it to increase or decrease the window size. You can type on the command line when the mouse cursor is inside of the window (the window borders change colors).
3. Before you invoke a command, make sure you are in the correct directory (use the pwd command to check). If not, use the change directory command (cd <desired directory path name>)
4. Check that you have the required files in the directory (type ls to list the files).
5. To invoke a command from the command line, type the name of the command and any options, and then press the Enter key.
6. If you get no messages indicating a problem, the command is being processed.
   Messages may be written to the window during the operation indicating its status. You cannot invoke more commands in this window until the operation is completed.
7. When the command is finished, you will see the prompt again and can type in the command line.

• run Catalyst database utilities (catDB) in a UNIX shell window.
• run Catalyst database search (catSearch) in a UNIX shell window.
• change the name of a journal file to journal.in in order to run the journal in Catalyst (cp <journal name> journal.in)
• display a list of the names and sizes of all files in a directory (ls -l)
• create a new directory for organizing your files (mkdir <directory name>)
• send files exported from Catalyst to another directory on the network, or bring compound files into a directory from which they can be imported into Catalyst
  (cp <from /path/filename> <to /path/filename>)
• remove obsolete files or databases from a directory (rm <file name>)
• remove core files after a system crash (rm core)
• read a text file (more <file name>)
• change to a different directory (cd <directory /path/name>)
• display your current directory path (pwd)

In the View Compound workbench you can set up a conformer generation process to run in the background and then bring the data into Catalyst. You do not need to use a UNIX shell window to do this. See "To Generate Conformers."

In the Generate Hypothesis workbench you can set up a hypothesis generation process to run in the background and then bring the data into Catalyst; you do not need to use a UNIX shell window to do this. See "To Generate a Hypothesis Automatically."