Miscellaneous

Available commands: comment , C , FILE , HELP , PROMPT , RECALL , SETENV and SHDF .

This type of command is designed to make EDPDB more user-friendly and/or to provide the user with help when needed.

comment

Any text-string following a semicolon (;) or an exclamation mark (!) in an input statement will be considered as a comment and is omitted during command interpretation.

Function: Miscellaneous

Syntax:
1) ; comment
2) ! comment
3) command ;comment
4) command !comment
Note:
1) The first two forms are called comment statement, and the other two are called commands with comments.
2) A comment statement starting with a semicolon in a macro file will not be echoed. A comment statement starting with an exclamation mark will be echoed if the echo option is set to ON.

See also: SETENV and command interpretation

C

Clear the terminal screen.

Function: Miscellaneous

Syntax:
C

FILE

Show the file names which are currently used.

Function: Information, Control

Syntax:
1) FILE
2) FILE SCR file_name
2) FILE LOG file_name

Note:
1) The first form lists the currently used files. For the input PDB files, only the names of the first two and the last one will be listed.
2) Using the SCR option, the intermediate result will be redirected to a new scratch file, so that the old scratch file can be saved for other purposes.
3) Using the LOG option, the result that is usually piped to the sys$output will be redirected to a file.

See also: ACCESS, DISTANCE, HELP, READ, SHDF, SORT and @macro_file

Examples:
1) List the currently used files.

      file

2) Close the old scratch (.scr) file, say a.scr, and pipe the scratch output to a file called junk.scr. Then one can type the old scratch file.

      file scr junk.scr
      system wait type/page a.scr

3) Redirect some displayed result to a file tmp.log, and then switch back to the terminal.

      file log a.log
      ...
      file log tt:    ! for VMS terminal

HELP

Call EDPDB on-line help service. (Bug!)

Function: Information

Syntax:
1) HELP [category command_leading_keyword]
2) command_leading_keyword /?

Note:
1) In the first format, if no search information is specified, a "level by level" systematic search will start.
2) For the VMS version of EDPDB, the system help-library utility is used to run the on-line help. For the unix version, a separate program is used to mimic the VMS system utility. It may not have the full functions of the VMS version of on-line help.

PROMPT

One may reset the prompt, which consists of up to nine characters.

Function: Miscellaneous

Syntax:
PROMPT prompt_character_string

Examples:
1) Set the prompt to the text string CHK> followed by a space.

      setenv tolower off
      prompt 'CHK> '

2) Use the prompt to send messages, eg. from a macro file.

      prompt 'ok_1> '

RECALL

Recall a command, for saving typing.

Function: Miscellaneous Syntax:
1) RECALL
2) RECALL record_#
3) up/down arrows

Note:
1) The first form lists up to 16 previously input legal commands (the command RECALL is not included), which may or may not be completed. The second form will repeat a command in the history list.
2) The up/down arrows can recall a previously typed-in text string no matter the consequence of that input. The recalled text string can be edited, just like a DCL command in the DCL/VMS environment.

Examples:
1) List the command input history.

      recall

2) Recall a command which was not completed. For example, one wants to find the (4.5 Å) neighboring atoms of the CB atom of residue B40 from molecule A.

      nayb 4.5 B40 CB from molA
           ; errmsg: wrong group/zone information
           ; The problem is that molA is undefined.
      initial
      group molA from { chain A }
      recall -3
           ; repeat 'nayb 4.5 B40 CB from molA'.

SETENV

Change environmental variables.

Function: Definition, Information

Syntax:
1) SETENV
2) SETENV variable
3) SETENV variable new_variables

Note:
The first form shows the current values. The second form resets the value to the default. And the third form sets the user specified value to the variable.

Available variables include the following. DELIMITER , ECHO , EDP_DATA , INTERACTIVE , TOLOWER , VERBOSE , WILDCARD and WINDOW_SIZE .

DELIMITER

Set the parameter delimiter.

Syntax:
SETENV DELIMITER [one_character]

Note:
The default delimiter is a single quotation mark (').

Examples:
1) Assume that we have a macro file, read.edp, which accepts a text string as its parameter. We can use the delimiter to enclose a text string containing spaces or commas as a single parameter, which otherwise would be considered as multiple parameters.

      @read 'this is a test.'

2) If a quotation mark (') needs to be included in the text string, the delimiter has to be changed to something else.

      setenv delimiter #
      @read #it's a test.#

ECHO

Turn the echo option ON/OFF for input commands from a macro file.

Syntax:
SETENV ECHO [0,1,2]

Note:
The default option is 1.

Examples:
1) Turn the echo option off for the input from a macro.

      setenv echo 0
      @a_well_tested_macro

2) Turn the echo option on for the input from a macro.

      setenv echo 2
      @a_macro_to_be_tested

EDP_DATA

A user may setup his/her owner directory to keep the .edp macro files. By default, EDPDB reads an .edp file from the predefined directory: edp_data: for the VMS version and edp_data/ for the unix version, if it can not be found in the user's current directory. However, a user may change back and forth between the program-default and one's own default directory using this edp_data option.

Syntax:
SETENV EDP_DATA directory_name

Example:

      setenv edp_data [user.my_edp_lib]
           ; set default to the user specified directory
      @my_macro
      ...
      setenv edp_data
           ; back to the program default directory
      @an_edpdb_macro
      ...

INTERACTIVE

EDPDB can run interactively or batch mode. The VMS version program will check the current working mode automatically, and use it as the default. The default mode for the unix version is interactive. To speed up the calculation, an interactive user may switch between the interactive and non-interactive modes. By doing this, the program will turn on/off HELP, LIST and PAUSE, as well as some screen outputs.

Syntax:
1) SETENV INTERACTIVE
2) SETENV INTERACTIVE ON
3) SETENV INTERACTIVE OFF

Note:
The first form sets the mode to the default, without typing the scratch file on the screen. The second form sets the mode to the default, and will type the scratch file on the screen if the default mode is interactive. The third form sets the mode to 'non-interactive'.

Examples:
1) Displaying the scratch file can be time consuming, especially when it contains a large number of records. Therefore, the user may deactivate the display and read the file later.

      setenv interactive off   ; deactivate the display
      ...
      setenv interactive on    ; type the .scr file.
      ...

TOLOWER

By default, EDPDB converts all the characters in an input statement to lower case before interpreting the commands. All the build-in keyword are in lower case. The user can change the default so that the program will not perform the conversion to the input statement.

Syntax:
SETENV TOLOWER (ON, OFF)

Examples:
1) In the unix system, a file name is case sensitive. To read a file named, eg. UPPER_CASE.FILE, the tolower parameter should be set to off.

      setenv tolower off
      read UPPER_CASE.FILE
      setenv tolower on

VERBOSE

This option sets output to different levels so that some diagnastic information can be output if necessary. Usually the higher the level is, the more information may be output. The default level is zero.

Syntax:
SETENV VERBOSE level

Examples:
1) List all of the detailed results of a MATCH3D calculation.

      setenv verbose 6
      match3d a 4 4.0

WILDCARD

Set the wildcard, which is a single character and is used for example in the SHDF and ATOM commands.

Syntax:
SETENV WILDCARD [one_character]

Note:
The default wildcard is an asterisk (*).

Examples:
1) Assume that, in the input PDB file, one of the atom name is O5*. If we want to select this specific atom type and do not mix it with other atom types such as O5 or O5A, the default wildcard (*) must be changed.

      setenv wildcard & %
      atom O5*

WINDOW_SIZE

Set the number of lines per window. This function is useful only for the VMS version, because the unix version gets the value from the system directly.

Syntax:
SETENV WINDOW_SIZE [number_of_lines_per_window]

Examples:
1) Set the window size to 40 lines.

      setenv window_size 40

2) Set the window size to the default value.

      setenv window_size

SHDF

Show the values defined by DFXXXX command.

Function: Information

Syntax:
SHDF [(*, MAIN, CA, AB, ABC, ABCD, BRG, RES, NEWXYZ, CELL, SYMM)]

Note:
Dfxxxx series commands without following any parameters will display the corresponding definition too.