ANSIG v3.3: Command reference

Command reference






ASSIGN
BYE
COMPILE
CONTOURS
COORDINATES
CROSSPEAKS
DEASSIGN
DELETE
DUMP




ECHO
EXIT
GRAPHICS
HELP
HISTORY
IF
INITIALIZE
INPUT
INTO




LIST
MACRO
NOE
NOOP
QUIT
READ
RECOMPILE
RENAME
RETURN




SET
SHOW
STOP
SYSTEM
VARIABLE
WRITE

`BYE`

Exit from ANSIG. The exit file is not executed, even if it is defined. This is a synonym for QUIT.

The exit file will be executed before exiting ANSIG if the EXIT command is used instead.

Compile the AL procedure(s) in the given AL source code file. The AL procedures must not have been compiled already. If there is an error in the compilation, then no AL procedures from the file are retained, not even those that compiled successfully.

`CONTOURS spectrum [ f1 f2 ] filename`

Compute contours within the current area for the given spectrum and writes them to file. The contour file can be used as source of contours instead of computing contours directly each time from the matrix file.

In most cases, reading contours from file is only marginally faster for 2D spectra (and occasionally actually slower), but is usually significantly faster for 3D and even more so for 4D spectra.

If the spectrum is 2D, then no plane dimensions may be given. If the spectrum is 3D or 4D, then plane dimensions must be given. Contours will be computed only for this plane.

The view for the spectrum in the current window does not affect which part of the spectrum is used when creating the contour file. The current area is therefore interpreted directly in terms of the dimensions of the spectrum. It is therefore best to specify the current spectrum area explicitly using commands, rather than the current item in the graphics menu. Usually, one computes contours for the entire spectrum, in which case the current spectrum area should be set to the maximum.

Once the contour file has been made, it cannot be modified. In particular, it is not possible to concatenate several contour files into one single file.

See also: SET CONTOURS, SHOW SPECTRUM and contour files.

`COORDINATES [ filename ]`

Read a coordinate file in PDB, MSA (Connolly's MS atom file), DG (Havel's DISGEO atom file) RD (Diamond format, Frodo variant), CDS (Diamond format, MRC variant), or WAH (Hendrickson's PROLSQ) formats.

The file format is chosen on the basis of the filename extension; if it is not recognised, then PDB is assumed. More than one coordinate set may be loaded, depending on the dimensioning at compile-time of ANSIG.

If no file name is given, then the currently loaded coordinate sets are deleted.

The sequence names and residue types in the coordinate file must match the current sequence. The coordinate sets are handled independently of each other; their relative orientation is irrelevant for the facilities in ANSIG.

See also: SHOW COORDINATES and ASSIGN MATCHING

`DELETE macroname`

Delete the specified macro. This command cannot be given from inside a macro.

`DUMP filename`

Write a text file containing an assembler-like representation of the currently compiled AL procedures. First the headers of the intrinsic procedures are output, then the compiled procedures, then some statistics for the AL machine. This file is useful only for debugging the ANSIG source code, and so is almost certainly irrelevant for ordinary users.

`ECHO [ arguments... ]`

Display the arguments after command line processing. This command is useful for invoking an AL procedure or to display the value of a variable.

`EXIT`

Exit from the ANSIG program. If an exit file has been defined (in the control file), then it is executed before exiting.

If the exit file is not to be executed before exiting, then use either of the commands QUIT or BYE.

`HELP`

Start up the WWW browser (currently Netscape) on the top help file ansig.html in the help_dir directory as specified in the control file.

`HISTORY`

Output a list of the last 19 commands given. This list is used by the command history substitution mechanism.

`IF logical command1 [ ELSE command2 ]`

Execute the first command if the logical value is true, else execute the second command if given.

The command NOOP can be used as the first command if nothing is to be done when the logical value is true.

Warning: The entire line is processed in the usual way before the test is performed. In particular, this implies that all AL procedure invokations in the line are performed before the logical value is evaluated.

`INITIALIZE`

Reset the AL machine to its initial state; all compiled procedures are removed.

`INPUT filename`

Read commands from a command file. The syntax for the commands in the file is exactly the same as when entered by the user directly. The file format allows comments (started by exclamation-mark '!' and ended by end-of-line), and blank lines.

Calls from within the command file to other command files are allowed.

`MACRO macroname`

Start the definition of a macro. The macro name must not be a command, nor must it have been defined already. After the command is given, the command lines that constitute the macro should be entered. These are stored exactly as they are, without any processing at all.

The macro definition is finished by entering the command END_MACRO alone on a command line.

`NOOP`

Execute no operation. Useful mainly for the IF command.

`QUIT`

Exit from ANSIG. The exit file is not executed, even if it is defined. This is the same command as BYE.

The exit file will be executed before exiting ANSIG if the EXIT command is used instead.

`READ filename`

Read a file containing symbols (i e variables and lists).

If a symbol already exists, then an error will result if the clobber parameter has been set to false (the default). Otherwise the symbol is overwritten, and its old value is destroyed.

See also: WRITE, SHOW LIST and SHOW VARIABLES.

`RECOMPILE`

Initialize the AL machine, removing all compiled AL procedures, and then recompile all AL procedure files. ANSIG retains a memory of which AL procedure files have been successfully compiled during a session.

This command is useful when developing an AL procedure; edit the AL procedure file in another window, and recompile when the AL source file has been written to disk.

`RENAME oldsymbol newsymbol`

Rename a list or a variable. The new name must not already be used.

`RETURN`

Stop execution of the current macro or commands file, and change back to input from the calling macro, commands file or user.

`STOP`

Stop execution of all recursively called macros and input files and returns to await input from the user. This command is mainly useful as a panic exit from within macros or input files.