INCLAN Reference Manual

The user interface of the program CYANA is based on INCLAN, a powerful interactive command language that allows the use of variables, mathematical and character expressions, macros, flow control (loops, conditional statements, jumps), parallelization on shared-memory and distributed-memory systems, and the production of graphics.

INCLAN separates the user interface from the specific functions of the underlying program. It allows new commands to be implemented quickly, either in the compiled source code of the program or as interpreted INCLAN scripts (macros). In both cases the command line syntax follows the same, uniform rules, and is automatically checked by INCLAN for consistency and correct data typing. The output of the program is controlled and formatted by INCLAN, which allows the amount and destination of informative output to be defined in a uniform way. The INCLAN command language is an interpreted language that combines features of Unix shell scripts, e.g. the use variable substitutions in the command line, with those of high-level programming languages, e.g. sophisticated mathematical functions and expressions.

The current version of INCLAN is implemented in Fortran-95, and is used as the command interpreter of several program packages written in Fortran and C++, including CYANA, DYANA, GARANT, OPALp, and PROSA.

In the following, literal INCLAN input and output is shown in Courier font. Non-literal input is shown in italics. Optional arguments are enclosed in square brackets “[…]”. In an argument list the ellipsis “…” indicates that the preceding parameter can be repeated.

• Special characters

INCLAN Commands

• alias
• ask
• break
• do
• eval, show, set, unset, external
• exit
• goto, go to
• if
• label
• parameter
• print, error
• quit
• readline
• remove
• return
• sleep
• special characters
• subroutine, command
• syntax
• system
• type
• var

INCLAN Variables

• echo
• erract
• info
• intrinsics
• label
• nparam
• nproc
• path
• prompt
• protocol
• timing

INCLAN Graphics

• plot arc
• plot caro, plot cross, plot dot, plot plus, plot square, plot triangle
• plot clip
• plot close
• plot comment
• plot curve
• plot errorbar
• plot file
• plot fit
• plot frame
• plot function
• plot label
• plot line
• plot mif, plot ps
• plot polygon
• plot rectangle
• plot scale
• plot set
• plot shape
• plot spline
• plot text
• plot write