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Jul 1 2004
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The following notational and typographical conventions are used
throughout the manual.
- Bold. Command names may appear in bold in syntax descriptions.
(e.g. montecarlo ). Type them as they appear in the text.
- Typewriter font is used for command words,
examples and ICM-shell prompts. This text can also be
copied into the shell.
- Italic font is used for command or function arguments which
should be replaced with actual values.
For example, if you see
/whatever/your/ICM/directory/
and your ICM directory actually is
/usr/pub/icm
the latter is what you should actually type.
Short prefixes shown in parentheses may be used to specify argument type:
integer (i),
real (r),
string (s),
logical (l),
preference (p),
iarray (I),
rarray (R),
sarray (S),
matrix (M),
sequence (seq),
profile (prf),
alignment (ali),
map (m),
graphics object, or grob (g),
structure factor (sf),
atom selection (as),
residue selection (rs),
molecule selection (ms),
object selection (os),
variable selection, e.g. a subset of torsion angles, (vs), and
table (T).
These prefixes are also used to construct formal argument names for
macros.
For example, I_Color would mean an integer array with color
information, or s_ObjName would mean a string variable or
constant (e.g. "crn" ) specifying the object name.
- Optional arguments appear in square brackets [ ].
- Braces { } are used for mutually exclusive groups or
arguments. For example:
set charge as_ { r_Charge | add r_Increment }
means either
set charge as_ r_Charge
or
set charge as_ add r_Increment
- The default values in ICM macros are shown in parenthesis and in typewriter font:
icmPocketFinder as_receptorMol r_threshold (3.) l_display (yes)
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