Version 2.1.0 now handles KaSim 3.1 style grammar, with the following exceptions:

Spatial Kappa %agent: declarations do not allow link definitions
Spatial Kappa only accepts single site states outside of %agent:
declarations - ie A(xbc) is invalid
The --implicit-signature command line option is not allowed - agents
must be declared
Tokens are not supported, and the ':' and '|' characters are reused by
Spatial Kappa for other purposes
Spatial Kappa %init: declarations only accept integer quantities
Spatial Kappa does not allow the expressions [E+] and [E-]
Spatial Kappa only accepts variable names in %plot: declarations
Spatial Kappa does not support the %def: declaration, or the $PRINT,
$TRACK or $FLUX perturbation effects
Deprecated syntax in KaSim 3.1 is not supported in Spatial Kappa:
- %mod: bool_expr do effect_list until bool_expr
- %mod: bool_expr set effect_list
- Assignment operator :=
KaSim 3.1 allows nesting of perturbation effects (like (effect1;
((effect3;effect4); (effect5; effect6)))). Spatial kappa only allows
parentheses around all effects (like ((effect1; effect3;effect4;
effect5; effect6)))
KaSim 3.1 allows $ADD and $DEL effects to skip the quantity (defaults
to 1), although this isn't mentioned in the manual. Spatial kappa
doesn't allow skipping
Spatial Kappa does not allow $SNAPSHOT and $STOP perturbation effects
to supply an output filename
Spatial Kappa does not allow bidirectional transitions, or different
rates for unary and binary transitions
Spatial Kappa does not support links of the form !x.y

Some of the above will be implemented soon, the remaining ones are intended to remain different.

Upgrade grammar to be compatible with that of KaSim #2

Description