Upgrade grammar to be compatible with that of KaSim

[donal-s]

Suggestion from V. The spatial grammar could be based on the Kappa grammar currently handled by KaSim. Also the translator output from spatial to non spatial Kappa could target the KaSim Kappa grammar.

[donal-s]

Partial implementation of the KaSim grammar now readable. Yet to do %agent and default state choice for agents, among other things...

[donal-s]

v1.1.0 will handle most KaSim model files. %agent declarations are ignored, and default state choice is not yet implemented.

[donal-s]

Now we're onto KaSim 3.0 - keeping up will take a while :)

[donal-s]

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(x~b~c) 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.