10.2. Rule Composition

10.2.1. Unary Operators

Special rules can be constructed from graphs.

Explore in the playground.

include("../000_basics/050_formoseGrammar.py")
glycolaldehyde.print()
# A graph G can be used to construct special rules:
# (\emptyset <- \emptyset -> G)
bindExp = rcBind(glycolaldehyde)
# (G <- \emptyset -> \emptyset)
unbindExp = rcUnbind(glycolaldehyde)
# (G <- G -> G)
idExp = rcId(glycolaldehyde)
# These are really rule composition expressions that have to be evaluated:
rc = rcEvaluator(inputRules)
# Each expression results in a lists of rules:
bindRules = rc.eval(bindExp)
unbindRules = rc.eval(unbindExp)
idRules = rc.eval(idExp)
post.summarySection("Bind Rules")
for p in bindRules:
   p.print()
post.summarySection("Unbind Rules")
for p in unbindRules:
   p.print()
post.summarySection("Id Rules")
for p in idRules:
   p.print()

10.2.2. Parallel Composition

A pair of rules can be merged to a new rule implementing the parallel transformation.

Explore in the playground.

include("../000_basics/050_formoseGrammar.py")
rc = rcEvaluator(inputRules)
# The special global object 'rcParallel' is used to make a pseudo-operator:
exp = rcId(formaldehyde) *rcParallel*  rcUnbind(glycolaldehyde)
rules = rc.eval(exp)
for p in rules:
   p.print()

10.2.3. Supergraph Composition

A pair of rules can (maybe) be composed using a sueprgraph relation.

Explore in the playground.

include("../000_basics/050_formoseGrammar.py")
rc = rcEvaluator(inputRules)
exp = rcId(formaldehyde) *rcParallel*  rcId(glycolaldehyde)
exp = exp *rcSuper* ketoEnol_F
rules = rc.eval(exp)
for p in rules:
   p.print()

10.2.4. Overall Formose Reaction

A complete pathway can be composed to obtain the overall rules.

Explore in the playground.

include("../000_basics/050_formoseGrammar.py")
rc = rcEvaluator(inputRules)
exp = (
   rcId(glycolaldehyde)
   *rcSuper* ketoEnol_F
   *rcParallel* rcId(formaldehyde)
   *rcSuper(allowPartial=False)* aldolAdd_F
   *rcSuper* ketoEnol_F
   *rcParallel* rcId(formaldehyde)
   *rcSuper(allowPartial=False)* aldolAdd_F
   *rcSuper* ketoEnol_F
   *rcSuper* ketoEnol_B
   *rcSuper* aldolAdd_B
   *rcSuper* ketoEnol_B
   *rcSuper(allowPartial=False)*
   (rcId(glycolaldehyde) *rcParallel* rcId(glycolaldehyde))
)
rules = rc.eval(exp)
for p in rules:
   p.print()