all-classes.heta

// Component
// Base element annotation
{
  id: <ID>,
  space: <ID>,
  class: <String>, // class of component
  title: <String>, // Human readable name of component
  notes: <String>, // any notes, supports Markdown
  tags: <String[]>, // tags for component
  aux: <Dict>, // Any user defined properties
  ...
};

''' Notes '''
sp1::cmd @Component 'Title' {
  tags: [a, b, c],
  aux: {},
  ...
};

// Record <= Component
// describes value which can change its value in time
p1 @Record {
  boundary: <Boolean>,    // if true it cannot be changed by @Process or @Reaction
  units: <UnitExpr>,      // units describing the value
  assignments: {
    [<ID>]: <MathExpr>,   // any number of key/value pairs describing value changes
    ...
  }
};

// record assignments
p1 .= <MathExpr>;         // calculated at start, uses start_ switcher
p1 := <MathExpr>;         // calculated at each time point, uses ode_ switcher
p1 [sw1]= <MathExpr>;     // calculated at sw1 switcher
p1 []= <MathExpr>;        // the same as .=

// Process <= Record 
// change record values using ODEs
pr1 @Process {
  actors: <ProcessExpr>/<Actor[]> // describes records to change
};

// correct ProcessExpr
1*A = 2*B + 3*C
A => 2B + 3C      // mark as irreversible
A <=> B + B + 3C  // mark as reversible

// TimeSwitcher <= Component
// run reassignment of records at specific time points
sw1 @TimeSwitcher {
  start: <Number>, // required, when switcher is called
  period: <Integer>, // >0, if set, the switcher will be called with period
  stop: <Number>
};

// Const <= Component
// numerical value which does not change in time
k1 @Const {
  units: <UnitExpr>,      // units describing the value
  num: <Number>,          // required, constant value
  free: <Boolean>         // if true the value is marked for fitting
};

// Compartment <= Record <= Component
// describes volumes where Species instances are located
comp1 @Compartment {
  // no specific properties
};

// Species <= Record <= Component
// describes particles in some location
s @Species {
  isAmount: <Boolean>, // 
  compartment: <ID> // required, reference to Compartment
};

// Reaction <= Process <= Record
// The same as Process, but all target references should be Species
r1 @Reaction {
  actors: <ProcessExpr>/<Reactant[]>,   // 
  modifiers: <Modifier[]>/<Id[]>        // array of references to Species
};

// ===

pmid @ReferenceDefinition {
  prefix: "https://pubmed.org",
  suffix: /
};

pow #defineFunction {
  args: [x, y],
  expr: x^y
};

kDa #defineUnit {components: [
  { kind: g, multiplier: 1e3, exponent: 1},
  { kind: mole, exponent: -1}
]};