Predicates
The clorm predicates the ASP program is written against.
Classes:
| Name | Description |
|---|---|
activity |
An activity node in the new AF map. |
keptSpeciesKey |
Activity-key wrapper: the AF activity reuses an input PD species by identity. |
logicalOperator |
A logical operator node in the new AF map. |
logicalOperatorInput |
An input edge of a logical operator: one activity feeding it. |
logicalOperatorKey |
Activity-source wrapper: the AF influence is sourced by a logical operator. |
modulates |
A modulation edge: source influences target with an effect of unknown sign. |
negativelyInfluences |
A negative-influence edge (source inhibits target). |
new |
Top-level marker: this fact belongs to the new AF map being constructed. |
positivelyInfluences |
A positive-influence edge (source activates target). |
promotedSubunitKey |
Activity-key wrapper: a PD subunit of a dissolved complex is promoted. |
triggers |
A triggering edge (necessary stimulation): source is required for target. |
unknownModulates |
A modulation edge whose existence is uncertain. |
unknownNegativelyInfluences |
A negative-influence edge whose existence is uncertain. |
unknownPositivelyInfluences |
A positive-influence edge whose existence is uncertain. |
unknownTriggers |
A triggering edge whose existence is uncertain. |
Bases: Predicate
An activity node in the new AF map.
Always wrapped by new(...) in rule heads. The key field
carries the activity's identity — one of the two activity-key
wrappers.
Bases: Predicate
Activity-key wrapper: the AF activity reuses an input PD species by identity.
The single argument is the original CellDesigner species ID. The
solver looks it up in id_to_model_element to recover the
Species object.
Bases: Predicate
A logical operator node in the new AF map.
Always wrapped by new(...) in rule heads. key carries the
operator's identity; type_ is the operator-type token
(and | or | not_ | unknown). The NOT token is spelt
not_ -- with a trailing underscore -- because bare not is a
reserved clingo keyword (default negation) and cannot appear as a
term. The builder maps the token to the momapy operator class per
output language
(BooleanLogicGate subclass for CellDesigner, LogicalOperator
subclass for SBGN-AF). A single token field -- rather than one
predicate per type -- mirrors the internal influences/3
KIND-token idiom and avoids same-name collisions with the input
ontology's per-type operator functors.
Bases: Predicate
An input edge of a logical operator: one activity feeding it.
Always wrapped by new(...) in rule heads. The input is an activity
key, or -- for SBGN-PD, where a logical operator's input may refer to
another logical operator -- the key of that operator, mirroring how
_INFLUENCE_SOURCE widens an influence source.
Bases: Predicate
Activity-source wrapper: the AF influence is sourced by a logical operator.
The operator (AND / OR / NOT / unknown) is authored in the input PD map. The
single argument is the original gate ID -- a CellDesigner
BooleanLogicGate or an SBGN-PD LogicalOperator. The solver
looks it up in clingo_id_to_model_element to recover the gate
object. An operator is only ever an influence source, never a
target, so it widens _INFLUENCE_SOURCE but not the activity key.
Bases: Predicate
A modulation edge: source influences target with an effect of unknown sign.
Bases: Predicate
A negative-influence edge (source inhibits target).
Bases: Predicate
Top-level marker: this fact belongs to the new AF map being constructed.
As opposed to facts about the input PD map.
Bases: Predicate
A positive-influence edge (source activates target).
Bases: Predicate
Activity-key wrapper: a PD subunit of a dissolved complex is promoted.
The subunit becomes a top-level activity, added to model.species. The
single argument is the synthetic ASP ID of the subunit species.
Emitted by the no-complex mode.
Bases: Predicate
A triggering edge (necessary stimulation): source is required for target.
Bases: Predicate
A modulation edge whose existence is uncertain.
Bases: Predicate
A negative-influence edge whose existence is uncertain.
Bases: Predicate
A positive-influence edge whose existence is uncertain.
Bases: Predicate
A triggering edge whose existence is uncertain.