{% import 'macros_helpers.html' as helpers %} {% macro model(m) %} id{{ m.id }} name{{ m.name }} versionL{{ m.level }}V{{ m.version }} time{{ m.time_units }} substance{{ m.substance_units }} extent{{ m.extent_units }} volume{{ m.volume_units }} area{{ m.area_units }} length{{ m.length_units }} {% endmacro %} {% macro function_header(size) %} type FunctionDefinitions [{{ size }}] name math sbo cvterm {% endmacro %} {% macro function_content(item) %} FunctionDefinition {{ item.id }} {{ item.name }} {{ helpers.math(item) }} {{ helpers.sbo(item) }} {{ helpers.cvterm(item) }} {% endmacro %} {% macro unit_header(size) %} type UnitDefinitions [{{ size }}] name units sbo cvterm {% endmacro %} {% macro unit_content(item) %} UnitDefinition {{ item.id }} {{ item.name }} {{ item|SBML_unitDefinitionToString|SBML_stringToMathML }} {{ helpers.sbo(item) }} {{ helpers.cvterm(item) }} {% endmacro %} {% macro compartment_header(size) %} type Compartments [{{ size }}] name size constant spatial dimensions unit derived unit sbo cvterm {% endmacro %} {% macro compartment_content(item, values) %} Compartment {{ item.id }} {{ item.name }} {% if item.isSetSize() %} {{ item.size }} {% else %} {{ helpers.math(values[item.id]) }} {% endif %} {{ helpers.boolean(item.constant) }} {{ item.spatial_dimensions }} {{ item.units }} {{ helpers.derived_units(item) }} {{ helpers.sbo(item) }} {{ helpers.cvterm(item) }} {% endmacro %} {% macro species_header(size) %} type Species [{{ size }}] name compartment boundary condition constant initial amount initial concentration substance units derived units {# only substance units #} sbo cvterm {# XML #} {% endmacro %} {% macro species_content(item) %} Species {{ item.id }} {{ item.name }}
{{ item|SBML_formulaChargeString }} {{ item.compartment }} {{ helpers.boolean(item.boundary_condition) }} {{ helpers.boolean(item.constant) }} {% if item.isSetInitialAmount() %} {{ item.initial_amount }} {% endif %} {% if item.isSetInitialConcentration() %} {{ item.initial_concentration }} {% endif %} {{ item.substance_units }} {{ helpers.derived_units(item) }} {# {{ helpers.boolean(item.getHasOnlySubstanceUnits()) }} #} {{ helpers.sbo(item) }} {{ helpers.cvterm(item) }} {# {{ helpers.xml(item) }} #} {% endmacro %} {% macro parameter_header(size) %} type Parameters [{{ size }}] name value unit derived unit constant sbo cvterm {% endmacro %} {% macro parameter_content(item, values) %} Parameter {{ item.id }} {{ item.name }} {% if item.isSetValue() %} {{ item.value }} {% else %} {{ helpers.math(values[item.id]) }} {% endif %} {{ item.units }} {{ helpers.derived_units(item) }} {{ helpers.boolean(item.constant) }} {{ helpers.sbo(item) }} {{ helpers.cvterm(item) }} {% endmacro %} {% macro assignment_header(size) %} type InitialAssignments [{{ size }}]   assignment derived units sbo cvterm {% endmacro %} {% macro assignment_content(item) %} InitialAssignment {{ item.symbol }} {{ item.name }} = {{ helpers.math(item) }} {{ helpers.derived_units(item) }} {{ helpers.sbo(item) }} {{ helpers.cvterm(item) }} {% endmacro %} {% macro rule_header(size) %} type Rules [{{ size }}]   assignment derived units sbo cvterm {% endmacro %} {% macro rule_content(item) %} Rule {{ item|SBML_ruleVariableToString }} = {{ helpers.math(item) }} {{ helpers.derived_units(item) }} {{ helpers.sbo(item) }} {{ helpers.cvterm(item) }} {% endmacro %} {% macro constraint_header(size) %} type Constraints [{{ size }}] constraint sbo cvterm {% endmacro %} {% macro constraint_content(item) %} Constraint {{ item.id }} {{ helpers.math(item) }} {{ helpers.sbo(item) }} {{ helpers.cvterm(item) }} {% endmacro %} {% macro reaction_header(size) %} type Reactions [{{ size }}] name equation modifiers formula derived units sbo cvterm {% endmacro %} {% macro reaction_content(item) %} Reaction {{ item.id }} {{ item.name }} {% if item.reversible %} ⇆ {% else %} ➞ {% endif %} {{ item|SBML_reactionToString }} {% for mod in item.getListOfModifiers() %} {{ mod.getSpecies() }}
{% endfor %} {{ helpers.math(item.getKineticLaw()) }} {{ helpers.derived_units(item.getKineticLaw()) }} {{ helpers.sbo(item) }} {{ helpers.cvterm(item) }} {% endmacro %} {% macro event_header(size) %} type Events [{{ size }}] name trigger priority delay assignments sbo cvterm {% endmacro %} {% macro event_content(item) %} Event {{ item.id }} {{ item.name }} {{ helpers.math(item.getTrigger()) }}
initialValue = {{ item.getTrigger().initial_value }}
persistent = {{ item.getTrigger().persistent }}
{{ item.priority }} {{ item.delay }} {% for eva in item.getListOfEventAssignments() %} {{eva.getId()}} = {{ helpers.math(eva) }}
{% endfor %} {{ helpers.sbo(item) }} {{ helpers.cvterm(item) }} {% endmacro %}