docs/overview.rst
Overview of `wc_lang`
=====================
Units
-----
+-----------------------------+---------------------------------------------------------------+---------------------------------------------------------+-------------------------------------------------+-------------------------------------------------------+
| Quantity | Attributes | Dimensions | Units | Units class |
+=============================+===============================================================+=========================================================+=================================================+=======================================================+
| Time | :py:attr:`wc_lang.core.Model.time_units` | time | s | :py:class:`wc_lang.core.TimeUnit` |
+-----------------------------+---------------------------------------------------------------+---------------------------------------------------------+-------------------------------------------------+-------------------------------------------------------+
| Compartment density | | :py:attr:`wc_lang.core.Compartment.density` | mass / volume | g l^-1 | :py:class:`wc_lang.core.DensityUnit` |
| | | :py:attr:`wc_lang.core.Compartment.density_units` | | | |
+-----------------------------+---------------------------------------------------------------+---------------------------------------------------------+-------------------------------------------------+-------------------------------------------------------+
| Compartment volume | | :py:attr:`wc_lang.core.Compartment.volume` | volume | l^-1 | :py:class:`wc_lang.core.VolumeUnit` |
| | | :py:attr:`wc_lang.core.Compartment.volume_units` | | | |
+-----------------------------+---------------------------------------------------------------+---------------------------------------------------------+-------------------------------------------------+-------------------------------------------------------+
| | Distribution of initial | | :py:attr:`wc_lang.core.Concentration.distribution` | | molecule, | | molecule, | :py:class:`wc_lang.core.ConcentrationUnit` |
| | concentration of a | | :py:attr:`wc_lang.core.Concentration.mean` | | molecule volume\ :sup:`-1` | | M | |
| | species at the beginning | | :py:attr:`wc_lang.core.Concentration.std` | | | |
| | of the cell cycle | | :py:attr:`wc_lang.core.Concentration.units` | | | |
+-----------------------------+---------------------------------------------------------------+---------------------------------------------------------+-------------------------------------------------+-------------------------------------------------------+
| Species count | :py:attr:`wc_lang.core.Species.units` | molecule | molecule | :py:class:`wc_lang.core.MoleculeCountUnit` |
+-----------------------------+---------------------------------------------------------------+---------------------------------------------------------+-------------------------------------------------+-------------------------------------------------------+
| Observable count | | :py:attr:`wc_lang.core.ObservableExpression.expression` | molecule | molecule | :py:class:`wc_lang.core.MoleculeCountUnit` |
| | | :py:attr:`wc_lang.core.Observable.units` | | | |
+-----------------------------+---------------------------------------------------------------+---------------------------------------------------------+-------------------------------------------------+-------------------------------------------------------+
| Observable coefficient | :py:attr:`wc_lang.core.ObservableExpression.expression` | *dimensionless* | *none* | :py:class:`wc_lang.core.ObservableCoefficientUnit` |
+-----------------------------+---------------------------------------------------------------+---------------------------------------------------------+-------------------------------------------------+-------------------------------------------------------+
| Reaction participant | :py:attr:`wc_lang.core.SpeciesCoefficient.coefficient` | *dimensionless* | *none* | :py:class:`wc_lang.core.ReactionParticipantUnit` |
+-----------------------------+---------------------------------------------------------------+---------------------------------------------------------+-------------------------------------------------+-------------------------------------------------------+
| Reaction rate | | :py:attr:`wc_lang.core.RateLawExpression.expression` | time\ :sup:`-1` | s\ :sup:`-1`, | :py:class:`wc_lang.core.ReactionRateUnit` |
| | | :py:attr:`wc_lang.core.RateLaw.units` | | | |
| | | :py:attr:`wc_lang.core.DfbaObjective.reaction_rate_units` | | | |
| | | :py:attr:`wc_lang.core.DfbaObjReaction.units` | | | |
+-----------------------------+---------------------------------------------------------------+---------------------------------------------------------+-------------------------------------------------+-------------------------------------------------------+
| Reaction flux bounds | | :py:attr:`wc_lang.core.Reaction.flux_min` | volume\ :sup:`-1` time\ :sup:`-1` | M s^-1 | :py:class:`wc_lang.core.ReactionFluxUnit` |
| | | :py:attr:`wc_lang.core.Reaction.flux_max` | | | |
| | | :py:attr:`wc_lang.core.Reaction.flux_bound_units` | | | |
+-----------------------------+---------------------------------------------------------------+---------------------------------------------------------+-------------------------------------------------+-------------------------------------------------------+
| dFBA objective | | :py:attr:`wc_lang.core.DfbaObjectiveExpresssion.expression` | time\ :sup:`-1` | s^-1 | :py:class:`wc_lang.core.DfbaObjectiveUnit` |
| | | :py:attr:`wc_lang.core.DfbaObjective.units` | | | |
+-----------------------------+---------------------------------------------------------------+---------------------------------------------------------+-------------------------------------------------+-------------------------------------------------------+
| dFBA objective coefficient | | :py:attr:`wc_lang.core.DfbaObjectiveExpresssion.expression` | time | s | :py:class:`wc_lang.core.DfbaObjectiveCoefficientUnit` |
| | | :py:attr:`wc_lang.core.DfbaObjective.coefficient_units` | | | |
+-----------------------------+---------------------------------------------------------------+---------------------------------------------------------+-------------------------------------------------+-------------------------------------------------------+
| dFBA objective species | | :py:attr:`wc_lang.core.DfbaObjSpecies.value` | | volume^-1 time^-1, | | M s^-1 | :py:class:`wc_lang.core.DfbaObjSpeciesUnit` |
| | | :py:attr:`wc_lang.core.DfbaObjSpecies.units` | | gDCW^-1 time^-1 | | mol gDCW^-1 s^-1 | |
+-----------------------------+---------------------------------------------------------------+---------------------------------------------------------+-------------------------------------------------+-------------------------------------------------------+
| Function | | :py:attr:`wc_lang.core.FunctionExpression.expression` | *various* | *various* | |
| | | :py:attr:`wc_lang.core.Function.units` | | | |
+-----------------------------+---------------------------------------------------------------+---------------------------------------------------------+-------------------------------------------------+-------------------------------------------------------+
| Parameter | | :py:attr:`wc_lang.core.Parameter.value` | *various* | *various* | |
| | | :py:attr:`wc_lang.core.Parameter.units` | | | |
+-----------------------------+---------------------------------------------------------------+---------------------------------------------------------+-------------------------------------------------+-------------------------------------------------------+
| Stop condition | | :py:attr:`wc_lang.core.StopCondition.expression` | *dimensionless* | *none* | :py:class:`wc_lang.core.StopConditionUnit` |
| | | :py:attr:`wc_lang.core.StopCondition.units` | | | |
+-----------------------------+---------------------------------------------------------------+---------------------------------------------------------+-------------------------------------------------+-------------------------------------------------------+