Update PURE mixture, mechanisms, and parameters

Tests/Unit/test_chemicalReactionNetwork.py

@@ -228,7 +228,7 @@ def test_initial_condition_vector(self):
     def test_get_all_species_containing(self):
         # test that the species arument must be Species object
         with self.assertRaisesRegex(
-            ValueError, 'species argument must be an instance of Species!'
+            ValueError, 'species argument must be an instance of Species'
         ):
             self.crn.get_all_species_containing(species=self.species_list)
 

Tests/Unit/test_component_basic.py

@@ -11,7 +11,11 @@ def test_enzyme():
     products = 'P1'
     enzyme = 'E1'
 
-    e = Enzyme(enzyme=enzyme, substrates=substrates, products=products)
+    e = Enzyme(
+        enzyme=enzyme, substrates=substrates, products=products,
+    )
+    e.default_mechanism=None  # override failsafe
+
     assert any([s.name == 'S1' for s in e.substrates])
     assert any([p.name == 'P1' for p in e.products])
     assert enzyme == e.enzyme.name

Tests/Unit/test_component_membrane.py

@@ -21,6 +21,7 @@ def test_DiffusibleMolecule():
 
     assert dm.get_species().name == 'DP'
 
+    dm.default_mechanism = None  # override failsafe
     with pytest.raises(
         KeyError,
         match='Unable to find mechanism of type diffusion in Component',
@@ -46,6 +47,7 @@ def test_IntegralMembraneProtein():
 
     assert imp.get_species().name == 'MP1'
 
+    imp.default_mechanism = None  # override failsafe
     with pytest.raises(
         KeyError,
         match='Unable to find mechanism of type membrane_insertion in Component',
@@ -70,6 +72,7 @@ def test_MembraneChannel():
 
     assert mc.get_species().name == 'IMP1'
 
+    mc.default_mechanism = None  # override failsafe
     with pytest.raises(
         KeyError,
         match='Unable to find mechanism of type transport in Component',
@@ -94,6 +97,7 @@ def test_MembranePump():
 
     assert mp.get_species().name == 'MPump1'
 
+    mp.default_mechanism = None  # override failsafe
     with pytest.raises(
         KeyError,
         match='Unable to find mechanism of type transport in Component',
@@ -125,6 +129,7 @@ def test_MembraneSensor():
 
     assert ms.get_species().name == 'MSensor1'
 
+    ms.default_mechanism = None  # override failsafe
     with pytest.raises(
         KeyError,
         match='Unable to find mechanism of type membrane_sensor in Component',

biocrnpyler/__init__.py

@@ -11,6 +11,12 @@
 
 # All utilities
 from .utils import *
+from .utils.plotting import (
+    plot_all_species_containing as plot_all_species_containing,
+)
+from .utils.plotting import (
+    plot_gene_expression_data as plot_gene_expression_data,
+)
 
 try:
     from ._version import version as __version__

biocrnpyler/components/basic.py

@@ -6,6 +6,9 @@
 from ..core.component import Component
 from ..core.reaction import Reaction
 from ..core.species import Complex, Species
+from ..mechanisms.binding import One_Step_Binding
+from ..mechanisms.enzyme import MichaelisMenten
+from ..mechanisms.metabolite import OneStepPathway
 
 
 class DNA(Component):
@@ -402,7 +405,17 @@ def __init__(
                 else:
                     self.products.append(self.set_species(p))
 
-        Component.__init__(self=self, name=name, **kwargs)
+        if precursors is not None or products is not None:
+            default_mechanism = OneStepPathway()
+        else:
+            default_mechanism = None
+
+        Component.__init__(
+            self=self,
+            name=name,
+            default_mechanism=default_mechanism,
+            **kwargs,
+        )
 
     def get_species(self) -> Species:
         """Get the metabolite species.
@@ -602,7 +615,12 @@ def __init__(
         if name is None:
             name = self.species.name
 
-        Component.__init__(self=self, name=name, **kwargs)
+        Component.__init__(
+            self=self,
+            name=name,
+            default_mechanism=One_Step_Binding(),
+            **kwargs,
+        )
 
     def get_species(self) -> List[Species]:
         """Get the complex species.
@@ -773,7 +791,12 @@ def __init__(
         self.substrates = substrates
         self.products = products
 
-        Component.__init__(self=self, name=self.enzyme.name, **kwargs)
+        Component.__init__(
+            self=self,
+            name=self.enzyme.name,
+            default_mechanism=MichaelisMenten(),
+            **kwargs,
+        )
 
     @property
     def substrates(self) -> List:

biocrnpyler/components/combinatorial_conformation.py

@@ -140,8 +140,12 @@ def __init__(
 
         if name is None:
             name = str(self.internal_polymer.name)
-        Component.__init__(self, name=name, **kwargs)
-        self.add_mechanism(One_Step_Reversible_Conformation_Change())
+        Component.__init__(
+            self,
+            name=name,
+            default_mechanism=One_Step_Reversible_Conformation_Change(),
+            **kwargs,
+        )
 
     # Helper function to assert the correct class type
     def _assert_conformation(self, states, input_name='states'):

biocrnpyler/components/membrane.py

@@ -7,6 +7,14 @@
 from ..core.compartment import Compartment
 from ..core.component import Component
 from ..core.species import Species
+from ..mechanisms.signaling import Membrane_Signaling_Pathway_MM
+from ..mechanisms.transport import (
+    Facilitated_Transport_MM,
+    Membrane_Protein_Integration,
+    Primary_Active_Transport_MM,
+    Simple_Diffusion,
+    Simple_Transport,
+)
 
 
 class DiffusibleMolecule(Component):
@@ -108,7 +116,11 @@ def __init__(
             name = self.substrate.name + '_' + self.substrate.compartment.name
 
         Component.__init__(
-            self=self, name=name, attributes=attributes, **kwargs
+            self=self,
+            name=name,
+            attributes=attributes,
+            default_mechanism=Simple_Diffusion(),
+            **kwargs,
         )
 
     def get_species(self):
@@ -334,7 +346,12 @@ def __init__(
             + self.membrane_protein.compartment.name
         )
 
-        Component.__init__(self=self, name=name, **kwargs)
+        Component.__init__(
+            self=self,
+            name=name,
+            default_mechanism=Membrane_Protein_Integration(),
+            **kwargs,
+        )
 
     def get_species(self):
         """Get the membrane protein species before insertion.
@@ -504,7 +521,7 @@ def __init__(
             integral_membrane_protein = self.set_species(
                 integral_membrane_protein,
                 material_type='protein',
-                attributes='Passive' if direction is None else direction,
+                attributes=['Passive'] if direction is None else direction,
             )
         self.integral_membrane_protein = integral_membrane_protein
 
@@ -568,7 +585,12 @@ def __init__(
             + self.integral_membrane_protein.compartment.name
         )
 
-        Component.__init__(self=self, name=name, **kwargs)
+        Component.__init__(
+            self=self,
+            name=name,
+            default_mechanism=Simple_Transport(),
+            **kwargs,
+        )
 
     def get_species(self):
         """Get the integral membrane protein species.
@@ -782,14 +804,14 @@ def __init__(
                 self.membrane_pump = self.set_species(
                     membrane_pump,
                     material_type='protein',
-                    attributes='Passive',
+                    attributes=['Passive'],
                 )
                 self.membrane_pump.ATP = ATP
             else:
                 self.membrane_pump = self.set_species(
                     membrane_pump,
                     material_type='protein',
-                    attributes=direction,
+                    attributes=[direction],
                 )
                 self.membrane_pump.ATP = ATP
                 if direction == 'Importer':
@@ -812,19 +834,19 @@ def __init__(
                 self.integral_membrane_protein = self.set_species(
                     membrane_pump,
                     material_type='protein',
-                    attributes='Passive',
+                    attributes=['Passive'],
                 )
             elif membrane_pump.attributes[0] == 'Exporter':
                 self.membrane_pump = self.set_species(
                     membrane_pump,
                     material_type='protein',
-                    attributes='Exporter',
+                    attributes=['Exporter'],
                 )
             elif membrane_pump.attributes[0] == 'Importer':
                 self.membrane_pump = self.set_species(
                     membrane_pump,
                     material_type='protein',
-                    attributes='Importer',
+                    attributes=['Importer'],
                 )
                 self.energy = self.set_species(
                     'ATP',
@@ -867,7 +889,18 @@ def __init__(
             + self.membrane_pump.compartment.name
         )
 
-        Component.__init__(self=self, name=name, **kwargs)
+        # Determine the default mechanism
+        if 'Passive' in self.membrane_pump.attributes:
+            default_mechanism = Primary_Active_Transport_MM()
+        else:
+            default_mechanism = Facilitated_Transport_MM()
+
+        Component.__init__(
+            self=self,
+            name=name,
+            default_mechanism=default_mechanism,
+            **kwargs,
+        )
 
     def get_species(self):
         """Get the membrane pump protein species.
@@ -1137,7 +1170,12 @@ def __init__(
             + self.membrane_sensor_protein.compartment.name
         )
 
-        Component.__init__(self=self, name=name, **kwargs)
+        Component.__init__(
+            self=self,
+            name=name,
+            default_mechanism=Membrane_Signaling_Pathway_MM(),
+            **kwargs,
+        )
 
     def get_species(self):
         """Get the membrane sensor protein species.

biocrnpyler/core/chemical_reaction_network.py

@@ -604,7 +604,7 @@ def initial_condition_vector(
         return x0
 
     def get_all_species_containing(
-        self, species: Species, return_as_strings=False
+        self, species: Union[Species, str], return_as_strings=False
     ):
         """Find all species (complexes) that contain a given species.
 
@@ -613,8 +613,9 @@ def get_all_species_containing(
 
         Parameters
         ----------
-        species : Species
-            The species to search for within other species.
+        species : Species or str
+            The species to search for within other species.  If given as a
+            string, returns all species with that string as part of the name.
         return_as_strings : bool, default=False
             If True, returns species as string representations. If False,
             returns actual Species objects.
@@ -645,13 +646,15 @@ def get_all_species_containing(
 
         """
         return_list = []
-        if not isinstance(species, Species):
+        if not isinstance(species, (Species, str)):
             raise ValueError(
-                "species argument must be an instance of Species!"
+                "species argument must be an instance of Species or str."
             )
 
         for s in self._species:
-            if species in s.get_species(recursive=True):
+            if (
+                isinstance(species, str) and species in s.name
+            ) or species in s.get_species(recursive=True):
                 if return_as_strings:
                     return_list.append(repr(s))
                 else: