Updates on membrane mech and comp

Additionally cleans up comments and descriptions.

Tests/Unit/test_component_membrane.py

@@ -1,9 +1,23 @@
 #  Copyright (c) 2020, Build-A-Cell. All rights reserved.
 #  See LICENSE file in the project root directory for details.
 
-from biocrnpyler import IntegralMembraneProtein, MembraneChannel, MembranePump
+from biocrnpyler import DiffusibleMolecule, IntegralMembraneProtein, MembraneChannel, MembranePump, MembraneSensor
 import pytest
 
+def test_DiffusibleMolecule():
+    diffusion_molecule = 'DP'
+
+    dm = DiffusibleMolecule(substrate=diffusion_molecule)
+    assert diffusion_molecule == dm.substrate.name
+    assert diffusion_molecule== dm.product.name
+
+    assert dm.get_species().name == 'DP'
+
+    with pytest.raises(KeyError, match='Unable to find mechanism of type diffusion in Component'):
+        mp.update_species()
+
+    with pytest.raises(KeyError, match='Unable to find mechanism of type diffusion in Component'):
+        mp.update_reactions()
 
 def test_IntegralMembraneProtein():
     membrane_protein = 'MP1'
@@ -15,10 +29,10 @@ def test_IntegralMembraneProtein():
 
     assert mp.get_species().name == 'MP1'
 
-    with pytest.raises(KeyError, match='Unable to find mechanism of type catalysis in Component'):
+    with pytest.raises(KeyError, match='Unable to find mechanism of type membrane_insertion in Component'):
         mp.update_species()
 
-    with pytest.raises(KeyError, match='Unable to find mechanism of type catalysis in Component'):
+    with pytest.raises(KeyError, match='Unable to find mechanism of type membrane_insertion in Component'):
         mp.update_reactions()
 
 def test_MembraneChannel():
@@ -32,10 +46,10 @@ def test_MembraneChannel():
 
     assert imp.get_species().name == 'IMP1'
 
-    with pytest.raises(KeyError, match='Unable to find mechanism of type catalysis in Component'):
+    with pytest.raises(KeyError, match='Unable to find mechanism of type transport in Component'):
         imp.update_species()
 
-    with pytest.raises(KeyError, match='Unable to find mechanism of type catalysis in Component'):
+    with pytest.raises(KeyError, match='Unable to find mechanism of type transport in Component'):
         imp.update_reactions()
 
 def test_MembranePump(): 
@@ -49,8 +63,28 @@ def test_MembranePump():
 
     assert imp.get_species().name == 'MPump1'
 
-    with pytest.raises(KeyError, match='Unable to find mechanism of type catalysis in Component'):
+    with pytest.raises(KeyError, match='Unable to find mechanism of type transport in Component'):
         imp.update_species()
 
-    with pytest.raises(KeyError, match='Unable to find mechanism of type catalysis in Component'):
-        imp.update_reactions()
+    with pytest.raises(KeyError, match='Unable to find mechanism of type transport in Component'):
+        imp.update_reactions()
+
+def test_MembraneSensor():
+    membrane_sensor = 'MSensor1'
+    response_protein = 'RP1'
+    assigned_substrate = 'Sub_A1'
+    signal_substrate = 'Sub_S1'
+
+    ms = MembraneSensor(membrane_sensor, response_protein=response_protein, 
+                        assigned_substrate=assigned_substrate, signal_substrate=signal_substrate)
+    assert response_protein == ms.response_protein.name
+    assert assigned_substrate == ms.assigned_substrate.name
+    assert signal_substrate == ms.signal_substrate.name
+
+    assert ms.get_species().name == 'MSensor1'
+
+    with pytest.raises(KeyError, match='Unable to find mechanism of type membrane_sensor in Component'):
+            ms.update_species()
+
+    with pytest.raises(KeyError, match='Unable to find mechanism of type membrane_sensor in Component'):
+            ms.update_reactions()

Tests/Unit/test_membrane_signaling.py

@@ -0,0 +1,48 @@
+
+#  Copyright (c) 2020, Build-A-Cell. All rights reserved.
+#  See LICENSE file in the project root directory for details.
+
+from biocrnpyler import Species, Complex
+
+#Test Membrane Transport Mechanisms
+from biocrnpyler import Membrane_Signaling_Pathway_MM
+
+class test_membrane_signaling_MM():
+    tcs = Membrane_Signaling_Pathway_MM()
+    MSP = Species("MSP1")
+    MSP.ATP=2
+    RP = Species("RP1")
+    sub_assign = Species("S1")
+    sub_signal = Species("S2")
+    energy = Species("E1")
+    waste = Species("W1")
+    c1 =  Complex([sub_signal, MSP])
+    c2 =  Complex([MP.ATP*[energy], c1])
+    c3 =  Complex([c1, MP.ATP*[waste], sub_assign])
+    c4 =  Complex([c1, sub_assign])
+    c5 = Complex([c4, RP])
+    c6 = Complex([c1, RP, sub_assign])
+    c7 =  Complex([RP, sub_assign])
+
+    c_fake = Species("C")
+
+    #Test Update Species
+    assert len(tcs.update_species(MSP, RP, sub_assign, sub_signal, energy, waste)) == 13
+    assert c1 in tcs.update_species(MSP, RP, sub_assign, sub_signal, energy, waste)
+    assert c2 in tcs.update_species(MSP, RP, sub_assign, sub_signal, energy, waste)
+    assert c3 in tcs.update_species(MSP, RP, sub_assign, sub_signal, energy, waste)
+    assert c4 in tcs.update_species(MSP, RP, sub_assign, sub_signal, energy, waste)
+    assert c5 in tcs.update_species(MSP, RP, sub_assign, sub_signal, energy, waste)
+    assert c6 in tcs.update_species(MSP, RP, sub_assign, sub_signal, energy, waste)
+    assert c7 in tcs.update_species(MSP, RP, sub_assign, sub_signal, energy, waste)
+
+    assert c_fake in tcs.update_species(MSP, RP, sub_assign, sub_signal, energy, waste, complex = c_fake)
+
+    #Test Update Reactions
+    assert len(tcs.update_reactions(MSP, RP, sub_assign, sub_signal, energy, waste, kb1 = 2e-3, ku1 = 2e-10, 
+        kb2 = 2e-3, ku2 = 2e-10, k_hydro = 1e-1, ku3 = 2e-1, kb4 = 2e-3, ku4 = 2e-10, 
+        k_phosph = 1e-1, ku5 = 2e-1,ku6 = 2e-10)) == 8
+
+    assert len(tcs.update_reactions(MSP, RP, sub_assign, sub_signal, energy, waste, kb1 = 2e-3, ku1 = 2e-10,
+        kb2 = 2e-3, ku2 = 2e-10, k_hydro = 1e-1, ku3 = 2e-1, kb4 = 2e-3, ku4 = 2e-10, 
+        k_phosph = 1e-1, ku5 = 2e-1,ku6 = 2e-10, complex_species = c_fake,)) == 8

Tests/Unit/test_transport.py

@@ -5,7 +5,21 @@
 from biocrnpyler import Species, Complex
 
 #Test Membrane Transport Mechanisms
-from biocrnpyler import Membrane_Protein_Integration, Simple_Transport, Facilitated_Transport_MM, Primary_Active_Transport_MM
+from biocrnpyler import Simple_Diffusion, Membrane_Protein_Integration, Simple_Transport, Facilitated_Transport_MM, Primary_Active_Transport_MM
+
+class test_simple_diffusion():
+    sd = Simple_Diffusion()
+    substrate = Species("DMi")
+    product = Species("DMo")
+    c_fake = Species("C")
+
+    #Test Update Species
+    assert len(sd.update_species(substrate, product))==2
+    assert c1 in sd.update_species(substrate, product)
+
+    #Test Update Reactions
+    assert len(sd.update_reactions(substrate, product, k_diff = 1.0,)) == 1
+    assert len(sd.update_reactions(substrate, product, k_diff = 1.0, complex_species = c_fake,)) == 1
 
 class test_membrane_integration():
     mpi = Membrane_Protein_Integration()
@@ -84,5 +98,4 @@ class test_active_transport_MM():
 
     #Test Update Reactions
     assert len(pat.update_reactions(MP, substrate, product, energy, waste, k1 = 1.0, ku1 = 1.0, k2 = 1.0, ku2 = 1.0, k_trnsp = 1.0, ku3= 1.0, ku4= 1.0)) == 7
-    assert len(pat.update_reactions(MP, substrate, product, energy, waste, k1 = 1.0, ku1 = 1.0, k2 = 1.0, ku2 = 1.0, k_trnsp = 1.0, ku3= 1.0, ku4= 1.0, complex_species = c_fake,)) == 7
-
+    assert len(pat.update_reactions(MP, substrate, product, energy, waste, k1 = 1.0, ku1 = 1.0, k2 = 1.0, ku2 = 1.0, k_trnsp = 1.0, ku3= 1.0, ku4= 1.0, complex_species = c_fake,)) == 7

biocrnpyler/components_membrane.py

@@ -8,15 +8,15 @@
 from .reaction import Reaction
 from .species import Complex, Species
 
-class Diffusible_Molecule(Component):
+class DiffusibleMolecule(Component):
     """A class to represent transmembrane proteins or integral membrane proteins.
     This membrane class is to classify a membrane channel that will intergrate into the membrane.
     Uses a mechanism called "diffusion".
     """
     def __init__(self, substrate: Union[Species,str, Component], 
                  internal_compartment='Internal', external_compartment='External',
                  cell=None, attributes=None, **keywords):       
-        """Initialize a Diffusible_Molecule object to store molecule/substance related information.
+        """Initialize a DiffusibleMolecule object to store molecule/substance related information.
         :param substrate: name of the diffusible substrate, reference to an Species or Component
         :param internal_compartment: name of internal compartment 
         :param external_compartment: name of external compartment 

biocrnpyler/mechanism_signaling.py

@@ -80,8 +80,10 @@ def update_reactions(self, membrane_sensor_protein, response_protein, assigned_s
         if part_id is None and component is not None:
             part_id = component.name
 
-        if component is None and (kb1 is None or ku1 is None or kb2 is None or kex is None or kcat is None):
-            raise ValueError("Must pass in a Component or values for kb1, ku1, kb2, kex, and kcat.")
+        if component is None and (kb1 is None or ku1 is None or kb2 is None or ku2 is None or k_hydro is None 
+                                  or ku3 is None or kb4 is None or  ku4 is None or k_phosph is None 
+                                  or ku5 is None or ku6 is None):
+            raise ValueError("Must pass in a Component or values for kb1, ku1, kb2, ku2, k_hydro, ku3, kb4, ku4, k_phosph, ku5 and ku6.")
 
         if kb1 is None:
             kb1 = component.get_parameter("kb1", part_id = part_id, mechanism = self)

biocrnpyler/mechanisms_transport.py

@@ -71,8 +71,8 @@ def update_reactions(self, integral_membrane_protein, product, component=None, p
         if part_id is None and component is not None:
             part_id = component.name
 
-        if component is None and (kb is None or ku is None or kcat is None):
-            raise ValueError("Must pass in a Component or values for kb, ku, and kcat.")
+        if component is None and (kb1 is None or ku1 is None or kb2 is None or ku2 is None or kcat is None or kex is None):
+            raise ValueError("Must pass in a Component or values for kb1, ku1, kb2, ku2, kcat, and kex.")
 
         if kb1 is None:
             kb1 = component.get_parameter("kb1", part_id = part_id, mechanism = self)
@@ -150,7 +150,7 @@ def update_reactions(self, membrane_channel, substrate, product, component=None,
             part_id = component.name
 
         if component is None and (k_trnsp is None):
-            raise ValueError("Must pass in a Component or values for kb, ku, and kcat.")
+            raise ValueError("Must pass in a Component or values for k_trnsp.")
         if k_trnsp is None:
             k_trnsp = component.get_parameter("k_trnsp", part_id = part_id, mechanism = self)
         else:
@@ -190,8 +190,8 @@ def update_reactions(self, membrane_carrier, substrate, product, component = Non
         if part_id is None and component is not None:
             part_id = component.name
 
-        if component is None and (kb is None or ku is None or k1 is None):
-            raise ValueError("Must pass in a Component or values for kb, ku, and kcat.")
+        if component is None and (k1 is None or ku1 is None or ku2 is None or k_trnsp is None):
+            raise ValueError("Must pass in a Component or values for k1, ku1, ku2, and k_trnsp.")
 
         if k1 is None:
             k1 = component.get_parameter("k1", part_id = part_id, mechanism = self)