add documentation + code cleanup

Author: murrayrm

Tests/Unit/test_parameter.py

@@ -545,3 +545,150 @@ def test_findpath():
         os.environ['BCP_PATH'] = '/tmp:.:..'
     assert os.path.exists(bcp.find_file_in_bcp_path('__testfile__.tsv'))
     os.remove('../__testfile__.tsv')
+
+
+def test_parameter_ordering():
+    import biocrnpyler as bcp
+
+    # Create the components for testing
+    TetR = bcp.Protein('TetR')
+    aTc = bcp.Species('aTc')
+    TetR_inactive=bcp.ChemicalComplex([TetR.species, aTc])
+    ptet = bcp.RegulatedPromoter('ptet', TetR)
+    dna_GFP = bcp.DNAassembly(
+        'GFP', promoter=ptet, rbs='RBS', protein='GFP')
+
+    # Default case: test everything in PURE< with no parameters
+    default_mixture = bcp.BasicPURE(
+        'default', components=[dna_GFP, TetR_inactive])
+    default_crn = default_mixture.compile_crn()
+
+    # Find the binding reactions of TetR to DNA and aTc
+    aTc_TetR_index = dna_TetR_index = -1
+    for i, reaction in enumerate(default_crn.reactions):
+        if not isinstance(reaction.propensity_type, bcp.MassAction):
+            continue
+
+        inputs = [input.species for input in reaction.inputs]
+
+        # Find the binding of aTc to TetR
+        if aTc in inputs and TetR.species in inputs:
+            aTc_TetR_index = i
+
+        # Find the binding of TetR to DNA
+        if dna_GFP.species in inputs and TetR.species in inputs:
+            dna_TetR_index = i
+    assert aTc_TetR_index != -1 and dna_TetR_index != -1
+    assert default_crn.reactions[
+        dna_TetR_index].propensity_type.k_forward != 1
+    assert default_crn.reactions[
+        aTc_TetR_index].propensity_type.k_forward != 1
+
+    # Rebuild using given parameters
+    baseline_parameters = {
+        ('binding', None, 'kb'): 1,
+        ('binding', None, 'ku'): 0.1,
+        ('binding', None, 'cooperativity'): 2,
+    }
+    TetR_inactive=bcp.ChemicalComplex(
+        [TetR.species, aTc], parameters=baseline_parameters)
+    dna_GFP = bcp.DNAassembly(
+        'GFP', promoter=ptet, rbs='RBS', protein='GFP',
+        parameters=baseline_parameters)
+    baseline_mixture = bcp.BasicPURE(
+        'baseline', components=[dna_GFP, TetR_inactive])
+    baseline_crn = baseline_mixture.compile_crn()
+    assert baseline_crn.reactions[
+        dna_TetR_index].propensity_type.k_forward == 1
+    assert baseline_crn.reactions[
+        aTc_TetR_index].propensity_type.k_forward == 1
+
+    # Override using mechanism subtypes
+    mechtype_parameters = baseline_parameters | {
+        ('binding', 'dna_protein', 'kb'): 2,
+        ('binding', 'chemical_complex', 'kb'): 3,
+    }
+    TetR_inactive=bcp.ChemicalComplex(
+        [TetR.species, aTc], parameters=mechtype_parameters)
+    dna_GFP = bcp.DNAassembly(
+        'GFP', promoter=ptet, rbs='RBS', protein='GFP',
+        parameters=mechtype_parameters)
+    mechtype_mixture = bcp.BasicPURE(
+        'mechtype', components=[dna_GFP, TetR_inactive])
+    mechtype_crn = mechtype_mixture.compile_crn()
+    assert mechtype_crn.reactions[
+        dna_TetR_index].propensity_type.k_forward == 2
+    assert mechtype_crn.reactions[
+        aTc_TetR_index].propensity_type.k_forward == 3
+
+    # Override using part IDs
+    partid_parameters = mechtype_parameters | {
+        ('binding', 'ptet_TetR', 'kb'): 4,
+        ('binding', 'aTc_protein_TetR', 'kb'): 5,
+    }
+    TetR_inactive=bcp.ChemicalComplex(
+        [TetR.species, aTc], parameters=partid_parameters)
+    dna_GFP = bcp.DNAassembly(
+        'GFP', promoter=ptet, rbs='RBS', protein='GFP',
+        parameters=partid_parameters)
+    partid_mixture = bcp.BasicPURE(
+        'partid', components=[dna_GFP, TetR_inactive])
+    partid_crn = partid_mixture.compile_crn()
+    assert partid_crn.reactions[
+        dna_TetR_index].propensity_type.k_forward == 4
+    assert partid_crn.reactions[
+        aTc_TetR_index].propensity_type.k_forward == 5
+
+    # Override using mechanism name
+    mechname_parameters = baseline_parameters | {
+        ('one_step_cooperative_binding', None, 'kb'): 6,
+        ('binding', 'chemical_complex', 'kb'): 7,
+    }
+    TetR_inactive=bcp.ChemicalComplex(
+        [TetR.species, aTc], parameters=mechname_parameters)
+    dna_GFP = bcp.DNAassembly(
+        'GFP', promoter=ptet, rbs='RBS', protein='GFP',
+        parameters=mechname_parameters)
+    mechname_mixture = bcp.BasicPURE(
+        'mechname', components=[dna_GFP, TetR_inactive])
+    mechname_crn = mechname_mixture.compile_crn()
+    assert mechname_crn.reactions[
+        dna_TetR_index].propensity_type.k_forward == 6
+    assert mechname_crn.reactions[
+        aTc_TetR_index].propensity_type.k_forward == 7
+
+    # Override in mixture instead of components
+    mixture_parameters = baseline_parameters | {
+        ('one_step_cooperative_binding', None, 'kb'): 8,
+        ('binding', 'chemical_complex', 'kb'): 9,
+    }
+    TetR_inactive=bcp.ChemicalComplex([TetR.species, aTc])
+    dna_GFP = bcp.DNAassembly(
+        'GFP', promoter=ptet, rbs='RBS', protein='GFP')
+    mixture_mixture = bcp.BasicPURE(
+        'mixture', components=[dna_GFP, TetR_inactive],
+        parameters=mixture_parameters)
+    mixture_crn = mixture_mixture.compile_crn()
+    assert mixture_crn.reactions[
+        dna_TetR_index].propensity_type.k_forward == 8
+    assert mixture_crn.reactions[
+        aTc_TetR_index].propensity_type.k_forward == 9
+
+    # Override in components and not mixture
+    component_parameters = baseline_parameters | {
+        ('one_step_cooperative_binding', None, 'kb'): 10,
+        ('binding', 'chemical_complex', 'kb'): 11,
+    }
+    TetR_inactive=bcp.ChemicalComplex(
+        [TetR.species, aTc], parameters=component_parameters)
+    dna_GFP = bcp.DNAassembly(
+        'GFP', promoter=ptet, rbs='RBS', protein='GFP',
+        parameters=component_parameters)
+    mixture_mixture = bcp.BasicPURE(
+        'mixture', components=[dna_GFP, TetR_inactive],
+        parameters=mixture_parameters)
+    mixture_crn = mixture_mixture.compile_crn()
+    assert mixture_crn.reactions[
+        dna_TetR_index].propensity_type.k_forward == 10
+    assert mixture_crn.reactions[
+        aTc_TetR_index].propensity_type.k_forward == 11

biocrnpyler/components/basic.py

@@ -513,7 +513,7 @@ class ChemicalComplex(Component):
         List of attribute tags to associate with the complex species. The
         complex also inherits attributes from its constituent species.
     binding_type : str, default='chemical_complex'
-        Mechanism subtype for binding reaction parameters.
+        Part type for binding reaction parameters.
     **kwargs
         Additional keyword arguments passed to the `Component` base class
         constructor.

biocrnpyler/components/combinatorial_complex.py

@@ -37,7 +37,7 @@ class CombinatorialComplex(Component):
         Name of the component. If None, automatically generated from
         final_states names.
     binding_type : str, default='chemical_complex'
-        Mechanism subtype for binding reaction parameters.
+        Part type for binding reaction parameters.
     **kwargs
         Additional keyword arguments passed to the `Component` base class
         constructor.

biocrnpyler/components/dna/misc.py

@@ -36,7 +36,7 @@ class DNABindingSite(DNA_part):
     assembly : DNAassembly, optional
         The DNA assembly containing this binding site.
     binding_type : str, default='dna_protein'
-        Mechanism subtype for binding reaction parameters.
+        Part type for binding reaction parameters.
     **kwargs
         Additional keyword arguments passed to the parent `DNA_part` class.
 
@@ -258,7 +258,7 @@ class IntegraseSite(DNABindingSite):
         If True, integrase must bind before recombination. If False,
         recombination occurs without explicit binding (simplified model).
     binding_type : str, default='dna_protein'
-        Mechanism subtype for binding reaction parameters.
+        Part type for binding reaction parameters.
     **kwargs
         Additional keyword arguments passed to parent class.
 

biocrnpyler/components/dna/promoter.py

@@ -51,8 +51,6 @@ class Promoter(DNA_part):
     dna_to_bind : DNA or Species, optional
         The DNA species that serves as the transcription template. If None,
         uses the assembly's DNA when available.
-    binding_type : str, default='dna_protein'
-        Mechanism subtype for binding reaction parameters.
     **kwargs
         Additional keyword arguments passed to the parent `DNA_part` class.
 
@@ -109,12 +107,10 @@ def __init__(
         parameters=None,
         protein=None,
         dna_to_bind=None,
-        binding_type='dna_protein',
         **kwargs,
     ):
         self._dna_bind = dna_to_bind
         self.length = length
-        self.binding_type = binding_type
 
         if transcript is None and assembly is None:
             self.transcript = None
@@ -397,6 +393,8 @@ class RegulatedPromoter(Promoter):
         Custom mechanisms for this promoter.
     parameters : dict, optional
         Parameter values specific to this promoter.
+    binding_type : str, default='dna_protein'
+        Part type for binding reaction parameters.
     **kwargs
         Additional keyword arguments passed to parent class.
 
@@ -455,6 +453,7 @@ def __init__(
         length=0,
         mechanisms=None,
         parameters=None,
+        binding_type='dna_protein',
         **kwargs,
     ):
         Promoter.__init__(
@@ -478,6 +477,7 @@ def __init__(
             ]
 
         self.leak = leak
+        self.binding_type = binding_type
 
         self.add_mechanism(One_Step_Cooperative_Binding(), 'binding')
         self.complexes = []
@@ -631,6 +631,8 @@ class ActivatablePromoter(Promoter):
     leak : bool, default=False
         If True, allows basal transcription without activator. If False, no
         transcription occurs without activator binding.
+    binding_type : str, default='dna_protein'
+        Part type for binding reaction parameters.
     **kwargs
         Additional keyword arguments passed to parent `Promoter` class.
 
@@ -669,7 +671,13 @@ class ActivatablePromoter(Promoter):
     """
 
     def __init__(
-        self, name, activator, transcript=None, leak=False, **kwargs
+        self,
+        name,
+        activator,
+        transcript=None,
+        leak=False,
+        binding_type='dna_protein',
+        **kwargs,
     ):
         # Always call the superclass __init__() with **kwargs passed through
         Promoter.__init__(self, name=name, transcript=transcript, **kwargs)
@@ -682,6 +690,7 @@ def __init__(
         self.activator = self.set_species(activator)
 
         self.leak = leak  # toggles whether or not there is a leak reaction
+        self.binding_type = binding_type
 
         # Non-default Mechanisms are added to the Component with
         # .add_mechanism
@@ -777,6 +786,8 @@ class RepressiblePromoter(Promoter):
     leak : bool, default=False
         If True, allows residual transcription even at high repressor
         concentrations. If False, transcription is fully repressed.
+    binding_type : str, default='dna_protein'
+        Part type for binding reaction parameters.
     **kwargs
         Additional keyword arguments passed to parent `Promoter` class.
 
@@ -815,7 +826,13 @@ class RepressiblePromoter(Promoter):
     """
 
     def __init__(
-        self, name, repressor, transcript=None, leak=False, **kwargs
+        self,
+        name,
+        repressor,
+        transcript=None,
+        leak=False,
+        binding_type='dna_protein',
+        **kwargs,
     ):
         # Always call the superclass __init__() with **kwargs passed through
         Promoter.__init__(self, name=name, transcript=transcript, **kwargs)
@@ -828,6 +845,7 @@ def __init__(
         self.repressor = self.set_species(repressor)
 
         self.leak = leak  # toggles whether or not there is a leak reaction
+        self.binding_type = binding_type
 
         # Mechanisms are inherited from the Mixture unless set
         # specifically in self.default_mechanisms.
@@ -946,6 +964,8 @@ class CombinatorialPromoter(Promoter):
         Dictionary mapping regulator names to their cooperativity values
         (Hill coefficients) for binding, e.g., {'regulator1': 2,
         'regulator2': 1}.
+    binding_type : str, default='dna_protein'
+        Part type for binding reaction parameters.
     **kwargs
         Additional keyword arguments passed to parent class.
 
@@ -1024,6 +1044,7 @@ def __init__(
         protein=None,
         tx_capable_list=None,
         cooperativity=None,
+        binding_type='dna_protein',
         **kwargs,
     ):
         Promoter.__init__(
@@ -1079,6 +1100,7 @@ def __init__(
             self.tx_capable_list = [set(a) for a in newlist]
 
         self.leak = leak
+        self.binding_type = binding_type
         self.complex_combinations = {}
         self.tx_capable_complexes = []
         self.leak_complexes = []

biocrnpyler/core/component.py

@@ -690,8 +690,21 @@ def get_parameter(
 
         # Finally, try the mechanism parameter database
         if param is None and self.mechanisms is not None and check_mechanism:
-            if self.mechanisms.get(mechanism, None):
-                param = self.mechanisms[mechanism].get_parameter(
+            if isinstance(mechanism, Mechanism):
+                key = mechanism.mechanism_type
+            else:
+                key = mechanism
+
+            if self.mechanisms.get(key, None):
+                param = self.mechanisms[key].get_parameter(
+                    mechanism, part_id, param_name
+                )
+            elif (
+                self.mixture
+                and self.mixture.mechanisms
+                and self.mixture.mechanisms.get(key, None)
+            ):
+                param = self.mixture.mechanisms[key].get_parameter(
                     mechanism, part_id, param_name
                 )
 

biocrnpyler/core/parameter.py

@@ -54,9 +54,9 @@
 
 from ..utils.units import biocrnpyler_supported_units
 
-# This could later be extended
-ParameterKey = namedtuple('ParameterKey', 'mechanism part_id name')
-"""Named tuple defining a parameter key.
+
+class ParameterKey(namedtuple('ParameterKey', 'mechanism part_id name')):
+    """Named tuple defining a parameter key.
 
     Parameters
     ----------
@@ -69,7 +69,7 @@
         Name of the parameter. Must start with a letter and contain at
         least one character.
 
-"""
+    """
 
 
 class Parameter(object):
@@ -1671,7 +1671,7 @@ def find_parameter(self, mechanism, part_id, param_name):
 
         if not isinstance(part_id, list):
             part_id = [part_id]
-        part_id += [None]
+        part_id = part_id + [None]
         parameter_key_list = []
 
         # Create a parameter key for each part_id

biocrnpyler/mechanisms/binding_parameters.tsv

@@ -21,11 +21,11 @@ binding	chemical_complex	ku	10	uM/sec	90% binding
 binding	dna_protein	kb	0.2	/sec	TODO
 binding	dna_protein	ku	1e-3	uM/sec	TODO
 
-# One step cooperative binding
-cooperative_binding		cooperativity	2		number of binding modules to bind simultaneously
+# Default cooperativity
+binding		cooperativity	2		number of binding modules to bind simultaneously
 
 # Two step cooperative binding (oligimerization)
-cooperative_binding		kb1	1.0	/sec	forward rate constant for oligomerization (TODO)
-cooperative_binding		ku1	0.01	uM/sec	reverse rate constant for oligomerization (TODO)
-cooperative_binding		kb2	1.0	/sec	forward rate constant for oligomer-bindee binding (TODO)
-cooperative_binding		ku2	0.01	uM/sec	reverse rate constant for oligomer-bindee binding (TODO)
+two_step_cooperative_binding		kb1	1.0	/sec	forward rate constant for oligomerization (TODO)
+two_step_cooperative_binding		ku1	0.01	uM/sec	reverse rate constant for oligomerization (TODO)
+two_step_cooperative_binding		kb2	1.0	/sec	forward rate constant for oligomer-bindee binding (TODO)
+two_step_cooperative_binding		ku2	0.01	uM/sec	reverse rate constant for oligomer-bindee binding (TODO)