updated parameter processing

Tests/Combinatorial/test_construct_combinatorially.py

@@ -185,6 +185,7 @@ def test_combinatorial_DNAconstruct_in_Mixtures():
         for mclass, args in mixture_classes:
             # create the Mixture with parameters
             args['parameters'] = dict(parameters)
+            args['parameter_file'] = None
             m = mclass(**args)
 
             # Promoters and terminators are instances
@@ -221,6 +222,7 @@ def test_combinatorial_RNAconstruct_in_Mixtures():
         for mclass, args in mixture_classes:
             # create the Mixture with parameters
             args['parameters'] = dict(parameters)
+            args['parameter_file'] = None
             m = mclass(**args)
 
             # RBSs and CDSs are instances
@@ -252,6 +254,7 @@ def test_combinatorial_DNAconstruct_RNAconstruct_in_Mixtures():
         for mclass, args in mixture_classes:
             # create the Mixture with parameters
             args['parameters'] = dict(parameters)
+            args['parameter_file'] = None
             m = mclass(**args)
 
             # Promoters and terminators are instances

Tests/Combinatorial/test_mixtures_and_components_combinatorially.py

@@ -198,8 +198,12 @@ def setUp(self) -> None:
         self.parameters = {
             'kb': 1.0,
             'ku': 1.0,
+            'kb_ntps': 1.0,
+            'ku_ntps': 1.0,
             'ktx': 1.0,
             'ktl': 1.0,
+            'kb_fuel': 1.0,
+            'ku_fuel': 1.0,
             'kdeg': 1.0,
             'kdil': 1.0,
             'kexpress': 1.0,

Tests/Unit/test_compartment.py

@@ -135,7 +135,7 @@ def test_compartment_in_special_mixtures(self):
         )
         E = EnergyTxTlExtract(
             components=[activatable_assembly],
-            parameter_file='examples/Specialized Tutorials/txtl_toolbox_parameters.txt',
+            parameter_file='mixtures/extract_parameters.tsv',
         )
         CRN_1 = E.compile_crn()  # compile CRN
 

Tests/Unit/test_parameter.py

@@ -123,7 +123,7 @@ def test_parameter_entry(self):
                 parameter_value=1.0,
                 parameter_key={'part_id': 'id'},
                 parameter_info={'comment': 'comment', 'unit': 'M'},
-                unit='m',
+                unit='uM',
             )
 
         # Invalid keys
@@ -527,7 +527,7 @@ def test_findpath():
 
     # Make sure that files in package can be found
     assert os.path.exists(
-        bcp.find_file_in_bcp_path('components/tetr_parameters.tsv')
+        bcp.find_file_in_bcp_path('mechanisms/txtl_parameters.tsv')
     )
 
     # Make sure we can find files in current directory
@@ -545,3 +545,151 @@ 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: make sure we can compile with no additional paramters
+    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

Tests/Unit/test_plotting.py

@@ -228,7 +228,8 @@ def test_render_network_bokeh():
         ('rna_degradation_mm', None, 'kdeg'): 0.001,
         (None, None, 'cooperativity'): 2,
     }
-    txtl = bcp.TxTlExtract('mixture1', parameters=parameters)
+    txtl = bcp.TxTlExtract(
+        'mixture1', parameters=parameters, overwrite_parameters=True)
     dna = bcp.DNAassembly(
         'mydna',
         promoter=bcp.RegulatedPromoter('plac', ['laci']),

Tests/Unit/test_units.py

@@ -10,12 +10,15 @@
 
 
 def check(value, message):
-    """If 'value' is None, prints an error message constructed using
-    'message' and then exits with status code 1 (for libsbml). If 'value' is an integer,
+    """Utility function for printing SBML error messages.
+
+    If `value` is None, prints an error message constructed using 'message'
+    and then exits with status code 1 (for libsbml). If 'value' is an integer,
     it assumes it is a libSBML return status code.  If the code value is
     LIBSBML_OPERATION_SUCCESS, returns without further action; if it is not,
     prints an error message constructed using 'message' along with text from
     libSBML explaining the meaning of the code, and exits with status code 1.
+
     """
     if value == None:
         raise SystemExit(
@@ -52,3 +55,56 @@ def test_units_initialization(self):
             'Arguments are not of expected type. unit_id must be a string.',
         ):
             create_new_unit_definition(sbml_model, 24)
+
+
+def test_supported_units():
+    supported_units = biocrnpyler_supported_units()
+    for key in [
+        'nM',
+        'uM',
+        'mM',
+        'M',
+        'nL',
+        'uL',
+        'mL',
+        'L',
+        'sec',
+        'min',
+        'hrs',
+    ]:
+        assert key in supported_units
+
+    for base, aliases in [
+        ('second', ['s', 'sec', 'secs', 'seconds']),
+        ('minute', ['min', 'mins', 'minutes']),
+        ('hour', ['hr', 'hrs', 'hours']),
+    ]:
+        for alias in aliases:
+            assert supported_units[alias] == supported_units[base]
+
+
+def test_unit_conversion_variables():
+    from biocrnpyler.utils.units import (
+        nM,
+        uM,
+        mM,
+        M,
+        nL,
+        uL,
+        mL,
+        L,
+        sec,
+        min,
+        hrs,
+    )
+
+    assert nM == uM * 1e-3
+    assert mM == uM * 1e3
+    assert M == uM * 1e6
+
+    assert nL == uL * 1e-3
+    assert mL == uL * 1e3
+    assert L == uL * 1e6
+
+    assert min == sec * 60
+    assert hrs == min * 60

biocrnpyler/components/basic.py

@@ -512,6 +512,8 @@ class ChemicalComplex(Component):
     attributes : list of str, optional
         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'
+        Part type for binding reaction parameters.
     **kwargs
         Additional keyword arguments passed to the `Component` base class
         constructor.
@@ -574,6 +576,7 @@ def __init__(
         name: str = None,
         material_type='complex',
         attributes=None,
+        binding_type='chemical_complex',
         **kwargs,
     ):
         if not isinstance(species, list) or len(species) < 2:
@@ -582,6 +585,7 @@ def __init__(
                 "Species, strings, or Component objects."
             )
 
+        self.binding_type = binding_type
         self.internal_species = []  # a list of species inside the complex
 
         for s in species:
@@ -659,7 +663,7 @@ def update_reactions(self) -> List[Reaction]:
             bindee,
             complex_species=self.get_species(),
             component=self,
-            part_id=self.name,
+            part_id=[self.name, self.binding_type],
         )
         return reactions