Merge pull request #13 from zoltuz/master

adding some reporting

examples/geneexpr_3tube.py

@@ -18,8 +18,8 @@
 tube3 = txtl.newtube('geneexpr')
 
 # Define a DNA strand using strings (ala MATLAB)
-gene1 = txtl.assemble_dna('ptet(50)', 'BCD2(20)', 'tetR(1200)')
-txtl.add_dna(tube3, gene1, 1, 'plasmid')
+gene1 = txtl.assemble_dna(prom='ptet(50)', utr5='BCD2(20)', cds='tetR(1200)')
+txtl.add_dna(mixture=tube3, dna=gene1, conc=1, type='plasmid')
 
 #
 # Assemble a DNA strand using objects (semi-pythonic)
@@ -51,3 +51,6 @@
 
 # Create an SBML file containing the model
 txtl.write_sbml(well1, 'geneexpr.xml')
+
+# print out a basic report about the content of the well
+well1.print_report()

txtl/dna.py

@@ -140,6 +140,9 @@ def update_reactions(self, mixture, debug=False):
         for dna in [self.promoter, self.utr5, self.cds, self.ctag, self.utr3]:
             if dna != None:
                 dna.update_reactions(mixture)
+
+    def __str__(self):
+        return 'DNA Assembly: ' + self.name
 
 #
 # DNA component
@@ -212,6 +215,9 @@ def update_species(self, mixture, conc):
     def update_reactions(self, mixture):
         return None
 
+    def __str__(self):
+        return self.name
+
 #
 # Promoter subclasses
 #
@@ -251,6 +257,9 @@ def __init__(
         # Fill in any missing parameter values with defaults
         update_missing(self.parameters, Promoter.default_parameters)
 
+    def __str__(self):
+        return self.prefix + self.name
+
     def update_species(self, mixture, conc, parameters={}):
         assy = self.assy        # Get the DNA assembly we are part of
 

txtl/extract.py

@@ -35,7 +35,7 @@ def __init__(self, name, parameters={}):
         self.parameters = get_parameters(self.config_file, parameters)
 
 class StandardExtract(Extract):
-    mechanisms = {
+    default_mechanisms = {
         'transcription'         : transcription.basic(),
         'translation'           : translation.basic(),
         'DNA_degradation'       : degradation.dna_basic(),
@@ -125,6 +125,8 @@ def update_reactions(self, mixture):
         #! TODO: add reactions that are instantiated by extract
         # mechanism['RNA_degradation'].update_reactions(mixture, mechanisms)
         None
+    def __str__(self):
+        return "StandardExtract with %d mechanisms" % len(self.default_mechanisms)
 
 # Create a mixture containing extract
 def create_extract(name, type=StandardExtract, mechanisms={}):
@@ -150,7 +152,7 @@ def create_extract(name, type=StandardExtract, mechanisms={}):
     mixture.concentrations = [10.0/(10.0/3.0)]
 
     # Store default mechanisms and custom mechanisms
-    mixture.default_mechanisms = extract.mechanisms
+    mixture.default_mechanisms = extract.default_mechanisms
     mixture.custom_mechanisms = mechanisms
 
     # Store the parameters in the mixture so that components can access them

txtl/mechanism.py

@@ -35,10 +35,15 @@ class Mechanism:
     derived from this class.
 
     """
-    def __init__(self): return None
+    def __init__(self,name=''):
+        self.name = name
+
     def update_species(self, mixture, component, conc): return None
     def update_reactions(self, mixture, component): return None
 
+    def __str__(self):
+        return self.name
+
 # Utility function to retrieve mechanism list
 def get_mechanisms(mixture, component, custom={}):
     mechanisms = {}                                 # initalize mechanism

txtl/mechanisms/degradation.py

@@ -12,17 +12,25 @@
 
 class dna_basic(Mechanism):
     "Basic DNA degradation"
+    def __init__(self):
+        self.name = 'Basic DNA degradation'
+
     #! TODO: not implemented
 
 class rna_basic(Mechanism):
     "Basic RNA degradation"
+    def __init__(self):
+        self.name = 'Basic RNA degradation'
+
     def update_reactions(self, mixture, assy):
         parameters = mixture.parameters         # get parameter values
         add_reaction(mixture, [assy.rna], [], kf=parameters['RNA_deg'],
                      prefix="degradation_rna_basic_")
 
 class protein_basic(Mechanism):
     "Basic protein degradation"
+    def __init__(self):
+        self.name = 'Basic protein degradation'
     #! TODO: not implemented
 
 

txtl/mechanisms/maturation.py

@@ -12,6 +12,9 @@
 
 class protein_basic(Mechanism):
     "Basic protein maturation"
+    def __init__(self):
+        self.name = 'Basic protein maturation'
+
     def update_reactions(self, mixture, assy, debug=False):
         #! TODO: See if this protein is subject to maturation
         #! TODO: Create maturation reaction

txtl/mechanisms/transcription.py

@@ -14,6 +14,10 @@
 # Convert DNA to RNA
 class basic(Mechanism):
     "Basic transcription mechanism"
+
+    def __init__(self):
+        self.name = 'Basic Transcription'
+
     def update_reactions(self, mixture, assy, debug=False):
         parameters = assy.promoter.parameters   # get parameter values
 

txtl/mechanisms/translation.py

@@ -13,6 +13,9 @@
 
 class basic(Mechanism):
     "Basic translation mechanism"
+    def __init__(self):
+        self.name = 'Basic Translation'
+
     def update_reactions(self, mixture, assy, debug=False):
         parameters = assy.utr5.parameters       # get parameter values
 

txtl/mixture.py

@@ -63,7 +63,7 @@ def __init__(self, name=None, mechanisms={}, config_file=None):
         document, model, compartment = create_sbml_model()
 
         # Initialize instance variables
-        self.name = name;               # Save the name of the mixture
+        self.name = name                # Save the name of the mixture
         self._SBMLdoc = document        # SBML document container
         self.model = model              # SBML model object
         self.compartment = compartment  # SBML compartment
@@ -82,28 +82,43 @@ def __init__(self, name=None, mechanisms={}, config_file=None):
         if (config_file != None):
             self.parameters.update(load_config(config_file))
 
-    def write_sbml(self, filename):
-        "Generate an SBML file for the current mixture (model)"
-
+    def _update_sbml_model(self):
+        """Updating the internal SBML representation"""
         # Update all species in the mixture to make sure everything exists
-        for i in range(len(self.components)):
-            concentration = self.concentrations[i]
-            component = self.components[i]
-
+        assert (len(self.concentrations) == len(self.components))
+        for component, concentration in zip(self.components, self.concentrations):
             # Create all (global) parameters for this component
-            #! TODO: need to document this better; see extract.py
+            # ! TODO: need to document this better; see extract.py
             component.update_parameters(self)
 
             # Create all of the species for this component
             component.update_species(self, concentration)
 
+
+
         # Now go through and add all of the reactions that are required
         for component in self.components:
             component.update_reactions(self)
 
+    def print_report(self):
+        self._update_sbml_model()
+        # Now go through and add all of the reactions that are required
+        for component in self.components:
+            print(component)
+            for mechanism_name, mechanism_implementation in component.default_mechanisms.items():
+                print('\t' + mechanism_name + ": " + str(mechanism_implementation))
+
+    def write_sbml(self, filename):
+        "Generate an SBML file for the current mixture (model)"
+        self._update_sbml_model()
+
         # Write the model to a file
         libsbml.writeSBMLToFile(self._SBMLdoc, filename)
 
+    def __str__(self):
+        """Returning the name of the mixture"""
+        return self.name
+
 #
 # Functions for interacting with mixtures
 #
@@ -132,34 +147,37 @@ def add_dna(mixture, dna, conc, type=None):
 # Combine the components of two more more mixtures
 def combine_mixtures(mixtures, volumes=None, name=None):
     # Create a name if we were sent done
-    #! TODO: concatenate names of mixtures
 
     # Create a mixture for the results
+    if name is None:
+        name = 'Mix_of'
+
     outmixture = Mixture(name)
 
     # Keep track of the total amount of mixture we are creating (for scaling)
     # If no volumes are given, assume equal volumes of 1 unit each
-    total_volume = sum(volumes) if volumes != None else len(mixtures)
+    total_volume = sum(volumes) if volumes is not None else len(mixtures)
 
     # Add the components (and concentrations) of inputs to the output
-    for i in range(len(mixtures)):
+    for i, mixture in enumerate(mixtures):
         # Combine the mechanisms
         #! TODO: issue a warning if there are conflicting mechanisms
-        outmixture.default_mechanisms.update(mixtures[i].default_mechanisms)
-        outmixture.custom_mechanisms.update(mixtures[i].custom_mechanisms)
-
+        outmixture.default_mechanisms.update(mixture.default_mechanisms)
+        outmixture.custom_mechanisms.update(mixture.custom_mechanisms)
+        outmixture.name += '_' + str(mixture) # getting the name of a mixture
         # Components of new mixture are concatenation of mixture components
-        outmixture.components += mixtures[i].components
+        outmixture.components += mixture.components
 
         # Concentrations are scaled by the volume
-        scale = volume[i]/total_volume if volumes != None else 1/total_volume
-        for j in range(len(mixtures[i].concentrations)):
-            outmixture.concentrations += [mixtures[i].concentrations[j] * scale]
+        scale = volumes[i]/total_volume if volumes is not None else 1/total_volume
+        for concentration in mixture.concentrations:
+            outmixture.concentrations += [concentration * scale]
 
         # Combine parameter dictionaries from each mixture
         #! TODO: issue a warning if there are conflicting parameters
         outmixture.parameters.update(mixtures[i].parameters)
 
+    assert len(outmixture.concentrations) == len(outmixture.components)
     return outmixture
 
 # Write out the SBML description of the contexts of a mixture

txtl/sbmlutil.py

@@ -48,18 +48,17 @@ def add_species(mixture, type, name, ic=None, debug=False):
     model = mixture.model   # Get the model where we will store results
 
     # Construct the species name
-    prefix = type + " " if type != None else ""
+    prefix = type + " " if type is not None else ""
     species_name = prefix + name
 
     # Construct the species ID
     species_id = _id_from_name(species_name)
 
     # Check to see if this species is already present
     species = find_species(model, species_id)
-    if species == None:
+    if species is None:
         if debug: print("Adding species %s" % species_name)
         species = model.createSpecies()
-        prefix = type + " " if type != None else ""
         species.setName(species_name)
         species.setId(species_id)
         species.setCompartment(mixture.compartment.getId())
@@ -89,13 +88,13 @@ def find_species(mixture, species_name):
     #! TODO: Add error checking
     return model.getSpecies(species_id)
 
-# Helper function to add a pameter to the model
+# Helper function to add a parameter to the model
 def add_parameter(mixture, name, value=0, debug=False):
     model = mixture.model   # Get the model where we will store results
 
     # Check to see if this parameter is already present
     parameter = find_parameter(mixture, name)   #! TODO: add error checking
-    if parameter == None:
+    if parameter is None:
         if debug: print("Adding parameter %s" % name)
         parameter = model.createParameter()
         parameter.setId(name)                   #! TODO: add error checking
@@ -218,11 +217,11 @@ def add_reaction(mixture, reactants, products, kf, kr=None, id=None,
         param.setValue(float(kf))
     ratelaw.setFormula(ratestring);
 
-    # If the reverse rate is given, switch things around create reverse raaction
-    if (kr != None):
+    # If the reverse rate is given, switch things around create reverse reaction
+    if kr is not None:
         revreaction = add_reaction(mixture, products, reactants, kr, None,
                                    prefix=prefix)
-        return (reaction, revreaction)
+        return reaction, revreaction
 
     return reaction