def generate_categorization_report(sa,
reports_folder,
category_dict,
categories_to_print=[]):
"""
Method to generate categorization report
:param sa: SimulationAnalyzer object
:param reports_folder: path to the save the report to
:param category_dict: dictionary with reaction category as the key and list of reactions as the value
:param categories_to_print: list of reaction types to print, if "[]" all reaction types will be printed
"""
if categories_to_print == []:
categories_to_print = list(category_dict.keys())
with open(
reports_folder + "/categorization.tex",
"w",
) as f:
generate_latex_header(f)
for rxn_type, reactions in category_dict.items():
f.write("\n\n\n")
str_type = str("Reaction Type: " + rxn_type + " count: " +
str(len(reactions))).replace("_", " ")
f.write(str_type)
if rxn_type in categories_to_print:
f.write("\n\n\n")
for reaction_index in reactions:
sa.latex_emit_reaction(f, reaction_index)
generate_latex_footer(f)
def pathfinding_path_report(folder: str, rn: ReactionNetwork, paths):
entries_dict = {}
for entry in rn.entries_list:
entries_dict[entry.parameters["ind"]] = entry
if not os.path.isdir(folder):
os.mkdir(folder)
visualize_molecules(folder + "/molecule_diagrams", entries_dict)
pathways = []
for reaction_path in paths:
pathway = []
cost = reaction_path["cost"]
for node in reaction_path["full_path"]:
if type(node) == str:
dG = rn.graph.nodes[node]["free_energy"]
pathway.append(reaction_string_to_dict(node, dG))
pathways.append((cost, pathway))
with open(folder + "/pathway_report.tex", "w") as f:
generate_latex_header(f)
count = 1
for cost, pathway in pathways:
f.write("pathway " + str(count) + "\n\n")
f.write("pathway cost: " + str(cost) + "\n\n")
for reaction in pathway:
latex_emit_reaction(f, reaction)
f.write("\\newpage\n")
count += 1
generate_latex_footer(f)
def generate_list_of_all_species_report(self):
with open(
self.reports_folder + "/list_of_all_species.tex",
"w",
) as f:
generate_latex_header(f)
for species_index in range(self.number_of_species):
f.write("\n\n\n")
latex_emit_molecule(f, species_index)
generate_latex_footer(f)
def generate_list_of_all_reactions_report(self):
with open(
self.reports_folder + "/list_of_all_reactions.tex",
"w",
) as f:
generate_latex_header(f)
for reaction_index in range(self.number_of_reactions):
f.write("\n\n\n")
self.latex_emit_reaction(f, reaction_index)
generate_latex_footer(f)
def generate_consumption_report(self, mol_entry: MoleculeEntry):
target_species_index = mol_entry.parameters["ind"]
(
producing_reactions,
consuming_reactions,
final_counts,
) = self.extract_species_consumption_info(target_species_index)
histogram_file = (self.reports_folder + "/final_count_histogram_" +
str(target_species_index) + ".pdf")
visualize_molecule_count_histogram(final_counts, histogram_file)
with open(
self.reports_folder + "/consumption_report_" +
str(target_species_index) + ".tex",
"w",
) as f:
generate_latex_header(f)
f.write("consumption report for")
latex_emit_molecule(f, target_species_index)
f.write("\n\n")
f.write("molecule frequency at end of simulations")
f.write("\\raisebox{-.5\\height}{" +
"\\includegraphics[scale=0.5]{" +
"./final_count_histogram_" + str(target_species_index) +
".pdf" + "}}\n\n")
f.write("producing reactions:\n\n\n")
for reaction_index, frequency in sorted(
producing_reactions.items(), key=lambda item: -item[1]):
f.write(str(frequency) + " occurrences:\n")
self.latex_emit_reaction(f, reaction_index)
f.write("consuming reactions:\n\n\n")
for reaction_index, frequency in sorted(
consuming_reactions.items(), key=lambda item: -item[1]):
f.write(str(frequency) + " occurrences:\n")
self.latex_emit_reaction(f, reaction_index)
generate_latex_footer(f)
def generate_simulation_history_report(self, history_num):
with open(
self.reports_folder + "/simulation_history_report_" +
str(history_num) + ".tex",
"w",
) as f:
generate_latex_header(f)
f.write("simulation " + str(history_num))
f.write("\n\n\n")
for reaction_index in self.reaction_histories[history_num]:
f.write("\n\n\n")
self.latex_emit_reaction(f, reaction_index)
generate_latex_footer(f)
def generate_reaction_tally_report(self, cutoff: int):
self.compute_reaction_tally()
with open(self.reports_folder + "/reaction_tally_report.tex",
"w") as f:
generate_latex_header(f)
f.write("reaction tally report")
f.write("\n\n\n")
for (reaction_index,
number) in sorted(self.observed_reactions.items(),
key=lambda pair: -pair[1]):
if number > cutoff:
f.write(str(number) + " occourances of:")
self.latex_emit_reaction(f, reaction_index)
generate_latex_footer(f)
def generate_pathway_report(self, mol_entry: MoleculeEntry,
min_frequency: int):
target_species_index = mol_entry.parameters["ind"]
if target_species_index not in self.reaction_pathways_dict:
self.extract_reaction_pathways(target_species_index)
with open(
self.reports_folder + "/pathway_report_" +
str(target_species_index) + ".tex",
"w",
) as f:
pathways = self.reaction_pathways_dict[target_species_index]
generate_latex_header(f)
f.write("pathway report for\n\n")
latex_emit_molecule(f, target_species_index)
self.latex_emit_initial_state(f)
f.write("\\newpage\n\n\n")
for _, unique_pathway in sorted(
pathways.items(), key=lambda item: -item[1]["frequency"]):
frequency = unique_pathway["frequency"]
if frequency > min_frequency:
f.write(str(frequency) + " occurrences:\n")
for reaction_index in unique_pathway["pathway"]:
self.latex_emit_reaction(f, reaction_index)
f.write("\\newpage\n")
else:
break
generate_latex_footer(f)
def generate_pathway_report(self,
mol_entry: MoleculeEntry,
number_of_pathways=100,
sort_by_frequency=True):
target_species_index = mol_entry.parameters["ind"]
if target_species_index not in self.reaction_pathways_dict:
self.extract_reaction_pathways(target_species_index)
if sort_by_frequency:
suffix = "frequency"
else:
suffix = "cost"
with open(
self.reports_folder + "/pathway_report_" +
str(target_species_index) + "_" + suffix + ".tex",
"w",
) as f:
pathways = self.reaction_pathways_dict[target_species_index]
generate_latex_header(f)
f.write("pathway report for\n\n")
latex_emit_molecule(f, target_species_index)
if sort_by_frequency:
f.write("\n\ntop " + str(number_of_pathways) +
" pathways sorted by frequency")
else:
f.write("\n\ntop " + str(number_of_pathways) +
" pathways sorted by cost")
f.write("\\vspace{1cm}")
self.latex_emit_initial_state(f)
f.write("\\newpage\n\n\n")
if sort_by_frequency:
def sort_function(item):
return -item[1]["frequency"]
else:
def sort_function(item):
return item[1]["weight"]
count = 1
for _, unique_pathway in sorted(pathways.items(),
key=sort_function):
frequency = unique_pathway["frequency"]
weight = unique_pathway["weight"]
f.write("pathway " + str(count) + "\n\n")
f.write("path weight: " + str(weight) + "\n\n")
f.write(str(frequency) + " occurrences:\n")
for reaction_index in unique_pathway["pathway"]:
self.latex_emit_reaction(f, reaction_index)
f.write("\\newpage\n")
count += 1
if count > number_of_pathways:
break
generate_latex_footer(f)