def latex_emit_initial_state(self, f: TextIO):
f.write("\n\n initial state:\n\n\n")
for species_index in range(self.number_of_species):
num = self.initial_state[species_index]
if num > 0:
f.write(str(num) + " molecules of ")
latex_emit_molecule(f, species_index)
f.write("\n\n")
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_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_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)