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TIRAMISU/Main_exe_1.py

+import time
+import datetime
+import pickle 
+import sys
+import os
+sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), '..')))
+from TIRAMISU import read_model_new as rm
+from TIRAMISU import make_translation as mt
+from TIRAMISU import add_and_write_mechanism as awm
+with open(sys.argv[1], 'r') as file_input :
+    file = file_input.readlines()
+# with open("0.txt", 'r') as file_input :
+#     file = file_input.readlines()
+file=[x for x in file if x.strip()[0] != '!']
+core_path=file[0].strip()
+translate_path=file[1].strip()
+name_core=os.path.basename(core_path)
+name_translate=os.path.basename(translate_path)
+output=file[2].strip()
+n=10000
+n_find=False
+do_translation=True
+translation_find=False
+for line in file :
+    if "n=" in line[:2].strip() :
+        n_find=True
+        n=int(line.strip()[2:])
+    if "translation=" in line.strip()[:12] :
+        translation_find=True
+        tmp_bool=(line.strip()[12:]).casefold()
+        if 'true' in tmp_bool :
+            do_translation=True
+        elif 'false'in tmp_bool :
+            do_translation=False
+        else :
+            raise Exception('Error: translation keyword not True nor False.')
+        
+if n_find is False :
+    print('No maximum number of permutation specified (n=). Default is n=10000.')
+if translation_find is False :
+    print('No boolean for translation (translation=True or False). Default is translation=True.')
+print(f'\ntranslation={do_translation}')
+
+
+path_mech_core=f'{core_path}.mech'
+path_therm_core=f'{core_path}.therm'
+path_trans_core=f'{core_path}.trans'
+
+path_mech_to_translate=f'{translate_path}.mech'
+path_therm_to_translate=f'{translate_path}.therm'
+path_trans_to_translate=f'{translate_path}.trans'
+
+time_start = time.time()
+
+model_to_translate=rm.Model(path_mech_to_translate, path_therm_to_translate, output, path_trans_to_translate,verbose=False)
+model_core=rm.Model(path_mech_core, path_therm_core, output, path_trans_core, verbose=False)
+
+time_end = time.time()
+
+print(f'\nTotal time for model compilation = {time_end-time_start} seconds or {datetime.timedelta(seconds=(time_end-time_start))} ')
+print( f'\nmodel_to_translate Species = {len(model_to_translate.reactions[1])} Reactions = {len(model_to_translate.reactions[2])}')
+print( f'\nmodel_core Species = {len(model_core.reactions[1])} Reactions = {len(model_core.reactions[2])}')
+
+with open(f'{output}{name_translate}.pick', 'wb') as m1 :
+    pickle.dump( model_to_translate, m1)
+with open(f'{output}{name_core}.pick', 'wb') as m2 :
+    pickle.dump(model_core, m2)
+
+if do_translation is True :
+    time_start = time.time()
+    stock=mt.models_translation(model_to_translate,  model_core, output, 350, n)
+    time_end=time.time()
+    print(f'\nTotal time = {time_end-time_start} seconds or {datetime.timedelta(seconds=(time_end-time_start))} ')
+    
+print('\n\nOpen and complete translation in "tmp_species_traduction.tmp". Then change name to "tmp_species_traduction.inp".\nEND OF PART 1')
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