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TIRAMISU/Main_exe_2.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
+
+
+# =============================================================================
+# ############################# INITIALISATION  ###############################
+# =============================================================================
+
+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] != '!']
+n=10000
+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()
+intro='!'
+task='full'
+task_requested=False
+order_list=['kt']
+order_requested=False
+string_to_del=[]   
+list_to_del=[]  
+
+inp=f'{output}tmp_species_traduction.inp'
+with open(f'{output}{name_translate}.pick', 'rb') as m1 :
+    model_to_translate = pickle.load(m1)
+with open(f'{output}{name_core}.pick', 'rb') as m2 :
+    model_core = pickle.load(m2)
+translation, warning=mt.parse_file(inp)
+translation={key : value for key,value in translation.items() if key != value}
+count=0
+for element in translation :
+    if translation[element] not in model_core.reactions[1] :
+        print(f'{element} {translation[element]} not in species !')
+    else :
+        count+=1
+
+print(f'\nnb of species translated vs nb of translation : {count} {len(translation)}')
+print(f'nb of species/reactions in model_to_translate : {len(model_to_translate.reactions[1])} {len(model_to_translate.reactions[2])}')
+print(f'nb of species/reactions in model_core : {len(model_core.reactions[1])} {len(model_core.reactions[2])}\n')
+
+out= f'{output}new_model_TIRAMISU'
+md_translate=f'{name_translate}'
+md_core=f'{name_core}'
+to_add=[]
+
+depth=''
+
+# =============================================================================
+# ############################### PARAMETERS  #################################
+# =============================================================================
+
+for line in file :
+    if "introduction=" in line.strip()[:13] :
+        intro='!'+str(line.strip()[13:])
+    elif "n=" in line[:2].strip() :
+        n=int(line.strip()[2:])
+    elif "task=" in line.strip()[:5] :
+        task_request=True
+        if 'full' in line.strip()[5:].casefold() :
+            task='full'
+        elif 'extraction' in line.strip()[5:].casefold() :
+            task='extraction'
+        else :
+            raise Exception('Error: unknown merging task requested. Only "extraction" or "full" are accepted.')
+    elif "order=" in line.strip()[:6] :
+        order_requested=True
+        order_list=line.strip()[6:].split(',')
+        order_list=[x.strip().lower() for x in order_list]
+    elif "string_to_del=" in line.strip()[:14] :
+        string_to_del=line.strip()[14:].split(',')
+        string_to_del=[x.strip().lower() for x in string_to_del]
+    elif "list_to_del=" in line.strip()[:12] :
+        list_to_del=line.strip()[12:].split(',')
+        list_to_del=[x.strip().lower() for x in list_to_del]
+       
+# =============================================================================
+# ############################### VALIDATION  #################################
+# =============================================================================
+       
+if order_requested is False :
+    print('No mechanism designed as main ("kt", "k", "t", "n").\nk = model_core main for kinetic data and model_to_translate main for thermo data.\n'+\
+          't = model_to_translate main for kinetic data and core_mechanism main for thermo data.\n'+\
+          'kt = model_core main for kinetic and themo data.\nn = modle_to_translate main for kinetic and thermo data.\n'+\
+          'Default order task is order=kt. You can also specify a list of order to generate multiple mechanism in the form "order=order1, order2, order3, ...".\n'+\
+          '\nORDER FOR EXTRACTION_MERGING IS ALWAYS SET TO "kt" !!!')
+if task_requested is False :
+    print('No merging task requested ("extraction" or "full"). Default merging task is task=full.\n')  
+if string_to_del==[] :
+    print('No string to remove. You can specify to delete species containing a specific string with "string_to_del=chr1, chr2, chr3, ...".\n')
+if list_to_del==[] :
+    print('No species to remove. You can specify to delete specific species "list_to_del=species1, species2, species3, ...".\n')
+
+# =============================================================================
+# ############################### EXTRACTION  #################################
+# =============================================================================
+
+if task == 'extraction' :  
+    depth=1e10
+    depth_requested=False
+    list_to_add=[]
+    order_list=['kt']
+    for line in file :
+        if "depth=" in line.strip()[:6] :
+            depth_requested=True
+            depth=int(line.strip()[6:])
+        elif "mech_to_extract=" in line.strip()[:16] :
+            list_to_add=line.strip()[16:].split(',')
+            list_to_add=[x.strip().lower() for x in list_to_add]
+
+            
+            
+    if depth_requested is False :
+        print('No maximum depth requested ("depth="). Default behavior is that the extracting loop will continue until no new species are found.')  
+    if list_to_add==[] :
+        raise Exception('No species sub-mechanism to extract provided ("mech_to_extract=species1, species2, species3, ...").')
+        
+    print(f'EXTRACTION MERGING\n\nSub-mechanism to extract : {list_to_add}')
+    
+    model_to_translate_translated = mt.translate(model_to_translate, translation)
+    # model_to_translate_translated.spe_model={x : name_translate for x in model_to_translate_translated.spe}
+    time_start = time.time()
+    
+    to_add = awm.recursive_addition(list_to_add, model_to_translate_translated, model_core, warning, depth)
+    
+    print(f'time for recursive_addition : {time.time()-time_start}')
+    
+    if to_add == '' :
+        raise Exception('No species extracted ?!?.')
+    
+    print(f'\n\nLength of to_add : (reactions/species)\n{len(to_add[0])}  {len(to_add[1])}')
+    
+    print('\nCheck Lumping START')
+    
+    for reaction in model_to_translate_translated.rea :
+        if reaction.species[0] == reaction.species[1] : 
+            print(f'UN-LUMPING NEEDED : {reaction.species[0]} = {reaction.species[1]}')
+    print('Check Lumping END\n')
+
+# =============================================================================
+# ################################### FULL ####################################
+# =============================================================================
+
+elif task == 'full' :
+    print('FULL MERGING\n')
+
+    # prefix_to_del=['bb', 'pb', 'c6h5c3', 'c6h5c4', 'cyc']   
+    # list_to_del=['a1c2hac', 'a1c2h3ac', 'a2-x', 'a2o']  
+    
+    model_to_translate_translated = mt.translate(model_to_translate, translation)
+    # model_to_translate_translated.spe_model={x : name_translate for x in model_to_translate_translated.spe}
+
+# =============================================================================
+# ################################# MERGING ###################################
+# =============================================================================
+
+""" New order are 'k', 't', 'kt', 'n' depending on whether the core mechanism retains its kinetics, its thermodynamics, both or neither"""
+
+max_len_name=max(list(set([len(x.from_model) if x.from_model != '' else len(x.model) for x in model_core.rea]+
+                          [len(x.from_model) if x.from_model != '' else len(x.model) for x in model_to_translate_translated.rea])))
+
+for order in order_list :
+    
+    if order == 'kt' :
+        retained = f'kinetics and thermodynamics retained from {md_core}'
+    elif order == 'k' :
+        retained = f'kinetics retained from {md_core}, thermodynamics retained from {md_translate}'
+    elif order == 't' :
+        retained = f'kinetics retained from {md_translate}, thermodynamics retained from {md_core}'
+    elif order == 'n' :
+        retained = f'kinetics and thermodynamics retained from {md_translate}'
+    else :
+        raise Exception("Wrong order. New order are 'k', 't', 'kt', 'n' depending on whether the core mechanism retains its kinetics, its thermodynamics, both or neither")
+    
+    introduction=f'{intro}\n! n={n} '+(f'depth={int(depth)} ' if depth != '' else '') + f'{retained}' + f'\n! {datetime.date.today().strftime("%d/%m/%Y")}\n'
+    flag_extraction=False if to_add==[] else True
+    
+    awm.merging(out+f'_{order}', md_core, md_translate, max_len_name, model_core, model_to_translate_translated, order, custom=introduction, flag_extraction=flag_extraction, to_add=to_add)
+
+
+
+
+    
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