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Commit 638c7e2c authored by FAGES Timothee's avatar FAGES Timothee
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TIRAMISU/add_and_write_mechanism.py 0 → 100644
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import copy
import re
import os
def recursive_addition(to_add_mech, model1_translated, model2, warning, depth=1e10) :
warn_to_check=set()
new_species=[]
skip=0
for species in to_add_mech :
if species not in model1_translated.reactions[1] :
print(f'ERROR : {species} not in model1')
print(species, to_add_mech)
print(model1_translated.reactions[1])
return('')
if species in model2.spe :
while True and skip !=1 :
conti=input(f'I think the mech {species} is already in model2. Do you want to continue (y/y_all/n)?')
if conti == 'y' or conti == 'Y':
break
if conti == 'y_all' :
skip = 1
break
elif conti == 'n' or conti == 'N' :
return('ERROR : already in model2')
new_species.append([species, model1_translated.spe_model[species]])
new_reactions=[]
n_species=[x for x,y in new_species]
count_depth=0
last_reactions=[]
while (n_species != [] and count_depth < depth) :
print(n_species)
last2_reactions = copy.deepcopy(last_reactions)
last_reactions=[]
count_depth+=1
tmp_n_species=copy.deepcopy(n_species)
n_species = []
if tmp_n_species != [] :
for n_spe in tmp_n_species :
count=0
for reaction in model1_translated.reactions[2] :
if n_spe in reaction.species[0] or n_spe in reaction.species[1] :
if reaction in model2.reactions[2] :
print(reaction.species, "Error ?")
else :
if reaction not in new_reactions :
new_reactions.append(reaction)
else :
len1=len([0 for x in new_reactions[new_reactions.index(reaction)].supinfo if x.strip().startswith('dup')])
len2=len([0 for x in reaction.supinfo if x.strip().startswith('dup')])
if len1 == 0 and len2 != 0 :
print(f'\nERROR LUMPING : {new_reactions[new_reactions.index(reaction)].__dict__} {reaction.__dict__}\n')
new_reactions.remove(reaction)
new_reactions.append(reaction)
last_reactions.append(reaction)
elif len1 != 0 and len2 != 0 :
xor=[rea.speed for rea in new_reactions if rea==reaction]
# print(f'Faux xor : {xor}')
if reaction.speed not in xor :
new_reactions.append(reaction)
last_reactions.append(reaction)
# print(f'Xor : {xor}')
# print(f'{" + ".join(reaction.species[0])} = {" + ".join(reaction.species[1]):30} {reaction.third_body.upper() if reaction.third_body!=0 else ""}')
for side in reaction.species :
for species in side :
if species == "hv" :
print(f'REGARDE ! UN PHOTON ! {reaction.species}')
if species != "hv" and species not in [x for x,y in new_species] \
and species not in model2.spe :
if species in warning :
print(f'WARNING : {species} ENCOUNTERED IN REACTION AND NOT TRADUCTED (!CHECK)')
warn_to_check.add(species)
n_species.append(species)
new_species.append([species, model1_translated.spe_model[species]])
count+=1
else :
break
# list_to_check=[]
# for reaction in last_reactions :
# for species in [*reaction.species[0],reaction.species[1]]
# print(count)
for ind_spe, species in enumerate([x for x,y in new_species].copy()) :
if species in model2.reactions[1] :
print('Already there ....', species)
del new_species[ind_spe]
for reaction in new_reactions :
len1=len([0 for x in reaction.supinfo if x.strip().startswith('dup')])
if len1 != 0 :
len2=len([0 for x in new_reactions if x==reaction])
if len2 == 1 :
print(f'\nA reaction have been duplicated :\n{reaction.__dict__}\n')
new_reactions.append(reaction)
elif len2 < 1 :
print('FATAL ERROR')
print(f'DEPTH = {count_depth}')
print(f'\nNumber of species that can cause issue : {len(warn_to_check)}\n {warn_to_check}')
return(new_reactions, new_species)
def mechanism_writing(outp, md1, md2, model1_translated, model2, to_add, custom='') :
""" MECH """
with open(outp+'.mech', 'w') as out :
""" INTRODUCTION """
out.write(custom)
""" ELEMENTS """
out.write('elements\n'.upper())
elements=set(model1_translated.reactions[0]+model2.reactions[0])
for element in elements :
out.write(f'{element}\n'.upper())
""" SPECIES 2 """
out.write(f'end\n{"!"*80}\n!!!!!{" "*70}!!!!!\n!!!!!{md2+" SPECIES":^70}!!!!!\n!!!!!{" "*70}!!!!!\n{"!"*80}\nspecies\n'.upper())
for species in model2.reactions[1] :
out.write(f'{species}\n'.upper())
""" SPECIES 1 """
out.write(f'{"!"*80}\n!!!!!{" "*70}!!!!!\n!!!!!{md1+" SPECIES":^70}!!!!!\n!!!!!{" "*70}!!!!!\n{"!"*80}\n'.upper())
if to_add != '' :
for species in to_add[1] :
out.write(f'{species}\n'.upper())
""" REACTIONS 2 """
out.write(f'end\n{"!"*80}\n!!!!!{" "*70}!!!!!\n!!!!!{md2+" REACTIONS":^70}!!!!!\n!!!!!{" "*70}!!!!!\n{"!"*80}\nreactions\n'.upper())
for reaction in model2.reactions[2] :
if reaction.is_rev == True :
equal= '='
elif reaction.is_rev == False :
equal= '=>'
else :
print(f'ERROR, NO REV {reaction.__dict__}')
if reaction.third_body != 0 :
tb=f"+{reaction.third_body}"
if reaction.supinfo != [] :
low_check=["low/" for x in reaction.supinfo if 'low/' in x or 'low /' in x]
tcheb_check=["tcheb/" for x in reaction.supinfo if 'tcheb/' in x or 'tcheb /' in x]
if len(low_check) >= 1 or len(tcheb_check) >= 1 :
tb=f"(+{reaction.third_body})"
else :
tb=''
reactant=[]
product=[]
# print(reaction.speed[1])
for s, c in zip(reaction.species[0], reaction.coef[0]) :
if c == 1 :
c=''
elif int(c) == c :
c=int(c)
reactant.append(str(c) + str (s))
for s, c in zip(reaction.species[1], reaction.coef[1]) :
if c == 1 :
c=''
elif int(c) == c :
c=int(c)
product.append(str(c) + str (s))
final_reaction=f'{"+".join(reactant)}{tb if tb!= "" else ""}{equal}{"+".join(product)}{tb if tb!= "" else ""}'
# to_write=f'{final_reaction:48} {reaction.speed[0]}{reaction.speed[1]:<+7.3f}{reaction.speed[2]:+11.3e}'
to_write='{:<48}{:>+12.3e}{:>+9.3f}{:>+11.1f}'.format\
(final_reaction, reaction.speed[0], reaction.speed[1], reaction.speed[2])
if len(to_write)>80 :
print(f'Reaction from base model too big ! :\n{to_write}')
to_write=re.sub(r"\s+", " ", to_write)
print(to_write)
out.write((to_write+'\n').upper())
# print(to_write,len(to_write))
for sup in reaction.supinfo :
out.write(('\t'+sup+'\n').upper())
""" REACTIONS 1 """
out.write(f'{"!"*80}\n!!!!!{" "*70}!!!!!\n!!!!!{md1+" REACTIONS":^70}!!!!!\n!!!!!{" "*70}!!!!!\n{"!"*80}\n'.upper())
if to_add != '' :
for reaction in to_add[0] :
if reaction.is_rev == True :
equal= '='
elif reaction.is_rev == False :
equal= '=>'
else :
print(f'ERROR, NO REV {reaction.__dict__}')
if reaction.third_body != 0 :
tb=f"+{reaction.third_body}"
if reaction.supinfo != [] :
low_check=["low/" for x in reaction.supinfo if 'low/' in x or 'low /' in x]
tcheb_check=["tcheb/" for x in reaction.supinfo if 'tcheb/' in x or 'tcheb /' in x]
if len(low_check) >= 1 or len(tcheb_check) >= 1 :
tb=f"(+{reaction.third_body})"
else :
tb=''
reactant=[]
product=[]
# print(reaction.speed[1])
for s, c in zip(reaction.species[0], reaction.coef[0]) :
if c == 1 :
c=''
elif int(c) == c :
c=int(c)
reactant.append(str(c) + str (s))
for s, c in zip(reaction.species[1], reaction.coef[1]) :
if c == 1 :
c=''
elif int(c) == c :
c=int(c)
product.append(str(c) + str (s))
final_reaction=f'{"+".join(reactant)}{tb if tb!= "" else ""}{equal}{"+".join(product)}{tb if tb!= "" else ""}'
to_write='{:<48}{:>+12.3e}{:>+9.3f}{:>+11.1f}'.format\
(final_reaction, reaction.speed[0], reaction.speed[1], reaction.speed[2])
# to_write=f'{final_reaction:48} {reaction.speed[0]:<+12.3e}{reaction.speed[1]:<+7.3f}{reaction.speed[2]:+11.3e}'
if len(to_write)>80 :
print(f'Reaction from added model too big !\n{to_write}')
to_write=re.sub(r"\s+", " ", to_write)
print(to_write)
out.write((to_write+'\n').upper())
# print(to_write,len(to_write))
for sup in reaction.supinfo :
out.write(('\t'+sup+'\n').upper())
out.write('end'.upper())
""" THERMO """
with open(outp+'.therm', 'w') as out :
""" INTRODUCTION """
out.write(custom)
""" START """
out.write(f'thermo\n{300:>10.3f}{1000:>10.3f}{5000:>10.3f}\n'.upper())
out.write(f'{"!"*80}\n!!!!!{" "*70}!!!!!\n!!!!!{md2+" THERMO":^70}!!!!!\n!!!!!{" "*70}!!!!!\n{"!"*80}\n'.upper())
for species in model2.reactions[1] :
name=model2.therm[species]
ato_comp=name.atomic_composition
string=''
for ato in ato_comp :
string+=ato+' '*(5-len(str(ato_comp[ato]))-len(ato))+str(ato_comp[ato])
#
temp=name.temp_list
out.write(f'{name.species:<16}{" "*8}{string:<20}G{temp[0]:>10.2f}{temp[2]:>10.2f}{temp[1]:>8.2f}{" "*6}1\n'.upper())
for idx,item in enumerate(name.nasa_list) :
if idx in [4,9,13] :
if idx == 4 :
strsup=' 2'
if idx == 9 :
strsup=' 3'
if idx == 13 :
strsup=' '*15+' 4'
out.write(f'{item:>+15.8e}{strsup}\n'.upper())
else :
out.write(f'{item:>+15.8e}'.upper())
out.write(f'{"!"*80}\n!!!!!{" "*70}!!!!!\n!!!!!{md1+" THERMO":^70}!!!!!\n!!!!!{" "*70}!!!!!\n{"!"*80}\n'.upper())
if to_add != '' :
for species in to_add[1] :
name=model1_translated.therm[species]
ato_comp=name.atomic_composition
string=''
for ato in ato_comp :
string+=ato+' '*(5-len(str(ato_comp[ato]))-len(ato))+str(ato_comp[ato])
#
temp=name.temp_list
out.write(f'{name.species:<16}{" "*8}{string:<20}G{temp[0]:>10.2f}{temp[2]:>10.2f}{temp[1]:>8.2f}{" "*6}1\n'.upper())
for idx,item in enumerate(name.nasa_list) :
if idx in [4,9,13] :
if idx == 4 :
strsup=' 2'
if idx == 9 :
strsup=' 3'
if idx == 13 :
strsup=' '*15+' 4'
out.write(f'{item:>+15.8e}{strsup}\n'.upper())
else :
out.write(f'{item:>+15.8e}'.upper())
out.write('end'.upper())
""" TRANSPORT """
with open(outp+'.trans', 'w') as out :
""" INTRODUCTION """
out.write(custom)
""" START """
out.write(f'{"!"*80}\n!!!!!{" "*70}!!!!!\n!!!!!{md2+" TRANSPORT":^70}!!!!!\n!!!!!{" "*70}!!!!!\n{"!"*80}\n'.upper())
for species in model2.reactions[1] :
trans=model2.trans[species]
out.write(f'{trans.species:<20}{trans.geo:>10.0f}{trans.lj_p:>10.3f}{trans.lj_cd:>10.3f}{trans.dp:>10.3f}{trans.p:>10.3f}{trans.rr:>10.3f}\n'.upper())
out.write(f'{"!"*80}\n!!!!!{" "*70}!!!!!\n!!!!!{md1+" THERMO":^70}!!!!!\n!!!!!{" "*70}!!!!!\n{"!"*80}\n'.upper())
if to_add !='' and model1_translated.path_trans != '':
for species in to_add[1] :
trans=model1_translated.trans[species]
out.write(f'{trans.species:<20}{trans.geo:>10.0f}{trans.lj_p:>10.3f}{trans.lj_cd:>10.3f}{trans.dp:>10.3f}{trans.p:>10.3f}{trans.rr:>10.3f}\n'.upper())
else :
if model1_translated.path_trans == '' :
out.write('NOT COMPLETE\nNOT COMPLETE\n')
out.write('end'.upper())
def merging(outp, md_core, md_to_translate, max_len_name, model_core, model_to_translate_translated, order, custom='',flag_extraction=False, to_add=[]) :
#(out+f'_{order}', md_translate, md_core, max_len_name, model_to_translate_translated, model_core, order, custom=introduction, flag_extraction=flag_extraction, to_add=to_add)
def write_species(out, model1, model2, md1, md2, flag_extraction=False, to_add=[]) :
out.write(f'end\nspecies\n'.upper())#'{"!"*80}\n!!!!!{" "*70}!!!!!\n!!!!!{md1+" SPECIES":^70}!!!!!\n!!!!!{" "*70}!!!!!\n{"!"*80}\nspecies\n'.upper())
spe_list=[]
for species in model1.spe :
if species not in spe_list :
spe_list.append(species)
out.write((f'{species:<80}'+f'\t! *:_:* {model1.spe_model[species]} *:_:* \n').upper())
if flag_extraction == True :
# out.write(f'{"!"*80}\n!!!!!{" "*70}!!!!!\n!!!!!{md2+" SPECIES":^70}!!!!!\n!!!!!{" "*70}!!!!!\n{"!"*80}\n'.upper())
for species in to_add[1] :
if species[0] not in spe_list :
spe_list.append(species)
if species[0] not in model1.spe :
out.write((f'{species[0]:<80}'+f'\t! *:_:* {species[1]} *:_:* \n').upper())
elif model2 != '' :
# out.write(f'{"!"*80}\n!!!!!{" "*70}!!!!!\n!!!!!{md2+" SPECIES":^70}!!!!!\n!!!!!{" "*70}!!!!!\n{"!"*80}\n'.upper())
for species in model2.spe :
if species not in spe_list :
spe_list.append(species)
out.write((f'{species:<80}'+f'\t! *:_:* {model2.spe_model[species]} *:_:* \n').upper())
def write_reactions(out, model1, model2, md1, md2, max_len_name, flag_extraction=False, to_add=[]) :
out.write(f'end\nreactions\n'.upper())#{"!"*80}\n!!!!!{" "*70}!!!!!\n!!!!!{md1+" REACTIONS":^70}!!!!!\n!!!!!{" "*70}!!!!!\n{"!"*80}\nreactions\n'.upper())
rea_list=[]
for reaction in model1.rea :
if reaction not in rea_list :
rea_list.append(reaction)
out.write(reaction.print_reaction(path='return', pr=False, max_len_name=max_len_name))
if flag_extraction == True :
# out.write(f'{"!"*80}\n!!!!!{" "*70}!!!!!\n!!!!!{md2+" REACTIONS":^70}!!!!!\n!!!!!{" "*70}!!!!!\n{"!"*80}\n'.upper())
for reaction in to_add[0] :
if reaction not in rea_list :
rea_list.append(reaction)
out.write(reaction.print_reaction(path='return', pr=False, max_len_name=max_len_name))
elif model2 !='' :
# out.write(f'{"!"*80}\n!!!!!{" "*70}!!!!!\n!!!!!{md2+" REACTIONS":^70}!!!!!\n!!!!!{" "*70}!!!!!\n{"!"*80}\n'.upper())
for reaction in model2.rea :
if reaction not in rea_list :
rea_list.append(reaction)
out.write(reaction.print_reaction(path='return', pr=False, max_len_name=max_len_name))
out.write('end'.upper())
def write_therm(out, model1, model2, md1, md2, flag_extraction=False, to_add=[]) :
out.write(f'{"!"*80}\n!!!!!{" "*70}!!!!!\n!!!!!{md1+" THERMO":^70}!!!!!\n!!!!!{" "*70}!!!!!\n{"!"*80}\n'.upper())
spe_list=[]
# print(f'model1 : {model1.path_mech}')
for species in model1.spe :
if species not in spe_list :
# print(species)
spe_list.append(species)
name=model1.therm[species]
ato_comp=name.atomic_composition
string=''
for ato in ato_comp :
string+=ato+' '*(5-len(str(ato_comp[ato]))-len(ato))+str(ato_comp[ato])
temp=name.temp_list
out.write(f'{name.species:<16}{" "*8}{string:<20}G{temp[0]:>10.2f}{temp[2]:>10.2f}{temp[1]:>8.2f}{" "*6}1\n'.upper())
for idx,item in enumerate(name.nasa_list) :
if idx in [4,9,13] :
if idx == 4 :
strsup=' 2'
if idx == 9 :
strsup=' 3'
if idx == 13 :
strsup=' '*15+' 4'
out.write(f'{item:>+15.8e}{strsup}\n'.upper())
else :
out.write(f'{item:>+15.8e}'.upper())
if flag_extraction == True :
out.write(f'{"!"*80}\n!!!!!{" "*70}!!!!!\n!!!!!{md2+" THERMO":^70}!!!!!\n!!!!!{" "*70}!!!!!\n{"!"*80}\n'.upper())
for species in to_add[1] :
if species[0] not in spe_list :
spe_list.append(species[0])
name=model2.therm[species[0]]
ato_comp=name.atomic_composition
string=''
for ato in ato_comp :
string+=ato+' '*(5-len(str(ato_comp[ato]))-len(ato))+str(ato_comp[ato])
temp=name.temp_list
out.write(f'{name.species:<16}{" "*8}{string:<20}G{temp[0]:>10.2f}{temp[2]:>10.2f}{temp[1]:>8.2f}{" "*6}1\n'.upper())
for idx,item in enumerate(name.nasa_list) :
if idx in [4,9,13] :
if idx == 4 :
strsup=' 2'
if idx == 9 :
strsup=' 3'
if idx == 13 :
strsup=' '*15+' 4'
out.write(f'{item:>+15.8e}{strsup}\n'.upper())
else :
out.write(f'{item:>+15.8e}'.upper())
elif model2 !='' :
out.write(f'{"!"*80}\n!!!!!{" "*70}!!!!!\n!!!!!{md2+" THERMO":^70}!!!!!\n!!!!!{" "*70}!!!!!\n{"!"*80}\n'.upper())
for species in model2.spe :
if species not in spe_list :
spe_list.append(species)
name=model2.therm[species]
ato_comp=name.atomic_composition
string=''
for ato in ato_comp :
string+=ato+' '*(5-len(str(ato_comp[ato]))-len(ato))+str(ato_comp[ato])
temp=name.temp_list
out.write(f'{name.species:<16}{" "*8}{string:<20}G{temp[0]:>10.2f}{temp[2]:>10.2f}{temp[1]:>8.2f}{" "*6}1\n'.upper())
for idx,item in enumerate(name.nasa_list) :
if idx in [4,9,13] :
if idx == 4 :
strsup=' 2'
if idx == 9 :
strsup=' 3'
if idx == 13 :
strsup=' '*15+' 4'
out.write(f'{item:>+15.8e}{strsup}\n'.upper())
else :
out.write(f'{item:>+15.8e}'.upper())
out.write('end'.upper())
def write_trans(out, model1, model2, md1, md2, flag_extraction=False, to_add=[]) :
spe_list=[]
out.write(f'{"!"*80}\n!!!!!{" "*70}!!!!!\n!!!!!{md1+" TRANSPORT":^70}!!!!!\n!!!!!{" "*70}!!!!!\n{"!"*80}\n'.upper())
for species in model1.spe :
if species not in spe_list :
spe_list.append(species)
trans=model1.trans[species]
out.write(f'{trans.species:<20}{trans.geo:>10.0f}{trans.lj_p:>10.3f}{trans.lj_cd:>10.3f}{trans.dp:>10.3f}{trans.p:>10.3f}{trans.rr:>10.3f}\n'.upper())
if flag_extraction == True :
out.write(f'{"!"*80}\n!!!!!{" "*70}!!!!!\n!!!!!{md2+" TRANSPORT":^70}!!!!!\n!!!!!{" "*70}!!!!!\n{"!"*80}\n'.upper())
for species in to_add[1] :
if species[0] not in spe_list :
spe_list.append(species[0])
out.write(f'{trans.species:<20}{trans.geo:>10.0f}{trans.lj_p:>10.3f}{trans.lj_cd:>10.3f}{trans.dp:>10.3f}{trans.p:>10.3f}{trans.rr:>10.3f}\n'.upper())
elif model2 !='' :
out.write(f'{"!"*80}\n!!!!!{" "*70}!!!!!\n!!!!!{md2+" TRANSPORT":^70}!!!!!\n!!!!!{" "*70}!!!!!\n{"!"*80}\n'.upper())
for species in model2.spe :
if species not in spe_list :
spe_list.append(species)
trans=model2.trans[species]
out.write(f'{trans.species:<20}{trans.geo:>10.0f}{trans.lj_p:>10.3f}{trans.lj_cd:>10.3f}{trans.dp:>10.3f}{trans.p:>10.3f}{trans.rr:>10.3f}\n'.upper())
out.write('end'.upper())
""" MECH """
with open(outp+'.mech', 'w') as out :
""" INTRODUCTION """
out.write(custom)
""" ELEMENTS """
out.write('elements\n'.upper())
elements=set(model_core.elem+model_to_translate_translated.elem if model_to_translate_translated != '' else model_core.elem)
for element in elements :
out.write(f'{element}\n'.upper())
""" SPECIES """
if 'k' in order :
write_species(out, model_core, model_to_translate_translated, md_core, md_to_translate, flag_extraction, to_add)
write_reactions(out, model_core, model_to_translate_translated, md_core, md_to_translate, max_len_name, flag_extraction, to_add)
else :
write_species(out, model_to_translate_translated, model_core, md_to_translate, md_core, flag_extraction, to_add)
write_reactions(out, model_to_translate_translated, model_core, md_to_translate, md_core, max_len_name, flag_extraction, to_add)
""" THERMO """
with open(outp+'.therm', 'w') as out :
""" INTRODUCTION """
out.write(custom)
out.write('!'+order+'\n')
""" START """
out.write(f'thermo\n{300:>10.3f}{1000:>10.3f}{5000:>10.3f}\n'.upper())
if 't' in order :
write_therm(out, model_core, model_to_translate_translated, md_core, md_to_translate, flag_extraction, to_add)
else :
write_therm(out, model_to_translate_translated, model_core, md_to_translate, md_core, flag_extraction, to_add)
""" TRANSPORT """
if (model_core.path_trans != '' and model_to_translate_translated == '') or (model_core.path_trans != '' and model_to_translate_translated.path_trans != '') :
with open(outp+'.trans', 'w') as out :
""" INTRODUCTION """
out.write(custom)
out.write('!'+order+'\n')
""" START """
if 't' in order :
write_trans(out, model_core, model_to_translate_translated, md_core, md_to_translate, flag_extraction, to_add)
def writing_modified_mechanism(outp, new_md_name, true_model, list_species=[], list_reactions=[], dict_translation={}, verbose=True) :
model=copy.deepcopy(true_model)
# for species in list_species :
# print(f'nb reaction {len(write[1])}')
if list_species != [] :
rea_removed=[]
spe_removed=[]
for spe in copy.deepcopy(model.reactions[1]) :
if spe in list_species :
# print([spe])
spe_removed.append(model.reactions[1].pop(model.reactions[1].index(spe)))
model.therm.pop(spe)
model.trans.pop(spe)
for rea in copy.deepcopy(model.reactions[2]) :
testing=[x for x in [*rea.species[0],*rea.species[1]] if x in list_species]
if len(testing)>0 :
# print(testing)
for index,r in enumerate(model.reactions[2]) :
if r.eq_rea(rea) :
# print('a ',index)
break
# print('b ',index)
rea_removed.append(copy.deepcopy(model.reactions[2][index]))
del model.reactions[2][index]
with open(outp+new_md_name+'_spe&rea_removed.txt', 'w') as s_r :
for spe in spe_removed :
s_r.write(f'{spe}\n')
for rea in rea_removed :
if verbose == True :
rea.print_reaction(outp+new_md_name+'_spe&rea_removed.txt')
print('nb rea removed because of spe :', len(rea_removed))
print('nb spe removed :',len(spe_removed))
if list_reactions != [] :
rea_force_removed=[]
for rea in list_reactions :
for index,r in enumerate(copy.deepcopy(model.reactions[2])) :
if r.eq_rea(rea) :
rea_force_removed.append(copy.deepcopy(model.reactions[2][index]))
del model.reactions[2][index]
break
with open(outp+new_md_name+'_spe&rea_force_removed.txt', 'w') as cl :
pass
for rea in rea_force_removed :
rea.print_reaction(outp+new_md_name+'_spe&rea_force_removed.txt', pr=False)
print('nb rea force removed :', len(rea_force_removed))
if dict_translation != {} :
for spe in copy.deepcopy(model.reactions[1]) :
# print(spe)
if spe in dict_translation :
print('1 :'+spe)
tmp=model.reactions[1].index(spe)
model.reactions[1][tmp] = dict_translation[spe]
print('2 :'+model.reactions[1][tmp])
# for spe in dict_translate :
for index,rea in enumerate(copy.deepcopy(model.reactions[2])) :
for index2, side in enumerate(rea.species) :
for index3, spe in enumerate(side) :
if spe in dict_translation :
print(f'before : {model.reactions[2][index].species}')
model.reactions[2][index].species[index2][index3] = dict_translation[spe]
print(f'after : {model.reactions[2][index].species}')
spe_removed=[]
spe_set=set()
for rea in copy.deepcopy(model.reactions[2]) :
for spe in [*rea.species[0], *rea.species[1]] :
spe_set.add(spe)
for spe in copy.deepcopy(model.reactions[1]) :
if spe not in spe_set and spe not in ['he', 'ar', 'ne']:
print('No reaction for',spe)
spe_removed.append(model.reactions[1].pop(model.reactions[1].index(spe)))
model.therm.pop(spe)
model.trans.pop(spe)
with open(outp+new_md_name+'_norea_spe_removed.txt', 'w') as nr_s :
for spe in spe_removed :
nr_s.write(f'{spe}\n')
merging(outp+new_md_name, 'model', '', max(list(set([len(x.from_model) if x.from_model != '' else len(x.model) for x in model.rea]))),
model, '', 'kt', custom='' ,flag_extraction=False, to_add=[])
# def full_merging(output, prefix_to_del, spe_to_del, model_to_translate) :
# rea_to_del=[]
# for species in (copy.deepcopy(model_to_translate.spe)) :
# for pref in prefix_to_del :
# # print(pref, species)
# if pref in species :
# # print(pref, species)
# spe_to_del.append(model_to_translate.spe[model_to_translate.spe.index(species)])
# # print(len(model1.reactions[1]))
# print('Is spe_to_del well written ?',len(spe_to_del), len(set(spe_to_del)))
# print('Length therm start :',len(model_to_translate.therm))
# print('Length trans start :',len(model_to_translate.trans))
# for species in spe_to_del :
# if species in copy.deepcopy(model_to_translate.therm) :
# del model_to_translate.therm[species]
# for species in spe_to_del :
# if species in copy.deepcopy(model_to_translate.trans) :
# del model_to_translate.trans[species]
# print('Length therm end :',len(model_to_translate.therm))
# print('Length trans end :',len(model_to_translate.trans))
# with open(f'{output}removed_by_prefix.txt','w') as rm :
# for spe in spe_to_del :
# rm.write(f'{spe}\n')
# for species in spe_to_del :
# for reaction in copy.deepcopy(model_to_translate.rea) :
# if species in [*reaction.species[0],*reaction.species[1]] :
# rea_to_del.append(reaction.identifier)
# model_to_translate.spe=[x for x in model_to_translate.spe if x not in spe_to_del]
# batch_rea=[x for x in model_to_translate.rea if x.identifier not in rea_to_del]
# model_to_translate.rea=batch_rea
# return model_to_translate
\ No newline at end of file
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