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Fixed protein names for translation factors
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@Ashwin-Srinivasan
Ashwin-Srinivasan committed Jul 13, 2018
1 parent f4cdd0b commit f93c1fb
Showing 1 changed file with 46 additions and 37 deletions.
83 changes: 46 additions & 37 deletions wc_model_gen/rand_gen/translation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -86,41 +86,50 @@ def gen_reactions(self):
trnas.append(rna)
# print(len(trnas))
protsSet = set()
IF1 = random.choice(prots).id
IF1 = random.choice(prots)
IF1.name = 'IF1'
protsSet.add(IF1)
# print('here1')
IF2 = random.choice(prots).id
IF2 = random.choice(prots)
while IF2 in protsSet:
# print('here2')
IF2 = random.choice(prots).id
IF2 = random.choice(prots)
IF2.name = 'IF2'
protsSet.add(IF2)
IF3 = random.choice(prots).id
IF3 = random.choice(prots)
while IF3 in protsSet:
IF3 = random.choice(prots).id
IF3 = random.choice(prots)
IF3.name = 'IF3'
protsSet.add(IF3)
EFtu = random.choice(prots).id
EFtu = random.choice(prots)
while EFtu in protsSet:
EFtu = random.choice(prots).id
EFtu = random.choice(prots)
EFtu.name = "EFtu"
protsSet.add(EFtu)
EFts = random.choice(prots).id
EFts = random.choice(prots)
while EFts in protsSet:
EFts = random.choice(prots).id
EFts = random.choice(prots)
EFts.name = 'EFts'
protsSet.add(EFts)
EFg = random.choice(prots).id
EFg = random.choice(prots)
while EFg in protsSet:
EFg = random.choice(prots).id
EFg = random.choice(prots)
EFg.name = 'EFg'
protsSet.add(EFg)
RF1 = random.choice(prots).id
RF1 = random.choice(prots)
while RF1 in protsSet:
RF1 = random.choice(prots).id
RF1 = random.choice(prots)
RF1.name = 'RF1'
protsSet.add(RF1)
RF2 = random.choice(prots).id
RF2 = random.choice(prots)
while RF2 in protsSet:
RF2 = random.choice(prots).id
RF2 = random.choice(prots)
RF2.name = 'RF2'
protsSet.add(RF2)
RF3 = random.choice(prots).id
RF3 = random.choice(prots)
while RF3 in protsSet:
RF3 = random.choice(prots).id
RF3 = random.choice(prots)
RF3.name = 'RF3'
protsSet.add(RF3)
amino_acids = {}
trna = random.choice(trnas)
Expand Down Expand Up @@ -200,15 +209,15 @@ def gen_reactions(self):
reaction.participants.add(
specie.species_coefficients.get_or_create(coefficient=-1))
specie = self.model.species_types.get_one(
id=IF1).species.get_one(compartment=compartment)
id=IF1.id).species.get_one(compartment=compartment)
reaction.participants.add(
specie.species_coefficients.get_or_create(coefficient=-1))
specie = self.model.species_types.get_one(
id=IF2).species.get_one(compartment=compartment)
id=IF2.id).species.get_one(compartment=compartment)
reaction.participants.add(
specie.species_coefficients.get_or_create(coefficient=-1))
specie = self.model.species_types.get_one(
id=IF3).species.get_one(compartment=compartment)
id=IF3.id).species.get_one(compartment=compartment)
reaction.participants.add(
specie.species_coefficients.get_or_create(coefficient=-1))

Expand All @@ -226,15 +235,15 @@ def gen_reactions(self):
reaction.participants.add(
specie.species_coefficients.get_or_create(coefficient=1))
specie = self.model.species_types.get_one(
id=IF1).species.get_one(compartment=compartment)
id=IF1.id).species.get_one(compartment=compartment)
reaction.participants.add(
specie.species_coefficients.get_or_create(coefficient=1))
specie = self.model.species_types.get_one(
id=IF2).species.get_one(compartment=compartment)
id=IF2.id).species.get_one(compartment=compartment)
reaction.participants.add(
specie.species_coefficients.get_or_create(coefficient=1))
specie = self.model.species_types.get_one(
id=IF3).species.get_one(compartment=compartment)
id=IF3.id).species.get_one(compartment=compartment)
reaction.participants.add(
specie.species_coefficients.get_or_create(coefficient=1))

Expand All @@ -251,15 +260,15 @@ def gen_reactions(self):
reaction.participants.add(
specie.species_coefficients.get_or_create(coefficient=-1))
specie = self.model.species_types.get_one(
id=EFtu).species.get_one(compartment=compartment)
id=EFtu.id).species.get_one(compartment=compartment)
reaction.participants.add(
specie.species_coefficients.get_or_create(coefficient=-n_steps))
specie = self.model.species_types.get_one(
id=EFts).species.get_one(compartment=compartment)
id=EFts.id).species.get_one(compartment=compartment)
reaction.participants.add(
specie.species_coefficients.get_or_create(coefficient=-n_steps))
specie = self.model.species_types.get_one(
id=EFg).species.get_one(compartment=compartment)
id=EFg.id).species.get_one(compartment=compartment)
reaction.participants.add(
specie.species_coefficients.get_or_create(coefficient=-n_steps))
specie = self.model.species_types.get_one(
Expand Down Expand Up @@ -293,15 +302,15 @@ def gen_reactions(self):
reaction.participants.add(
specie.species_coefficients.get_or_create(coefficient=2 * n_steps))
specie = self.model.species_types.get_one(
id=EFtu).species.get_one(compartment=compartment)
id=EFtu.id).species.get_one(compartment=compartment)
reaction.participants.add(
specie.species_coefficients.get_or_create(coefficient=n_steps))
specie = self.model.species_types.get_one(
id=EFts).species.get_one(compartment=compartment)
id=EFts.id).species.get_one(compartment=compartment)
reaction.participants.add(
specie.species_coefficients.get_or_create(coefficient=n_steps))
specie = self.model.species_types.get_one(
id=EFg).species.get_one(compartment=compartment)
id=EFg.id).species.get_one(compartment=compartment)
reaction.participants.add(
specie.species_coefficients.get_or_create(coefficient=n_steps))
specie = self.model.species_types.get_one(
Expand All @@ -321,36 +330,36 @@ def gen_reactions(self):

if stop_codon == 'TAG':
specie = self.model.species_types.get_one(
id=RF1).species.get_one(compartment=compartment)
id=RF1.id).species.get_one(compartment=compartment)
reaction.participants.add(
specie.species_coefficients.get_or_create(coefficient=-1))
specie = self.model.species_types.get_one(
id=RF1).species.get_one(compartment=compartment)
id=RF1.id).species.get_one(compartment=compartment)
reaction.participants.add(
specie.species_coefficients.get_or_create(coefficient=1))
elif stop_codon == 'TGA':
specie = self.model.species_types.get_one(
id=RF2).species.get_one(compartment=compartment)
id=RF2.id).species.get_one(compartment=compartment)
reaction.participants.add(
specie.species_coefficients.get_or_create(coefficient=-1))
specie = self.model.species_types.get_one(
id=RF2).species.get_one(compartment=compartment)
id=RF2.id).species.get_one(compartment=compartment)
reaction.participants.add(
specie.species_coefficients.get_or_create(coefficient=1))
else:
rList = [RF1, RF2]
RF = random.choice(rList)
specie = self.model.species_types.get_one(
id=RF).species.get_one(compartment=compartment)
id=RF.id).species.get_one(compartment=compartment)
reaction.participants.add(
specie.species_coefficients.get_or_create(coefficient=-1))
specie = self.model.species_types.get_one(
id=RF).species.get_one(compartment=compartment)
id=RF.id).species.get_one(compartment=compartment)
reaction.participants.add(
specie.species_coefficients.get_or_create(coefficient=1))

specie = self.model.species_types.get_one(
id=RF3).species.get_one(compartment=compartment)
id=RF3.id).species.get_one(compartment=compartment)
reaction.participants.add(
specie.species_coefficients.get_or_create(coefficient=-1))
specie = self.model.species_types.get_one(
Expand Down Expand Up @@ -380,7 +389,7 @@ def gen_reactions(self):
reaction.participants.add(
specie.species_coefficients.get_or_create(coefficient=1))
specie = self.model.species_types.get_one(
id=RF3).species.get_one(compartment=compartment)
id=RF3.id).species.get_one(compartment=compartment)
reaction.participants.add(
specie.species_coefficients.get_or_create(coefficient=1))
specie = self.model.species_types.get_one(
Expand Down

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