/
exp_cost_model.py
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/
exp_cost_model.py
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#! /usr/bin/env python3
# I, Robert Rozanski, the copyright holder of this work, release this work into the public domain. This applies worldwide. In some countries this may not be legally possible; if so: I grant anyone the right to use this work for any purpose, without any conditions, unless such conditions are required by law.
from exp_repr import DetectionEntity, AdamTwoFactorExperiment, ReconstructionActivity, ReconstructionEnzReaction, ReconstructionTransporterRequired
from exp_repr import LocalisationEntity
from exp_repr import DetectionActivity
from mnm_repr import CellMembrane, CellMembraneOuterSide, CellMembraneInnerSide, Cytosol, Mitochondrium, MitochMatrix, MitochOuterMembrane, MitochOuterMembraneOuterSide, MitochOuterMembraneInnerSide, MitochInnerMembrane, MitochInnerMembraneOuterSide, MitochInnerMembraneInnerSide, GolgiMembrane, GolgiMembraneOuterSide, GolgiMembraneInnerSide, GolgiApparatus, Nucleus, NuclearMembrane, NuclearMembraneOuterSide, NuclearMembraneInnerSide, EndoplasmicReticulum, ERMembrane, ERMembraneOuterSide, ERMembraneInnerSide, Vacuole, VacuolarMembrane, VacuolarMembraneMediumSide, VacuolarMembraneCytosolSide, VacuolarMembraneInnerSide, PeroxisomalMembrane, PeroxisomalMembraneInnerSide, PeroxisomalMembraneOuterSide, Peroxisome, Medium
import mnm_repr
class CostModel:
def __init__(self, entities, compartments, activities, setup_conds, import_activities=[]):
self.generate_all_possible(entities, compartments, activities, setup_conds, import_activities)
def generate_all_possible(self, entities, compartments, activities, setup_conds, import_activities):
# exp types:
self.types = {AdamTwoFactorExperiment:None}# DetectionEntity:None, AdamTwoFactorExperiment:None,
# ReconstructionActivity:None, ReconstructionEnzReaction:None,
# ReconstructionTransporterRequired:None, LocalisationEntity:None,
# DetectionActivity:None
# compartments for checking localisation:
self.design_compartment = {'c_02':None, 'c_03':None, 'c_04':None, 'c_05':None,
'c_06':None, 'c_07':None, 'c_08':None, 'c_09':None, 'c_10':None, 'c_11':None,
'c_12':None, 'c_13':None, 'c_14':None, 'c_15':None, 'c_16':None, 'c_17':None,
'c_18':None, 'c_19':None, 'c_20':None, 'c_21':None, 'c_22':None, 'c_23':None,
'c_24':None, 'c_25':None, 'c_26':None, 'c_27':None, 'c_28':None, 'c_29':None,
'c_30':None, 'c_31':None, 'c_32':None, 'c_33':None, 'c_34':None}
# rest of elements:
self.design_deletable = {}
self.design_available = {}
self.design_activity_rec = {}
self.design_activity_det = {}
self.design_entity_loc = {}
self.design_entity_det = {}
self.intervention_add = {}
self.intervention_remove = {}
#
for act in import_activities:
self.intervention_add[mnm_repr.Add(act)] = 1
#
for st in setup_conds:
if (isinstance(st.entity, mnm_repr.Gene) or isinstance(st.compartment, Medium)): # all genes can be removed; metabs can only be removed from medium
self.intervention_remove[mnm_repr.Remove(st)] = None
if isinstance(st.entity, mnm_repr.Gene):
self.design_deletable[st.entity] = None
#
for ent in entities:
if isinstance(ent, mnm_repr.Gene):
continue
else: # Met, Prot, Cplx
self.design_available[ent] = None
self.design_entity_det[ent] = None
if isinstance(ent, mnm_repr.Metabolite):
self.intervention_add[mnm_repr.Add(mnm_repr.PresentEntity(ent, Medium()))] = None
else: # Prot, Cplx
self.design_entity_loc[ent] = None
#
for act in activities:
if act in import_activities:# don't test these additional import reactions: they're only to help with experiments
continue
elif isinstance(act, mnm_repr.Growth):
self.design_activity_det[act] = None
else:
self.design_activity_rec[act] = None
# def apply_basic_costs_<distribution>_<to_what>(self):
def remove_None_valued_elements(self):
for key in list(self.types.keys()):
if self.types[key] == None:
del self.types[key]
else:
pass
for key in list(self.design_compartment.keys()):
if self.design_compartment[key] == None:
del self.design_compartment[key]
else:
pass
for key in list(self.design_deletable.keys()):
if self.design_deletable[key] == None:
del self.design_deletable[key]
else:
pass
for key in list(self.design_available.keys()):
if self.design_available[key] == None:
del self.design_available[key]
else:
pass
for key in list(self.design_activity_det.keys()):
if self.design_activity_det[key] == None:
del self.design_activity_det[key]
else:
pass
for key in list(self.design_entity_loc.keys()):
if self.design_entity_loc[key] == None:
del self.design_entity_loc[key]
else:
pass
for key in list(self.design_entity_det.keys()):
if self.design_entity_det[key] == None:
del self.design_entity_det[key]
else:
pass
for key in list(self.intervention_add.keys()):
if self.intervention_add[key] == None:
del self.intervention_add[key]
else:
pass
for key in list(self.intervention_remove.keys()):
if self.intervention_remove[key] == None:
del self.intervention_remove[key]
else:
pass
for key in list(self.design_activity_rec.keys()):
if self.design_activity_rec[key] == None:
del self.design_activity_rec[key]
else:
pass
def calculate_derived_costs(self, activities):
# calculating costs for complexes
for ent in self.design_available: # loops through entities
if isinstance(ent, mnm_repr.Complex): # costs for complexes are derived from costs for their components
cplx_form = [a for a in activities if a.check_if_is_product(ent)] # find correcponding complex form. reactions
# costs for complexes can only be calculated if there is exactly 1 formation reaction
if len(cplx_form) == 1:
components = cplx_form[0].return_substrates()
# if all components have 'available' costs, then calculate cost for 'available' complex
costs_available = [self.design_available[comp] for comp in components]
if not (None in costs_available):
self.design_available[ent] = sum(costs_available)
else:
pass
# the same for 'detection' costs
costs_det = [self.design_entity_det[comp] for comp in components]
if not (None in costs_det):
self.design_entity_det[ent] = sum(costs_available)
else:
pass
# the same for 'localisation' costs
costs_loc = [self.design_entity_loc[comp] for comp in components]
if not (None in costs_loc):
self.design_entity_loc[ent] = sum(costs_available)
else:
pass
else:
pass
else:
pass
# calculating costs for activities: enzymes and transporters not included here; accounted for in design rules.
for act in self.design_activity_rec.keys():
if isinstance(act, mnm_repr.Growth) or isinstance(act, mnm_repr.Expression):
continue
else:
substrates_available_costs = [self.design_available[ent] for ent in act.return_substrates()]
try:
products_detection_costs = [self.design_entity_det[ent] for ent in act.return_products()]
except KeyError as err:
print('all act products: %s' % [(ent.ID, ent.version) for ent in act.return_products()])
print('dict: %s' % [(ent.ID, ent.version) for ent in self.design_entity_det])
if (None in substrates_available_costs):
continue
elif (None in products_detection_costs):
continue
else:
self.design_activity_rec[act] = sum(substrates_available_costs) + sum(products_detection_costs)
def set_all_basic_costs_to_1(self): # for testing
for key in self.types.keys():
self.types[key] = 1
for key in self.design_compartment.keys():
self.design_compartment[key] = 1
for key in self.design_deletable.keys():
self.design_deletable[key] = 1
for key in self.design_available.keys():
if isinstance(key, mnm_repr.Complex):
continue
else:
self.design_available[key] = 1
for key in self.design_activity_det.keys():
self.design_activity_det[key] = 1
for key in self.design_entity_loc.keys():
if isinstance(key, mnm_repr.Complex):
continue
else:
self.design_entity_loc[key] = 1
for key in self.design_entity_det.keys():
if isinstance(key, mnm_repr.Complex):
continue
else:
self.design_entity_det[key] = 1
for key in self.intervention_add.keys():
if self.intervention_add[key] != 0:# additional import activities should have 0... maybe :d
self.intervention_add[key] = 1
for key in self.intervention_remove.keys():
self.intervention_remove[key] = 1