Getting and setting reaction parameters and reactions
[1]:
import sys
sys.path.append('../..')
%matplotlib inline
[2]:
from basico import *
Load model
[3]:
biomod = load_example("LM-test1")
Getting/setting global quantities
It is possible to set:
'initial_value'
'initial_expression'
'expression'
'status'
'type'
[4]:
get_parameters()
[4]:
type | unit | initial_value | initial_expression | expression | value | rate | key | |
---|---|---|---|---|---|---|---|---|
name | ||||||||
epsilon | fixed | 0.78 | NaN | 0.0 | ModelValue_0 | |||
offset | fixed | 0.10 | NaN | 0.0 | ModelValue_1 | |||
signal | assignment | 0.10 | [P] * Values[epsilon] + Values[offset] | NaN | NaN | ModelValue_2 |
[5]:
set_parameters(name= 'offset', initial_value = 50)
[6]:
set_parameters('signal', expression='[P] * Values[epsilon] + Values[offset]')
[7]:
get_parameters()
[7]:
type | unit | initial_value | initial_expression | expression | value | rate | key | |
---|---|---|---|---|---|---|---|---|
name | ||||||||
epsilon | fixed | 0.78 | NaN | 0.0 | ModelValue_0 | |||
offset | fixed | 50.00 | NaN | 0.0 | ModelValue_1 | |||
signal | assignment | 50.00 | [P] * Values[epsilon] + Values[offset] | NaN | NaN | ModelValue_2 |
Getting/setting species (metabolites)
[8]:
get_species()
[8]:
compartment | type | unit | initial_concentration | initial_particle_number | initial_expression | expression | concentration | particle_number | rate | particle_number_rate | key | |
---|---|---|---|---|---|---|---|---|---|---|---|---|
name | ||||||||||||
E | compartment | reactions | mmol/ml | 0.010000 | 6.022142e+18 | NaN | NaN | NaN | NaN | Metabolite_1 | ||
S | compartment | reactions | mmol/ml | 10.000001 | 6.022142e+21 | NaN | NaN | NaN | NaN | Metabolite_0 | ||
ES | compartment | reactions | mmol/ml | 0.000000 | 0.000000e+00 | NaN | NaN | NaN | NaN | Metabolite_2 | ||
P | compartment | reactions | mmol/ml | 0.000000 | 0.000000e+00 | NaN | NaN | NaN | NaN | Metabolite_3 |
[9]:
get_species(name = 'E')['initial_concentration']
[9]:
name
E 0.01
ES 0.00
Name: initial_concentration, dtype: float64
Setting
if 'name' in kwargs:
metab.setObjectName(kwargs['name'])
if 'unit' in kwargs:
metab.setUnitExpression(kwargs['unit'])
if 'initial_concentration' in kwargs:
metab.setInitialConcentration(kwargs['initial_concentration']),
if 'initial_particle_number' in kwargs:
metab.setInitialValue(kwargs['initial_particle_number']),
if 'initial_expression' in kwargs:
metab.setInitialExpression(kwargs['initial_expression'])
if 'expression' in kwargs:
metab.setExpression(kwargs['expression'])
[10]:
set_species(name = 'E', new_name = 'Lilija')
[11]:
set_species(name = 'Lilija', initial_concentration = 123456)
[12]:
get_species(name = 'Lilija')
[12]:
compartment | type | unit | initial_concentration | initial_particle_number | initial_expression | expression | concentration | particle_number | rate | particle_number_rate | key | |
---|---|---|---|---|---|---|---|---|---|---|---|---|
name | ||||||||||||
Lilija | compartment | reactions | mmol/ml | 123456.0 | 7.434694e+25 | NaN | NaN | NaN | NaN | Metabolite_1 |
[13]:
# change it back
set_species(new_name = 'E', name = 'Lilija')
Getting/setting reaction parameters
[14]:
get_reaction_parameters()
[14]:
value | reaction | type | mapped_to | |
---|---|---|---|---|
name | ||||
(R1).k1 | 130.0 | R1 | local | |
(R1).k2 | 1.0 | R1 | local | |
(R2).k1 | 1.0 | R2 | local |
Setting only the following is possible:
'new_name'
'value'
[15]:
set_reaction_parameters(name = '(R1).k1', value=123)
[16]:
get_reaction_parameters()
[16]:
value | reaction | type | mapped_to | |
---|---|---|---|---|
name | ||||
(R1).k1 | 123.0 | R1 | local | |
(R1).k2 | 1.0 | R1 | local | |
(R2).k1 | 1.0 | R2 | local |
Getting/setting reactions
[17]:
get_reactions()
[17]:
scheme | flux | particle_flux | function | |
---|---|---|---|---|
name | ||||
R1 | S + E = ES | NaN | NaN | Mass action (reversible) |
R2 | ES -> E + P | NaN | NaN | Mass action (irreversible) |
Setting scheme
[18]:
set_reaction(name = 'R1', scheme = 'S + E + F = ES')
[19]:
get_reactions()
[19]:
scheme | flux | particle_flux | function | |
---|---|---|---|---|
name | ||||
R1 | S + E + F = ES | NaN | NaN | Mass action (reversible) |
R2 | ES -> E + P | NaN | NaN | Mass action (irreversible) |
Setting reaction name
[20]:
set_reaction(name = 'R1', new_name = 'Reaction 1')
[21]:
get_reactions()
[21]:
scheme | flux | particle_flux | function | |
---|---|---|---|---|
name | ||||
Reaction 1 | S + E + F = ES | NaN | NaN | Mass action (reversible) |
R2 | ES -> E + P | NaN | NaN | Mass action (irreversible) |
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