def _get_denominator(self, reaction, mode):
def get_substr_term(s):
term = self._get_substrate_term(s)
term = term[:term.rfind(')') + 1]
term = 'sqrt(%s)' % term
return term
text = ' * '.join(
[get_substr_term(s) for s in misc.get_participants(reaction)])
return '(%s)' % text
def _get_denominator(self, reaction, mode):
def get_substr_term(s):
term = self._get_substrate_term(s)
term = term[:term.rfind(')') + 1]
term = 'sqrt(%s)' % term
return term
text = ' * '.join([get_substr_term(s)
for s in misc.get_participants(reaction)])
return '(%s)' % text
def _create_local_params(self, reaction, params, mode):
'''
create the local parameters for a reaction
@type reaction: libsbml.reaction
@param reaction: the reaction, if paramter is associated with
a reaction
@type params: list
@param params: list of local (assigned to a reaction) parameters,
as generated by pack_parameters function
@type mode: string
@param mode: parametrisation type ('cat' | 'weg' | 'hal')
'''
local_param_count = 0
# iterate over all parameter types for this mode
for p_type in self.mode2params[mode]:
# get options
scope, deps, id_temp, required = self.param2options[p_type]
if scope == 'global': # this function is for global parameters
continue
# get the value
p_value = params[local_param_count]
local_param_count += 1
# based on dependencies,
# add one parameter for reaction / reactant / modifier
if deps == '':
self._add_param(p_type, p_value, reaction)
elif deps == 's':
for i, s in enumerate(misc.get_participants(reaction)):
self._add_param(p_type, p_value[i], reaction, s)
elif deps == 'k': # here go the k_i_vec and k_a_vec
for i, s in enumerate(misc.get_modifiers(reaction)):
sboterm = s.getSBOTerm()
if p_value[i] is None:
continue
else:
if sboterm in self.sbo_act and p_type == 'k_a_vec':
self._add_param(p_type, p_value[i], reaction, s)
elif sboterm in self.sbo_inh and p_type == 'k_i_vec':
self._add_param(p_type, p_value[i], reaction, s)
elif deps == 'm': # here go the inh_ratio_vec and act_ratio_vec
for i, s in enumerate(reaction.getListOfModifiers()):
if p_value[i] is None:
continue
self._add_param(p_type,
p_value[i],
reaction=reaction,
species=s)
def _create_local_params(self, reaction, params, mode):
'''
create the local parameters for a reaction
@type reaction: libsbml.reaction
@param reaction: the reaction, if paramter is associated with
a reaction
@type params: list
@param params: list of local (assigned to a reaction) parameters,
as generated by pack_parameters function
@type mode: string
@param mode: parametrisation type ('cat' | 'weg' | 'hal')
'''
local_param_count = 0
# iterate over all parameter types for this mode
for p_type in self.mode2params[mode]:
# get options
scope, deps, id_temp, required = self.param2options[p_type]
if scope == 'global': # this function is for global parameters
continue
# get the value
p_value = params[local_param_count]
local_param_count += 1
# based on dependencies,
# add one parameter for reaction / reactant / modifier
if deps == '':
self._add_param(p_type, p_value, reaction)
elif deps == 's':
for i, s in enumerate(misc.get_participants(reaction)):
self._add_param(p_type, p_value[i], reaction, s)
elif deps == 'k': # here go the k_i_vec and k_a_vec
for i, s in enumerate(misc.get_modifiers(reaction)):
sboterm = s.getSBOTerm()
if p_value[i] is None:
continue
else:
if sboterm in self.sbo_act and p_type == 'k_a_vec':
self._add_param(p_type, p_value[i], reaction, s)
elif sboterm in self.sbo_inh and p_type == 'k_i_vec':
self._add_param(p_type, p_value[i], reaction, s)
elif deps == 'm': # here go the inh_ratio_vec and act_ratio_vec
for i, s in enumerate(reaction.getListOfModifiers()):
if p_value[i] is None:
continue
self._add_param(p_type, p_value[i], reaction=reaction,
species=s)
def _get_denominator(self, reaction, mode):
get_substr_term = lambda s: self._get_substrate_term(s).replace(
'(', '( 1 + ')
text = ' * '.join(
[get_substr_term(s) for s in misc.get_participants(reaction)])
return '(%s)' % text
def _get_numerator(self, reaction, mode):
'''
get the numerator for the kinetic law
@type reaction: libsbml.reaction
@param reaction: the reaction
@type mode: string
@param mode: parametrisation type ('cat' | 'weg' | 'hal')
'''
# define little functionto get s^stoich
def get_substrate_term(s):
s_id = s.getSpecies()
if s.getStoichiometry() != 1:
s_id += '^' + str(s.getStoichiometry())
return s_id
# define little function to get KM^stoich
def get_km_term(s):
km_id = self.param2options['km_vec'][2].replace(
'$REAC$', reaction.getId()).replace('$SPECIES$',
s.getSpecies())
if s.getStoichiometry() != 1:
km_id += '^' + str(s.getStoichiometry())
return km_id
# get the id templates for kf, kb and hill coeff.
kf_id_temp = self.param2options['kf'][2]
kb_id_temp = self.param2options['kb'][2]
hill_id_temp = self.param2options['hill_coeff'][2]
# generate the numerator term dpending on parameterization type
if mode == 'cat':
forw_term = kf_id_temp.replace('$REAC$', reaction.getId()) + ' * '
back_term = kb_id_temp.replace('$REAC$', reaction.getId()) + ' * '
forw_term += ' * '.join([
self._get_substrate_term(s)
for s in reaction.getListOfReactants()
])
back_term += ' * '.join([
self._get_substrate_term(s)
for s in reaction.getListOfProducts()
])
if reaction.getNumReactants() == 0:
forw_term = '0'
elif reaction.getNumProducts() == 0:
back_term = '0'
term = '( ( %s ) - ( %s ) )' % (forw_term, back_term)
elif mode == 'hal':
react_term = ' * '.join([get_substrate_term(s)
for s in reaction.getListOfReactants()]) \
or '0'
prod_term = ' * '.join([get_substrate_term(s)
for s in reaction.getListOfProducts()]) \
or '0'
km_term = ' * '.join(
[get_km_term(s) for s in misc.get_participants(reaction)])
kv = self.param2options['kv'][2].replace('$REAC$',
reaction.getId())
keq = self.param2options['keq'][2].replace('$REAC$',
reaction.getId())
hill_coeff = hill_id_temp.replace('$REAC$', reaction.getId())
term = '''( %s * ( ( ((%s)^(%s/2.)) * %s) - (((%s)^(-%s/2.)) * %s)
) )''' % (kv, keq, hill_coeff, react_term, keq, hill_coeff,
prod_term)
term = '(%s) / sqrt(%s)' % (term, km_term)
elif mode == 'weg':
mu_id_temp = self.param2options['mu_vec'][2]
def get_mu_term(s):
mu_id = mu_id_temp.replace('$SPECIES$', s.getSpecies())
if s.getStoichiometry() != 1:
mu_id = str(s.getStoichiometry()) + '*' + mu_id
return mu_id
mu_f_term = ' + '.join([get_mu_term(s)
for s in reaction.getListOfReactants()]) \
or '0'
mu_b_term = ' + '.join([get_mu_term(s)
for s in reaction.getListOfProducts()]) \
or '0'
mu_term = '(%s) - (%s)' % (mu_b_term, mu_f_term)
hill_coeff = hill_id_temp.replace('$REAC$', reaction.getId())
react_term = ' * '.join([get_substrate_term(s)
for s in reaction.getListOfReactants()])\
or '0'
prod_term = ' * '.join([get_substrate_term(s)
for s in reaction.getListOfProducts()]) \
or '0'
km_term = ' * '.join(
[get_km_term(s) for s in misc.get_participants(reaction)])
kv = self.param2options['kv'][2].replace('$REAC$',
reaction.getId())
term = '''( %s * (( exp(-%s * (%s)/(2*R*temp)) * (%s) ) -
(exp(%s * (%s)/(2*R*temp)) * (%s)) ) / sqrt(%s))''' \
% (kv, hill_coeff, mu_term, react_term, hill_coeff, mu_term,
prod_term, km_term)
else:
# in case somebody chose a mode we do not know
raise Exception('Implement')
return term
def _pack_parameters(self, mode):
'''
get the parameters from the sbtab and pack them in a way that they can
be added easily. Parameters are separated in local ones (associated
with a reaction) and global ones.
@type mode: string
@param mode: parametrisation type ('cat' | 'weg' | 'hal')
@rtype: tuple
@return: tuple of (global_parameters, local_parameters) where
global parameters is the list of global params (1 entry
for each param type) and local_parameter is the list of
local params (1 entry for each reaction)
'''
# get the global params
global_params = []
# get global params for all parameters specified for this mode
for p_type in self.mode2params[mode]:
p_vec = []
scope, deps, dummy, required = self.param2options[p_type]
if scope == 'local':
continue
# if param. depends on species, get one param for each species, if
# it depends on reaction get one for each reaction
if deps == 's' or deps == 'k':
for s in self._model.getListOfSpecies():
if misc.is_enzyme(s):
continue
p_value = self._get_sbtab_entry(p_type, species=s)
p_vec.append(p_value)
elif deps == 'r':
for r in self._model.getListOfReactions():
p_value = self._get_sbtab_entry(p_type, reaction=r)
p_vec.append(p_value)
global_params.append(p_vec)
# get local parameters (one set for each reaction)
local_params = []
for r in self._model.getListOfReactions():
reaction_params = []
for p_type in self.mode2params[mode]:
scope, deps, dummy, required = self.param2options[p_type]
if scope == 'global':
continue
if deps == '':
p_vec = self._get_sbtab_entry(p_type, reaction=r)
elif deps == 's':
p_vec = []
for s in misc.get_participants(r):
p_value = self._get_sbtab_entry(
p_type,
reaction=r,
species=self._model.getSpecies(s.getSpecies()))
p_vec.append(p_value)
elif deps == 'k':
p_vec = []
for s in misc.get_modifiers(r):
p_value = self._get_sbtab_entry(
p_type,
reaction=r,
species=self._model.getSpecies(s.getSpecies()))
p_vec.append(p_value)
elif deps == 'm':
p_vec = []
for m in r.getListOfModifiers():
p_value = self._get_sbtab_entry(
p_type,
reaction=r,
species=self._model.getSpecies(m.getSpecies()))
p_vec.append(p_value)
reaction_params.append(p_vec)
local_params.append(reaction_params)
return (global_params, local_params)
def _get_denominator(self, reaction, mode):
get_substr_term = lambda s: self._get_substrate_term(s).replace('(', '( 1 + ')
text = ' * '.join([get_substr_term(s)
for s in misc.get_participants(reaction)])
return '(%s)' % text
def _get_numerator(self, reaction, mode):
'''
get the numerator for the kinetic law
@type reaction: libsbml.reaction
@param reaction: the reaction
@type mode: string
@param mode: parametrisation type ('cat' | 'weg' | 'hal')
'''
# define little functionto get s^stoich
def get_substrate_term(s):
s_id = s.getSpecies()
if s.getStoichiometry() != 1:
s_id += '^' + str(s.getStoichiometry())
return s_id
# define little function to get KM^stoich
def get_km_term(s):
km_id = self.param2options['km_vec'][2].replace('$REAC$',
reaction.getId()).replace('$SPECIES$',
s.getSpecies())
if s.getStoichiometry() != 1:
km_id += '^' + str(s.getStoichiometry())
return km_id
# get the id templates for kf, kb and hill coeff.
kf_id_temp = self.param2options['kf'][2]
kb_id_temp = self.param2options['kb'][2]
hill_id_temp = self.param2options['hill_coeff'][2]
# generate the numerator term dpending on parameterization type
if mode == 'cat':
forw_term = kf_id_temp.replace('$REAC$', reaction.getId()) + ' * '
back_term = kb_id_temp.replace('$REAC$', reaction.getId()) + ' * '
forw_term += ' * '.join([self._get_substrate_term(s)
for s in reaction.getListOfReactants()])
back_term += ' * '.join([self._get_substrate_term(s)
for s in reaction.getListOfProducts()])
if reaction.getNumReactants() == 0:
forw_term = '0'
elif reaction.getNumProducts() == 0:
back_term = '0'
term = '( ( %s ) - ( %s ) )' % (forw_term, back_term)
elif mode == 'hal':
react_term = ' * '.join([get_substrate_term(s)
for s in reaction.getListOfReactants()]) \
or '0'
prod_term = ' * '.join([get_substrate_term(s)
for s in reaction.getListOfProducts()]) \
or '0'
km_term = ' * '.join([get_km_term(s)
for s in misc.get_participants(reaction)])
kv = self.param2options['kv'][2].replace('$REAC$',
reaction.getId())
keq = self.param2options['keq'][2].replace('$REAC$',
reaction.getId())
hill_coeff = hill_id_temp.replace('$REAC$', reaction.getId())
term = '''( %s * ( ( ((%s)^(%s/2.)) * %s) - (((%s)^(-%s/2.)) * %s)
) )''' % (kv, keq, hill_coeff, react_term, keq, hill_coeff,
prod_term)
term = '(%s) / sqrt(%s)' % (term, km_term)
elif mode == 'weg':
mu_id_temp = self.param2options['mu_vec'][2]
def get_mu_term(s):
mu_id = mu_id_temp.replace('$SPECIES$', s.getSpecies())
if s.getStoichiometry() != 1:
mu_id = str(s.getStoichiometry()) + '*' + mu_id
return mu_id
mu_f_term = ' + '.join([get_mu_term(s)
for s in reaction.getListOfReactants()]) \
or '0'
mu_b_term = ' + '.join([get_mu_term(s)
for s in reaction.getListOfProducts()]) \
or '0'
mu_term = '(%s) - (%s)' % (mu_b_term, mu_f_term)
hill_coeff = hill_id_temp.replace('$REAC$', reaction.getId())
react_term = ' * '.join([get_substrate_term(s)
for s in reaction.getListOfReactants()])\
or '0'
prod_term = ' * '.join([get_substrate_term(s)
for s in reaction.getListOfProducts()]) \
or '0'
km_term = ' * '.join([get_km_term(s)
for s in misc.get_participants(reaction)])
kv = self.param2options['kv'][2].replace('$REAC$',
reaction.getId())
term = '''( %s * (( exp(-%s * (%s)/(2*R*temp)) * (%s) ) -
(exp(%s * (%s)/(2*R*temp)) * (%s)) ) / sqrt(%s))''' \
% (kv, hill_coeff, mu_term, react_term, hill_coeff, mu_term,
prod_term, km_term)
else:
# in case somebody chose a mode we do not know
raise Exception('Implement')
return term
def _pack_parameters(self, mode):
'''
get the parameters from the sbtab and pack them in a way that they can
be added easily. Parameters are separated in local ones (associated
with a reaction) and global ones.
@type mode: string
@param mode: parametrisation type ('cat' | 'weg' | 'hal')
@rtype: tuple
@return: tuple of (global_parameters, local_parameters) where
global parameters is the list of global params (1 entry
for each param type) and local_parameter is the list of
local params (1 entry for each reaction)
'''
# get the global params
global_params = []
# get global params for all parameters specified for this mode
for p_type in self.mode2params[mode]:
p_vec = []
scope, deps, dummy, required = self.param2options[p_type]
if scope == 'local':
continue
# if param. depends on species, get one param for each species, if
# it depends on reaction get one for each reaction
if deps == 's' or deps == 'k':
for s in self._model.getListOfSpecies():
if misc.is_enzyme(s):
continue
p_value = self._get_sbtab_entry(p_type, species=s)
p_vec.append(p_value)
elif deps == 'r':
for r in self._model.getListOfReactions():
p_value = self._get_sbtab_entry(p_type, reaction=r)
p_vec.append(p_value)
global_params.append(p_vec)
# get local parameters (one set for each reaction)
local_params = []
for r in self._model.getListOfReactions():
reaction_params = []
for p_type in self.mode2params[mode]:
scope, deps, dummy, required = self.param2options[p_type]
if scope == 'global':
continue
if deps == '':
p_vec = self._get_sbtab_entry(p_type, reaction=r)
elif deps == 's':
p_vec = []
for s in misc.get_participants(r):
p_value = self._get_sbtab_entry(p_type, reaction=r,
species=self._model.getSpecies(s.getSpecies()))
p_vec.append(p_value)
elif deps == 'k':
p_vec = []
for s in misc.get_modifiers(r):
p_value = self._get_sbtab_entry(p_type, reaction=r,
species=self._model.getSpecies(s.getSpecies()))
p_vec.append(p_value)
elif deps == 'm':
p_vec = []
for m in r.getListOfModifiers():
p_value = self._get_sbtab_entry(p_type, reaction=r,
species=self._model.getSpecies(m.getSpecies()))
p_vec.append(p_value)
reaction_params.append(p_vec)
local_params.append(reaction_params)
return (global_params, local_params)