def pore_bind(subunit, sp_site1, sp_site2, sc_site, size, cargo, c_site,
klist):
"""Generate rules to bind a monomer to a circular homomeric pore.
The pore structure is defined by the `pore_species` macro -- `subunit`
monomers bind to each other from `sp_site1` to `sp_site2` to form a closed
ring. The binding reaction takes the form pore + cargo <> pore:cargo.
Parameters
----------
subunit : Monomer or MonomerPattern
Subunit of which the pore is composed.
sp_site1, sp_site2 : string
Names of the sites where one copy of `subunit` binds to the next.
sc_site : string
Name of the site on `subunit` where it binds to the cargo `cargo`.
size : integer
Number of subunits in the pore at which binding will occur.
cargo : Monomer or MonomerPattern
Cargo that binds to the pore complex.
c_site : string
Name of the site on `cargo` where it binds to `subunit`.
klist : list of Parameters or numbers
List containing forward and reverse rate constants for the binding
reaction (in that order). Rate constants should either be both Parameter
objects or both numbers. If Parameters are passed, they will be used
directly in the generated Rules. If numbers are passed, Parameters
will be created with automatically generated names based on <TODO>
and these parameters will be included at the end of the returned
component list.
"""
macros._verify_sites(subunit, sc_site)
macros._verify_sites(cargo, c_site)
def pore_bind_rule_name(rule_expression, size):
# Get ReactionPatterns
react_p = rule_expression.reactant_pattern
prod_p = rule_expression.product_pattern
# Build the label components
# Pore is always first complex of LHS due to how we build the rules
subunit = react_p.complex_patterns[0].monomer_patterns[0].monomer
if len(react_p.complex_patterns) == 2:
# This is the complexation reaction
cargo = react_p.complex_patterns[1].monomer_patterns[0]
else:
# This is the dissociation reaction
cargo = prod_p.complex_patterns[1].monomer_patterns[0]
return '%s_%d_%s' % (subunit.name, size,
macros._monomer_pattern_label(cargo))
components = ComponentSet()
# Set up some aliases that are invariant with pore size
subunit_free = subunit({sc_site: None})
cargo_free = cargo({c_site: None})
#for size, klist in zip(range(min_size, max_size + 1), ktable):
# More aliases which do depend on pore size
pore_free = macros.pore_species(subunit_free, sp_site1, sp_site2, size)
# This one is a bit tricky. The pore:cargo complex must only introduce
# one additional bond even though there are multiple subunits in the
# pore. We create partial patterns for bound pore and cargo, using a
# bond number that is high enough not to conflict with the bonds within
# the pore ring itself.
# Start by copying pore_free, which has all cargo binding sites empty
pore_bound = pore_free.copy()
# Get the next bond number not yet used in the pore structure itself
cargo_bond_num = size + 1
# Assign that bond to the first subunit in the pore
pore_bound.monomer_patterns[0].site_conditions[sc_site] = cargo_bond_num
# Create a cargo source pattern with that same bond
cargo_bound = cargo({c_site: cargo_bond_num})
# Finally we can define the complex trivially; the bond numbers are
# already present in the patterns
pc_complex = pore_bound % cargo_bound
# Create the rules
name_func = functools.partial(pore_bind_rule_name, size=size)
components |= macros._macro_rule('pore_bind',
pore_free + cargo_free | pc_complex,
klist[0:2], ['kf', 'kr'],
name_func=name_func)
return components
# Maximum number of subunits in a pore
max_size = 6
# Size at which pores are "competent" to transport cargo
min_transport_size = 4
# Build handy rate "sets" (in this formulation, rates don't vary with pore size)
assembly_rates = [[2e-4, 1e-3]] * (max_size - 1)
transport_rates = [[3e-5, 1e-3, 1e1]] * (max_size - min_transport_size + 1)
# Assemble the pore
# (specify t=None so the pore can't fall apart while it's bound to cargo)
assemble_pore_sequential(Bax(t=None), 's1', 's2', max_size, assembly_rates)
# Transport Smac
pore_transport(Bax, 's1', 's2', 't', min_transport_size, max_size,
Smac(loc='m'), 't', Smac(loc='c'), transport_rates)
# Add an observable for each pore size
for size in range(1, max_size + 1):
Observable('Bax%d' % size, pore_species(Bax, 's1', 's2', size))
# Observe unbound Smac in each compartment
Observable('mSmac', Smac(loc='m', t=None))
Observable('cSmac', Smac(loc='c'))
if __name__ == '__main__':
print __doc__, "\n", model
print "\nNOTE: This model code is designed to be imported and programatically " \
"manipulated,\nnot executed directly. The above output is merely a " \
"diagnostic aid. Please see\n" \
"run_bax_pore_sequential.py for example usage."
def pore_bind(subunit, sp_site1, sp_site2, sc_site, size, cargo, c_site,
klist):
"""Generate rules to bind a monomer to a circular homomeric pore.
The pore structure is defined by the `pore_species` macro -- `subunit`
monomers bind to each other from `sp_site1` to `sp_site2` to form a closed
ring. The binding reaction takes the form pore + cargo <> pore:cargo.
Parameters
----------
subunit : Monomer or MonomerPattern
Subunit of which the pore is composed.
sp_site1, sp_site2 : string
Names of the sites where one copy of `subunit` binds to the next.
sc_site : string
Name of the site on `subunit` where it binds to the cargo `cargo`.
size : integer
Number of subunits in the pore at which binding will occur.
cargo : Monomer or MonomerPattern
Cargo that binds to the pore complex.
c_site : string
Name of the site on `cargo` where it binds to `subunit`.
klist : list of Parameters or numbers
List containing forward and reverse rate constants for the binding
reaction (in that order). Rate constants should either be both Parameter
objects or both numbers. If Parameters are passed, they will be used
directly in the generated Rules. If numbers are passed, Parameters
will be created with automatically generated names based on <TODO>
and these parameters will be included at the end of the returned
component list.
"""
macros._verify_sites(subunit, sc_site)
macros._verify_sites(cargo, c_site)
def pore_bind_rule_name(rule_expression, size):
# Get ReactionPatterns
react_p = rule_expression.reactant_pattern
prod_p = rule_expression.product_pattern
# Build the label components
# Pore is always first complex of LHS due to how we build the rules
subunit = react_p.complex_patterns[0].monomer_patterns[0].monomer
if len(react_p.complex_patterns) == 2:
# This is the complexation reaction
cargo = react_p.complex_patterns[1].monomer_patterns[0]
else:
# This is the dissociation reaction
cargo = prod_p.complex_patterns[1].monomer_patterns[0]
return '%s_%d_%s' % (subunit.name, size,
macros._monomer_pattern_label(cargo))
components = ComponentSet()
# Set up some aliases that are invariant with pore size
subunit_free = subunit({sc_site: None})
cargo_free = cargo({c_site: None})
#for size, klist in zip(range(min_size, max_size + 1), ktable):
# More aliases which do depend on pore size
pore_free = macros.pore_species(subunit_free, sp_site1, sp_site2, size)
# This one is a bit tricky. The pore:cargo complex must only introduce
# one additional bond even though there are multiple subunits in the
# pore. We create partial patterns for bound pore and cargo, using a
# bond number that is high enough not to conflict with the bonds within
# the pore ring itself.
# Start by copying pore_free, which has all cargo binding sites empty
pore_bound = pore_free.copy()
# Get the next bond number not yet used in the pore structure itself
cargo_bond_num = size + 1
# Assign that bond to the first subunit in the pore
pore_bound.monomer_patterns[0].site_conditions[sc_site] = cargo_bond_num
# Create a cargo source pattern with that same bond
cargo_bound = cargo({c_site: cargo_bond_num})
# Finally we can define the complex trivially; the bond numbers are
# already present in the patterns
pc_complex = pore_bound % cargo_bound
# Create the rules
name_func = functools.partial(pore_bind_rule_name, size=size)
components |= macros._macro_rule('pore_bind',
pore_free + cargo_free <> pc_complex,
klist[0:2], ['kf', 'kr'],
name_func=name_func)
return components
# Maximum number of subunits in a pore
max_size = 6
# Size at which pores are "competent" to transport cargo
min_transport_size = 4
# Build handy rate "sets" (in this formulation, rates don't vary with pore size)
assembly_rates = [[2e-4, 1e-3]] * (max_size - 1)
transport_rates = [[3e-5, 1e-3, 1e1]] * (max_size - min_transport_size + 1)
# Assemble the pore
# (specify t=None so the pore can't fall apart while it's bound to cargo)
assemble_pore_sequential(Bax(t=None), 's1', 's2', max_size, assembly_rates)
# Transport Smac
pore_transport(Bax, 's1', 's2', 't', min_transport_size, max_size,
Smac(loc='m'), 't', Smac(loc='c'), transport_rates)
# Add an observable for each pore size
for size in range(1, max_size + 1):
Observable('Bax%d' % size, pore_species(Bax, 's1', 's2', size))
# Observe unbound Smac in each compartment
Observable('mSmac', Smac(loc='m', t=None))
Observable('cSmac', Smac(loc='c'))
if __name__ == '__main__':
print __doc__, "\n", model
print "\nNOTE: This model code is designed to be imported and programatically " \
"manipulated,\nnot executed directly. The above output is merely a " \
"diagnostic aid. Please see\n" \
"run_bax_pore_sequential.py for example usage."