def complex_assemble_one_step(stmt, model):
pairs = itertools.combinations(stmt.members, 2)
for pair in pairs:
# Make a rule name
nugget_name = '_'.join([get_agent_rule_str(m) for m in pair])
nugget_name += '_bind'
action_name = nugget_name + '_act'
kf_bind = 1e-6
nugget = Nugget(nugget_name, nugget_name, kf_bind)
action_id = nugget.add_node(action_name)
# Initialize dicts/lists for this nugget
nugget.add_typing(action_id, 'bnd')
for agent in pair:
agent_id = nugget.add_agent(agent)
agent_bs = get_binding_site_name(agent)
agent_bs_id = nugget.add_node(agent_bs)
nugget.add_edge(agent_bs_id, agent_id)
nugget.add_edge(agent_bs_id, action_id)
# Add to the Kami typing dict
nugget.add_typing(agent_bs_id, 'locus')
# Typing dicts linking the nugget to the Action Graph and to the
# Kami graph
typing_dict_ag = {'from': nugget_name, 'to': 'action_graph',
'mapping': {}, 'total': False,
'ignore_attrs': False}
typing_dict_kami = {'from': nugget_name, 'to': 'kami',
'mapping': nugget.get_typing_dict(), 'total': True,
'ignore_attrs': True}
# Add the graphs for this nugget to the graphs and typing lists
model['typing'] += [typing_dict_ag, typing_dict_kami]
model['graphs'].append(nugget.get_nugget_dict())
# In reverse reaction, assume that dissocition is unconditional
nugget_name = '_'.join([get_agent_rule_str(m) for m in pair])
nugget_name += '_dissociate'
action_name = nugget_name + '_act'
kr_bind = 1e-1
nugget = Nugget(nugget_name, nugget_name, kr_bind)
action_id = nugget.add_node(action_name)
nugget.add_typing(action_id, 'brk')
for agent in pair:
agent_bs = get_binding_site_name(agent)
agent_id = nugget.add_node(agent.name)
agent_bs_id = nugget.add_node(agent_bs)
nugget.add_edge(agent_bs_id, agent_id)
nugget.add_edge(agent_bs_id, action_id)
nugget.add_typing(agent_id, 'agent')
nugget.add_typing(agent_bs_id, 'locus')
# Typing dicts linking the nugget to the Action Graph and to the
# Kami graph
typing_dict_ag = {'from': nugget_name, 'to': 'action_graph',
'mapping': {}, 'total': False,
'ignore_attrs': False}
typing_dict_kami = {'from': nugget_name, 'to': 'kami',
'mapping': nugget.get_typing_dict(), 'total': True,
'ignore_attrs': True}
# Add the graphs for this nugget to the graphs and typing lists
model['typing'] += [typing_dict_ag, typing_dict_kami]
model['graphs'].append(nugget.get_nugget_dict())
def _mod_demod_assemble_one_step(stmt, model, is_mod):
# Define some basic parameters for the modification
mc = stmt._get_mod_condition()
mod_condition_name = mc.mod_type
mod_site = get_mod_site_name(mc)
rule_enz_str = get_agent_rule_str(stmt.enz)
rule_sub_str = get_agent_rule_str(stmt.sub)
nugget_name = '%s_%s_%s_%s' % \
(rule_enz_str, mod_condition_name, rule_sub_str, mod_site)
action_name = nugget_name + '_act'
kf_mod = 1e-6
nugget = Nugget(nugget_name, nugget_name, kf_mod)
enz_id = nugget.add_agent(stmt.enz)
sub_id = nugget.add_agent(stmt.sub)
st = states[mod_condition_name]
from_state, to_state = (st[0], st[1]) if is_mod else (st[1], st[0])
mod_site_id = nugget.add_node(mod_site, {'val': from_state})
action_id = nugget.add_node(action_name, {'val': to_state})
nugget.add_typing(mod_site_id, 'state')
nugget.add_typing(action_id, 'mod')
nugget.add_edge(mod_site_id, sub_id)
nugget.add_edge(action_id, mod_site_id)
nugget.add_edge(enz_id, action_id)
# Typing dicts linking the nugget to the Action Graph and to the
# Kami graph
typing_dict_ag = {
'from': nugget_name,
'to': 'action_graph',
'mapping': {},
'total': False,
'ignore_attrs': False
}
typing_dict_kami = {
'from': nugget_name,
'to': 'kami',
'mapping': nugget.get_typing_dict(),
'total': True,
'ignore_attrs': True
}
# Add the graphs for this nugget to the graphs and typing lists
model['typing'] += [typing_dict_ag, typing_dict_kami]
model['graphs'].append(nugget.get_nugget_dict())
def _mod_demod_assemble_one_step(stmt, model, is_mod):
# Define some basic parameters for the modification
mc = stmt._get_mod_condition()
mod_condition_name = mc.mod_type
mod_site = get_mod_site_name(mc)
rule_enz_str = get_agent_rule_str(stmt.enz)
rule_sub_str = get_agent_rule_str(stmt.sub)
nugget_name = '%s_%s_%s_%s' % \
(rule_enz_str, mod_condition_name, rule_sub_str, mod_site)
action_name = nugget_name + '_act'
kf_mod = 1e-6
nugget = Nugget(nugget_name, nugget_name, kf_mod)
enz_id = nugget.add_agent(stmt.enz)
sub_id = nugget.add_agent(stmt.sub)
st = states[mod_condition_name]
from_state, to_state = (st[0], st[1]) if is_mod else (st[1], st[0])
mod_site_id = nugget.add_node(mod_site, {'val': from_state})
action_id = nugget.add_node(action_name, {'val': to_state})
nugget.add_typing(mod_site_id, 'state')
nugget.add_typing(action_id, 'mod')
nugget.add_edge(mod_site_id, sub_id)
nugget.add_edge(action_id, mod_site_id)
nugget.add_edge(enz_id, action_id)
# Typing dicts linking the nugget to the Action Graph and to the
# Kami graph
typing_dict_ag = {'from': nugget_name, 'to': 'action_graph',
'mapping': {}, 'total': False,
'ignore_attrs': False}
typing_dict_kami = {'from': nugget_name, 'to': 'kami',
'mapping': nugget.get_typing_dict(), 'total': True,
'ignore_attrs': True}
# Add the graphs for this nugget to the graphs and typing lists
model['typing'] += [typing_dict_ag, typing_dict_kami]
model['graphs'].append(nugget.get_nugget_dict())
def get_create_observable(model, agent):
site_pattern = pa.get_site_pattern(agent)
obs_name = pa.get_agent_rule_str(agent) + '_obs'
try:
monomer = model.monomers[pa._n(agent.name)]
except KeyError:
raise MissingMonomerError('%s is not in the model ' % agent.name)
try:
monomer_state = monomer(site_pattern)
except Exception as e:
msg = 'Site pattern %s invalid for monomer %s' % \
(site_pattern, monomer.name)
raise MissingMonomerSiteError(msg)
obs = Observable(obs_name, monomer(site_pattern))
model.add_component(obs)
return obs
def get_create_observable(model, agent):
site_pattern = pa.get_site_pattern(agent)
obs_name = pa.get_agent_rule_str(agent) + '_obs'
try:
monomer = model.monomers[pa._n(agent.name)]
except KeyError:
raise MissingMonomerError('%s is not in the model ' % agent.name,
agent)
try:
monomer_state = monomer(site_pattern)
except Exception as e:
msg = 'Site pattern %s invalid for monomer %s' % \
(site_pattern, monomer.name)
raise MissingMonomerSiteError(msg)
obs = Observable(obs_name, monomer(site_pattern))
try:
model.add_component(obs)
except ComponentDuplicateNameError as e:
pass
return obs
def test_rule_name_str_5():
a = Agent('BRAF', mods=[ModCondition('phosphorylation', 'serine', '123')])
s = pa.get_agent_rule_str(a)
assert s == 'BRAF_phosphoS123'
def test_rule_name_str_3():
a = Agent('GRB2', bound_conditions=[BoundCondition(Agent('EGFR'), False)])
s = pa.get_agent_rule_str(a)
assert s == 'GRB2_nEGFR'
def test_rule_name_str_1():
s = pa.get_agent_rule_str(Agent('BRAF'))
assert s == 'BRAF'
def complex_assemble_one_step(stmt, model):
pairs = itertools.combinations(stmt.members, 2)
for pair in pairs:
# Make a rule name
nugget_name = '_'.join([get_agent_rule_str(m) for m in pair])
nugget_name += '_bind'
action_name = nugget_name + '_act'
kf_bind = 1e-6
nugget = Nugget(nugget_name, nugget_name, kf_bind)
action_id = nugget.add_node(action_name)
# Initialize dicts/lists for this nugget
nugget.add_typing(action_id, 'bnd')
for agent in pair:
agent_id = nugget.add_agent(agent)
agent_bs = get_binding_site_name(agent)
agent_bs_id = nugget.add_node(agent_bs)
nugget.add_edge(agent_bs_id, agent_id)
nugget.add_edge(agent_bs_id, action_id)
# Add to the Kami typing dict
nugget.add_typing(agent_bs_id, 'locus')
# Typing dicts linking the nugget to the Action Graph and to the
# Kami graph
typing_dict_ag = {
'from': nugget_name,
'to': 'action_graph',
'mapping': {},
'total': False,
'ignore_attrs': False
}
typing_dict_kami = {
'from': nugget_name,
'to': 'kami',
'mapping': nugget.get_typing_dict(),
'total': True,
'ignore_attrs': True
}
# Add the graphs for this nugget to the graphs and typing lists
model['typing'] += [typing_dict_ag, typing_dict_kami]
model['graphs'].append(nugget.get_nugget_dict())
# In reverse reaction, assume that dissocition is unconditional
nugget_name = '_'.join([get_agent_rule_str(m) for m in pair])
nugget_name += '_dissociate'
action_name = nugget_name + '_act'
kr_bind = 1e-1
nugget = Nugget(nugget_name, nugget_name, kr_bind)
action_id = nugget.add_node(action_name)
nugget.add_typing(action_id, 'brk')
for agent in pair:
agent_bs = get_binding_site_name(agent)
agent_id = nugget.add_node(agent.name)
agent_bs_id = nugget.add_node(agent_bs)
nugget.add_edge(agent_bs_id, agent_id)
nugget.add_edge(agent_bs_id, action_id)
nugget.add_typing(agent_id, 'agent')
nugget.add_typing(agent_bs_id, 'locus')
# Typing dicts linking the nugget to the Action Graph and to the
# Kami graph
typing_dict_ag = {
'from': nugget_name,
'to': 'action_graph',
'mapping': {},
'total': False,
'ignore_attrs': False
}
typing_dict_kami = {
'from': nugget_name,
'to': 'kami',
'mapping': nugget.get_typing_dict(),
'total': True,
'ignore_attrs': True
}
# Add the graphs for this nugget to the graphs and typing lists
model['typing'] += [typing_dict_ag, typing_dict_kami]
model['graphs'].append(nugget.get_nugget_dict())
def test_rule_name_str_5():
a = Agent('BRAF', mods=[ModCondition('phosphorylation', 'serine', '123')])
s = pa.get_agent_rule_str(a)
assert s == 'BRAF_phosphoS123'
def test_rule_name_str_3():
a = Agent('GRB2',
bound_conditions=[BoundCondition(Agent('EGFR'), False)])
s = pa.get_agent_rule_str(a)
assert s == 'GRB2_nEGFR'
def test_rule_name_str_1():
s = pa.get_agent_rule_str(Agent('BRAF'))
assert s == 'BRAF'
