def __init__(self, label = 'another reaction', rate = float(10.0), propensity_scheme = 'classic', propensity_function_maker = None, parent = None, occurrences = [], used = None, produced = None, visible_attributes = ['label', 'propensity_scheme', 'rate', 'used', 'produced']): self.system = None self.rate = rate if occurrences is None: self.occurrences = [] else: self.occurrences = occurrences #instances of these are somehow coupled unless a # used and produced list is passed to init, # EVEN an empty list will do (used = [] does not!) if used is None: self.used = [] else: self.used = used if produced is None: self.produced = [] else: self.produced = produced self.propensity = 1.0 self.propensity_minimum = 1e-30 self.propensity_scheme = propensity_scheme parameter_space_templates =\ [lgeo.interface_template_p_space_axis(parent = self, p_sp_bounds = [0.0000001, 1000.0], instance = self, key = 'rate')] modular_object.__init__(self, label = label, parent = parent, visible_attributes = visible_attributes, parameter_space_templates = parameter_space_templates)
def __init__(self, *args, **kwargs):
if 'label' not in kwargs.keys(): kwargs['label'] = 'variable'
self.impose_default('value', 1.0, **kwargs)
self.brand_new = True
parameter_space_templates = [lgeo.interface_template_p_space_axis(instance = self,
p_sp_bounds = ['-10e64', '10e64'],
parent = self, key = 'value')]
modular_object.__init__(self, *args,
parameter_space_templates = parameter_space_templates, **kwargs)
def __init__(self, *args, **kwargs):
if "label" not in kwargs.keys():
kwargs["label"] = "variable"
self.impose_default("value", 1.0, **kwargs)
self.brand_new = True
parameter_space_templates = [
lgeo.interface_template_p_space_axis(
instance=self, p_sp_bounds=["-10e64", "10e64"], parent=self, key="value"
)
]
modular_object.__init__(self, *args, parameter_space_templates=parameter_space_templates, **kwargs)
def __init__(self, *args, **kwargs):
if 'label' not in kwargs.keys(): kwargs['label'] = 'variable'
self.impose_default('value', 1.0, **kwargs)
self.brand_new = True
parameter_space_templates =\
[lgeo.interface_template_p_space_axis(instance = self,
p_sp_bounds = ['-10e64', '10e64'],
parent = self, key = 'value')]
modular_object.__init__(self, *args,
parameter_space_templates =\
parameter_space_templates, **kwargs)
def set_settables(self, *args, **kwargs):
ensem = args[1]
self.parent = ensem
window = args[0]
if self.brand_new:
ensem.run_params["plot_targets"].append(self.label)
plan = ensem.run_params["output_plans"]["Simulation"]
plan.targeted.append(self.label)
plan.rewidget(True)
for subtargeted in plan.outputs:
subtargeted.append(self.label)
self.brand_new = not self.brand_new
# dictionary_support = lgm.dictionary_support_mason(window)
where_reference = ensem.run_params["variables"]
cartographer_support = lgm.cartographer_mason(window)
self.handle_widget_inheritance(*args, **kwargs)
self.parameter_space_templates = [
lgeo.interface_template_p_space_axis(
parent=self, p_sp_bounds=self._p_sp_bounds_[0], instance=self, key="value"
)
]
self.parameter_space_templates[0].set_settables(*args, **kwargs)
self.widg_templates.append(
lgm.interface_template_gui(
widgets=["spin"],
doubles=[[True]],
initials=[[float(self.value)]],
instances=[[self]],
keys=[["value"]],
box_labels=["Variable Value"],
mason=cartographer_support,
parameter_space_templates=[self.parameter_space_templates[0]],
)
)
self.widg_templates.append(
lgm.interface_template_gui(
widgets=["text"],
# mason = dictionary_support,
# wheres = [[where_reference]],
keys=[["label"]],
instances=[[self]],
initials=[[self.label]],
box_labels=["Variable Name"],
)
)
modular_object.set_settables(self, *args, from_sub=True)
def __init__(self, label = 'another species', initial_count = 0, current_count = None, visible_attributes = \ ['label', 'initial_count'], parent = None): self.system = None self.initial_count = initial_count if current_count == None: self.current_count = initial_count else: self.current_count = current_count self.brand_new = True parameter_space_templates =\ [lgeo.interface_template_p_space_axis(instance = self, key = 'initial_count', p_sp_bounds = [0, 1000000], p_sp_increment = 1, p_sp_continuous = False, parent = self)] modular_object.__init__(self, label = label, visible_attributes = visible_attributes, parameter_space_templates = parameter_space_templates)
def __init__(self, label = 'another species', initial_count = 0,
current_count = None, visible_attributes = \
['label', 'initial_count'], parent = None):
self.system = None
self.initial_count = initial_count
if current_count == None: self.current_count = initial_count
else: self.current_count = current_count
self.brand_new = True
parameter_space_templates =\
[lgeo.interface_template_p_space_axis(instance = self,
key = 'initial_count', p_sp_bounds = [0, 1000000],
p_sp_increment = 1, p_sp_continuous = False,
parent = self)]
modular_object.__init__(
self,
label=label,
visible_attributes=visible_attributes,
parameter_space_templates=parameter_space_templates)
def set_settables(self, *args, **kwargs):
ensem = args[1]
self.parent = ensem
window = args[0]
if self.brand_new:
ensem.run_params['plot_targets'].append(self.label)
plan = ensem.run_params['output_plans']['Simulation']
plan.targeted.append(self.label)
plan.rewidget(True)
for subtargeted in plan.outputs:
subtargeted.append(self.label)
self.brand_new = not self.brand_new
#dictionary_support = lgm.dictionary_support_mason(window)
where_reference = ensem.run_params['variables']
cartographer_support = lgm.cartographer_mason(window)
self.handle_widget_inheritance(*args, **kwargs)
self.parameter_space_templates =\
[lgeo.interface_template_p_space_axis(parent = self,
p_sp_bounds = self._p_sp_bounds_[0],
instance = self, key = 'value')]
self.parameter_space_templates[0].set_settables(*args, **kwargs)
self.widg_templates.append(
lgm.interface_template_gui(
widgets = ['spin'],
doubles = [[True]],
initials = [[float(self.value)]],
instances = [[self]],
keys = [['value']],
box_labels = ['Variable Value'],
mason = cartographer_support,
parameter_space_templates =\
[self.parameter_space_templates[0]]))
self.widg_templates.append(
lgm.interface_template_gui(
widgets=['text'],
#mason = dictionary_support,
#wheres = [[where_reference]],
keys=[['label']],
instances=[[self]],
initials=[[self.label]],
box_labels=['Variable Name']))
lfu.modular_object_qt.set_settables(self, *args, from_sub=True)
def set_settables(self, *args, **kwargs):
ensem = args[1]
window = args[0]
spec_list = ensem.run_params['species'].keys()
cartographer_support = lgm.cartographer_mason(window)
self.handle_widget_inheritance(*args, **kwargs)
self.parameter_space_templates =\
[lgeo.interface_template_p_space_axis(parent = self,
p_sp_bounds = self._p_sp_bounds_[0],
instance = self, key = 'rate')]
self.parameter_space_templates[0].set_settables(*args, **kwargs)
left_template = lgm.interface_template_gui(
panel_position=(0, 2),
mason=cartographer_support,
layout='vertical',
keys=[['label'], ['rate']],
instances=[[self], [self]],
widgets=['text', 'text'],
minimum_sizes=[[(400, 100)], [(100, 100)]],
box_labels=['Reaction Name', 'Reaction Rate'],
initials=[[self.label], [self.rate]],
parameter_space_templates=[
None, self.parameter_space_templates[0]
])
self.verify_agents(spec_list)
agents_template = lgm.interface_template_gui(
panel_position=(0, 0),
layout='horizontal',
widgets=['check_spin_list', 'check_spin_list'],
keys=[['used'], ['produced']],
instances=[[self], [self]],
labels=[spec_list, spec_list],
box_labels=['Reagents', 'Products'])
self.widg_templates.append(
lgm.interface_template_gui(
widgets=['splitter'],
orientations=[['horizontal']],
templates=[[left_template, agents_template]]))
modular_object.set_settables(self, *args, from_sub=True)
def set_settables(self, *args, **kwargs): ensem = args[1] window = args[0] spec_list = ensem.run_params['species'].keys() cartographer_support = lgm.cartographer_mason(window) self.handle_widget_inheritance(*args, **kwargs) self.parameter_space_templates =\ [lgeo.interface_template_p_space_axis(parent = self, p_sp_bounds = self._p_sp_bounds_[0], instance = self, key = 'rate')] self.parameter_space_templates[0].set_settables(*args, **kwargs) left_template = lgm.interface_template_gui( panel_position = (0, 2), mason = cartographer_support, layout = 'vertical', keys = [['label'], ['rate']], instances = [[self], [self]], widgets = ['text', 'text'], minimum_sizes = [[(400, 100)], [(100, 100)]], box_labels = ['Reaction Name', 'Reaction Rate'], initials = [[self.label], [self.rate]], parameter_space_templates = [None, self.parameter_space_templates[0]]) self.verify_agents(spec_list) agents_template = lgm.interface_template_gui( panel_position = (0, 0), layout = 'horizontal', widgets = ['check_spin_list', 'check_spin_list'], keys = [['used'], ['produced']], instances = [[self], [self]], labels = [spec_list, spec_list], box_labels = ['Reagents', 'Products']) self.widg_templates.append( lgm.interface_template_gui( widgets = ['splitter'], orientations = [['horizontal']], templates = [[left_template, agents_template]])) modular_object.set_settables(self, *args, from_sub = True)
def __init__(self,
label='another reaction',
rate=float(10.0),
propensity_scheme='classic',
propensity_function_maker=None,
parent=None,
occurrences=[],
used=None,
produced=None,
visible_attributes=[
'label', 'propensity_scheme', 'rate', 'used', 'produced'
]):
self.system = None
self.rate = rate
if occurrences is None: self.occurrences = []
else: self.occurrences = occurrences
#instances of these are somehow coupled unless a
# used and produced list is passed to init,
# EVEN an empty list will do (used = [] does not!)
if used is None: self.used = []
else: self.used = used
if produced is None: self.produced = []
else: self.produced = produced
self.propensity = 1.0
self.propensity_minimum = 1e-30
self.propensity_scheme = propensity_scheme
parameter_space_templates =\
[lgeo.interface_template_p_space_axis(parent = self,
p_sp_bounds = [0.0000001, 1000.0],
instance = self, key = 'rate')]
modular_object.__init__(
self,
label=label,
parent=parent,
visible_attributes=visible_attributes,
parameter_space_templates=parameter_space_templates)
def set_settables(self, *args, **kwargs): window = args[0] self.parent = args[1] ensem = self.parent cartographer_support = lgm.cartographer_mason(window) self.handle_widget_inheritance(*args, **kwargs) if self.brand_new: ensem.run_params['plot_targets'].append(self.label) plan = ensem.run_params['output_plans']['Simulation'] plan.targeted.append(self.label) plan.rewidget(True) for subtargeted in plan.outputs: subtargeted.append(self.label) self.brand_new = not self.brand_new label_data_links = [lfu.interface_template_dependance( (self, 'label', self.label), linkages = [(ensem.run_params, 'plot_targets', True, 'append_list')])] #this will cause a bug if a propensity_function_maker class # with a .key attribute which should not be linked to the # species name exists - so do not use one with this module #on the other hand, a subclass which uses .key exploits this # this bug can be fixed with name mangling on the base class!! label_data_links.extend([lfu.interface_template_dependance( (self, 'label', self.label), linkages =\ [(ensem.run_params['output_plans']['Simulation'], 'targeted', True, 'append_list')])]) [label_data_links.extend([lfu.interface_template_dependance( (self, 'label', self.label), linkages =\ [(ensem.run_params['output_plans']['Simulation'], 'outputs', True, 'append_list_nested', dex)])]) for dex in range(4)] label_data_links.extend( [lfu.interface_template_dependance( (self, 'label', self.label), linkages = [(rxn, 'used', True, 'append_tuples_list', 0, 0)]) for rxn in ensem.run_params['reactions']]) label_data_links.extend( [lfu.interface_template_dependance( (self, 'label', self.label), linkages = [(rxn, 'produced', True, 'append_tuples_list', 0, 0)]) for rxn in ensem.run_params['reactions']]) window = args[1] self.handle_widget_inheritance(*args, **kwargs) self.parameter_space_templates =\ [lgeo.interface_template_p_space_axis(instance = self, key = 'initial_count', parent = self, p_sp_bounds = self._p_sp_bounds_[0], p_sp_increment = self._p_sp_increments_[0], p_sp_continuous = False)] self.parameter_space_templates[0].set_settables(*args, **kwargs) self.widg_templates.append( lgm.interface_template_gui( mason = cartographer_support, widgets = ['spin'], instances = [[self]], keys = [['initial_count']], minimum_values = [[0]], maximum_values = [[sys.maxint]], initials = [[self.initial_count]], box_labels = ['Initial Count'], parameter_space_templates =\ [self.parameter_space_templates[0]])) self.widg_templates.append( lgm.interface_template_gui( keys = [['label']], minimum_sizes = [[(150, 50)]], instances = [[self]], widgets = ['text'], box_labels = ['Species Name'])) modular_object.set_settables(self, *args, from_sub = True)
def set_settables(self, *args, **kwargs):
window = args[0]
self.parent = args[1]
ensem = self.parent
cartographer_support = lgm.cartographer_mason(window)
self.handle_widget_inheritance(*args, **kwargs)
if self.brand_new:
ensem.run_params['plot_targets'].append(self.label)
plan = ensem.run_params['output_plans']['Simulation']
plan.targeted.append(self.label)
plan.rewidget(True)
for subtargeted in plan.outputs:
subtargeted.append(self.label)
self.brand_new = not self.brand_new
label_data_links = [
lfu.interface_template_dependance(
(self, 'label', self.label),
linkages=[(ensem.run_params, 'plot_targets', True,
'append_list')])
]
#this will cause a bug if a propensity_function_maker class
# with a .key attribute which should not be linked to the
# species name exists - so do not use one with this module
#on the other hand, a subclass which uses .key exploits this
# this bug can be fixed with name mangling on the base class!!
label_data_links.extend([lfu.interface_template_dependance(
(self, 'label', self.label), linkages =\
[(ensem.run_params['output_plans']['Simulation'],
'targeted', True, 'append_list')])])
[label_data_links.extend([lfu.interface_template_dependance(
(self, 'label', self.label), linkages =\
[(ensem.run_params['output_plans']['Simulation'],
'outputs', True, 'append_list_nested', dex)])])
for dex in range(4)]
label_data_links.extend([
lfu.interface_template_dependance(
(self, 'label', self.label),
linkages=[(rxn, 'used', True, 'append_tuples_list', 0, 0)])
for rxn in ensem.run_params['reactions']
])
label_data_links.extend([
lfu.interface_template_dependance(
(self, 'label', self.label),
linkages=[(rxn, 'produced', True, 'append_tuples_list', 0, 0)])
for rxn in ensem.run_params['reactions']
])
window = args[1]
self.handle_widget_inheritance(*args, **kwargs)
self.parameter_space_templates =\
[lgeo.interface_template_p_space_axis(instance = self,
key = 'initial_count', parent = self,
p_sp_bounds = self._p_sp_bounds_[0],
p_sp_increment = self._p_sp_increments_[0],
p_sp_continuous = False)]
self.parameter_space_templates[0].set_settables(*args, **kwargs)
self.widg_templates.append(
lgm.interface_template_gui(
mason = cartographer_support,
widgets = ['spin'],
instances = [[self]],
keys = [['initial_count']],
minimum_values = [[0]],
maximum_values = [[sys.maxint]],
initials = [[self.initial_count]],
box_labels = ['Initial Count'],
parameter_space_templates =\
[self.parameter_space_templates[0]]))
self.widg_templates.append(
lgm.interface_template_gui(keys=[['label']],
minimum_sizes=[[(150, 50)]],
instances=[[self]],
widgets=['text'],
box_labels=['Species Name']))
modular_object.set_settables(self, *args, from_sub=True)
