def trapped_inactivated_state_blocker(output_dir, save_model=False):
mc = example_models.construct_four_state_chain()
mc.mirror_model(prefix='d_')
drug_rates = [('I', 'd_I', 'drug_on', 'drug_off')]
for r in drug_rates:
mc.add_both_transitions(*r)
positive_rate_expr = ('a*exp(b*V)', ('a', 'b'))
negative_rate_expr = ('a*exp(-b*V)', ('a', 'b'))
kon_rate_expr = ('k*D', ('k'))
koff_rate_expr = ('l', ('l'))
rate_dictionary = dict(zip(['k_1', 'k_3', 'k_2', 'k_4', 'drug_on', 'drug_off'],
[positive_rate_expr] * 2 + [negative_rate_expr]
* 2 + [kon_rate_expr] + [koff_rate_expr]))
mc.parameterise_rates(rate_dictionary, ['V', 'D'])
mc.draw_graph(os.path.join(output_dir, "%s_trapped_inactivated_state_blocker.html" % mc.name), show_parameters=True)
myokitmodel = mc.generate_myokit_model(drug_binding=True)
print(myokitmodel.code())
if save_model:
myokit.save(filename=os.path.join("%s_trapped_inactivated_state_blocker.mmt") % mc.name, model=myokitmodel)
def mmt_import(importer, source, target=None):
"""
Imports a model and saves it in mmt format.
"""
import myokit
# Get importer
importer = myokit.formats.importer(importer)
# Get logger
logger = importer.logger()
# If a target is specified, set the importer to live logging mode
if target:
logger.set_live(True)
logger.log_flair(str(importer.__class__.__name__))
# Import
m = importer.model(source)
# If a target is specified, save the output
if target:
# Save or output model to new location
logger.log('Saving output to ' + str(target))
myokit.save(target, m)
logger.log('Done.')
else:
# Write it to screen
print(myokit.save(None, m))
def test_parameterise_rates(self):
"""
Test the MarkovChain.parameterise_rates function.
"""
mc = example_models.construct_four_state_chain()
# Expressions to be used for the rates. The variable V (membrane
# voltage) is shared across expressions and so it should only appear
# once in the parameter list.
# Output system of equations
logging.debug("ODE system is %s",
str(mc.get_transition_matrix(use_parameters=True)))
# Output reduced system of equations
logging.debug(
"Reduced ODE system is :%s",
str(
mc.eliminate_state_from_transition_matrix(
list(mc.graph.nodes)[:-1], use_parameters=True)))
# Output list of parameters
param_list = mc.get_parameter_list()
logging.debug("parameters are %s", mc.get_parameter_list())
self.assertEqual(param_list.count('V'), 1)
# Generate myokit code
myokit_model = mc.generate_myokit_model()
myokit.save(os.path.join(self.output_dir, 'beattie_model.mmt'),
myokit_model)
myokit_model = mc.generate_myokit_model(eliminate_state='IC')
myokit.save(os.path.join(self.output_dir, 'beattie_model_reduced.mmt'),
myokit_model)
def save(self):
"""
Tests if the correct parts are saved/loaded from disk using the
``save()`` method.
"""
opath = os.path.join(myotest.DIR_OUT, 'loadsavetest.mmt')
if os.path.exists(opath):
os.remove(opath)
# Test example loading
m, p, x = myokit.load('example')
self.assertIsInstance(m, myokit.Model)
self.assertIsInstance(p, myokit.Protocol)
self.assertIsInstance(x, str)
# Save all three and reload
try:
myokit.save(opath, m, p, x)
mm, pp, xx = myokit.load(opath)
self.assertEqual(m.code(), mm.code())
self.assertEqual(p.code(), pp.code())
self.assertEqual(x, xx)
finally:
if os.path.exists(opath):
os.remove(opath)
# Save only model
try:
myokit.save(opath, model=m)
with open(opath, 'r') as f:
text = f.read()
self.assertTrue('[[model]]' in text)
self.assertFalse('[[protocol]]' in text)
self.assertFalse('[[script]]' in text)
mm, pp, xx = myokit.load(opath)
self.assertEqual(mm.code(), m.code())
self.assertEqual(pp, None)
self.assertEqual(xx, None)
finally:
if os.path.exists(opath):
os.remove(opath)
# Save only protocol
try:
myokit.save(opath, protocol=p)
with open(opath, 'r') as f:
text = f.read()
self.assertFalse('[[model]]' in text)
self.assertTrue('[[protocol]]' in text)
self.assertFalse('[[script]]' in text)
mm, pp, xx = myokit.load(opath)
self.assertEqual(mm, None)
self.assertEqual(pp.code(), p.code())
self.assertEqual(xx, None)
finally:
if os.path.exists(opath):
os.remove(opath)
# Save only script
try:
myokit.save(opath, script=x)
with open(opath, 'r') as f:
text = f.read()
self.assertFalse('[[model]]' in text)
self.assertFalse('[[protocol]]' in text)
self.assertTrue('[[script]]' in text)
mm, pp, xx = myokit.load(opath)
self.assertEqual(mm, None)
self.assertEqual(pp, None)
self.assertEqual(xx, x)
finally:
if os.path.exists(opath):
os.remove(opath)
# Save all but model
try:
myokit.save(opath, protocol=p, script=x)
with open(opath, 'r') as f:
text = f.read()
self.assertFalse('[[model]]' in text)
self.assertTrue('[[protocol]]' in text)
self.assertTrue('[[script]]' in text)
mm, pp, xx = myokit.load(opath)
self.assertEqual(mm, None)
self.assertEqual(pp.code(), p.code())
self.assertEqual(xx, x)
finally:
if os.path.exists(opath):
os.remove(opath)
# Save all but protocol
try:
myokit.save(opath, model=m, script=x)
with open(opath, 'r') as f:
text = f.read()
self.assertTrue('[[model]]' in text)
self.assertFalse('[[protocol]]' in text)
self.assertTrue('[[script]]' in text)
mm, pp, xx = myokit.load(opath)
self.assertEqual(mm.code(), m.code())
self.assertEqual(pp, None)
self.assertEqual(xx, x)
finally:
if os.path.exists(opath):
os.remove(opath)
# Save all but script
try:
myokit.save(opath, model=m, protocol=p)
with open(opath, 'r') as f:
text = f.read()
self.assertTrue('[[model]]' in text)
self.assertTrue('[[protocol]]' in text)
self.assertFalse('[[script]]' in text)
mm, pp, xx = myokit.load(opath)
self.assertEqual(mm.code(), m.code())
self.assertEqual(pp.code(), p.code())
self.assertEqual(xx, None)
finally:
if os.path.exists(opath):
os.remove(opath)
def test_save(self):
# Test if the correct parts are saved/loaded from disk using the
# ``save()`` method.
# Test example loading
m, p, x = myokit.load('example')
self.assertIsInstance(m, myokit.Model)
self.assertIsInstance(p, myokit.Protocol)
self.assertTrue(isinstance(x, basestring))
# Save all three and reload
with TemporaryDirectory() as d:
opath = d.path('test.mmt')
myokit.save(opath, m, p, x)
mm, pp, xx = myokit.load(opath)
self.assertEqual(m.code(), mm.code())
self.assertEqual(p.code(), pp.code())
self.assertEqual(x, xx)
# Save only model
with TemporaryDirectory() as d:
opath = d.path('test.mmt')
myokit.save(opath, model=m)
with open(opath, 'r') as f:
text = f.read()
self.assertTrue('[[model]]' in text)
self.assertFalse('[[protocol]]' in text)
self.assertFalse('[[script]]' in text)
mm, pp, xx = myokit.load(opath)
self.assertEqual(mm.code(), m.code())
self.assertEqual(pp, None)
self.assertEqual(xx, None)
# Save only protocol
with TemporaryDirectory() as d:
opath = d.path('test.mmt')
myokit.save(opath, protocol=p)
with open(opath, 'r') as f:
text = f.read()
self.assertFalse('[[model]]' in text)
self.assertTrue('[[protocol]]' in text)
self.assertFalse('[[script]]' in text)
mm, pp, xx = myokit.load(opath)
self.assertEqual(mm, None)
self.assertEqual(pp.code(), p.code())
self.assertEqual(xx, None)
# Save only script
with TemporaryDirectory() as d:
opath = d.path('test.mmt')
myokit.save(opath, script=x)
with open(opath, 'r') as f:
text = f.read()
self.assertFalse('[[model]]' in text)
self.assertFalse('[[protocol]]' in text)
self.assertTrue('[[script]]' in text)
mm, pp, xx = myokit.load(opath)
self.assertEqual(mm, None)
self.assertEqual(pp, None)
self.assertEqual(xx, x)
# Save all but model
with TemporaryDirectory() as d:
opath = d.path('test.mmt')
myokit.save(opath, protocol=p, script=x)
with open(opath, 'r') as f:
text = f.read()
self.assertFalse('[[model]]' in text)
self.assertTrue('[[protocol]]' in text)
self.assertTrue('[[script]]' in text)
mm, pp, xx = myokit.load(opath)
self.assertEqual(mm, None)
self.assertEqual(pp.code(), p.code())
self.assertEqual(xx, x)
# Save all but protocol
with TemporaryDirectory() as d:
opath = d.path('test.mmt')
myokit.save(opath, model=m, script=x)
with open(opath, 'r') as f:
text = f.read()
self.assertTrue('[[model]]' in text)
self.assertFalse('[[protocol]]' in text)
self.assertTrue('[[script]]' in text)
mm, pp, xx = myokit.load(opath)
self.assertEqual(mm.code(), m.code())
self.assertEqual(pp, None)
self.assertEqual(xx, x)
# Save all but script
with TemporaryDirectory() as d:
opath = d.path('test.mmt')
myokit.save(opath, model=m, protocol=p)
with open(opath, 'r') as f:
text = f.read()
self.assertTrue('[[model]]' in text)
self.assertTrue('[[protocol]]' in text)
self.assertFalse('[[script]]' in text)
mm, pp, xx = myokit.load(opath)
self.assertEqual(mm.code(), m.code())
self.assertEqual(pp.code(), p.code())
self.assertEqual(xx, None)
# Save all as strings
with TemporaryDirectory() as d:
opath = d.path('test.mmt')
myokit.save(opath, m, p, x)
with open(opath, 'r') as f:
text1 = f.read()
myokit.save(opath, m.code(), p.code(), x)
with open(opath, 'r') as f:
text2 = f.read()
self.assertEqual(text1, text2)
# Save all as strings without [[model]] or [[protocol]] tage
with TemporaryDirectory() as d:
opath = d.path('test.mmt')
myokit.save(opath, m, p, x)
with open(opath, 'r') as f:
text1 = f.read()
mcode = '\n'.join(m.code().splitlines()[1:])
pcode = '\n'.join(p.code().splitlines()[1:])
myokit.save(opath, mcode, pcode, x)
with open(opath, 'r') as f:
text2 = f.read()
self.assertEqual(text1, text2)
# Save all, compare with string generated version
with TemporaryDirectory() as d:
opath = d.path('test.mmt')
myokit.save(opath, model=m, protocol=p, script=x)
with open(opath, 'r') as f:
text = f.read()
self.assertEqual(text, myokit.save(model=m, protocol=p, script=x))
def clamp_experiment_model(model_filename,
clamped_variable_annot: str,
pace_variable_annotation: str,
protocol=None,
save_new_mmt_filename=None):
"""
This function loads a mmt model, sets the equation for the desired variable
to engine.pace (bound with the protocol), and returns the Myokit.model
generated this way. If the user provides the argument for
save_new_mmt_filename, the new model is also saved in the hard drive.
:param model_filename: str
Path and filename to the MMT model loaded.
:param clamped_variable_annot: str
MMT model annotation for the model variable clamped. This variable's
values will be set by the protocol.
:param pace_variable_annotation: str
Model annotation for the variable bound to pace, used to read out
information from the Myokit protocol. Usually, the annotation is either
engine.pace or environment.pace
:param protocol: Myokit.Protocol()
If specified by the user, the protocol will be added to the MMT file
saved.
:param save_new_mmt_filename: str
Path and filename to the location where the user wants to save the
model ready for clamping simulations.
:return: m: Myokit.Model()
Returns a Myokit.Model() ready to be used with a clamping protocol to
generate a Myokit.Simulation().
"""
# Check that model_filename is provided as a mmt file
if model_filename[-4:] != '.mmt':
raise ValueError('The model_filename should lead to a MMT model.')
# Load the MMT file depending on whether a protocol is entered as function
# input
if protocol is not None:
m = myokit.load_model(model_filename)
else:
m, protocol, script = myokit.load(model_filename)
# Analyse the clamped_variable_annot to find component name and variable
# name
i = clamped_variable_annot.index('.')
component_name = clamped_variable_annot[0:i]
variable_name = clamped_variable_annot[i + 1:]
# Change the model to clamp the selected value
original_protocol_component = m.get(component_name,
class_filter=myokit.Component)
variable_found = False
for variable in original_protocol_component.variables():
if variable.name() == variable_name:
if variable.is_state():
# Set the variable type to constant if needed
variable.demote()
# Bind the variable to the pace (= read from protocol)
variable.set_rhs(pace_variable_annotation)
variable_found = True
if not variable_found:
raise ValueError('The variable ' + clamped_variable_annot +
' could not be found.')
# Save the new model and protocol if the user provided the argument
# save_new_mmt_filename
if save_new_mmt_filename is not None:
if protocol is not None:
myokit.save(save_new_mmt_filename, model=m, protocol=protocol)
else:
myokit.save(save_new_mmt_filename, model=m)
return m
