Add thirty models

markov_builder/models/thirty_models/__init__.py

@@ -13,11 +13,28 @@
 from .model12 import model_12
 from .model13 import model_13
 from .model14 import model_14
+from .model15 import model_15
+from .model16 import model_16
+from .model17 import model_17
+from .model18 import model_18
+from .model19 import model_19
 from .model20 import model_20
+from .model21 import model_21
+from .model22 import model_22
+from .model23 import model_23
+from .model24 import model_24
+from .model25 import model_25
+from .model26 import model_26
+from .model27 import model_27
+from .model28 import model_28
+from .model29 import model_29
 from .model30 import model_30
 
 
 __all__ = ['model_00', 'model_01', 'model_02', 'model_03', 'model_04',
            'model_05', 'model_06', 'model_07', 'model_08', 'model_09',
            'model_10', 'model_11', 'model_12', 'model_13', 'model_14',
-           'model_20', 'model_30']
+           'model_15', 'model_16', 'model_17', 'model_18', 'model_19',
+           'model_20', 'model_21', 'model_22', 'model_23', 'model_24',
+           'model_25', 'model_26', 'model_27', 'model_28', 'model_29',
+           'model_30']

markov_builder/models/thirty_models/model15.py

@@ -0,0 +1,82 @@
+from numpy import nan
+from markov_builder.MarkovChain import MarkovChain
+
+
+class model_15(MarkovChain):
+    description = "IKr Markov model 15 (Sanmitra Ghosh)"
+
+    # States
+    states = ('C3', 'C2', 'C1', 'O', 'I')
+
+    # Transitions derived directly from dot() equations
+    rates = [
+        ('C3', 'C2', 'a1', 'b1'),
+        ('C2', 'C1', 'a2', 'b2'),
+        ('C1', 'O', 'a3', 'b3'),
+        ('O', 'I', 'a4', 'b4'),
+    ]
+
+    # Open state
+    open_state = 'O'
+
+    # Rate expressions (verbatim from .mmt)
+    rate_dictionary = {
+        'a1': ('p1 * exp(p2 * V)',),
+        'b1': ('p3 * exp(-p4 * V)',),
+
+        'a2': ('p5 * exp(p6 * V)',),
+        'b2': ('p7 * exp(-p8 * V)',),
+
+        'a3': ('p9 * exp(p10 * V)',),
+        'b3': ('p11 * exp(-p12 * V)',),
+
+        'a4': ('p13 * exp(p14 * V)',),
+        'b4': ('p15 * exp(-p16 * V)',),
+    }
+
+    # Shared variables and parameters
+    shared_variables_dict = {
+        'V': nan,
+
+        'p1': 2.26e-4,
+        'p2': 0.06990,
+        'p3': 3.45e-5,
+        'p4': 0.05462,
+
+        'p5': 0.08730,
+        'p6': 8.91e-3,
+        'p7': 5.15e-3,
+        'p8': 0.03158,
+
+        'p9': 2.26e-4,
+        'p10': 0.06990,
+        'p11': 3.45e-5,
+        'p12': 0.05462,
+
+        'p13': 0.08730,
+        'p14': 8.91e-3,
+        'p15': 5.15e-3,
+        'p16': 0.03158,
+
+        'p17': 0.15240,
+    }
+
+    # Current expression
+    auxiliary_expression = 'p17 * state_O * (V - E_Kr)'
+    auxiliary_symbol = 'I_Kr'
+
+    auxiliary_parameters = {
+        'E_Kr': -88,
+    }
+
+    def __init__(self):
+        super().__init__(
+            states=self.states,
+            open_state=self.open_state,
+            transition_rates=self.rates,
+            rate_expressions=self.rate_dictionary,
+            auxiliary_expression=self.auxiliary_expression,
+            auxiliary_symbol=self.auxiliary_symbol,
+            shared_variables=self.shared_variables_dict,
+            auxiliary_parameters=self.auxiliary_parameters,
+        )

markov_builder/models/thirty_models/model16.py

@@ -0,0 +1,81 @@
+from numpy import nan
+from markov_builder.MarkovChain import MarkovChain
+
+
+class model_16(MarkovChain):
+    description = "IKr Markov model 16 (Wang et al. 1997, Sanmitra Ghosh)"
+
+    # States
+    states = ('C3', 'C2', 'C1', 'O', 'I')
+
+    # Transitions derived from dot() equations
+    rates = [
+        ('C3', 'C2', 'a1', 'b1'),
+        ('C2', 'C1', 'a2', 'b2'),
+        ('C1', 'O', 'a3', 'b3'),
+        ('O', 'I', 'a4', 'b4'),
+    ]
+
+    # Open state
+    open_state = 'O'
+
+    # Rate expressions (verbatim from .mmt)
+    rate_dictionary = {
+        'a1': ('p1 * exp(p2 * V)',),
+        'b1': ('p3 * exp(-p4 * V)',),
+
+        'a3': ('p5 * exp(p6 * V)',),
+        'b3': ('p7 * exp(-p8 * V)',),
+
+        'a4': ('p9 * exp(p10 * V)',),
+        'b4': ('p11 * exp(-p12 * V)',),
+
+        # Voltage-independent rates
+        'a2': ('p13',),
+        'b2': ('p14',),
+    }
+
+    # Shared variables and parameters
+    shared_variables_dict = {
+        'V': nan,
+
+        'p1': 2.26e-4,
+        'p2': 0.06990,
+        'p3': 3.45e-5,
+        'p4': 0.05462,
+
+        'p5': 0.08730,
+        'p6': 8.91e-3,
+        'p7': 5.15e-3,
+        'p8': 0.03158,
+
+        'p9': 0.08730,
+        'p10': 8.91e-3,
+        'p11': 5.15e-3,
+        'p12': 0.03158,
+
+        'p13': 0.08730,
+        'p14': 8.91e-3,
+
+        'p15': 0.15240,
+    }
+
+    # Current expression
+    auxiliary_expression = 'p15 * state_O * (V - E_Kr)'
+    auxiliary_symbol = 'I_Kr'
+
+    auxiliary_parameters = {
+        'E_Kr': -85,
+    }
+
+    def __init__(self):
+        super().__init__(
+            states=self.states,
+            open_state=self.open_state,
+            transition_rates=self.rates,
+            rate_expressions=self.rate_dictionary,
+            auxiliary_expression=self.auxiliary_expression,
+            auxiliary_symbol=self.auxiliary_symbol,
+            shared_variables=self.shared_variables_dict,
+            auxiliary_parameters=self.auxiliary_parameters,
+        )

markov_builder/models/thirty_models/model17.py

@@ -0,0 +1,77 @@
+from numpy import nan
+from markov_builder.MarkovChain import MarkovChain
+
+
+class model_17(MarkovChain):
+    description = "IKr Markov model (Sanmitra Ghosh)"
+
+    # States
+    states = ('C3', 'C2', 'C1', 'O', 'I')
+
+    # Transitions inferred directly from dot() equations
+    rates = [
+        # C3 <-> C2
+        ('C3', 'C2', '3*am', 'bm'),
+
+        # C2 <-> C1
+        ('C2', 'C1', '2*am', '2*bm'),
+
+        # C1 <-> O
+        ('C1', 'O', 'am', '3*bm'),
+
+        # C1 <-> I
+        ('C1', 'I', 'a2', 'b2'),
+
+        # O <-> I
+        ('O', 'I', 'a1', 'b1'),
+    ]
+
+    # Open state
+    open_state = 'O'
+
+    # Rate expressions (verbatim from .mmt)
+    rate_dictionary = {
+        'am': ('p1 * exp(p2 * V)',),
+        'bm': ('p3 * exp(-p4 * V)',),
+        'a1': ('p5 * exp(p6 * V)',),
+        'b1': ('p7 * exp(-p8 * V)',),
+        'a2': ('p9 * exp(p10 * V)',),
+        'b2': ('(a2 * 3 * bm * b1) / (am * a1)',),
+    }
+
+    # Shared variables and parameters
+    shared_variables_dict = {
+        'V': nan,
+
+        'p1': 2.26e-4,
+        'p2': 0.06990,
+        'p3': 3.45e-5,
+        'p4': 0.05462,
+        'p5': 0.08730,
+        'p6': 8.91e-3,
+        'p7': 5.15e-3,
+        'p8': 0.03158,
+        'p9': 5.15e-3,
+        'p10': 0.03158,
+        'p11': 0.15240,
+    }
+
+    # Current expression
+    auxiliary_expression = 'p11 * state_O * (V - E_Kr)'
+    auxiliary_symbol = 'I_Kr'
+
+    auxiliary_parameters = {
+        'E_Kr': -85,
+    }
+
+    def __init__(self):
+        super().__init__(
+            states=self.states,
+            open_state=self.open_state,
+            transition_rates=self.rates,
+            rate_expressions=self.rate_dictionary,
+            auxiliary_expression=self.auxiliary_expression,
+            auxiliary_symbol=self.auxiliary_symbol,
+            shared_variables=self.shared_variables_dict,
+            auxiliary_parameters=self.auxiliary_parameters,
+        )

markov_builder/models/thirty_models/model18.py

@@ -0,0 +1,98 @@
+from numpy import nan
+from markov_builder.MarkovChain import MarkovChain
+
+
+class model_18(MarkovChain):
+    description = "IKr Markov model 18 (Sanmitra Ghosh)"
+
+    # States
+    states = ('C3', 'C2', 'C1', 'O', 'I')
+
+    # Transitions derived directly from dot() equations
+    rates = [
+        # C3 <-> C2
+        ('C3', 'C2', 'a1', 'b1'),
+
+        # C2 <-> C1
+        ('C2', 'C1', 'a2', 'b2'),
+
+        # C1 <-> O
+        ('C1', 'O', 'a3', 'b3'),
+
+        # O <-> I
+        ('O', 'I', 'a4', 'b4'),
+
+        # C1 <-> I
+        ('C1', 'I', 'a5', 'b5'),
+    ]
+
+    # Open state
+    open_state = 'O'
+
+    # Rate expressions (verbatim from .mmt)
+    rate_dictionary = {
+        'a1': ('p1 * exp(p2 * V)',),
+        'b1': ('p3 * exp(-p4 * V)',),
+
+        'a2': ('p5 * exp(p6 * V)',),
+        'b2': ('p7 * exp(-p8 * V)',),
+
+        'a3': ('p9 * exp(p10 * V)',),
+        'b3': ('p11 * exp(-p12 * V)',),
+
+        'a4': ('p13 * exp(p14 * V)',),
+        'b4': ('p15 * exp(-p16 * V)',),
+
+        'a5': ('p17 * exp(p18 * V)',),
+        'b5': ('(a5 * b3 * b4) / (a3 * a4)',),
+    }
+
+    # Shared variables and parameters
+    shared_variables_dict = {
+        'V': nan,
+
+        'p1': 2.26e-4,
+        'p2': 0.06990,
+        'p3': 3.45e-5,
+        'p4': 0.05462,
+
+        'p5': 0.08730,
+        'p6': 8.91e-3,
+        'p7': 5.15e-3,
+        'p8': 0.03158,
+
+        'p9': 5.15e-3,
+        'p10': 0.03158,
+        'p11': 2.26e-4,
+        'p12': 0.06990,
+
+        'p13': 3.45e-5,
+        'p14': 0.05462,
+        'p15': 0.08730,
+        'p16': 8.91e-3,
+
+        'p17': 5.15e-3,
+        'p18': 0.03158,
+
+        'p19': 0.15240,
+    }
+
+    # Current expression
+    auxiliary_expression = 'p19 * state_O * (V - E_Kr)'
+    auxiliary_symbol = 'I_Kr'
+
+    auxiliary_parameters = {
+        'E_Kr': -85,
+    }
+
+    def __init__(self):
+        super().__init__(
+            states=self.states,
+            open_state=self.open_state,
+            transition_rates=self.rates,
+            rate_expressions=self.rate_dictionary,
+            auxiliary_expression=self.auxiliary_expression,
+            auxiliary_symbol=self.auxiliary_symbol,
+            shared_variables=self.shared_variables_dict,
+            auxiliary_parameters=self.auxiliary_parameters,
+        )