fix fake elasticities in Symca to assign -1 to products and modifiers

Author: jmrohwer

psctb/analyse/_symca/_symca.py

@@ -52,7 +52,7 @@ def __init__(self, mod, auto_load=False, internal_fixed=False, ignore_steady_sta
             warnings.warn_explicit("\nIgnoring steady-state solution: Steady-state variables set to 1. Note that parameter scan functionality is unavailable.",
                                    Warning,
                                    filename=get_filename_from_caller(),
-                                   lineno=36)
+                                   lineno=42)
             SMCAtools.populate_with_fake_elasticities(mod)
             SMCAtools.populate_with_fake_fluxes(mod)
             SMCAtools.populate_with_fake_ss_concentrations(mod)

psctb/analyse/_symca/symca_toolbox.py

@@ -8,14 +8,15 @@
 # from os import mkdir
 import sys
 #from re import sub
+from pysces import ModelMap
 from sympy import Symbol, sympify, nsimplify, fraction, S
 from sympy.matrices import Matrix, diag, NonSquareMatrixError
 from .ccobjects import CCBase, CCoef
 from ...utils.misc import DotDict
 from ...utils.misc import formatter_factory
 from ...utils import ConfigReader
-from ...utils.misc import ec_list, flux_list, ss_species_list
-
+from ...utils.misc import ec_list, prod_ec_list, mod_ec_list, \
+                          flux_list, ss_species_list
 
 ## Everything in this file can be a function rather than a static method
 ## better yet, almost everything can be part of symca. Finally everything can
@@ -638,6 +639,10 @@ def generic_populate(mod, function, value = 1):
     @staticmethod
     def populate_with_fake_elasticities(mod):
         SymcaToolBox.generic_populate(mod, ec_list)
+        # set product elasticities to -1 to avoid divide by zero errors in Symca
+        SymcaToolBox.generic_populate(mod, prod_ec_list, value=-1)
+        # same for modifiers as these are mostly allosteric inhibitors
+        SymcaToolBox.generic_populate(mod, mod_ec_list, value=-1)
 
     @staticmethod
     def populate_with_fake_fluxes(mod):

psctb/utils/misc/_misc.py

@@ -10,13 +10,16 @@
 from numpy import array, errstate, nanmin, nanmax, nonzero, float64,\
     bool_, string_, ones
 from pysces.PyscesModel import PysMod
+from pysces import ModelMap
 from IPython.display import HTML
 from sympy import sympify
 from functools import wraps
 from ..config import ConfigReader
 
 __all__ = ['cc_list',
            'ec_list',
+           'prod_ec_list',
+           'mod_ec_list',
            'rc_list',
            'prc_list',
            'silence_print',
@@ -84,7 +87,7 @@ def is_species(attr, model):
 
 @memoize
 def is_reaction(attr, model):
-    if attr.endswith('J_'):
+    if attr.startswith('J_'):
         attr = attr[2:]
     if attr in model.reactions:
         return True
@@ -795,6 +798,55 @@ def ec_list(mod):
     ecs.sort()
     return ecs
 
+@memoize
+def prod_ec_list(mod):
+    """
+    Returns a list of product elasticity coefficients of a model.
+
+    Returns
+    -------
+    list of str
+        The prod_ec_list is sorted alphabetically.
+
+    See Also
+    --------
+    ec_list, cc_list, rc_list, prc_list
+
+    """
+    ecs = []
+    model_map = ModelMap(mod)
+    for top_reaction in mod.reactions:
+        r = getattr(model_map, top_reaction)
+        for base_product in r.hasProducts():
+            ec = 'ec%s_%s' % (top_reaction, base_product)
+            ecs.append(str(ec))
+    ecs.sort()
+    return ecs
+
+@memoize
+def mod_ec_list(mod):
+    """
+    Returns a list of modifier elasticity coefficients of a model.
+
+    Returns
+    -------
+    list of str
+        The mod_ec_list is sorted alphabetically.
+
+    See Also
+    --------
+    ec_list, cc_list, rc_list, prc_list
+
+    """
+    ecs = []
+    modifiers = dict(mod.__modifiers__)
+    for top_reaction in modifiers:
+        for base_species in modifiers[top_reaction]:
+            ec = 'ec%s_%s' % (top_reaction, base_species)
+            ecs.append(str(ec))
+    ecs.sort()
+    return ecs
+
 @memoize
 def ec_dict(mod):
     ecs = {}