import sys
import os
import errno
import warnings
import inspect
import re
import collections
import weakref
import copy
import itertools
import sympy
try:
reload
except NameError:
from imp import reload
try:
basestring
except NameError:
# Under Python 3, do not pretend that bytes are a valid string
basestring = str
long = int
[docs]def Initial(*args):
"""Declare an initial condition (see Model.initial)."""
return SelfExporter.default_model.initial(*args)
[docs]def MatchOnce(pattern):
"""Make a ComplexPattern match-once."""
cp = as_complex_pattern(pattern).copy()
cp.match_once = True
return cp
# A module may define a global with this name (_pysb_doctest_...) to request
# that SelfExporter not issue any ModelExistsWarnings from doctests defined
# therein. (This is the best method we could come up with to manage this
# behavior, as doctest doesn't offer per-doctest setup/teardown.)
_SUPPRESS_MEW = '_pysb_doctest_suppress_modelexistswarning'
[docs]class SelfExporter(object):
"""
Make model components appear in the calling module's namespace.
This class is for pysb internal use only. Do not construct any instances.
"""
do_export = True
default_model = None
target_globals = None # the globals dict to which we'll export our symbols
target_module = None # the module to which we've exported
@staticmethod
[docs] def export(obj):
"""Export an object by name and add it to the default model."""
if not SelfExporter.do_export:
return
if not isinstance(obj, (Model, Component)):
raise Exception("%s is not a type that is understood by SelfExporter" % str(type(obj)))
# determine the module from which we were called (we need to do this here so we can
# calculate stacklevel for use in the warning at the bottom of this method)
cur_module = inspect.getmodule(inspect.currentframe())
caller_frame = inspect.currentframe()
# walk up through the stack until we hit a different module
stacklevel = 1
while inspect.getmodule(caller_frame) == cur_module:
stacklevel += 1
caller_frame = caller_frame.f_back
# use obj's name as the symbol to export it to (unless modified below)
export_name = obj.name
if isinstance(obj, Model):
new_target_module = inspect.getmodule(caller_frame)
if SelfExporter.default_model is not None \
and new_target_module is SelfExporter.target_module:
# Warn, unless running a doctest whose containing module set the
# magic global which tells us to suppress it.
if not (
caller_frame.f_code.co_filename.startswith('<doctest ') and
caller_frame.f_globals.get(_SUPPRESS_MEW)):
warnings.warn("Redefining model! (You can probably ignore "
"this if you are running code interactively)",
ModelExistsWarning, stacklevel)
SelfExporter.cleanup()
SelfExporter.target_module = new_target_module
SelfExporter.target_globals = caller_frame.f_globals
SelfExporter.default_model = obj
# if not set, assign model's name from the module it lives in. very sneaky and fragile.
if obj.name is None:
if SelfExporter.target_module == sys.modules['__main__']:
# user ran model .py directly
model_path = inspect.getfile(sys.modules['__main__'])
model_filename = os.path.basename(model_path)
module_name = re.sub(r'\.py$', '', model_filename)
elif SelfExporter.target_module is not None:
# model is imported by some other script (typical case)
module_name = SelfExporter.target_module.__name__
else:
# user is defining a model interactively (not really supported, but we'll try)
module_name = '_interactive_'
obj.name = module_name # internal name for identification
export_name = 'model' # symbol name for export
elif isinstance(obj, Component):
if SelfExporter.default_model == None:
raise Exception("A Model must be declared before declaring any model components")
SelfExporter.default_model.add_component(obj)
# load obj into target namespace under obj.name
if export_name in SelfExporter.target_globals:
warnings.warn("'%s' already defined" % (export_name), SymbolExistsWarning, stacklevel)
SelfExporter.target_globals[export_name] = obj
@staticmethod
[docs] def cleanup():
"""Delete previously exported symbols."""
if SelfExporter.default_model is None:
return
for name in [c.name for c in SelfExporter.default_model.all_components()] + ['model']:
if name in SelfExporter.target_globals:
del SelfExporter.target_globals[name]
SelfExporter.default_model = None
SelfExporter.target_globals = None
SelfExporter.target_module = None
@staticmethod
[docs] def rename(obj, new_name):
"""Rename a previously exported symbol"""
if new_name in SelfExporter.target_globals:
msg = "'%s' already defined" % new_name
warnings.warn(msg, SymbolExistsWarning, 2)
if obj.name in SelfExporter.target_globals:
obj = SelfExporter.target_globals[obj.name]
SelfExporter.target_globals[new_name] = obj
del SelfExporter.target_globals[obj.name]
else:
raise ValueError("Could not find object in global namespace by its"
"name '%s'" % obj.name)
[docs]class Component(object):
"""
The base class for all the named things contained within a model.
Parameters
----------
name : string
Name of the component. Must be unique within the containing model.
Attributes
----------
name : string
Name of the component.
model : weakref(Model)
Containing model.
"""
def __init__(self, name, _export=True):
if not re.match(r'[_a-z][_a-z0-9]*\Z', name, re.IGNORECASE):
raise InvalidComponentNameError(name)
self.name = name
self.model = None # to be set in Model.add_component
self._export = _export
if self._export:
self._do_export()
def __getstate__(self):
# clear the weakref to parent model (restored in Model.__setstate__)
state = self.__dict__.copy()
del state['model']
# Force _export to False; we don't want the unpickling process to
# trigger SelfExporter.export!
state['_export'] = False
return state
def _do_export(self):
try:
SelfExporter.export(self)
except ComponentDuplicateNameError as e:
# re-raise to hide the stack trace below this point -- it's irrelevant to the user
# and makes the error harder to understand
raise e
[docs] def rename(self, new_name):
"""Change component's name.
This is typically only needed when deriving one model from another and
it would be desirable to change a component's name in the derived
model."""
self.model()._rename_component(self, new_name)
if self._export:
SelfExporter.rename(self, new_name)
self.name = new_name
[docs]class Monomer(Component):
"""
Model component representing a protein or other molecule.
Parameters
----------
sites : list of strings, optional
Names of the sites.
site_states : dict of string => string, optional
Allowable states for sites. Keys are sites and values are lists of
states. Sites which only take part in bond formation and never take on a
state may be omitted.
Attributes
----------
Identical to Parameters (see above).
Notes
-----
A Monomer instance may be \"called\" like a function to produce a
MonomerPattern, as syntactic sugar to approximate rule-based modeling
language syntax. It is typically called with keyword arguments where the arg
names are sites and values are site conditions such as bond numbers or
states (see the Notes section of the :py:class:`MonomerPattern`
documentation for details). To help in situations where kwargs are unwieldy
(for example if a site name is computed dynamically or stored in a variable)
a dict following the same layout as the kwargs may be passed as the first
and only positional argument instead.
"""
def __init__(self, name, sites=None, site_states=None, _export=True):
Component.__init__(self, name, _export)
# Create default empty containers.
if sites is None:
sites = []
if site_states is None:
site_states = {}
# ensure sites is some kind of list (presumably of strings) but not a string itself
if not isinstance(sites, collections.Iterable) or isinstance(sites, basestring):
raise ValueError("sites must be a list of strings")
# ensure no duplicate sites
sites_seen = {}
for site in sites:
sites_seen.setdefault(site, 0)
sites_seen[site] += 1
sites_dup = [site for site, count in sites_seen.items() if count > 1]
if sites_dup:
raise Exception("Duplicate sites specified: " + str(sites_dup))
# ensure site_states keys are all known sites
unknown_sites = [site for site in site_states if not site in sites_seen]
if unknown_sites:
raise Exception("Unknown sites in site_states: " + str(unknown_sites))
# ensure site_states values are all strings
invalid_sites = [site for (site, states) in site_states.items() if not all([type(s) == str for s in states])]
if invalid_sites:
raise Exception("Non-string state values in site_states for sites: " + str(invalid_sites))
self.sites = list(sites)
self.site_states = site_states
def __call__(self, conditions=None, **kwargs):
"""
Return a MonomerPattern object based on this Monomer.
See the Notes section of this class's documentation for details.
Parameters
----------
conditions : dict, optional
See MonomerPattern.site_conditions.
**kwargs : dict
See MonomerPattern.site_conditions.
"""
return MonomerPattern(self, extract_site_conditions(conditions, **kwargs), None)
def __repr__(self):
value = '%s(%s' % (self.__class__.__name__, repr(self.name))
if self.sites:
value += ', %s' % repr(self.sites)
if self.site_states:
value += ', %s' % repr(self.site_states)
value += ')'
return value
[docs]class MonomerPattern(object):
"""
A pattern which matches instances of a given monomer.
Parameters
----------
monomer : Monomer
The monomer to match.
site_conditions : dict
The desired state of the monomer's sites. Keys are site names and values
are described below in Notes.
compartment : Compartment or None
The desired compartment where the monomer should exist. None means
\"don't-care\".
Attributes
----------
Identical to Parameters (see above).
Notes
-----
The acceptable values in the `site_conditions` dict are as follows:
* ``None`` : no bond
* *str* : state
* *int* : a bond (to a site with the same number in a ComplexPattern)
* *list of int* : multi-bond (not valid in Kappa)
* ``ANY`` : \"any\" bond (bound to something, but don't care what)
* ``WILD`` : \"wildcard\" bond (bound or not bound)
* *tuple of (str, int)* : state with specified bond
* *tuple of (str, WILD)* : state with wildcard bond
* *tuple of (str, ANY)* : state with any bond
If a site is not listed in site_conditions then the pattern will match any
state for that site, i.e. \"don't write, don't care\".
"""
def __init__(self, monomer, site_conditions, compartment):
# ensure all keys in site_conditions are sites in monomer
unknown_sites = [site for site in site_conditions if site not in monomer.sites]
if unknown_sites:
raise Exception("MonomerPattern with unknown sites in " + str(monomer) + ": " + str(unknown_sites))
# ensure each value is one of: None, integer, list of integers, string,
# (string,integer), (string,WILD), ANY, WILD
invalid_sites = []
for (site, state) in site_conditions.items():
# pass through to next iteration if state type is ok
if state == None:
continue
elif type(state) == int:
continue
elif type(state) == list and all(isinstance(s, int) for s in state):
continue
elif type(state) == str:
continue
elif type(state) == tuple and type(state[0]) == str and (type(state[1]) == int or state[1] is WILD or state[1] is ANY):
continue
elif state is ANY:
continue
elif state is WILD:
continue
invalid_sites.append(site)
if invalid_sites:
raise Exception("Invalid state value for sites: " + '; '.join(['%s=%s' % (s,str(site_conditions[s])) for s in invalid_sites]))
# ensure compartment is a Compartment
if compartment and not isinstance(compartment, Compartment):
raise Exception("compartment is not a Compartment object")
self.monomer = monomer
self.site_conditions = site_conditions
self.compartment = compartment
[docs] def is_concrete(self):
"""
Return a bool indicating whether the pattern is 'concrete'.
'Concrete' means the pattern satisfies ALL of the following:
1. All sites have specified conditions
2. If the model uses compartments, the compartment is specified.
"""
# 1.
sites_ok = self.is_site_concrete()
# 2.
compartment_ok = not self.monomer.model().compartments or self.compartment
return compartment_ok and sites_ok
[docs] def is_site_concrete(self):
"""
Return a bool indicating whether the pattern is 'site-concrete'.
'Site-concrete' means all sites have specified conditions."""
# assume __init__ did a thorough enough job of error checking that this is is all we need to do
return len(self.site_conditions) == len(self.monomer.sites)
def __call__(self, conditions=None, **kwargs):
"""Build a new MonomerPattern with updated site conditions. Can be used
to obtain a shallow copy by passing an empty argument list."""
# The new object will have references to the original monomer and
# compartment, and a shallow copy of site_conditions which has been
# updated according to our args (as in Monomer.__call__).
site_conditions = self.site_conditions.copy()
site_conditions.update(extract_site_conditions(conditions, **kwargs))
return MonomerPattern(self.monomer, site_conditions, self.compartment)
def __add__(self, other):
if isinstance(other, MonomerPattern):
return ReactionPattern([ComplexPattern([self], None), ComplexPattern([other], None)])
if isinstance(other, ComplexPattern):
return ReactionPattern([ComplexPattern([self], None), other])
elif other == None:
return as_reaction_pattern(self)
else:
return NotImplemented
def __mod__(self, other):
if isinstance(other, MonomerPattern):
return ComplexPattern([self, other], None)
else:
return NotImplemented
def __rshift__(self, other):
return build_rule_expression(self, other, False)
def __rrshift__(self, other):
return build_rule_expression(other, self, False)
def __ne__(self, other):
return build_rule_expression(self, other, True)
def __pow__(self, other):
if isinstance(other, Compartment):
mp_new = self()
mp_new.compartment = other
return mp_new
else:
return NotImplemented
def __repr__(self):
value = '%s(' % self.monomer.name
value += ', '.join([
k + '=' + repr(self.site_conditions[k])
for k in self.monomer.sites
if k in self.site_conditions
])
value += ')'
if self.compartment is not None:
value += ' ** ' + self.compartment.name
return value
[docs]class ComplexPattern(object):
"""
A bound set of MonomerPatterns, i.e. a pattern to match a complex.
In BNG terms, a list of patterns combined with the '.' operator.
Parameters
----------
monomer_patterns : list of MonomerPatterns
MonomerPatterns that make up the complex.
compartment : Compartment
Location restriction. None means don't care.
match_once : bool, optional
If True, the pattern will only count once against a species in which the
pattern can match the monomer graph in multiple distinct ways. If False
(default), the pattern will count as many times as it matches the
monomer graph, leading to a faster effective reaction rate.
Attributes
----------
Identical to Parameters (see above).
"""
def __init__(self, monomer_patterns, compartment, match_once=False):
# ensure compartment is a Compartment
if compartment and not isinstance(compartment, Compartment):
raise Exception("compartment is not a Compartment object")
self.monomer_patterns = monomer_patterns
self.compartment = compartment
self.match_once = match_once
[docs] def is_concrete(self):
"""
Return a bool indicating whether the pattern is 'concrete'.
'Concrete' means the pattern satisfies ANY of the following:
1. All monomer patterns are concrete
2. The compartment is specified AND all monomer patterns are site-concrete
"""
# 1.
mp_concrete_ok = all(mp.is_concrete() for mp in self.monomer_patterns)
# 2.
compartment_ok = self.compartment is not None and \
all(mp.is_site_concrete() for mp in self.monomer_patterns)
return mp_concrete_ok or compartment_ok
[docs] def is_equivalent_to(self, other):
"""Checks for equality with another ComplexPattern"""
# Didn't implement __eq__ to avoid confusion with __ne__ operator used for Rule building
# FIXME the literal site_conditions comparison requires bond numbering to be identical,
# so some sort of canonicalization of that numbering is necessary.
if not isinstance(other, ComplexPattern):
raise Exception("Can only compare ComplexPattern to another ComplexPattern")
return (self.compartment == other.compartment and
sorted((repr(mp.monomer), mp.site_conditions, mp.compartment)
for mp in self.monomer_patterns) ==
sorted((repr(mp.monomer), mp.site_conditions, mp.compartment)
for mp in other.monomer_patterns))
[docs] def copy(self):
"""
Implement our own brand of shallow copy.
The new object will have references to the original compartment, and
copies of the monomer_patterns.
"""
return ComplexPattern([mp() for mp in self.monomer_patterns], self.compartment, self.match_once)
def __call__(self, conditions=None, **kwargs):
"""Build a new ComplexPattern with updated site conditions."""
kwargs = extract_site_conditions(conditions, **kwargs)
# Ensure we don't have more than one of any Monomer in our patterns.
mp_monomer = lambda mp: id(mp.monomer)
patterns_sorted = sorted(self.monomer_patterns, key=mp_monomer)
pgroups = itertools.groupby(patterns_sorted, mp_monomer)
pcounts = [(monomer, sum(1 for mp in mps)) for monomer, mps in pgroups]
dup_monomers = [monomer.name for monomer, count in pcounts if count > 1]
if dup_monomers:
raise DuplicateMonomerError("ComplexPattern has duplicate "
"Monomers: " + str(dup_monomers))
# Ensure all specified sites are present in some Monomer.
self_site_groups = (mp.monomer.sites for mp in self.monomer_patterns)
self_sites = list(itertools.chain(*self_site_groups))
unknown_sites = set(kwargs).difference(self_sites)
if unknown_sites:
raise UnknownSiteError("Unknown sites in argument list: " +
", ".join(unknown_sites))
# Ensure no specified site is present in multiple Monomers.
used_sites = [s for s in self_sites if s in kwargs]
sgroups = itertools.groupby(sorted(used_sites))
scounts = [(name, sum(1 for s in sites)) for name, sites in sgroups]
dup_sites = [name for name, count in scounts if count > 1]
if dup_sites:
raise DuplicateSiteError("ComplexPattern has duplicate sites: " +
str(dup_sites))
# Copy self so we can modify it in place before returning it.
cp = self.copy()
# Build map from site name to MonomerPattern.
site_map = {}
for mp in cp.monomer_patterns:
site_map.update(dict.fromkeys(mp.monomer.sites, mp))
# Apply kwargs to our ComplexPatterns.
for site, condition in kwargs.items():
site_map[site].site_conditions[site] = condition
return cp
def __add__(self, other):
if isinstance(other, ComplexPattern):
return ReactionPattern([self, other])
elif isinstance(other, MonomerPattern):
return ReactionPattern([self, ComplexPattern([other], None)])
elif other == None:
return as_reaction_pattern(self)
else:
return NotImplemented
def __mod__(self, other):
if isinstance(other, MonomerPattern):
return ComplexPattern(self.monomer_patterns + [other], self.compartment, self.match_once)
elif isinstance(other, ComplexPattern):
if self.compartment is not other.compartment:
raise ValueError("merged ComplexPatterns must specify the same compartment")
elif self.match_once != other.match_once:
raise ValueError("merged ComplexPatterns must have the same value of match_once")
return ComplexPattern(self.monomer_patterns + other.monomer_patterns, self.compartment, self.match_once)
else:
return NotImplemented
def __rmod__(self, other):
if isinstance(other, MonomerPattern):
return ComplexPattern([other] + self.monomer_patterns, self.compartment, self.match_once)
else:
return NotImplemented
def __rshift__(self, other):
return build_rule_expression(self, other, False)
def __rrshift__(self, other):
return build_rule_expression(other, self, False)
def __ne__(self, other):
return build_rule_expression(self, other, True)
def __pow__(self, other):
if isinstance(other, Compartment):
cp_new = self.copy()
cp_new.compartment = other
return cp_new
else:
return NotImplemented
def __repr__(self):
ret = ' % '.join([repr(p) for p in self.monomer_patterns])
if self.compartment is not None:
ret = '(%s) ** %s' % (ret, self.compartment.name)
if self.match_once:
ret = 'MatchOnce(%s)' % ret
return ret
[docs]class ReactionPattern(object):
"""
A pattern for the entire product or reactant side of a rule.
Essentially a thin wrapper around a list of ComplexPatterns. In BNG terms, a
list of complex patterns combined with the '+' operator.
Parameters
----------
complex_patterns : list of ComplexPatterns
ComplexPatterns that make up the reaction pattern.
Attributes
----------
Identical to Parameters (see above).
"""
def __init__(self, complex_patterns):
self.complex_patterns = complex_patterns
def __add__(self, other):
if isinstance(other, MonomerPattern):
return ReactionPattern(self.complex_patterns + [ComplexPattern([other], None)])
elif isinstance(other, ComplexPattern):
return ReactionPattern(self.complex_patterns + [other])
elif other == None:
return self
else:
return NotImplemented
def __rshift__(self, other):
"""Irreversible reaction"""
return build_rule_expression(self, other, False)
def __rrshift__(self, other):
return build_rule_expression(other, self, False)
def __ne__(self, other):
"""Reversible reaction"""
return build_rule_expression(self, other, True)
def __repr__(self):
if len(self.complex_patterns):
return ' + '.join([repr(p) for p in self.complex_patterns])
else:
return 'None'
[docs]class RuleExpression(object):
"""
A container for the reactant and product patterns of a rule expression.
Contains one ReactionPattern for each of reactants and products, and a bool
indicating reversibility. This is a temporary object used to implement
syntactic sugar through operator overloading. The Rule constructor takes an
instance of this class as its first argument, but simply extracts its fields
and discards the object itself.
Parameters
----------
reactant_pattern, product_pattern : ReactionPattern
The reactants and products of the rule.
is_reversible : bool
If True, the reaction is reversible. If False, it's irreversible.
Attributes
----------
Identical to Parameters (see above).
"""
def __init__(self, reactant_pattern, product_pattern, is_reversible):
self.reactant_pattern = reactant_pattern
self.product_pattern = product_pattern
self.is_reversible = is_reversible
def __repr__(self):
operator = '<>' if self.is_reversible else '>>'
return '%s %s %s' % (repr(self.reactant_pattern), operator,
repr(self.product_pattern))
[docs]def as_complex_pattern(v):
"""Internal helper to 'upgrade' a MonomerPattern to a ComplexPattern."""
if isinstance(v, ComplexPattern):
return v
elif isinstance(v, Monomer):
return ComplexPattern([v()], None)
elif isinstance(v, MonomerPattern):
return ComplexPattern([v], None)
else:
raise InvalidComplexPatternException
[docs]def as_reaction_pattern(v):
"""Internal helper to 'upgrade' a Complex- or MonomerPattern or None to a
complete ReactionPattern."""
if isinstance(v, ReactionPattern):
return v
elif v is None:
return ReactionPattern([])
else:
try:
return ReactionPattern([as_complex_pattern(v)])
except InvalidComplexPatternException:
raise InvalidReactionPatternException
[docs]def build_rule_expression(reactant, product, is_reversible):
"""Internal helper for operators which return a RuleExpression."""
# Make sure the types of both reactant and product are acceptable.
try:
reactant = as_reaction_pattern(reactant)
product = as_reaction_pattern(product)
except InvalidReactionPatternException:
return NotImplemented
# Synthesis/degradation rules cannot be reversible.
if (reactant is None or product is None) and is_reversible:
raise InvalidReversibleSynthesisDegradationRule
return RuleExpression(reactant, product, is_reversible)
[docs]class Parameter(Component, sympy.Symbol):
"""
Model component representing a named constant floating point number.
Parameters are used as reaction rate constants, compartment volumes and
initial (boundary) conditions for species.
Parameters
----------
value : number, optional
The numerical value of the parameter. Defaults to 0.0 if not specified.
The provided value is converted to a float before being stored, so any
value that cannot be coerced to a float will trigger an exception.
Attributes
----------
Identical to Parameters (see above).
"""
def __new__(cls, name, value=0.0, _export=True):
return super(sympy.Symbol, cls).__new__(cls, name)
def __getnewargs__(self):
return (self.name, self.value, False)
def __init__(self, name, value=0.0, _export=True):
Component.__init__(self, name, _export)
self.value = float(value)
def get_value(self):
return self.value
# This is needed to make sympy's evalf machinery treat this class like a
# Symbol.
@property
def func(self):
return sympy.Symbol
def __repr__(self):
return '%s(%s, %s)' % (self.__class__.__name__, repr(self.name), repr(self.value))
def __str__(self):
return repr(self)
[docs]class Compartment(Component):
"""
Model component representing a bounded reaction volume.
Parameters
----------
parent : Compartment, optional
Compartment which contains this one. If not specified, this will be the
outermost compartment and its parent will be set to None.
dimension : integer, optional
The number of spatial dimensions in the compartment, either 2 (i.e. a
membrane) or 3 (a volume).
size : Parameter, optional
A parameter object whose value defines the volume or area of the
compartment. If not specified, the size will be fixed at 1.0.
Attributes
----------
Identical to Parameters (see above).
Notes
-----
The compartments of a model must form a tree via their `parent` attributes
with a three-dimensional (volume) compartment at the root. A volume
compartment may have any number of two-dimensional (membrane) compartments
as its children, but never another volume compartment. A membrane
compartment may have a single volume compartment as its child, but nothing
else.
Examples
--------
Compartment('cytosol', dimension=3, size=cyto_vol, parent=ec_membrane)
"""
def __init__(self, name, parent=None, dimension=3, size=None, _export=True):
Component.__init__(self, name, _export)
if parent != None and isinstance(parent, Compartment) == False:
raise Exception("parent must be a predefined Compartment or None")
#FIXME: check for only ONE "None" parent? i.e. only one compartment can have a parent None?
if size is not None and not isinstance(size, Parameter):
raise Exception("size must be a parameter (or omitted)")
self.parent = parent
self.dimension = dimension
self.size = size
def __repr__(self):
return '%s(name=%s, parent=%s, dimension=%s, size=%s)' % \
(self.__class__.__name__, repr(self.name), repr(self.parent), repr(self.dimension), repr(self.size))
[docs]class Rule(Component):
"""
Model component representing a reaction rule.
Parameters
----------
rule_expression : RuleExpression
RuleExpression containing the essence of the rule (reactants, products,
reversibility).
rate_forward : Parameter
Forward reaction rate constant.
rate_reverse : Parameter, optional
Reverse reaction rate constant (only required for reversible rules).
delete_molecules : bool, optional
If True, deleting a Monomer from a species is allowed to fragment the
species into multiple pieces (if the deleted Monomer was the sole link
between those pieces). If False (default) then fragmentation is
disallowed and the rule will not match a reactant species if applying
the rule would fragment a species.
move_connected : bool, optional
If True, a rule that transports a Monomer between compartments will
co-transport anything connected to that Monomer by a path in the same
compartment. If False (default), connected Monomers will remain where
they were.
Attributes
----------
Identical to Parameters (see above), plus the component elements of
`rule_expression`: reactant_pattern, product_pattern and is_reversible.
"""
def __init__(self, name, rule_expression, rate_forward, rate_reverse=None,
delete_molecules=False, move_connected=False,
_export=True):
Component.__init__(self, name, _export)
if not isinstance(rule_expression, RuleExpression):
raise Exception("rule_expression is not a RuleExpression object")
validate_expr(rate_forward, "forward rate")
if rule_expression.is_reversible:
validate_expr(rate_reverse, "reverse rate")
self.rule_expression = rule_expression
self.reactant_pattern = rule_expression.reactant_pattern
self.product_pattern = rule_expression.product_pattern
self.is_reversible = rule_expression.is_reversible
self.rate_forward = rate_forward
self.rate_reverse = rate_reverse
self.delete_molecules = delete_molecules
self.move_connected = move_connected
# TODO: ensure all numbered sites are referenced exactly twice within each of reactants and products
[docs] def is_synth(self):
"""Return a bool indicating whether this is a synthesis rule."""
return len(self.reactant_pattern.complex_patterns) == 0
[docs] def is_deg(self):
"""Return a bool indicating whether this is a degradation rule."""
return len(self.product_pattern.complex_patterns) == 0
def __repr__(self):
ret = '%s(%s, %s, %s' % \
(self.__class__.__name__, repr(self.name),
repr(self.rule_expression), self.rate_forward.name)
if self.is_reversible:
ret += ', %s' % self.rate_reverse.name
if self.delete_molecules:
ret += ', delete_molecules=True'
if self.move_connected:
ret += ', move_connected=True'
ret += ')'
return ret
[docs]def validate_expr(obj, description):
"""Raises an exception if the argument is not an expression."""
if not isinstance(obj, (Parameter, Expression)):
description_upperfirst = description[0].upper() + description[1:]
msg = "%s must be a Parameter or Expression" % description_upperfirst
raise ExpressionError(msg)
[docs]def validate_const_expr(obj, description):
"""Raises an exception if the argument is not a constant expression."""
validate_expr(obj, description)
if isinstance(obj, Expression) and not obj.is_constant_expression():
description_upperfirst = description[0].upper() + description[1:]
msg = ("%s must be a Parameter or constant Expression" %
description_upperfirst)
raise ConstantExpressionError(msg)
[docs]class Observable(Component, sympy.Symbol):
"""
Model component representing a linear combination of species.
Observables are useful in correlating model simulation results with
experimental measurements. For example, an observable for "A()" will report
on the total number of copies of Monomer A, regardless of what it's bound to
or the state of its sites. "A(y='P')" would report on all instances of A
with site 'y' in state 'P'.
Parameters
----------
reaction_pattern : ReactionPattern
The list of ComplexPatterns to match.
match : 'species' or 'molecules'
Whether to match entire species ('species') or individual fragments
('molecules'). Default is 'molecules'.
Attributes
----------
reaction_pattern : ReactionPattern
See Parameters.
match : 'species' or 'molecules'
See Parameters.
species : list of integers
List of species indexes for species matching the pattern.
coefficients : list of integers
List of coefficients by which each species amount is to be multiplied to
correct for multiple pattern matches within a species.
Notes
-----
ReactionPattern is used here as a container for a list of ComplexPatterns,
solely so users could utilize the ComplexPattern '+' operator overload as
syntactic sugar. There are no actual "reaction" semantics in this context.
"""
def __new__(cls, name, reaction_pattern, match='molecules', _export=True):
return super(sympy.Symbol, cls).__new__(cls, name)
def __getnewargs__(self):
return (self.name, self.reaction_pattern, self.match, False)
def __init__(self, name, reaction_pattern, match='molecules', _export=True):
try:
reaction_pattern = as_reaction_pattern(reaction_pattern)
except InvalidReactionPatternException as e:
raise type(e)("Observable pattern does not look like a ReactionPattern")
if match not in ('molecules', 'species'):
raise ValueError("Match must be 'molecules' or 'species'")
Component.__init__(self, name, _export)
self.reaction_pattern = reaction_pattern
self.match = match
self.species = []
self.coefficients = []
# This is needed to make sympy's evalf machinery treat this class like a
# Symbol.
@property
def func(self):
return sympy.Symbol
def __repr__(self):
ret = '%s(%s, %s' % (self.__class__.__name__, repr(self.name),
repr(self.reaction_pattern))
if self.match != 'molecules':
ret += ', match=%s' % repr(self.match)
ret += ')'
return ret
def __str__(self):
return repr(self)
[docs]class Expression(Component, sympy.Symbol):
"""
Model component representing a symbolic expression of other variables.
Parameters
----------
expr : sympy.Expr
Symbolic expression.
Attributes
----------
expr : sympy.Expr
See Parameters.
"""
def __new__(cls, name, expr, _export=True):
return super(sympy.Symbol, cls).__new__(cls, name)
def __getnewargs__(self):
return (self.name, self.expr, False)
def __init__(self, name, expr, _export=True):
Component.__init__(self, name, _export)
self.expr = expr
[docs] def expand_expr(self):
"""Return expr rewritten in terms of terminal symbols only."""
subs = ((a, a.expand_expr()) for a in self.expr.atoms()
if isinstance(a, Expression))
return self.expr.subs(subs)
[docs] def is_constant_expression(self):
"""Return True if all terminal symbols are Parameters or numbers."""
return all(isinstance(a, Parameter) or
(isinstance(a, Expression) and a.is_constant_expression()) or
isinstance(a, sympy.Number)
for a in self.expr.atoms())
def get_value(self):
return self.expr.evalf()
# This is needed to make sympy's evalf machinery treat this class like a
# Symbol.
@property
def func(self):
return sympy.Symbol
def __repr__(self):
ret = '%s(%s, %s)' % (self.__class__.__name__, repr(self.name),
repr(self.expr))
return ret
def __str__(self):
return repr(self)
[docs]class Model(object):
"""
A rule-based model containing monomers, rules, compartments and parameters.
Parameters
----------
name : string, optional
Name of the model. If not specified, will be set to the name of the file
from which the constructor was called (with the .py extension stripped).
base : Model, optional
If specified, the model will begin as a copy of `base`. This can be used
to achieve a simple sort of model extension and enhancement.
Attributes
----------
name : string
Name of the model. See Parameter section above.
base : Model or None
See Parameter section above.
monomers, compartments, parameters, rules, observables : ComponentSet
The Component objects which make up the model.
initial_conditions : list of tuple of (ComplexPattern, Parameter)
Specifies which species are present in the model's starting
state (t=0) and how much there is of each one. The
ComplexPattern defines the species identity, and it must be
concrete (see ComplexPattern.is_concrete). The
Parameter defines the amount or concentration of the species.
species : list of ComplexPattern
List of all complexes which can be produced by the model, starting from
the initial conditions and successively applying the rules. Each
ComplexPattern is concrete.
odes : list of sympy.Expr
Mathematical expressions describing the time derivative of the amount of
each species, as generated by the rules.
reactions : list of dict
Structures describing each possible unidirectional reaction that can be
produced by the model. Each structure stores the name of the rule that
generated the reaction ('rule'), the mathematical expression for the
rate of the reaction ('rate'), tuples of species indexes for the
reactants and products ('reactants', 'products'), and a bool indicating
whether the reaction is the reverse component of a bidirectional
reaction ('reverse').
reactions_bidirectional : list of dict
Similar to `reactions` but with only one entry for each bidirectional
reaction. The fields are identical except 'reverse' is replaced by
'reversible', a bool indicating whether the reaction is reversible. The
'rate' is the forward rate minus the reverse rate.
annotations : list of Annotation
Structured annotations of model components. See the Annotation class for
details.
"""
_component_types = (Monomer, Compartment, Parameter, Rule, Observable,
Expression)
def __init__(self, name=None, base=None, _export=True):
self.name = name
self.base = base
self._export = _export
self.monomers = ComponentSet()
self.compartments = ComponentSet()
self.parameters = ComponentSet()
self.rules = ComponentSet()
self.observables = ComponentSet()
self.expressions = ComponentSet()
self.species = []
self.odes = []
self.reactions = []
self.reactions_bidirectional = []
self.initial_conditions = []
self.annotations = []
#####
self.diffusivities = []
#####
if self._export:
SelfExporter.export(self)
if self.base is not None:
if not isinstance(self.base, Model):
raise ValueError("base must be a Model")
model_copy = copy.deepcopy(self.base)
for component in model_copy.all_components():
self.add_component(component)
component._do_export()
self.initial_conditions = model_copy.initial_conditions
def __setstate__(self, state):
# restore the 'model' weakrefs on all components
self.__dict__.update(state)
for c in self.all_components():
c.model = weakref.ref(self)
[docs] def reload(self):
"""
Reload a model after its source files have been edited.
This method does not yet reload the model contents in-place, rather it
returns a new model object. Thus the correct usage is ``model =
model.reload()``.
If the model script imports any modules, these will not be reloaded. Use
python's reload() function to reload them.
"""
# forcibly removes the .pyc file and reloads the model module
model_pyc = SelfExporter.target_module.__file__
if model_pyc[-3:] == '.py':
model_pyc += 'c'
try:
os.unlink(model_pyc)
except OSError as e:
# ignore "no such file" errors, re-raise the rest
if e.errno != errno.ENOENT:
raise
try:
reload(SelfExporter.target_module)
except SystemError as e:
# This one specific SystemError occurs when using ipython to 'run' a model .py file
# directly, then reload()ing the model, which makes no sense anyway. (just re-run it)
if e.args == ('nameless module',):
raise Exception('Cannot reload a model which was executed directly in an interactive'
'session. Please import the model file as a module instead.')
else:
raise
# return self for "model = model.reload()" idiom, until a better solution can be found
return SelfExporter.default_model
[docs] def all_component_sets(self):
"""Return a list of all ComponentSet objects."""
set_names = [t.__name__.lower() + 's' for t in Model._component_types]
sets = [getattr(self, name) for name in set_names]
return sets
[docs] def all_components(self):
"""Return a ComponentSet containing all components in the model."""
cset_all = ComponentSet()
for cset in self.all_component_sets():
cset_all |= cset
return cset_all
[docs] def parameters_rules(self):
"""Return a ComponentSet of the parameters used in rules."""
# rate_reverse is None for irreversible rules, so we'll need to filter those out
cset = ComponentSet(p for r in self.rules for p in (r.rate_forward, r.rate_reverse)
if p is not None)
# intersect with original parameter list to retain ordering
return self.parameters & cset
[docs] def parameters_initial_conditions(self):
"""Return a ComponentSet of initial condition parameters."""
cset = ComponentSet(ic[1] for ic in self.initial_conditions)
# intersect with original parameter list to retain ordering
return self.parameters & cset
[docs] def parameters_compartments(self):
"""Return a ComponentSet of compartment size parameters."""
cset = ComponentSet(c.size for c in self.compartments)
# intersect with original parameter list to retain ordering
return self.parameters & cset
[docs] def parameters_unused(self):
"""Return a ComponentSet of unused parameters."""
cset_used = self.parameters_rules() | self.parameters_initial_conditions() | self.parameters_compartments()
return self.parameters - cset_used
# def expressions_constant(self):
# """Return a ComponentSet of constant expressions."""
# cset = ComponentSet(e for e in self.expressions
# if all(isinstance(a, (Parameter, sympy.Number))
# for a in e.expand_expr().atoms()))
# return cset
[docs] def expressions_constant(self):
"""Return a ComponentSet of constant expressions."""
cset = ComponentSet(e for e in self.expressions
if e.is_constant_expression())
return cset
[docs] def expressions_dynamic(self):
"""Return a ComponentSet of non-constant expressions."""
return self.expressions - self.expressions_constant()
[docs] def add_component(self, other):
"""Add a component to the model."""
# We have a container for each type of component. This code determines
# the right one based on the class of the object being added.
for t, cset in zip(Model._component_types, self.all_component_sets()):
if isinstance(other, t):
cset.add(other)
other.model = weakref.ref(self)
break
else:
raise Exception("Tried to add component of unknown type '%s' to "
"model" % type(other))
[docs] def add_annotation(self, annotation):
"""Add an annotation to the model."""
self.annotations.append(annotation)
[docs] def get_annotations(self, subject):
"""Return all annotations for the given subject."""
annotations = []
for a in self.annotations:
if a.subject is subject:
annotations.append(a)
return annotations
def _rename_component(self, component, new_name):
"""
Change a component's name.
This has to be done through the Model because the ComponentSet needs to
be updated as well as the component's `name` field.
"""
for cset in self.all_component_sets():
if component in cset:
cset.rename(component, new_name)
def _validate_initial_condition_pattern(self, pattern):
"""
Make sure a pattern is valid for an initial condition.
Patterns must satisfy all of the following:
* Able to be cast as a ComplexPattern
* Concrete (see ComplexPattern.is_concrete)
* Distinct from any existing initial condition pattern
* match_once is False (nonsensical in this context)
Parameters
----------
pattern : MonomerPattern or ComplexPattern
Pattern to validate
Returns
-------
The validated pattern, upgraded to a ComplexPattern.
"""
try:
complex_pattern = as_complex_pattern(pattern)
except InvalidComplexPatternException as e:
raise InvalidInitialConditionError("Not a ComplexPattern")
if not complex_pattern.is_concrete():
raise InvalidInitialConditionError("Pattern not concrete")
if any(complex_pattern.is_equivalent_to(other_cp)
for other_cp, value in self.initial_conditions):
# FIXME until we get proper canonicalization this could produce
# false negatives
raise InvalidInitialConditionError("Duplicate species")
if complex_pattern.match_once:
raise InvalidInitialConditionError("MatchOnce not allowed here")
return complex_pattern
[docs] def initial(self, pattern, value):
"""
Add an initial condition.
An initial condition is made up of a species and its amount or
concentration.
Parameters
----------
pattern : ComplexPattern
A concrete pattern defining the species to initialize.
value : Parameter
Amount of the species the model will start with.
"""
complex_pattern = self._validate_initial_condition_pattern(pattern)
validate_const_expr(value, "initial condition value")
self.initial_conditions.append( (complex_pattern, value) )
[docs] def update_initial_condition_pattern(self, before_pattern, after_pattern):
"""
Update the pattern associated with an initial condition.
Leaves the Parameter object associated with the initial condition
unchanged while modifying the pattern associated with that condition.
For example this is useful for changing the state of a site on a
monomer or complex associated with an initial condition without having
to create an independent initial condition, and parameter, associated
with that alternative state.
Parameters
----------
before_pattern : ComplexPattern
The concrete pattern specifying the (already existing) initial
condition. If the model does not contain an initial condition
for the pattern, a ValueError is raised.
after_pattern : ComplexPattern
The concrete pattern specifying the new pattern to use to replace
before_pattern.
"""
# Get the initial condition index
ic_index_list = [i for i, ic in enumerate(self.initial_conditions)
if ic[0].is_equivalent_to(as_complex_pattern(before_pattern))]
# If the initial condition to replace is not found, raise an error
if not ic_index_list:
raise ValueError("No initial condition found for pattern %s" %
before_pattern)
# If more than one matching initial condition is found, raise an
# error (this should never happen, because duplicate initial conditions
# are not allowed to be created)
assert len(ic_index_list) == 1
ic_index = ic_index_list[0]
# Make sure the new initial condition pattern is valid
after_pattern = self._validate_initial_condition_pattern(after_pattern)
# Since everything checks out, replace the old initial condition
# pattern with the new one. Because initial_conditions are tuples (and
# hence immutable), we cannot simply replace the pattern; instead we
# must delete the old one and add the new one.
# We retain the old parameter object:
p = self.initial_conditions[ic_index][1]
del self.initial_conditions[ic_index]
self.initial_conditions.append( (after_pattern, p) )
[docs] def get_species_index(self, complex_pattern):
"""
Return the index of a species.
Parameters
----------
complex_pattern : ComplexPattern
A concrete pattern specifying the species to find.
"""
# FIXME I don't even want to think about the inefficiency of this, but at least it works
try:
return next((i for i, s_cp in enumerate(self.species) if s_cp.is_equivalent_to(complex_pattern)))
except StopIteration:
return None
[docs] def has_synth_deg(self):
"""Return true if model uses synthesis or degradation reactions."""
return any(r.is_synth() or r.is_deg() for r in self.rules)
[docs] def enable_synth_deg(self):
"""Add components needed to support synthesis and degradation rules."""
if self.monomers.get('__source') is None:
self.add_component(Monomer('__source', _export=False))
if self.monomers.get('__sink') is None:
self.add_component(Monomer('__sink', _export=False))
if self.parameters.get('__source_0') is None:
self.add_component(Parameter('__source_0', 1.0, _export=False))
source_cp = as_complex_pattern(self.monomers['__source']())
if not any(source_cp.is_equivalent_to(other_cp) for other_cp, value in self.initial_conditions):
self.initial(source_cp, self.parameters['__source_0'])
[docs] def reset_equations(self):
"""Clear out fields generated by bng.generate_equations or the like."""
self.species = []
self.odes = []
self.reactions = []
self.reactions_bidirectional = []
for obs in self.observables:
obs.species = []
obs.coefficients = []
def __repr__(self):
return ("<%s '%s' (monomers: %d, rules: %d, parameters: %d, "
"expressions: %d, compartments: %d) at 0x%x>" %
(self.__class__.__name__, self.name,
len(self.monomers), len(self.rules), len(self.parameters),
len(self.expressions), len(self.compartments), id(self)))
[docs]class InvalidComplexPatternException(Exception):
"""Expression can not be cast as a ComplexPattern."""
pass
[docs]class InvalidReactionPatternException(Exception):
"""Expression can not be cast as a ReactionPattern."""
pass
[docs]class InvalidReversibleSynthesisDegradationRule(Exception):
"""Synthesis or degradation rule defined as reversible."""
def __init__(self):
Exception.__init__(self, "Synthesis and degradation rules may not be"
"reversible.")
[docs]class ExpressionError(ValueError):
"""Expected an Expression but got something else."""
pass
[docs]class ConstantExpressionError(ValueError):
"""Expected a constant Expression but got something else."""
pass
[docs]class ModelExistsWarning(UserWarning):
"""A second model was declared in a module that already contains one."""
pass
[docs]class SymbolExistsWarning(UserWarning):
"""A component declaration or rename overwrote an existing symbol."""
pass
[docs]class InvalidComponentNameError(ValueError):
"""Inappropriate component name."""
def __init__(self, name):
ValueError.__init__(self, "Not a valid component name: '%s'" % name)
[docs]class InvalidInitialConditionError(ValueError):
"""Invalid initial condition pattern."""
class DuplicateMonomerError(ValueError):
pass
class DuplicateSiteError(ValueError):
pass
class UnknownSiteError(ValueError):
pass
[docs]class ComponentSet(collections.Set, collections.Mapping, collections.Sequence):
"""
An add-and-read-only container for storing model Components.
It behaves mostly like an ordered set, but components can also be retrieved
by name *or* index by using the [] operator (like a combination of a dict
and a list). Components cannot be removed or replaced, but they can be
renamed. Iteration returns the component objects.
Parameters
----------
iterable : iterable of Components, optional
Initial contents of the set.
"""
# The implementation is based on a list instead of a linked list (as
# OrderedSet is), since we only allow add and retrieve, not delete.
def __init__(self, iterable=None):
self._elements = []
self._map = {}
self._index_map = {}
if iterable is not None:
for value in iterable:
self.add(value)
def __iter__(self):
return iter(self._elements)
def __contains__(self, c):
if not isinstance(c, Component):
raise TypeError("Can only work with Components, got a %s" % type(c))
return c.name in self._map and self[c.name] is c
def __len__(self):
return len(self._elements)
def add(self, c):
if c not in self:
if c.name in self._map:
raise ComponentDuplicateNameError(
"Tried to add a component with a duplicate name: %s"
% c.name)
self._elements.append(c)
self._map[c.name] = c
self._index_map[c.name] = len(self._elements) - 1
def __getitem__(self, key):
# Must support both Sequence and Mapping behavior. This means
# stringified integer Mapping keys (like "0") are forbidden, but since
# all Component names must be valid Python identifiers, integers are
# ruled out anyway.
if isinstance(key, (int, long, slice)):
return self._elements[key]
else:
return self._map[key]
def get(self, key, default=None):
if isinstance(key, (int, long)):
raise ValueError("get is undefined for integer arguments, use []"
"instead")
try:
return self[key]
except KeyError:
return default
def iterkeys(self):
for c in self:
yield c.name
def itervalues(self):
return self.__iter__()
def iteritems(self):
for c in self:
yield (c.name, c)
def keys(self):
return [c.name for c in self]
def values(self):
return [c for c in self]
def items(self):
return zip(self.keys(), self)
def index(self, c):
# We can implement this in O(1) ourselves, whereas the Sequence mixin
# implements it in O(n).
if not c in self:
raise ValueError("%s is not in ComponentSet" % c)
return self._index_map[c.name]
def __and__(self, other):
# We reimplement this because collections.Set's __and__ mixin iterates
# over other, not self. That implementation ends up retaining the
# ordering of other, but we'd like to keep the ordering of self instead.
# We require other to be a ComponentSet too so we know it will support
# "in" efficiently.
if not isinstance(other, ComponentSet):
return collections.Set.__and__(self, other)
return ComponentSet(value for value in self if value in other)
def __rand__(self, other):
return self.__and__(other)
def __ror__(self, other):
return self.__or__(other)
def __rxor__(self, other):
return self.__xor__(other)
def __repr__(self):
return 'ComponentSet([\n' + \
''.join(' %s,\n' % repr(x) for x in self) + \
' ])'
[docs] def rename(self, c, new_name):
"""Change the name of component `c` to `new_name`."""
for m in self._map, self._index_map:
m[new_name] = m[c.name]
del m[c.name]
[docs]class ComponentDuplicateNameError(ValueError):
"""A component was added with the same name as an existing one."""
pass
[docs]class RedundantSiteConditionsError(ValueError):
"""Both conditions dict and kwargs both passed to create pattern."""
def __init__(self):
ValueError.__init__(
self,
("Site conditions may be specified as EITHER keyword arguments "
"OR a single dict"))
# Some light infrastructure for defining symbols that act like "keywords", i.e.
# they are immutable singletons that stringify to their own name. Regular old
# classes almost fit the bill, except that their __str__ method prepends the
# complete module hierarchy to the base class name. The KeywordMeta class here
# implements an alternate __str__ method which just returns the base name.
class KeywordMeta(type):
def __repr__(cls):
return cls.__name__
def __str__(cls):
return repr(cls)
class Keyword(object): __metaclass__ = KeywordMeta
# The keywords.
[docs]class ANY(Keyword):
"""Site must have a bond, but identity of binding partner is irrelevant.
Use ANY in a MonomerPattern site_conditions dict to indicate that a site
must have a bond without specifying what the binding partner should be.
Equivalent to the "+" bond modifier in BNG."""
pass
[docs]class WILD(Keyword):
"""Site may be bound or unbound.
Use WILD as part of a (state, WILD) tuple in a MonomerPattern
site_conditions dict to indicate that a site must have the given state,
irrespective of the presence or absence of a bond. (Specifying only the
state implies there must not be a bond). A bare WILD in a site_conditions
dict is also permissible, but as this has the same meaning as the much
simpler option of leaving the given site out of the dict entirely, this
usage is deprecated.
Equivalent to the "?" bond modifier in BNG."""
pass
warnings.simplefilter('always', ModelExistsWarning)
warnings.simplefilter('always', SymbolExistsWarning)