def do(self, time):
"""
Assign all molecules to a collection of reactants. Use the combined
collections of products as the new molecules.
Uses :py:mod:`umpf` for parallelism.
:param float time: Time to simulate, at a rate of one step per unit.
:rtype: yields :py:class:`achemkit.Event` objects.
"""
self.maxtime += time
while self.time < self.maxtime:
self.mols = tuple(self.rng.sample(self.mols, len(self.mols)))
newmols = ()
allreactants = []
while len(self.mols) > 0:
noreactants = get_sample(self.achem.noreactants)
if noreactants <= len(self.mols):
reactants = self.mols[:noreactants]
self.mols = self.mols[noreactants:]
allreactants.append(OrderedFrozenBag(reactants))
else:
break
allproducts = umpf.map(self.achem.react, allreactants)
results = itertools.izip(allreactants, allproducts)
for reactants, products in results:
e = Event(self.time, reactants, products)
newmols += tuple(products)
yield e
self.mols = newmols
self.time += 1.0
def do(self, time):
"""
Assign all molecules to a collection of reactants. Use the combined
collections of products as the new molecules.
Uses :py:mod:`umpf` for parallelism.
:param float time: Time to simulate, at a rate of one step per unit.
:rtype: yields :py:class:`achemkit.Event` objects.
"""
self.maxtime += time
while self.time < self.maxtime:
self.mols = tuple(self.rng.sample(self.mols, len(self.mols)))
newmols = ()
allreactants = []
while len(self.mols) > 0:
noreactants = get_sample(self.achem.noreactants)
if noreactants <= len(self.mols):
reactants = self.mols[:noreactants]
self.mols = self.mols[noreactants:]
allreactants.append(OrderedFrozenBag(reactants))
else:
break
allproducts = umpf.map(self.achem.react, allreactants)
results = zip(allreactants, allproducts)
for reactants, products in results:
e = Event(self.time, reactants, products)
newmols += tuple(products)
yield e
self.mols = newmols
self.time += 1.0
def Uniform(nmols, nreactions, nreactants, nproducts, rates = 1.0, cls = ReactionNetwork, rng = None):
"""
Generates a random :py:class:`~achemkit.reactionnet.ReactionNetwork` by assigning reaction randomly between all molecular species.
Arguments:
nmols
Number of molecules in the reaction network.
.. note::
:py:class:`achemkit.reactionnet.ReactionNetwork` tracks molecules by their reactions, so if a molecule is not part of any reaction
it will not appear at all e.g. in :py:attr:`~achemkit.reactionnet.ReactionNetwork.seen`. This could lead to differences from `nmols`.
nreactions
Number of reaction in the reaction network.
.. note::
The value of `nreactions` is the number of times a reaction will be added to the :py:class:`~achemkit.reactionnet.ReactionNetwork`. If it
is already in the :py:class:`~achemkit.reactionnet.ReactionNetwork`, it will be replaced. This can lead to :class:`achemkit.reactionnet.ReactionNetwork` with less
than `nreactions` reactions.
nreactants
Number of reactants for each reaction in the reaction network. Can be a single value or a tuple/list which will be uniformly sampled from (duplicates can be used to give a non-uniform distribution).
.. note::
If this is a tuple/list it will be sampled for each reaction.
nproducts
Number of products for each reaction in the reaction network. Can be a single value or a tuple/list which will be uniformly sampled from (duplicates can be used to give a non-uniform distribution).
If this is None, then `nreactants` must be a list/tuple of tuples of (`nreactants`, `nproducts`) pairs that will be uniformly sampled from. Or `nreactants` must be a dictionary with keys of (`nreactants`, `nproducts`) and values of weightings, which will be sampled from.
.. note::
If this is a tuple/list it will be sampled for each reaction.
rates
Rate of each reaction in the reaction network. Can be a single value or a tuple/list which will be uniformly sampled from (duplicates can be used to give a non-uniform distribution).
.. note::
If this is a tuple/list it will be sampled for each reaction.
cls
Alternative class to use for constructing the return rather than :py:class:`achemkit.reactionnet.ReactionNetwork`.
rng
Random number generator to use. If not specifed, one will be generated at random.
These arguments can be a single value, a tuple/list which will be uniformly sampled from, or a dictionary of value/weighting which will be sampled from
For example:
``Uniform(5,3,2,1)`` will generate 5 molecules with 3 reactions between them where each reaction has two reactants and one product.
``Uniform(5,3,(1,2), (1,2))`` will generate 5 molecules with 3 reactions between them where each reaction has one or two reactants and one or two products.
``Uniform(5,3,((2,1),(1,2)), None)`` will generate 5 molecules with 3 reactions between them where each reaction has either two reactants and one product or one reactant and two products.
"""
if rng is None:
rng = random.Random(random.random())
if isinstance(nmols, int):
nmols = ["M%d"%i for i in xrange(nmols)]
nreactions = get_sample(nreactions, rng)
if nproducts is None:
#its a tuple not a generator because its the same variable name
newnreactants = []
newnproducts = []
for nreactant, nproduct in [get_sample(nreactants, rng) for i in xrange(nreactions)]:
newnreactants.append(nreactant)
newnproducts.append(nproduct)
nproducts = newnreactants
nreactants = newnproducts
else:
#its a tuple not a generator because its the same variable name
nreactants = [get_sample(nreactants, rng) for i in xrange(nreactions)]
nproducts = [get_sample(nproducts, rng) for i in xrange(nreactions)]
rates = [get_sample(rates, rng) for i in xrange(nreactions)]
outrates = {}
for thisnreactants, thisnproducts, thisrate in zip(nreactants, nproducts, rates):
reactants = [get_sample(nmols, rng) for j in xrange(thisnreactants)]
products = [get_sample(nmols, rng) for j in xrange(thisnproducts)]
reactants = OrderedFrozenBag(reactants)
products = OrderedFrozenBag(products)
outrates[(reactants, products)] = thisrate
return cls(outrates)
def Linear(natoms, maxlength, pform, pbreak, directed = True, rates = 1.0, cls = ReactionNetwork, rng = None):
"""
Generates a random :py:class:`~achemkit.reactionnet.ReactionNetwork` from molecules that are strings of atoms and can join together or break apart.
Based on the paper Autocatalytic sets of proteins. 1986. Journal of Theoretical Biology 119:1-24 by Kauffman, Stuart A. but without the explicit catalytic activity.
Arguments:
natoms
Number of atoms to use. Can be a single value or a tuple/list which will be uniformly sampled from (duplicates can be used to give a non-uniform distribution), or a dict of value:weight which will be sampled from.
.. note::
:py:class:`achemkit.reactionnet.ReactionNetwork` tracks molecules by their reactions, so if a molecule is not part of any reaction
it will not appear at all e.g. in :py:attr:`~achemkit.reactionnet.ReactionNetwork.seen`.
maxlength
Maximum number of atoms in a molecule. If this is None, then they are unbounded; this might cause problems with a computational explosion. Can be a single value or a tuple/list which will be uniformly sampled from (duplicates can be used to give a non-uniform distribution), or a dict of value:weight which will be sampled from.
pform
Probability that a pair of molecules will join together per orientation. Must be between 0 and 1. Can be a single value or a tuple/list which will be uniformly sampled from (duplicates can be used to give a non-uniform distribution), or a dict of value:weight which will be sampled from.
pbreak
Probability that any pair of atoms will break. Must be between 0 and 1.Can be a single value or a tuple/list which will be uniformly sampled from (duplicates can be used to give a non-uniform distribution), or a dict of value:weight which will be sampled from.
directed
If false, molecules have no intrinsic direction so AlphBeta is equivlanet to BetaAlpha.
rates
Rate of each reaction in the reaction network. Can be a single value, or a tuple/list which will be uniformly sampled from (duplicates can be used to give a non-uniform distribution), or a dict of value:weight which will be sampled from.
cls
Alternative class to use for constructing the return rather than :py:class:`achemkit.reactionnet.ReactionNetwork`.
rng
Random number generator to use. If not specifed, one will be generated at random.
"""
if rng is None:
rng = random.Random(random.random())
natoms = get_sample(natoms, rng)
maxlength = get_sample(maxlength, rng)
pform = get_sample(pform, rng)
pbreak = get_sample(pbreak, rng)
assert pform >= 0.0
assert pform <= 1.0
assert pbreak >= 0.0
assert pbreak <= 1.0
#these are lists not sets because sets have machine-dependant ordering, which prevents reproducibility for the same random seed.
molecules = []
new = []
#create some inital atoms
#of the form Abc where first letter is capitalized
alpha = "abcdefghijklmnopqrstuvwxyz"
assert natoms > 0
for i in xrange(natoms):
name = alpha[i%len(alpha)]
while i >= len(alpha):
i /= len(alpha)
name = alpha[(i%len(alpha))-1] + name
name = name.strip().capitalize()
new.append(name)
outrates = {}
assert maxlength > 0
def mol_to_atoms(mol, cache = {}):
if mol not in cache:
cache[mol] = tuple(filter(lambda x: len(x) > 0, re.split(r"([A-Z][a-z]*)", mol)))
return cache[mol]
def mol_len(mol):
#return len(mol)
return len(mol_to_atoms(mol))
def mol_reverse(mol):
rmol = ""
for atom in mol_to_atoms(mol):
rmol = atom + rmol
return rmol
def mol_order(mol):
rmol = mol_reverse(mol)
if mol < rmol:
return mol
else:
return rmol
def atoms_to_mol(atoms):
mol = ""
for atom in atoms:
mol = mol + atom
return mol
while len(new) > 0:
oldnew = new
new = []
#decomposition
for z in oldnew:
for i in xrange(1, mol_len(z)):
if rng.random() < pbreak:
a = atoms_to_mol(mol_to_atoms(z)[:i])
b = atoms_to_mol(mol_to_atoms(z)[i:])
if not directed:
a = mol_order(a)
b = mol_order(b)
reaction = (OrderedFrozenBag((z,)), OrderedFrozenBag(sorted((a,b))))
if reaction not in outrates:
outrates[reaction] = get_sample(rates, rng)
if a not in molecules and a not in new:
new.append(a)
if b not in molecules and b not in new:
new.append(b)
for a, b in itertools.chain(itertools.product(oldnew, molecules), combinations_with_replacement(oldnew, 2)):
if maxlength is None or mol_len(a) + mol_len(b) <= maxlength:
combinations = ((a,b), (b,a))
if not directed:
combinations += ((mol_reverse(a), b), (a, mol_reverse(b)))
for x,y in combinations:
if rng.random() < pform:
z = x + y
if not directed:
z = mol_order(z)
#because we may have revereed them, we have to order them again
if not directed:
reactants = OrderedFrozenBag(sorted((mol_order(x), mol_order(y))))
else:
reactants = OrderedFrozenBag(sorted((x, y)))
products = OrderedFrozenBag((z,))
reaction = (reactants, products)
if reaction not in outrates:
outrates[reaction] = get_sample(rates, rng)
if z not in molecules and z not in new:
new.append(z)
for z in oldnew:
molecules.append(z)
return cls(outrates)
def Uniform(nmols, nreactions, nreactants, nproducts, rates = 1.0, cls = ReactionNetwork, rng = None):
"""
Generates a random :py:class:`~achemkit.reactionnet.ReactionNetwork` by assigning reaction randomly between all molecular species.
Arguments:
nmols
Number of molecules in the reaction network.
.. note::
:py:class:`achemkit.reactionnet.ReactionNetwork` tracks molecules by their reactions, so if a molecule is not part of any reaction
it will not appear at all e.g. in :py:attr:`~achemkit.reactionnet.ReactionNetwork.seen`. This could lead to differences from `nmols`.
nreactions
Number of reaction in the reaction network.
.. note::
The value of `nreactions` is the number of times a reaction will be added to the :py:class:`~achemkit.reactionnet.ReactionNetwork`. If it
is already in the :py:class:`~achemkit.reactionnet.ReactionNetwork`, it will be replaced. This can lead to :class:`achemkit.reactionnet.ReactionNetwork` with less
than `nreactions` reactions.
nreactants
Number of reactants for each reaction in the reaction network. Can be a single value or a tuple/list which will be uniformly sampled from (duplicates can be used to give a non-uniform distribution).
.. note::
If this is a tuple/list it will be sampled for each reaction.
nproducts
Number of products for each reaction in the reaction network. Can be a single value or a tuple/list which will be uniformly sampled from (duplicates can be used to give a non-uniform distribution).
If this is None, then `nreactants` must be a list/tuple of tuples of (`nreactants`, `nproducts`) pairs that will be uniformly sampled from. Or `nreactants` must be a dictionary with keys of (`nreactants`, `nproducts`) and values of weightings, which will be sampled from.
.. note::
If this is a tuple/list it will be sampled for each reaction.
rates
Rate of each reaction in the reaction network. Can be a single value or a tuple/list which will be uniformly sampled from (duplicates can be used to give a non-uniform distribution).
.. note::
If this is a tuple/list it will be sampled for each reaction.
cls
Alternative class to use for constructing the return rather than :py:class:`achemkit.reactionnet.ReactionNetwork`.
rng
Random number generator to use. If not specifed, one will be generated at random.
These arguments can be a single value, a tuple/list which will be uniformly sampled from, or a dictionary of value/weighting which will be sampled from
For example:
``Uniform(5,3,2,1)`` will generate 5 molecules with 3 reactions between them where each reaction has two reactants and one product.
``Uniform(5,3,(1,2), (1,2))`` will generate 5 molecules with 3 reactions between them where each reaction has one or two reactants and one or two products.
``Uniform(5,3,((2,1),(1,2)), None)`` will generate 5 molecules with 3 reactions between them where each reaction has either two reactants and one product or one reactant and two products.
"""
if rng is None:
rng = random.Random(random.random())
if isinstance(nmols, int):
nmols = ["M%d"%i for i in range(nmols)]
nreactions = get_sample(nreactions, rng)
if nproducts is None:
#its a tuple not a generator because its the same variable name
newnreactants = []
newnproducts = []
for nreactant, nproduct in [get_sample(nreactants, rng) for i in range(nreactions)]:
newnreactants.append(nreactant)
newnproducts.append(nproduct)
nproducts = newnreactants
nreactants = newnproducts
else:
#its a tuple not a generator because its the same variable name
nreactants = [get_sample(nreactants, rng) for i in range(nreactions)]
nproducts = [get_sample(nproducts, rng) for i in range(nreactions)]
rates = [get_sample(rates, rng) for i in range(nreactions)]
outrates = {}
for thisnreactants, thisnproducts, thisrate in zip(nreactants, nproducts, rates):
reactants = [get_sample(nmols, rng) for j in range(thisnreactants)]
products = [get_sample(nmols, rng) for j in range(thisnproducts)]
reactants = OrderedFrozenBag(reactants)
products = OrderedFrozenBag(products)
outrates[(reactants, products)] = thisrate
return cls(outrates)
def Linear(natoms, maxlength, pform, pbreak, directed = True, rates = 1.0, cls = ReactionNetwork, rng = None):
"""
Generates a random :py:class:`~achemkit.reactionnet.ReactionNetwork` from molecules that are strings of atoms and can join together or break apart.
Based on the paper Autocatalytic sets of proteins. 1986. Journal of Theoretical Biology 119:1-24 by Kauffman, Stuart A. but without the explicit catalytic activity.
Arguments:
natoms
Number of atoms to use. Can be a single value or a tuple/list which will be uniformly sampled from (duplicates can be used to give a non-uniform distribution), or a dict of value:weight which will be sampled from.
.. note::
:py:class:`achemkit.reactionnet.ReactionNetwork` tracks molecules by their reactions, so if a molecule is not part of any reaction
it will not appear at all e.g. in :py:attr:`~achemkit.reactionnet.ReactionNetwork.seen`.
maxlength
Maximum number of atoms in a molecule. If this is None, then they are unbounded; this might cause problems with a computational explosion. Can be a single value or a tuple/list which will be uniformly sampled from (duplicates can be used to give a non-uniform distribution), or a dict of value:weight which will be sampled from.
pform
Probability that a pair of molecules will join together per orientation. Must be between 0 and 1. Can be a single value or a tuple/list which will be uniformly sampled from (duplicates can be used to give a non-uniform distribution), or a dict of value:weight which will be sampled from.
pbreak
Probability that any pair of atoms will break. Must be between 0 and 1.Can be a single value or a tuple/list which will be uniformly sampled from (duplicates can be used to give a non-uniform distribution), or a dict of value:weight which will be sampled from.
directed
If false, molecules have no intrinsic direction so AlphBeta is equivlanet to BetaAlpha.
rates
Rate of each reaction in the reaction network. Can be a single value, or a tuple/list which will be uniformly sampled from (duplicates can be used to give a non-uniform distribution), or a dict of value:weight which will be sampled from.
cls
Alternative class to use for constructing the return rather than :py:class:`achemkit.reactionnet.ReactionNetwork`.
rng
Random number generator to use. If not specifed, one will be generated at random.
"""
if rng is None:
rng = random.Random(random.random())
natoms = get_sample(natoms, rng)
maxlength = get_sample(maxlength, rng)
pform = get_sample(pform, rng)
pbreak = get_sample(pbreak, rng)
assert pform >= 0.0
assert pform <= 1.0
assert pbreak >= 0.0
assert pbreak <= 1.0
#these are lists not sets because sets have machine-dependant ordering, which prevents reproducibility for the same random seed.
molecules = []
new = []
#create some inital atoms
#of the form Abc where first letter is capitalized
alpha = "abcdefghijklmnopqrstuvwxyz"
assert natoms > 0
for i in range(natoms):
name = alpha[i%len(alpha)]
while i >= len(alpha):
i /= len(alpha)
name = alpha[(i%len(alpha))-1] + name
name = name.strip().capitalize()
new.append(name)
outrates = {}
assert maxlength > 0
def mol_to_atoms(mol, cache = {}):
if mol not in cache:
cache[mol] = tuple([x for x in re.split(r"([A-Z][a-z]*)", mol) if len(x) > 0])
return cache[mol]
def mol_len(mol):
#return len(mol)
return len(mol_to_atoms(mol))
def mol_reverse(mol):
rmol = ""
for atom in mol_to_atoms(mol):
rmol = atom + rmol
return rmol
def mol_order(mol):
rmol = mol_reverse(mol)
if mol < rmol:
return mol
else:
return rmol
def atoms_to_mol(atoms):
mol = ""
for atom in atoms:
mol = mol + atom
return mol
while len(new) > 0:
oldnew = new
new = []
#decomposition
for z in oldnew:
for i in range(1, mol_len(z)):
if rng.random() < pbreak:
a = atoms_to_mol(mol_to_atoms(z)[:i])
b = atoms_to_mol(mol_to_atoms(z)[i:])
if not directed:
a = mol_order(a)
b = mol_order(b)
reaction = (OrderedFrozenBag((z,)), OrderedFrozenBag(sorted((a,b))))
if reaction not in outrates:
outrates[reaction] = get_sample(rates, rng)
if a not in molecules and a not in new:
new.append(a)
if b not in molecules and b not in new:
new.append(b)
for a, b in itertools.chain(itertools.product(oldnew, molecules), combinations_with_replacement(oldnew, 2)):
if maxlength is None or mol_len(a) + mol_len(b) <= maxlength:
combinations = ((a,b), (b,a))
if not directed:
combinations += ((mol_reverse(a), b), (a, mol_reverse(b)))
for x,y in combinations:
if rng.random() < pform:
z = x + y
if not directed:
z = mol_order(z)
#because we may have revereed them, we have to order them again
if not directed:
reactants = OrderedFrozenBag(sorted((mol_order(x), mol_order(y))))
else:
reactants = OrderedFrozenBag(sorted((x, y)))
products = OrderedFrozenBag((z,))
reaction = (reactants, products)
if reaction not in outrates:
outrates[reaction] = get_sample(rates, rng)
if z not in molecules and z not in new:
new.append(z)
for z in oldnew:
molecules.append(z)
return cls(outrates)
