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- ReactionVessel
-
- GillespieVessel(ReactionVessel, Multiset.Multiset)
- WellStirredVessel
class GillespieVessel(ReactionVessel, Multiset.Multiset) |
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- Method resolution order:
- GillespieVessel
- ReactionVessel
- Multiset.Multiset
Methods defined here:
- __init__(self, nav=1000)
- initialize empty reaction vessel for stochastic simulation;
'nav' is the initial N_A * V quantity (Avogadro constant
times volume of the vessel); typically a smaller nav
(hence smaller volume) leads to more prominent stochastic
fluctuations
- close(self)
- create data structures necessary for stochastic simulation;
convert the macroscopic kinetic constants (k) to
microscopic equivalents (c) using Wolkenhauer's relation
- deposit(self, mol, conc)
- deposit a concentration 'conc' of molecule 'mol';
first must convert 'conc' [S] to number of molecules (ns)
to be injected: [S] = ns / NAV => ns = [S] * NAV
- factorial(self, n, m=1)
- recursively computes the factorial of n, stopping at m:
factorial(n, m) = n*(n-1)*...*m for 1 < m < n
- get_conc(self, mol)
- calculate concentration of molecule 'mol': [S] = ns / NAV
- get_nav(self)
- current N_A * V value
- get_volume(self)
- volume of the vessel
- integrate(self, dt=1.0)
- iterate Gillespie SSA for an interval of size at least dt
- iterate(self)
- one iteration of the Gillespie stochastic simulation algorithm
- nchoosek(self, n, k)
- computes the binomial coefficient or "n choose k" function:
C(n,k) for two integers n & k, where n > k
C(n,k) = n!/((k!)(n-k)!) = n(n-1)(n-2)...(n-k+1)/k!
efficient when either k or (n-k) is small (n can be big)
- nspecies(self)
- total number of possible molecular species (static)
- nspecies_mset(self)
- number of species currently present in the multiset (dynamic)
- perform_reaction(self, rno)
- perform a given reaction, extracting the needed educts
from the multiset and injecting the resulting products
- propensity(self)
- calculate reaction propensities, store them in wv[j], total=wt
- react(self, dice)
- perform the reaction pointed by the given dice
relies on pre-calculated propensity values stored in wv[j]
- set_coefficient(self, i, k)
- update kinetic coefficient for reaction, together with its
corresponding mesoscopic value
- set_nav(self, newnav)
- sets the value of N_A*V = NAV:
this is useful when we have the parameters from the ODE
(initial concentrations, kinetic constants k) and want to
perform a stochastic simulation based on the same
parameters
in order to adjust NAV we use the relation:
[S] = ns / NAV => ns = [S]*NAV
thus by setting NAV small, we make the reactor small for
the same concentration, that is, the number of molecules
in the reactor will be smaller, hence the stochastic
effects can be more easily seen; increase NAV to simulate
larger particle numbers in the reactor, for a given
concentration.
- set_volume(self, newvol)
- sets the volume of the vessel, recalculating NAV = N_A*V
and the mesoscopic kinetic constants accordingly
- trace(self)
- print internal variables, for debug purposes
- trace_conc(self, prefix='')
- print concentrations, like trace_mult but concentrations
are calculated as [S] = ns / NAV
- trace_mult(self, prefix='')
- print molecule counts to tab-separated line for plotting.
a one-letter prefix can be given to print only molecules
starting with that letter
- wolkenhauer(self, j)
- calculate the microscopic stochastic rate constants (c)
from the macroscopic ones (k), according to [Wolkenhauer2004]:
c = k / (NAV)^(m - 1) * prod_i=1;L(li!)
where:
. m is the total number of colliding molecules (size of
educt multiset)
. L is the number of species in the educt multiset
. li is the educt stoichiometric coefficient of substance i
. NAV = N_A * V (CAUTION!!! must be refreshed if NAV changes!!)
Methods inherited from ReactionVessel:
- add(self, reaction)
- add a new chemical reaction to the vessel's set of reactions;
'reaction' must be an object of the Reaction class
- get_coefficient(self, i)
- get kinetic coefficient for reaction
- get_names(self)
- list of all possible molecular species (set S of S,R,A)
- nreactions(self)
- total number of reactions: |R| in S,R,A
- parse(self, reactlist)
- invoke the ReactionParser to parse a list of reactions
- parse_file(self, fname)
- invoke the ReactionParser to parse the file named 'fname'
- parse_input(self, infile)
- invoke the ReactionParser to parse an already open input file
- parse_stdin(self)
- invoke the ReactionParser to parse the standard input (stdin)
- trace_title(self, prefix='')
- output tab-separated title line for plotting;
an optional prefix can be given to print only molecules
starting with that character
- vtime(self)
- current simulation time
Methods inherited from Multiset.Multiset:
- absorb(self, victim)
- absorb victim multiset into my own (victim will return empty)
- clear(self)
- delete all molecules from the multiset
- divide(self)
- divide multiset in two parts; returns daughter multiset created
- empty(self)
- true if this multiset is empty
- expel(self, mol, mult=1)
- expel a given amount of a molecule from the multiset;
returns the number of molecules actually expelled
- expelrnd(self)
- expel a random molecule from the multiset
- inject(self, mol, mult=1)
- inject a given amount of a molecule in the multiset
- keys(self)
- list containing the set of different objects in the multiset
- mult(self, mol='')
- multiplicity: number of molecules of type 'mol' present
in the multiset
- nmolecules(self)
- total number of molecules in the multiset
- rndmol(self)
- peek at a random molecule from the multiset, without
removing it
- topkeys(self)
- list of molecules in the multiset, ordered by decreasing
multiplicity
- trace_frequencies(self)
- print a histogram of molecule multiplicities
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class ReactionVessel |
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Methods defined here:
- __init__(self)
- initialize empty reaction vessel
- add(self, reaction)
- add a new chemical reaction to the vessel's set of reactions;
'reaction' must be an object of the Reaction class
- get_coefficient(self, i)
- get kinetic coefficient for reaction
- get_names(self)
- list of all possible molecular species (set S of S,R,A)
- nreactions(self)
- total number of reactions: |R| in S,R,A
- nspecies(self)
- total number of molecular species: |S| in S,R,A
- parse(self, reactlist)
- invoke the ReactionParser to parse a list of reactions
- parse_file(self, fname)
- invoke the ReactionParser to parse the file named 'fname'
- parse_input(self, infile)
- invoke the ReactionParser to parse an already open input file
- parse_stdin(self)
- invoke the ReactionParser to parse the standard input (stdin)
- set_coefficient(self, i, k)
- update kinetic coefficient for reaction
- trace(self)
- print internal variables, for debug purposes
- trace_title(self, prefix='')
- output tab-separated title line for plotting;
an optional prefix can be given to print only molecules
starting with that character
- vtime(self)
- current simulation time
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class WellStirredVessel(ReactionVessel) |
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Methods defined here:
- __init__(self)
- initialize empty reaction vessel for ODE integration
- apply_dilution(self)
- apply dilution to vessel capacity: normalize the
concentrations to the vessel capacity, such that the sum
of concentrations of all species in the system does not
exceed the vessel capacity
- close(self)
- after all reactions have been parsed, this method should
be called in order to create all the data structures
needed for numeric integration
- deposit(self, mol, conc)
- increase the concentration of molecule 'mol' by an amount
'conc'
- get_coefficient(self, i)
- get kinetic coefficient for reaction (overrides default
ReactionVessel method in order to use vector kv directly;
the result of both methods should be the same though)
- get_conc(self, mol)
- get the concentration of molecule 'mol'
- get_dilution(self)
- get vessel capacity (measured in concentration)
- integrate(self, dt=1.0)
- ODE integration for one timestep of size dt
- reset(self, mol='', conc=0.0)
- reset the concentration of molecule 'mol' to 'conc';
if 'mol' is not specified (mol='') then set the
concentration of all molecules to the value 'conc';
hence a reset() without parameters will reset all the
concentration values to zero
- set_coefficient(self, i, k)
- update kinetic coefficient for reaction
- set_conc(self, mol, conc)
- set the concentration of molecule 'mol' to 'conc'
- set_dilution(self, cap)
- set dilution to vessel capacity, where 'cap' is the
maximum concentration that the vessel should contain
- trace(self)
- print internal variables, for debug purposes
- trace_conc(self)
- trace concentrations to tab-separated line for plotting
Methods inherited from ReactionVessel:
- add(self, reaction)
- add a new chemical reaction to the vessel's set of reactions;
'reaction' must be an object of the Reaction class
- get_names(self)
- list of all possible molecular species (set S of S,R,A)
- nreactions(self)
- total number of reactions: |R| in S,R,A
- nspecies(self)
- total number of molecular species: |S| in S,R,A
- parse(self, reactlist)
- invoke the ReactionParser to parse a list of reactions
- parse_file(self, fname)
- invoke the ReactionParser to parse the file named 'fname'
- parse_input(self, infile)
- invoke the ReactionParser to parse an already open input file
- parse_stdin(self)
- invoke the ReactionParser to parse the standard input (stdin)
- trace_title(self, prefix='')
- output tab-separated title line for plotting;
an optional prefix can be given to print only molecules
starting with that character
- vtime(self)
- current simulation time
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