<commit_before>###########################################################################
# Simulates data for given model, moments, parameters, initial conditions
# and method (moment expansion or LNA)
#########################################################################

import numpy as np
import matplotlib.pyplot as plt
from sympy import Matrix

from CVODE import CVODE

#########################################################################
# Arguments:
# mfkoutput     Name of output file from MFK/LNA (specify using --ODEout)
# trajout       Name of output file with simulated trajectories (specify 
#               using --simout)
# lib           Name of C file for solver (specify with --library)
# t             List of timepoints
# param         List of kinetic parameters
# initcond      List of initial conditions for each moment
#               (t, param, initcond are specified in --timeparam file)
# maxorder      Maximum order of moments to output to plot/datafile
#               (defaults to maxorder in MFK output, specify using
#               --maxorder if fewer required)
########################################################################

#######################################################################
# Variables within function:
# moment_list   Contains the names for each moment (e.g. [1,0,1], where
#               numbers are the power that each species is raised to
# soln          Array returned by CVODE, each row is a list of moments/
#               values at a particular timepoint
# mu            List where each item is a timecourse (as list) for a
#               particular moment/value
#
# Simulate function returns (mu, moment_list) i.e. trajectories and 
# corresponding list of names identifying the moments
########################################################################

def simulate(mfkoutput, trajout, lib, t, param, initcond, maxorder):

    # Get required info from mfkoutput, and if not all initial conditions
    # are specified set the remainder to 0 as default

    LHSfile = open(mfkoutput)<commit_msg>moved docstring to an appropriate place<commit_after>###########################################################################
# Simulates data for given model, moments, parameters, initial conditions
# and method (moment expansion or LNA)
#########################################################################

import numpy as np
import matplotlib.pyplot as plt
from sympy import Matrix

from CVODE import CVODE

#######################################################################
# Variables within function:
# moment_list   Contains the names for each moment (e.g. [1,0,1], where
#               numbers are the power that each species is raised to
# soln          Array returned by CVODE, each row is a list of moments/
#               values at a particular timepoint
# mu            List where each item is a timecourse (as list) for a
#               particular moment/value
#
# Simulate function returns (mu, moment_list) i.e. trajectories and 
# corresponding list of names identifying the moments
########################################################################

def simulate(mfkoutput, trajout, lib, t, param, initcond, maxorder):
    """

    :param mfkoutput: Name of output file from MFK/LNA (specified by --ODEout)
    :param trajout: Name of output file for this function (where simulated trajectories would be stored, i.e. --simout)
    :param lib: Name of the C file for solver (i.e. --library)
    :param t: List of timepoints
    :param param: List of kinetic parameters
    :param initcond: List of initial conditions for each moment (in timeparameters file)
    :param maxorder: Maximum order of moments to output to either plot or datafile. (Defaults to maximum order of moments)
    :return:
    """

    # Get required info from mfkoutput, and if not all initial conditions
    # are specified set the remainder to 0 as default

    LHSfile = open(mfkoutput)
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