def setup_single_state(sequence, name):
'''Simple function that sets up a System with one Macromolecule
and one State. Returns the State object.
'''
sys = System()
mol = sys.add_macromolecule(sequence, name)
return mol.get_apo_state()
sat_pct_error = 0.05
percentD = True # Is the data in percent D (True) or Deuterium units?
time_error = 0.02
fwd_exchange_ph = 7.4
fwd_exchange_t = 293
back_exchange_est = 0.35 # Back exchange for the entire system
back_exchange_ph = 3.0 #
back_exchange_t = 277
###########################################
####
# System Setup
sys = system.System("test_system", noclobber=False)
mol = sys.add_macromolecule(inseq, name="Test")
state = mol.get_apo_state()
# HDX model setup
hmod = model.ResidueGridModel(state, 20, protection_factors=True)
##############
# Get rates for each residue
act_sat = numpy.random.normal(saturation_est, sat_pct_error * saturation_est)
act_timepoints = [
numpy.random.normal(tp, tp * time_error) for tp in timepoints
]
fwd_rates = [-1]
back_rates = [-1]
###########################################
### Simulation Parameters
num_exp_bins = 40 # Number of log(kex) values for sampling. 15-20 is generally sufficient.
init = "random" # How to initialize - either "random" or "enumerate". Enumerate is slower but sampling will converge faster
nsteps = 10000 # equilibrium steps. 5000 to 10000
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
### Here the real work begins....
### You should not have to change anything beneath this line.
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
############################################
### System Setup:
# Initialize model
sys = system.System(output_dir = outputdir, noclobber=False)
mol = sys.add_macromolecule(sequence, "Test")
state = mol.get_apo_state()
state2 = mol.add_state("Apo2")
# Alternatively, you can use this single line macro, which is equivalent
#state = system.setup_single_state(sequence, "UVR8", output_dir = "test_output")
# Import data
dataset = hxio.import_HXcolumns("simulated_data.dat", # HX Columns input file
sequence, # FASTA sequence string
name="Data", # A string identifier for the dataset (optional)
percentD=False, # Is the data in percent deuterium (True) or absolute deuterons (False)
conditions=None, # A data.Conditions object specifying pH, Temp, etc... None uses a standard set of conditions
error_estimate=2.0, # The initial estimate for experimental SD in % deuterium untis.
n_fastamides=2, # Number of fast exchanging N-terminal amides
offset=offset) # Numbering offset between data and FASTA file. (positive or negative integer)
### Simulation Parameters
num_exp_bins = 71 # Number of log(kex) values for sampling. 15-20 is generally sufficient.
init = "random" # How to initialize - either "random" or "enumerate". Enumerate is slower but sampling will converge faster
nsteps = 5000 # equilibrium steps. 5000 to 10000
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
### Here the real work begins....
### You should not have to change anything beneath this line.
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
############################################
### System Setup:
# Initialize model
sys = system.System(output_dir=outputdir, noclobber=False)
mol = sys.add_macromolecule(sequence, "UVR8")
state = mol.get_apo_state()
state1 = mol.add_state(name="Apo2")
state2 = mol.add_state(name="Apo3")
# Alternatively, you can use this single line macro, which is equivalent
#state = system.setup_single_state(sequence, "UVR8", output_dir = "test_output")
# Import data
dataset = hxio.import_HXcolumns(
infile, # HX Columns input file
sequence, # FASTA sequence string
name="Data", # A string identifier for the dataset (optional)
percentD=
False, # Is the data in percent deuterium (True) or absolute deuterons (False)
conditions=
None, # A data.Conditions object specifying pH, Temp, etc... None uses a standard set of conditions
error_estimate=
rep_deut = 50
###########################################
### Simulation Parameters
num_exp_bins = 20 # Number of log(kex) values for sampling. 20 is generally sufficient.
init = "random" # How to initialize - either "random" or "enumerate". Enumerate is slower but sampling will converge faster
annealing_steps = 200 # steps per temperature in annealing - 100-200 sufficient
nsteps = 10000 # equilibrium steps. 5000 to 10000
num_best_models = 200 # Number of best models to consider for analysis
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# Input Data
sys = system.System()
mol = sys.add_macromolecule(name="Test", sequence=inseq)
state = mol.get_apo_state()
c = data.Conditions()
d = data.Dataset("Test", c, sequence=inseq)
pep = d.create_peptide("AAA", start_residue=1)
pep.add_timepoints([tp_time])
tp = pep.get_timepoint_by_time(tp_time)
tp.add_replicate(rep_deut)
state.add_dataset(d)
output_model = model.ResidueGridModel(state, grid_size=num_exp_bins)
state.set_output_model(output_model)
sampler = sampling.MCSampler(state, sigma_sample_level="timepoint")
###########################################
### Simulation Parameters
num_exp_bins = 50 # Number of log(kex) values for sampling. 20 is generally sufficient.
init = "enumerate" # How to initialize - either "random" or "enumerate". Enumerate is slower but sampling will converge faster
annealing_steps = 100 # steps per temperature in annealing - 100-200 sufficient
nsteps = 1000 # equilibrium steps. 5000 to 10000
###############################
### System Setup:
###############################
# Initialize model
sys = system.System(output_dir=outputdir, noclobber=False)
mol = sys.add_macromolecule(inseq, "CytC", initialize_apo=False)
# Import data
datasets = hxio.import_HDXWorkbench(
workbench_file, # Workbench input file
macromolecule=mol,
sequence=None, # FASTA sequence string
error_estimate=sigma0
) # The initial estimate for experimental SD in % deuterium untis.
#sys = system.System(output_dir=outputdir, noclobber=False)
#mol = sys.add_macromolecule(inseq, "CytC", initialize_apo=True)
state = mol.get_apo_state()
conditions = [data.Conditions(294, 6.5, 0.8), data.Conditions(294, 7.4, 0.8)]