annealing_steps = 200 # steps per temperature in annealing - 100-200 sufficient
nsteps = 10000 # equilibrium steps. 5000 to 10000
###############################
### System Setup:
###############################
# Initialize model
sys = system.System(output_dir=outputdir, noclobber=False)
mol = sys.add_macromolecule(inseq, "VDR", initialize_apo=False)
# Import data
datasets = hxio.import_HDXWorkbench(
workbench_file, # Workbench input file
macromolecule=mol,
sequence=None, # FASTA sequence string
sigma0=sigma0
) # The initial estimate for experimental SD in % deuterium untis.
print(datasets)
# Add data to molecule states and initialize models
for s in range(len(mol.get_states())):
print(s)
state = mol.get_states()[s]
state.add_dataset(datasets[s])
output_model = state.set_output_model(
model.ResidueGridModel(state, grid_size=num_exp_bins))
sys.output.initialize_output_model_file(state, output_model.pf_grids)
sampler = sampling.MCSampler(sys, sigma_sample_level="timepoint")
# First, run a short minimization step
def test_import_workbench(self):
infile = input_path + "Workbench_VDR_VD3_01.csv"
datasets = hxio.import_HDXWorkbench(infile)
self.assertEqual(len(datasets), 2)
import hxio
from matplotlib import pyplot as plt
# Script for plotting timepoint avg vs. std from a HDXWorkbench file
datafiles = ["Data_Export_HDX_Workbench.csv"]
error_dict = {}
i = 0
pctd_error = []
d2_error = []
for df in datafiles:
datasets = hxio.import_HDXWorkbench(df)
for d in datasets:
j = 0
d_error = {}
for pep in d.get_peptides():
#print(pep.sequence)
nam = pep.get_number_of_observable_amides()
for tp in pep.get_timepoints():
(avg, sd) = tp.get_avg_sd()
#print(tp.time, avg, sd)
d_error[j] = {
"sd": sd,
"avg": avg,
"amides": nam,
"time": tp.time
}
if sd is not None and avg is not None:
pctd_error.append((avg, sd))
d2_error.append(((avg * nam) / 100, sd * (avg) / 100))
300 : [22.86113],
900 : [31.88971],
3600 : [42.51679] }
print "Hello"
###############################
### System Setup:
###############################
# Initialize model (name, FASTA sequence, offset)
sys = system.System(output_dir=outputdir, noclobber=False)
mol = sys.add_macromolecule(sequence, "Single", initialize_apo=False)
datasets = hxio.import_HDXWorkbench(workbench_file, # Workbench input file
macromolecule=mol,
sequence=None, # FASTA sequence string
error_estimate=sigma0)
sys.get_output().write_datasets()
for state in mol.get_states():
output_model = model.ResidueGridModel(state, grid_size=num_exp_bins)
state.set_output_model(output_model)
sys.output.initialize_output_model_file(state, output_model.pf_grids)
state.initialize()
sampler = sampling.MCSampler(sys, sigma_sample_level=None)
# First, run a short minimization step
#sampler.run(50, 0.0001)
'''
for dataset in datasets: