def initialize_dataset():
d = data.Dataset("Test", data.Conditions(), sequence="MEGAMAN")
d.create_peptide("MEGA", start_residue=1)
d.create_peptide("MEGAMA", start_residue=1)
d.create_peptide("GAMAN", start_residue=3)
d.create_peptide("AMAN", start_residue=4)
return d
def initialize_system_and_dataset():
sequence = "MEGAMAN"
sys = system.System()
mol = sys.add_macromolecule(sequence, "test_molecule")
d = data.Dataset("Test", data.Conditions(), sequence=sequence)
d.create_peptide("MEGA", start_residue=1)
d.create_peptide("MEGAMA", start_residue=1)
d.create_peptide("GAMAN", start_residue=3)
d.create_peptide("AMAN", start_residue=4)
for pep in d.get_peptides():
pep.add_timepoints([10, 100, 1000])
mol.get_state(0).add_dataset(d)
return mol.get_state(0)
60: [3.90336438867],
300: [18.0515175821],
900: [44.9670559903],
3600: [90.8274310554]
}
###############################
### System Setup:
###############################
# Initialize model (name, FASTA sequence, offset)
sys = system.System(output_dir=outputdir, noclobber=False)
mol = sys.add_macromolecule(inseq, "Single_sim")
state = mol.get_apo_state()
dataset = data.Dataset("Sim",
data.Conditions(),
inseq,
offset=0,
error_estimate=sigma0)
pep = dataset.create_peptide(inseq, 1)
for d in dat.keys():
tp = pep.add_timepoint(d)
for r in dat[d]:
tp.add_replicate(r, 1)
state.add_dataset(dataset)
sys.get_output().write_datasets()
def initialize(self):
c = data.Conditions()
d = data.Dataset("Test", c, sequence="EWESEEESSEFF")
return d
def test_conditions(self):
c = data.Conditions()
self.assertEqual(c.saturation, 1.0)
def initialize_dataset(self):
c = data.Conditions()
d = data.Dataset("Test", c, sequence="LALALAND")
return d
mol0 = sys0.add_macromolecule(inseq, "CytC", initialize_apo=False)
# Import data
datasets = hxio.import_HDXWorkbench(
workbench_file, # Workbench input file
macromolecule=mol0,
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)]
datasets[0].conditions = conditions[1]
datasets[1].conditions = conditions[0]
ds = datasets[0]
#state.add_dataset(ds)
ds.calculate_intrinsic_rates()
ds.calculate_observable_rate_bounds()
ds.max_rate = ds.get_max_rate()
# Add data to molecule states and initialize models
for s in range(len(mol.get_states())):
state = mol.get_states()[s]
mod = model.ResidueGridModel(state, grid_size=num_exp_bins)
3600: [51.97321428571825, 37.898809523810655, 41.9226190476218],
}
'''
dat = { 10 : [3.903],
30 : [11.258],
60 : [30.113],
300 : [76.145],
900 : [97.221],
3600 : [99.9999] }
'''
###############################
### System Setup:
###############################
# create dataset
dataset = data.Dataset("Sim", data.Conditions(), inseq, offset=0)
pep = dataset.create_peptide(inseq, 1)
for d in dat.keys():
tp = pep.add_timepoint(d)
for r in dat[d]:
tp.add_replicate(r, 1)
# Initialize model (name, FASTA sequence, offset)
sys = system.System(output_dir=outputdir, noclobber=False)
mol = sys.add_macromolecule(inseq, "Single_pep")
state = mol.get_apo_state()
state.add_dataset(dataset)
om = model.ResidueGridModel(state, grid_size=num_exp_bins)
state.set_output_model(om)
sys.output.initialize_output_model_file(state, om.pf_grids)