# We need to store the experiments before adding them to the set
ligand_protein_experiments = list()
ligand_buffer_experiments = list()
# Scaling factors per replicate
factors = list()
# Define ligand to protein experiments
for cell_concentration in cell_concentrations:
for replicate in range(nreplicates):
name = '%s into CAII %d' % (ligand.name, replicate + 1)
experiment = ITCHeuristicExperiment(
name=name,
syringe_source=ligand_solution,
cell_source=caii_solution,
protocol=binding_protocol,
cell_concentration=cell_concentration,
buffer_source=buffer_trough,
cell_volume=cell_volume)
# optimize the syringe_concentration using heuristic equations and known binding constants
# TODO extract m, v and V0 from protocol somehow?
# Warning, you're possibly not getting the setup you want. Consider not using the Heuristic Experiment
experiment.heuristic_syringe(ligand_ka, 10, strict=False)
# rescale if syringe > stock. Store factor.
factors.append(experiment.rescale())
ligand_protein_experiments.append(experiment)
# Define corresponding ligand into buffer experiments
for experiment in ligand_protein_experiments:
experiment = copy.deepcopy(experiment)
# We need to store the experiments before adding them to the set
host_guest_experiments = list()
buff_guest_experiments = list()
# Scaling factors per replicate
factors = list()
# Define host into guest experiments.
for replicate in range(1):
name = 'host into %s' % guests[guest_index].name
experiment = ITCHeuristicExperiment(
name=name,
syringe_source=host_solution,
cell_source=guest_solutions[guest_index],
protocol=binding_protocol,
cell_concentration=0.2 *
millimolar *
cell_scaling,
buffer_source=buffer_trough)
# optimize the syringe_concentration using heuristic equations and known binding constants
# TODO extract m, v and V0 from protocol somehow?
experiment.heuristic_syringe(
guest_compound_Ka[guest_index],
10,
3. *
microliters,
202.8 *
microliters)
# rescale if syringe > stock. Store factor.
factors.append(experiment.rescale())
for guest_index in range(nguests):
# We need to store the experiments before adding them to the set
host_guest_experiments = list()
buff_guest_experiments = list()
# Scaling factors per replicate
factors = list()
# Define host into guest experiments.
for replicate in range(1):
name = 'host into %s' % guests[guest_index].name
experiment = ITCHeuristicExperiment(
name=name,
syringe_source=host_solution,
cell_source=guest_solutions[guest_index],
protocol=binding_protocol,
cell_volume=cell_volume,
cell_concentration=cell_concentration,
buffer_source=buffer_trough)
# optimize the syringe_concentration using heuristic equations and known binding constants
optimal_rm.append(experiment.heuristic_syringe(
guest_compound_Ka[guest_index],
strict=False))
# rescale if syringe > stock. Store factor.
factors.append(experiment.rescale())
host_guest_experiments.append(experiment)
# Define buffer into guest experiments.
for replicate in range(1):
name = 'buffer into %s' % guests[guest_index].name
experiment = ITCHeuristicExperiment(
# Scaling factors per replicate
factors = list()
# Define drug to protein experiments.
for replicate in range(1):
if count == 2:
protocol = binding_cleaning_protocol
else:
protocol = binding_protocol
name = '%s into HSA %d' % (drug.name, replicate + 1 )
experiment = ITCHeuristicExperiment(
name=name,
syringe_source=drug_solution,
cell_source=hsa_solution,
protocol=protocol,
cell_concentration=0.040 *
ureg.millimolar *
cell_scaling,
buffer_source=buffer_trough)
# optimize the syringe_concentration using heuristic equations and known binding constants
# TODO extract m, v and V0 from protocol somehow?
experiment.heuristic_syringe(
drug_ka,
10,
3. *
ureg.microliter,
202.8 *
ureg.microliter)
# rescale if syringe > stock. Store factor.
factors.append(experiment.rescale())
for ligand, ligand_solution, ligand_ka in zip(ligands, ligand_solutions,
ligand_kas):
# Perform specified number of replicates
for replicate in range(nreplicates):
#
# Injection protocol
#
# Titrate ligand into protein experiment based on guess of affinity
name = f'titration of {ligand.name} into {receptor.name} (replicate {replicate+1})'
receptor_experiment = ITCHeuristicExperiment(
name=name,
syringe_source=ligand_solution,
cell_source=receptor_solution,
protocol=binding_protocol_with_cleaning,
cell_concentration=cell_concentration,
buffer_source=buffer_trough,
cell_volume=cell_volume)
# Optimize the syringe_concentration using heuristic equations and known binding constants
n_injections = 10 # TODO: Extract this from binding_protocol object
receptor_experiment.heuristic_syringe(ligand_ka,
n_injections,
strict=False)
ligand_experiment = copy.deepcopy(receptor_experiment)
ligand_experiment.name = f'titration of {ligand.name} into buffer (replicate {replicate+1})'
ligand_experiment.cell_source = buffer_trough
ligand_experiment.cell_dilution_factor = 0
ligand_experiment.cell_concentration = None
for drug, drug_solution, drug_ka in zip(drugs, drug_solutions, drug_kas):
# We need to store the experiments before adding them to the set
drug_protein_experiments = list()
drug_buffer_experiments = list()
# Scaling factors per replicate
factors = list()
# Define drug to protein experiments.
for replicate in range(1):
name = '%s into HSA %d' % (drug.name, replicate + 1)
experiment = ITCHeuristicExperiment(name=name,
syringe_source=drug_solution,
cell_source=hsa_solution,
protocol=binding_protocol,
cell_concentration=0.040 *
ureg.millimolar * cell_scaling,
buffer_source=buffer_trough,
cell_volume=cell_volume)
# optimize the syringe_concentration using heuristic equations and known binding constants
# TODO extract m, v and V0 from protocol somehow?
## I am not sure what this part is doing?
# Warning, you're possibly not getting the setup you want. Consider not using the Heuristic Experiment
experiment.heuristic_syringe(drug_ka, 10, strict=False)
# rescale if syringe > stock. Store factor.
factors.append(experiment.rescale())
drug_protein_experiments.append(experiment)
# Define drug into buffer experiments.
for guest_index in range(nguests):
# We need to store the experiments before adding them to the set
host_guest_experiments = list()
buff_guest_experiments = list()
# Scaling factors per replicate
factors = list()
# Define host into guest experiments.
for replicate in range(1):
name = 'host into %s' % guests[guest_index].name
experiment = ITCHeuristicExperiment(
name=name,
syringe_source=host_solution,
cell_source=guest_solutions[guest_index],
protocol=binding_protocol,
cell_volume=cell_volume,
cell_concentration=cell_concentration,
buffer_source=buffer_trough)
# optimize the syringe_concentration using heuristic equations and known binding constants
optimal_rm.append(
experiment.heuristic_syringe(guest_compound_Ka[guest_index],
strict=False))
# rescale if syringe > stock. Store factor.
factors.append(experiment.rescale())
host_guest_experiments.append(experiment)
# Define buffer into guest experiments.
for replicate in range(1):
name = 'buffer into %s' % guests[guest_index].name
# We need to store the experiments before adding them to the set
drug_protein_experiments = list()
drug_buffer_experiments = list()
# Scaling factors per replicate
factors = list()
# Define drug to protein experiments.
for replicate in range(1):
name = '%s into HSA %d' % (drug.name, replicate + 1 )
experiment = ITCHeuristicExperiment(
name=name,
syringe_source=drug_solution,
cell_source=hsa_solution,
protocol=binding_protocol,
cell_concentration=0.040 *
ureg.millimolar *
cell_scaling,
buffer_source=buffer_trough,
cell_volume=cell_volume)
# optimize the syringe_concentration using heuristic equations and known binding constants
# TODO extract m, v and V0 from protocol somehow?
## I am not sure what this part is doing?
# Warning, you're possibly not getting the setup you want. Consider not using the Heuristic Experiment
experiment.heuristic_syringe(drug_ka, 10, strict=False)
# rescale if syringe > stock. Store factor.
factors.append(experiment.rescale())
drug_protein_experiments.append(experiment)
