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(
name=name,
syringe_source=buffer_trough,
cell_source=guest_solutions[guest_index],
protocol=blank_protocol,
cell_volume=cell_volume,
cell_concentration=cell_concentration,
buffer_source=buffer_trough)
# rescale to match host into guest experiment concentrations.
experiment.rescale(tfactor=factors[replicate])
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)
experiment.cell_source = buffer_trough
experiment.cell_concentration *= 0
ligand_buffer_experiments.append(experiment)
# TODO, since we are changing ligands, we'd have to wash the syringe.
# Add ligand to protein experiment(s) to set
for ligand_protein_experiment in ligand_protein_experiments:
itc_experiment_set.addExperiment(ligand_protein_experiment)
# pprint.pprint(ligand_protein_experiment.__dict__)
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())
drug_protein_experiments.append(experiment)
# Define drug into buffer
for replicate in range(1):
name = '%s into buffer %d' % (drug.name, replicate + 1)
experiment = ITCHeuristicExperiment(
name=name,
syringe_source=drug_solution,
cell_source=buffer_trough,
protocol=binding_protocol,
buffer_source=buffer_trough)
# rescale to match drug to protein experiment concentrations.
experiment.rescale(tfactor=factors[replicate])
drug_buffer_experiments.append(experiment)
