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)