예제 #1
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    'cleaning protocol',
    sample_prep_method='Plates Clean.setup',  # thorough cleaning
    itc_method='water5inj.inj',
    analysis_method='Control',
    experimental_conditions=dict(target_temperature=25,
                                 equilibration_time=60,
                                 stir_rate=1000,
                                 reference_power=5),
    injections=5 *
    [dict(volume_inj=7.5, duration_inj=15, spacing=150, filter_period=5)],
)

# Define ITC Experiment.

# use specified protocol by default
itc_experiment_set = ITCExperimentSet(
    name='Bovine carbonic anhydrase (CAII) experiments')
# Add available plates for experiments.
destination_plate = Labware(RackLabel='DestinationPlate', RackType='ITC Plate')
itc_experiment_set.addDestinationPlate(destination_plate)

nreplicates = 1  # number of replicates of each experiment

# Add cleaning experiment.
name = 'initial cleaning water titration'
itc_experiment_set.addExperiment(
    ITCExperiment(name=name,
                  syringe_source=water_trough,
                  cell_source=water_trough,
                  protocol=cleaning_protocol,
                  cell_volume=cell_volume))
예제 #2
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    )
# Protocol for cleaning protocol
cleaning_protocol = ITCProtocol(
    'cleaning protocol',
    sample_prep_method='Plates Clean.setup',
    itc_method='water5inj.inj',
    analysis_method='Control',
    experimental_conditions=dict(target_temperature=25, equilibration_time=60, stir_rate=1000, reference_power=5),
    injections=5 * [dict(volume_inj=7.5, duration_inj=15, spacing=150, filter_period=5)],
    )


# Define ITC Experiment.

# use specified protocol by default
itc_experiment_set = ITCExperimentSet(name='SAMPL4-CB7 host-guest experiments')
# Add available plates for experiments.
itc_experiment_set.addDestinationPlate(
    Labware(
        RackLabel='DestinationPlate',
        RackType='ITC Plate'))
itc_experiment_set.addDestinationPlate(
    Labware(
        RackLabel='DestinationPlate2',
        RackType='ITC Plate'))

nreplicates = 1  # number of replicates of each experiment

# Add cleaning experiment.
name = 'initial cleaning water titration'
itc_experiment_set.addExperiment(
예제 #3
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binding_protocol = ITCProtocol(
    '1:1 binding protocol',
    sample_prep_method='Plates Standard.setup',
    itc_method='Chodera_HSA.inj',  # TODO Define new protocol with more injections?
    analysis_method='Onesite')  # TODO better default analysis?
# Protocol for cleaning protocol
binding_cleaning_protocol = ITCProtocol(
    'cleaning protocol',
    sample_prep_method='Plates Clean.setup',
    itc_method='Chodera_HSA.inj',
    analysis_method='Onesite')

# Define ITC Experiment.

# use specified protocol by default
itc_experiment_set = ITCExperimentSet(name='Human Serum Albumin experiments')
# Add available plates for experiments.
itc_experiment_set.addDestinationPlate(
    Labware(
        RackLabel='DestinationPlate',
        RackType='ITC Plate'))
itc_experiment_set.addDestinationPlate(
    Labware(
        RackLabel='DestinationPlate2',
        RackType='ITC Plate'))

nreplicates = 1  # number of replicates of each experiment


# Add water control titrations.
for replicate in range(1):
예제 #4
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buffer_masses = {'Compound 10': 10.065 * ureg.gram}
compound_masses = {'Compound 10': 15.05 * ureg.milligram}
ligand_solutions = list()
for (index, ligand) in enumerate(ligands):
    ligand_solution = SimpleSolution(
        compound=ligand,
        compound_mass=compound_masses[ligand.name],
        solvent=buffer,
        solvent_mass=buffer_masses[ligand.name],
        location=PipettingLocation(source_plate.RackLabel,
                                   source_plate.RackType, index + 1))
    ligand_solutions.append(ligand_solution)

# For convenience, report concentrations
print('STOCK SOLUTION CONCENTRATIONS:')
location = ITCExperimentSet.human_readable(receptor_solution.location)
print(
    f"{receptor_solution.name:20} in {location:32} : {receptor_solution.compound_mass.to('milligrams')} receptor in {receptor_solution.solvent_mass.to('grams')} solvent : {receptor_solution.concentration.to('millimolar'):30}"
)
for ligand_solution in ligand_solutions:
    location = ITCExperimentSet.human_readable(ligand_solution.location)
    print(
        f"{ligand_solution.name:20} in {location:32} : {ligand_solution.compound_mass.to('milligrams')} compound in {ligand_solution.solvent_mass.to('grams')} solvent : {ligand_solution.concentration.to('millimolar'):30}"
    )
print('')

# Define ITC protocol.

# Receptor cell concentrations to evaluate
#cell_concentrations = [0.010 * ureg.millimolar, 0.020 * ureg.millimolar, 0.030 * ureg.millimolar]
#cell_concentrations = [0.020 * ureg.millimolar]
    'cleaning protocol',
    sample_prep_method='Plates Clean.setup',
    itc_method='water5inj.inj',
    analysis_method='Control',
    experimental_conditions=dict(target_temperature=25,
                                 equilibration_time=60,
                                 stir_rate=1000,
                                 reference_power=5),
    injections=5 *
    [dict(volume_inj=7.5, duration_inj=15, spacing=150, filter_period=5)],
)

# Define ITC Experiment.

# use specified protocol by default
itc_experiment_set = ITCExperimentSet(name='HDR')
# Add available plates for experiments.
itc_experiment_set.addDestinationPlate(
    Labware(RackLabel='DestinationPlate', RackType='ITC Plate'))
itc_experiment_set.addDestinationPlate(
    Labware(RackLabel='DestinationPlate2', RackType='ITC Plate'))

nreplicates = 1  # number of replicates of each experiment

# Add cleaning experiment.
name = 'initial cleaning water titration'
itc_experiment_set.addExperiment(
    ITCExperiment(
        name=name,
        syringe_source=water_trough,
        cell_source=water_trough,

cleaning_protocol = ITCProtocol(
    'cleaning protocol',
    sample_prep_method='Plates Clean.setup',
    itc_method='ChoderaWaterWater5.inj',
    analysis_method='Onesite',
    experimental_conditions=dict(target_temperature=25, equilibration_time=60, stir_rate=1000, reference_power=5),
    injections=5 * [
        dict(volume_inj=7.5, duration_inj=15, spacing=150, filter_period=5)],
    )

# Define ITC Experiment.

# use specified protocol by default
itc_experiment_set = ITCExperimentSet(name='Human Serum Albumin experiments')
# Add available plates for experiments.
itc_experiment_set.addDestinationPlate(
    Labware(
        RackLabel='DestinationPlate',
        RackType='ITC Plate'))
itc_experiment_set.addDestinationPlate(
    Labware(
        RackLabel='DestinationPlate2',
        RackType='ITC Plate'))

nreplicates = 1  # number of replicates of each experiment


# #  Initial cleaning is skipped.
# name = 'initial cleaning water titration'