#Ka (association constants) TODO Add this to the compound properties? (maybe a dict with protein as key)
aspirin_ka = 547198.10 / ureg.molar # http://omicsonline.org/2157-7544/2157-7544-2-107.pdf first site estimate
naproxen_ka = 1.7 / (10 * ureg.micromolar) # http://pubs.acs.org/doi/pdf/10.1021/jp062734p
indoxylsulfate_ka = 9.1E5 / ureg.molar # 10.1023/A:1011014629551
# Define troughs on the instrument
water_trough = Labware(RackLabel='Water', RackType='Trough 100ml')
buffer_trough = Labware(RackLabel='Buffer', RackType='Trough 100ml')
# Define source labware.
source_plate = Labware(RackLabel='SourcePlate', RackType='5x3 Vial Holder')
# Define source solutions in the vial holder
# TODO : Define solutions once prepared with the Quantos
hsa_solution = SimpleSolution(compound=hsa, compound_mass=10.05014 * ureg.milligram, solvent=buffer, solvent_mass=3.4245 * ureg.gram, location=PipettingLocation(
source_plate.RackLabel,
source_plate.RackType,
1)) # 10, where we expected 15. Is it the quantos, the dialysis, or the HSA powder that is the problem?
indoxylsulfate_solution = SimpleSolution(compound=indoxylsulfate, compound_mass=10.4 * ureg.milligram, solvent=buffer, solvent_mass=10.3894 * ureg.gram, location=PipettingLocation(
source_plate.RackLabel,
source_plate.RackType,
2))
naproxen_sodium_solution = SimpleSolution(compound=naproxen_sodium, compound_mass=25.245 * ureg.milligram, solvent=buffer, solvent_mass=10.0728 * ureg.gram, location=PipettingLocation(
source_plate.RackLabel,
source_plate.RackType,
3))
drugs = [indoxylsulfate, naproxen_sodium]
drug_solutions = [indoxylsulfate_solution, naproxen_sodium_solution]
drug_kas = [indoxylsulfate_ka, naproxen_ka]
# Define troughs on the instrument
water_trough = Labware(RackLabel='Water', RackType='Trough 100ml')
buffer_trough = Labware(RackLabel='Buffer', RackType='Trough 100ml')
# Define source labware.
source_plate = Labware(RackLabel='SourcePlate', RackType='5x3 Vial Holder')
protein_source_plate = Labware(RackLabel='ProteinSourcePlate',
RackType='ITC Plate')
# Define source solutions in the vial holder
caii_mass = 48.913e-6 * ureg.moles / ureg.liter * 29246 * ureg.grams / ureg.moles * 1.58 * ureg.milliliters
caii_solution = SimpleSolution(compound=caii,
compound_mass=caii_mass,
solvent=buffer,
solvent_mass=1.58 * ureg.grams,
location=PipettingLocation(
protein_source_plate.RackLabel,
protein_source_plate.RackType,
1)) # Well A1 of ITC plate
# aqueous solubility of CBS is 453 mg/L---stay well below this!
cbs_solution = SimpleSolution(
compound=cbs,
compound_mass=5.43 * ureg.milligram,
solvent=buffer,
solvent_mass=12.0006 * ureg.gram,
location=PipettingLocation(source_plate.RackLabel, source_plate.RackType,
1)) # Well A1 of vial holder
ligands = [cbs]
ligand_solutions = [cbs_solution]
buffer_trough = Labware(RackLabel='Buffer', RackType='Trough 100ml')
# Define source labware.
source_plate = Labware(RackLabel='SourcePlate', RackType='5x3 Vial Holder')
protein_source_plate = Labware(RackLabel='ProteinSourcePlate',
RackType='ITC Plate')
# Define source solutions in the vial holder
protein_volume = 0.5 * ureg.milliliter
protein_concentration = (1.872 * ureg.milligram / ureg.milliliter)
protein_mass = protein_concentration * protein_volume
solvent_mass = protein_volume * buffer.density
receptor_solution = SimpleSolution(compound=receptor,
compound_mass=protein_mass,
solvent=buffer,
solvent_mass=solvent_mass,
location=PipettingLocation(
protein_source_plate.RackLabel,
protein_source_plate.RackType,
1)) # Well A1 of ITC plate
solubility_safety = 0.5 # fraction of solubility to prepare solution for
max_compound_mass = 15.0 * ureg.milligram # maximum mass we may want to dispense
ligand_solutions = list()
for (index, ligand) in enumerate(ligands):
target_concentration = solubility_safety * ligand.solubility
target_buffer_mass = 10.0 * ureg.gram
target_buffer_volume = target_buffer_mass / buffer.density
target_compound_mass = target_concentration * target_buffer_volume
target_compound_mass = min(target_compound_mass, max_compound_mass)
ligand_solution = SimpleSolution(compound=ligand,
) # http://pubs.acs.org/doi/pdf/10.1021/jp062734p with (BSA, with 200 uM NaCl)
# Define troughs on the instrument
water_trough = Labware(RackLabel='Water', RackType='Trough 100ml')
buffer_trough = Labware(RackLabel='Buffer', RackType='Trough 100ml')
# Define source labware.
source_plate = Labware(RackLabel='SourcePlate', RackType='5x3 Vial Holder')
# Define source solutions in the vial holder
#TODO : Define solutions once prepared with the Quantos. Enter compound mass and solvent mass values. - MI
#I entered compound mass and solvent mass that matches 40 uM
hsa_solution = SimpleSolution(compound=hsa,
compound_mass=9.40 * ureg.milligram,
solvent=buffer,
solvent_mass=3.4245 * ureg.gram,
location=PipettingLocation(
source_plate.RackLabel,
source_plate.RackType, 1))
aspirin_solution = SimpleSolution(compound=aspirin,
compound_mass=20.235 * ureg.milligram,
solvent=buffer,
solvent_mass=10.0973 * ureg.gram,
location=PipettingLocation(
source_plate.RackLabel,
source_plate.RackType, 2))
naproxen_sodium_solution = SimpleSolution(
compound=naproxen_sodium,
compound_mass=25.275 * ureg.milligram,
# Define troughs on the instrument.
water_trough = Labware(RackLabel='Water', RackType='Trough 100ml')
buffer_trough = Labware(RackLabel='Buffer', RackType='Trough 100ml')
# Define source labware.
source_plate = Labware(RackLabel='SourcePlate', RackType='5x3 Vial Holder')
# Define source solutions on the deck.one
# TODO : Use actual compound and solvent masses.
# NOTE: Host solution is diluted by 10x.
host_solution = SimpleSolution(compound=host,
compound_mass=11.54 * ureg.milligram,
solvent=buffer,
solvent_mass=10.2002 * ureg.gram,
location=PipettingLocation(
source_plate.RackLabel,
source_plate.RackType, 1))
guest_solutions = list()
# Dispensed by quantos
guest_compound_masses = Quantity([1.38], ureg.milligram)
# Dispensed by quantos
guest_solvent_masses = Quantity([11.4985], ureg.gram)
for guest_index in range(nguests):
guest_solutions.append(
SimpleSolution(compound=guests[guest_index],
compound_mass=guest_compound_masses[guest_index],
solvent=buffer,
) # http://pubs.acs.org/doi/pdf/10.1021/jp062734p
indoxylsulfate_ka = 9.1E5 / ureg.molar # 10.1023/A:1011014629551
# Define troughs on the instrument
water_trough = Labware(RackLabel='Water', RackType='Trough 100ml')
buffer_trough = Labware(RackLabel='Buffer', RackType='Trough 100ml')
# Define source labware.
source_plate = Labware(RackLabel='SourcePlate', RackType='5x3 Vial Holder')
# Define source solutions in the vial holder
# TODO : Define solutions once prepared with the Quantos
hsa_solution = SimpleSolution(compound=hsa,
compound_mass=13.8 * ureg.milligram,
solvent=buffer,
solvent_mass=0.5 * ureg.gram,
location=PipettingLocation(
source_plate.RackLabel,
source_plate.RackType, 1))
indoxylsulfate_solution = SimpleSolution(compound=indoxylsulfate,
compound_mass=15 * ureg.milligram,
solvent=buffer,
solvent_mass=10 * ureg.gram,
location=PipettingLocation(
source_plate.RackLabel,
source_plate.RackType, 2))
naproxen_sodium_solution = SimpleSolution(compound=naproxen_sodium,
compound_mass=15 * ureg.milligram,
solvent=buffer,
solvent_mass=10 * ureg.gram,
caii_buffer_trough = Labware(RackLabel='Buffer', RackType='Trough 100ml')
PHIPA_buffer_trough = Labware(RackLabel='SecondBuffer',
RackType='Trough 100ml')
# Define source labware.
source_plate = Labware(RackLabel='SourcePlate', RackType='5x3 Vial Holder')
protein_source_plate = Labware(RackLabel='ProteinSourcePlate',
RackType='ITC Plate')
# Define source solutions in the vial holder
# TODO : Define solutions once prepared with the Quantos
#caii_solution = SimpleSolution(compound=caii, compound_mass=5 * ureg.milligram, solvent=caii_buffer, solvent_mass=0.7 * ureg.gram, location=PipettingLocation(
caii_solution = SimpleSolution(compound=caii,
compound_mass=2.5 * ureg.milligram,
solvent=caii_buffer,
solvent_mass=1.5 * ureg.gram,
location=PipettingLocation(
protein_source_plate.RackLabel,
protein_source_plate.RackType,
1)) # Well A1 of ITC plate
# 124 uM @ 1.5 mL
PHIPA_solution = SimpleSolution(compound=PHIPA,
compound_mass=2.6 * ureg.milligram,
solvent=PHIPA_buffer,
solvent_mass=1.5 * ureg.gram,
location=PipettingLocation(
protein_source_plate.RackLabel,
protein_source_plate.RackType,
2)) # Well B1 of ITC plate
cbs_solution = SimpleSolution(