from itctools.labware import Labware, PipettingLocation
import pprint
import copy
# The sample cell volume in microliters
cell_volume = 202.8
# Define solvents.
water = Solvent('water', density=0.9970479 * ureg.gram / ureg.milliliter)
buffer = Solvent(
'buffer', density=1.014 * ureg.gram /
ureg.milliliter) # TODO is our density the same as the HOST-GUEST buffer?
# Define compounds.
caii = Compound('CAII',
molecular_weight=29246.0 * (ureg.gram / ureg.mole),
purity=1.)
cbs = Compound('CBS',
molecular_weight=201.2 * (ureg.gram / ureg.mole),
purity=0.97)
#Ka (association constants) TODO Add this to the compound properties? (maybe a dict with protein as key)
cbs_ka = 50 * 1.203e6 / ureg.molar
# 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',
"""
Script for generation of input files for Aspirin and Naproxen binding to HSA by ITC.
"""
from itctools.itctools import ureg
from itctools.procedures import ITCProtocol, ITCExperimentSet, ITCExperiment, ITCHeuristicExperiment
from itctools.materials import Solvent, Compound, SimpleSolution
from itctools.labware import Labware, PipettingLocation
import pprint
# Define solvents.
water = Solvent('water', density=0.9970479 * ureg.gram / ureg.milliliter)
buffer = Solvent('buffer', density=1.014 * ureg.gram / ureg.milliliter) # TODO is our density the same as the HOST-GUEST buffer?
# Define compounds.
hsa = Compound('HumanSerumAlbumin', molecular_weight=66500 * (ureg.gram / ureg.mole), purity=.95)
indoxylsulfate = Compound('Indoxylsulfate potassium', molecular_weight=251.30 * (ureg.gram / ureg.mole), purity=1.)
naproxen_sodium = Compound('Naproxen Sodium', molecular_weight=252.24 * (ureg.gram / ureg.mole), purity=1.)
# These are insoluble in water without added DMSO
aspirin = Compound('AcetylsalicylicAcid', molecular_weight=180.15742 * (ureg.gram / ureg.mole), purity=.99)
naproxen = Compound('Naproxen', molecular_weight=230.3 * (ureg.gram / ureg.mole), purity=.98)
#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')
]
nreplicates = 1 # number of replicates of each protein-ligand experiment
# The sample cell volume in microliters
cell_volume = 202.8
# Define solvents.
water = Solvent('water', density=0.9970479 * ureg.gram / ureg.milliliter)
buffer = Solvent(
'buffer', density=1.014 * ureg.gram /
ureg.milliliter) # TODO is our density the same as the HOST-GUEST buffer?
# Define receptor
receptor = Compound('receptor',
molecular_weight=14117.0 * (ureg.gram / ureg.mole),
purity=1.)
# Define compounds.
ligands = list()
ligand_kas = list()
print('COMPOUNDS')
for compound_id in compound_ids:
molecular_weight = solubilities_df.loc[compound_id]['MW'] * (ureg.gram /
ureg.mole)
purity = purities_df.loc[compound_id]['Purity'] / 100.0
solubility = solubilities_df.loc[compound_id][
'ESOL Solubility (mg/ml)'] * (ureg.milligram / ureg.milliliter)
compound = Compound(f'Compound {compound_id}',
molecular_weight=molecular_weight,
purity=purity,
from itctools.materials import Solvent, Compound, SimpleSolution
from itctools.labware import Labware, PipettingLocation
import pprint
# The sample cell volume in microliters
cell_volume = 202.8
# Define solvents.
water = Solvent('water', density=0.9970479 * ureg.gram / ureg.milliliter)
buffer = Solvent(
'buffer', density=1.014 * ureg.gram /
ureg.milliliter) # TODO is our density the same as the HOST-GUEST buffer?
# Define compounds.
hsa = Compound('HumanSerumAlbumin',
molecular_weight=65000 * (ureg.gram / ureg.mole),
purity=.95)
naproxen_sodium = Compound('Naproxen Sodium',
molecular_weight=252.24 * (ureg.gram / ureg.mole),
purity=1.)
# TODO : update aspirin molecular weight - MI
aspirin = Compound('AcetylsalicylicAcid',
molecular_weight=180.15742 * (ureg.gram / ureg.mole),
purity=.99)
# Ka (association constants) TODO Add this to the compound properties? (maybe a dict with protein as key)
aspirin_ka = 2.76 / ureg.micromolar # http://omicsonline.org/2157-7544/2157-7544-2-107.pdf (first site estimate at 298K)
naproxen_ka = 1.73e7 / (
ureg.molar
) # http://pubs.acs.org/doi/pdf/10.1021/jp062734p with (BSA, with 200 uM NaCl)
# Define solvents.
water = Solvent('water', density=0.9970479 * ureg.gram / ureg.milliliter)
buffer = Solvent('buffer', density=1.014 * ureg.gram / ureg.milliliter)
# The sample cell volume in microliters
cell_volume = 202.8
# Define compounds.
# each experiment takes about 50 mins, cleaning takes 2.5
nguests = 1
assert (nguests == 1)
host = Compound('host',
molecular_weight=1134.987 * ureg.gram / ureg.mole,
purity=0.98)
guest_molecular_weights = [215.76]
# the guest compound Ka is very large.
guest_compound_Ka = Quantity([np.exp(32)],
ureg.liter / ureg.mole) # see dGtoKa.py
guests = [
Compound(name='guest%02d' % (guest_index + 1),
molecular_weight=guest_molecular_weights[guest_index] *
ureg.gram / ureg.mole,
purity=0.975) for guest_index in range(nguests)
]
# Define troughs on the instrument.
# The sample cell volume in microliters
cell_volume = 202.8
# Define solvents.
water = Solvent('water', density=0.9970479 * ureg.gram / ureg.milliliter)
caii_buffer = Solvent(
'caii_buffer', density=1.014 * ureg.gram /
ureg.milliliter) # TODO is our density the same as the HOST-GUEST buffer?
PHIPA_buffer = Solvent(
'PHIPA_buffer', density=1.014 * ureg.gram /
ureg.milliliter) # TODO is our density the same as the HOST-GUEST buffer?
# Define compounds.
caii = Compound('CAII',
molecular_weight=29246.0 * (ureg.gram / ureg.mole),
purity=1.)
cbs = Compound('CBS',
molecular_weight=201.2 * (ureg.gram / ureg.mole),
purity=0.97)
PHIPA = Compound('PHIPA',
molecular_weight=14117.0 * (ureg.gram / ureg.mole),
purity=1.)
cacl = Compound('CaCl2*2H2O',
molecular_weight=147.01 * (ureg.gram / ureg.mole),
purity=0.97)
hepes = Compound('HEPES',
molecular_weight=238.3012 * (ureg.gram / ureg.mole),
purity=0.97)