def get_charge_profile(self, conformation='AVR', grid=[0., 14., .1]):
"""Get charge profile for conformation as function of pH.
Args:
conformation: conformation to test
grid: grid of pH values [min, max, step]
Returns:
list of charge state values
"""
charge_profile = []
for ph in make_grid(*grid):
conf = self.conformations[conformation]
q_unfolded, q_folded = conf.calculate_charge(
self.version.parameters, ph=ph)
charge_profile.append([ph, q_unfolded, q_folded])
return charge_profile
def get_folding_profile(self,
conformation='AVR',
reference="neutral",
grid=[0., 14., 0.1]):
"""Get a folding profile.
Args:
conformation: conformation to select
reference: reference state
direction: folding direction (folding)
grid: the grid of pH values [min, max, step_size]
options: options object
Returns:
TODO - figure out what these are
1. profile
2. opt
3. range_80pct
4. stability_range
"""
# calculate stability profile
profile = []
for ph in make_grid(*grid):
conf = self.conformations[conformation]
ddg = conf.calculate_folding_energy(ph=ph, reference=reference)
profile.append([ph, ddg])
# find optimum
opt = [None, 1e6]
for point in profile:
opt = min(opt, point, key=lambda v: v[1])
# find values within 80 % of optimum
range_80pct = [None, None]
values_within_80pct = [p[0] for p in profile if p[1] < 0.8 * opt[1]]
if len(values_within_80pct) > 0:
range_80pct = [min(values_within_80pct), max(values_within_80pct)]
# find stability range
stability_range = [None, None]
stable_values = [p[0] for p in profile if p[1] < 0.0]
if len(stable_values) > 0:
stability_range = [min(stable_values), max(stable_values)]
return profile, opt, range_80pct, stability_range