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De-lint groups.py

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I did my best (via Google) to make sure that renamed public members and
methods had minimal impact on others' code.
This commit is contained in:
Nathan Baker
2020-05-24 11:13:06 -07:00
parent 6cbcac3be9
commit a534d97016
10 changed files with 703 additions and 650 deletions
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20
propka/coupled_groups.py
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@@ -33,7 +33,7 @@ class NonCovalentlyCoupledGroups:
return {'coupling_factor': -1.0}
# calculate intrinsic pKa's, if not already done
for group in [group1, group2]:
if not hasattr(group, 'intrinsic_pKa'):
if group.intrinsic_pka is None:
group.calculate_intrinsic_pka()
use_ph = self.parameters.pH
if self.parameters.pH == 'variable':
@@ -70,12 +70,12 @@ class NonCovalentlyCoupledGroups:
and return_on_fail:
return {'coupling_factor': -1.0}
# check intrinsic pka diff
if abs(group1.intrinsic_pKa - group2.intrinsic_pKa) \
> self.parameters.max_intrinsic_pKa_diff and return_on_fail:
if abs(group1.intrinsic_pka - group2.intrinsic_pka) \
> self.parameters.max_intrinsic_pka_diff and return_on_fail:
return {'coupling_factor': -1.0}
# if everything is OK, calculate the coupling factor and return all info
factor = self.get_free_energy_diff_factor(default_energy, swapped_energy) \
* self.get_pka_diff_factor(group1.intrinsic_pKa, group2.intrinsic_pKa) \
* self.get_pka_diff_factor(group1.intrinsic_pka, group2.intrinsic_pka) \
* self.get_interaction_factor(interaction_energy)
return {'coupling_factor': factor, 'default_energy': default_energy,
'swapped_energy': swapped_energy,
@@ -95,8 +95,8 @@ class NonCovalentlyCoupledGroups:
"""
intrinsic_pka_diff = abs(pka1-pka2)
res = 0.0
if intrinsic_pka_diff <= self.parameters.max_intrinsic_pKa_diff:
res = 1-(intrinsic_pka_diff/self.parameters.max_intrinsic_pKa_diff)**2
if intrinsic_pka_diff <= self.parameters.max_intrinsic_pka_diff:
res = 1-(intrinsic_pka_diff/self.parameters.max_intrinsic_pka_diff)**2
return res
def get_free_energy_diff_factor(self, energy1, energy2):
@@ -147,7 +147,7 @@ class NonCovalentlyCoupledGroups:
info(' Detecting non-covalently coupled residues')
info('-' * 103)
info(' Maximum pKa difference: %4.2f pKa units' \
% self.parameters.max_intrinsic_pKa_diff)
% self.parameters.max_intrinsic_pka_diff)
info(' Minimum interaction energy: %4.2f pKa units' \
% self.parameters.min_interaction_energy)
info(' Maximum free energy diff.: %4.2f pKa units' \
@@ -263,7 +263,7 @@ class NonCovalentlyCoupledGroups:
str_ = ' ' + '-' * 113 + '\n'
for group in system:
str_ += self.tagged_format(' %-8s|' % tag,
group.getDeterminantString(),
group.get_determinant_string(),
all_labels)
return str_ + '\n'
@@ -355,8 +355,8 @@ class NonCovalentlyCoupledGroups:
(group1.label, group2.label, data['coupling_factor'],
data['default_energy'], data['swapped_energy'],
data['default_energy'] - data['swapped_energy'], data['pH'],
data['interaction_energy'], group1.intrinsic_pKa, group2.intrinsic_pKa,
group1.intrinsic_pKa-group2.intrinsic_pKa, data['swapped_pka1'],
data['interaction_energy'], group1.intrinsic_pka, group2.intrinsic_pka,
group1.intrinsic_pka-group2.intrinsic_pka, data['swapped_pka1'],
data['swapped_pka2'], data['pka_shift1'], data['pka_shift2'])
return str_