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Update string formatting to modern version.

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Focuses only on complex formatting.
This commit is contained in:
Nathan Baker
2020-05-27 16:26:52 -07:00
parent 557ab19312
commit 6e7c188dbd
7 changed files with 90 additions and 77 deletions
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78
propka/coupled_groups.py
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@@ -146,31 +146,27 @@ class NonCovalentlyCoupledGroups:
"""
self.parameters = conformation.parameters
if verbose:
info('')
info(' Warning: When using the -d option, pKa values based on '
'\'swapped\' interactions')
info(' will be writting to the output .pka file')
info('')
info('-' * 103)
info(' Detecting non-covalently coupled residues')
info('-' * 103)
info(' Maximum pKa difference: %4.2f pKa units'
% 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'
% self.parameters.max_free_energy_diff)
info(' Minimum swap pKa shift: %4.2f pKa units'
% self.parameters.min_swap_pka_shift)
info(' pH: %6s '
% str(self.parameters.pH))
info(' Reference: %s'
% self.parameters.reference)
info(' Min pKa: %4.2f'
% self.parameters.min_pka)
info(' Max pKa: %4.2f'
% self.parameters.max_pka)
info('')
info_fmt = (
'\n'
' Warning: When using the -d option, pKa values based on \n'
'\'swapped\' interactions\n'
' will be writting to the output .pka file\n'
'\n'
'{sep}\n'
'\n'
' Detecting non-covalently coupled residues\n'
'{sep}\n'
' Maximum pKa difference: {c.max_intrinsic_pka_diff:>4.2f} pKa units\n'
' Minimum interaction energy: {c.min_interaction_energy:>4.2f} pKa units\n'
' Maximum free energy diff.: {c.max_free_energy_diff:>4.2f} pKa units\n'
' Minimum swap pKa shift: {c.min_swap_pka_shift:>4.2f} pKa units\n'
' pH: {c.pH:>6} \n'
' Reference: {c.reference}\n'
' Min pKa: {c.min_pka:>4.2f}\n'
' Max pKa: {c.max_pka:>4.2f}\n'
'\n')
sep = "-" * 103
info(info_fmt.format(sep=sep, c=self))
# find coupled residues
titratable_groups = conformation.get_titratable_groups()
if not conformation.non_covalently_coupled_groups:
@@ -364,20 +360,24 @@ class NonCovalentlyCoupledGroups:
formatted string with information.
"""
str_ = (
""" %s and %s coupled (prot.state): %5.2f
Energy levels: %6.2f, %6.2f (difference: %6.2f) at pH %6.2f
Interaction energy: %6.2f
Intrinsic pka's: %6.2f, %6.2f (difference: %6.2f)
Swapped pKa's: %6.2f, %6.2f (difference: %6.2f, %6.2f)"""
% (
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['swapped_pka2'],
data['pka_shift1'], data['pka_shift2']))
" {label1} and {label2} coupled (prot.state): {coupl_fact:>5.2f}\n"
" Energy levels: {def_energy:>6.2f}, {swap_energy:>6.2f} "
"(difference: {diff_energy:>6.2f}) at pH {ph:>6.2f}\n"
" Interaction energy: {int_energy:>6.2f}\n"
" Intrinsic pka's: {pka1:>6.2f}, {pka2:>6.2f} "
"(difference: {diff_pka:>6.2f})\n"
" Swapped pKa's: {swap1:>6.2f}, {swap2:>6.2f} "
"(difference: {shift1:>6.2f}, {shift2:>6.2f})"
).format(
label1=group1.label, label2=group2.label,
coupl_fact=data['coupling_factor'], def_energy=data['default_energy'],
swap_energy=data['swapped_energy'],
diff_energy=data['default_energy']-data['swapped_energy'], ph=data['pH'],
int_energy=data['interaction_energy'], pka1=group1.intrinsic_pka,
pka2=group2.intrinsic_pka,
diff_pka=group1.intrinsic_pka-group2.intrinsic_pka,
swap1=data['swapped_pka1'], swap2=data['swapped_pka2'],
shift1=data['pka_shift1'], shift2=data['pka_shift2'])
return str_