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Output performed with loggers. Adds options --no-print. (#12)

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Output performed with loggers.  Adds --quiet and --verbose options.
This commit is contained in:
Toni G
2016-04-29 08:21:35 +02:00
committed by Matvey Adzhigirey
parent ca6224433a
commit 5fbbdd4868
23 changed files with 4987 additions and 217 deletions
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45
propka/coupled_groups.py
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@@ -3,6 +3,7 @@ from __future__ import division
from __future__ import print_function
import math, propka.output, propka.group, propka.lib, itertools
from propka.lib import info, warning
class non_covalently_couple_groups:
@@ -129,22 +130,22 @@ class non_covalently_couple_groups:
self.parameters = conformation.parameters
if verbose:
print('')
print(' Warning: When using the -d option, pKa values based on \'swapped\' interactions')
print(' will be writting to the output .pka file')
print('')
print('-'*103)
print(' Detecting non-covalently coupled residues')
print('-'*103)
print(' Maximum pKa difference: %4.2f pKa units'%self.parameters.max_intrinsic_pKa_diff)
print(' Minimum interaction energy: %4.2f pKa units'%self.parameters.min_interaction_energy)
print(' Maximum free energy diff.: %4.2f pKa units'%self.parameters.max_free_energy_diff)
print(' Minimum swap pKa shift: %4.2f pKa units'%self.parameters.min_swap_pka_shift)
print(' pH: %6s ' %str(self.parameters.pH))
print(' Reference: %s' %self.parameters.reference)
print(' Min pKa: %4.2f'%self.parameters.min_pka)
print(' Max pKa: %4.2f'%self.parameters.max_pka)
print('')
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('')
# find coupled residues
titratable_groups = conformation.get_titratable_groups()
@@ -169,7 +170,7 @@ class non_covalently_couple_groups:
map = propka.output.make_interaction_map('Non-covalent coupling map for %s'%conformation,
conformation.get_non_covalently_coupled_groups(),
lambda g1,g2: g1 in g2.non_covalently_coupled_groups)
print(map)
info(map)
for system in conformation.get_coupled_systems(conformation.get_non_covalently_coupled_groups(),propka.group.Group.get_non_covalently_coupled_groups):
self.print_system(conformation, list(system))
@@ -177,7 +178,7 @@ class non_covalently_couple_groups:
def print_system(self, conformation, system):
print('System containing %d groups:'%len(system))
info('System containing %d groups:' % len(system))
# make list of interactions withi this system
interactions = list(itertools.combinations(system,2))
@@ -187,7 +188,7 @@ class non_covalently_couple_groups:
for interaction in interactions:
data = self.is_coupled_protonation_state_probability(interaction[0], interaction[1],conformation.calculate_folding_energy, return_on_fail=False)
coup_info += self.make_data_to_string(data,interaction[0],interaction[1])+'\n\n'
print(coup_info)
info(coup_info)
# make list of possible combinations of swap to try out
combinations = propka.lib.generate_combinations(interactions)
@@ -211,7 +212,7 @@ class non_covalently_couple_groups:
#for interaction in combination:
# self.swap_interactions([interaction[0]], [interaction[1]])
print(swap_info)
info(swap_info)
return
#
@@ -236,7 +237,7 @@ class non_covalently_couple_groups:
all_labels = [g.label for g in system]
s = ' '+'-'*113+'\n'
for group in system:
s += self.tagged_print(' %-8s|'%tag,group.getDeterminantString(), all_labels)
s += self.tagged_format(' %-8s|' % tag, group.getDeterminantString(), all_labels)
return s+'\n'
@@ -287,7 +288,7 @@ class non_covalently_couple_groups:
# Output methods
#
def tagged_print(self, tag, s, labels):
def tagged_format(self, tag, s, labels):
s = "%s %s"%(tag,s)
s = s.replace('\n','\n%s '%tag)
for label in labels: