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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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15
propka/conformation_container.py
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@@ -6,6 +6,7 @@ from __future__ import division
from __future__ import print_function
import propka.group, propka.determinants, propka.determinant, propka.ligand, propka.output, propka.coupled_groups, functools
from propka.lib import info, warning
class Conformation_container:
def __init__(self, name='', parameters=None, molecular_container=None):
@@ -50,7 +51,7 @@ class Conformation_container:
map = propka.output.make_interaction_map('Covalent coupling map for %s'%self,
self.get_covalently_coupled_groups(),
lambda g1,g2: g1 in g2.covalently_coupled_groups)
print(map)
info(map)
# check if we should set a common charge centre as well
if self.parameters.common_charge_centre:
@@ -96,7 +97,7 @@ class Conformation_container:
#self.get_titratable_groups(),
self.get_covalently_coupled_groups(),
lambda g1,g2: g1 in g2.covalently_coupled_groups)
print(map)
info(map)
return
@@ -168,7 +169,7 @@ class Conformation_container:
#
def calculate_pka(self, version, options):
print('\nCalculating pKas for',self)
info('\nCalculating pKas for', self)
# calculate desolvation
for group in self.get_titratable_groups()+self.get_ions():
@@ -193,7 +194,7 @@ class Conformation_container:
penalised_labels = self.coupling_effects()
if self.parameters.remove_penalised_group and len(penalised_labels)>0:
print('Removing penalised groups!!!')
info('Removing penalised groups!!!')
for g in self.get_titratable_groups():
g.remove_determinants(penalised_labels)
@@ -297,7 +298,7 @@ class Conformation_container:
def calculate_folding_energy(self, pH=None, reference=None):
ddg = 0.0
for group in self.groups:
#print('Folding energy for %s at pH %f: %f'%(group,pH,group.calculate_folding_energy(self.parameters, pH=pH, reference=reference)))
#info('Folding energy for %s at pH %f: %f'%(group,pH,group.calculate_folding_energy(self.parameters, pH=pH, reference=reference)))
ddg += group.calculate_folding_energy(self.parameters, pH=pH, reference=reference)
return ddg
@@ -379,7 +380,7 @@ class Conformation_container:
def add_atom(self, atom):
#print(self,'adding',atom)
#info(self,'adding',atom)
self.atoms.append(atom)
if not atom.conformation_container:
atom.conformation_container = self
@@ -446,5 +447,5 @@ class Conformation_container:
key += atom.resNumb*1000
if len(atom.name) > len(atom.element):
key += ord(atom.name[len(atom.element)])
#print(atom,ord(atom.name[len(atom.element)]), '|%s||%s|'%(atom.name,atom.element))
#info(atom,ord(atom.name[len(atom.element)]), '|%s||%s|'%(atom.name,atom.element))
return key