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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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47
propka/parameters.py
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@@ -5,6 +5,7 @@ from __future__ import print_function
import math
import propka.lib as lib
import sys, os
from propka.lib import info, warning
import pkg_resources
@@ -99,7 +100,7 @@ class Parameters:
self.parse_to_string_dictionary(words)
#print(words)
#info(words)
return
@@ -138,7 +139,7 @@ class Parameters:
return
def parse_string(self, words):
#print('self.%s = \'%s\''%tuple(words))
#info('self.%s = \'%s\''%tuple(words))
exec('self.%s = \'%s\''%tuple(words))
return
@@ -158,12 +159,12 @@ class Parameters:
return
def print_interaction_parameters(self):
print('--------------- Model pKa values ----------------------')
info('--------------- Model pKa values ----------------------')
for k in self.model_pkas.keys():
print('%3s %8.2f'%(k,self.model_pkas[k]))
info('%3s %8.2f' % (k, self.model_pkas[k]))
print('')
print('--------------- Interactions --------------------------')
info('')
info('--------------- Interactions --------------------------')
agroups = ['COO', 'HIS', 'CYS', 'TYR', 'SER', 'N+', 'LYS', 'AMD', 'ARG', 'TRP', 'ROH', 'CG', 'C2N', 'N30', 'N31', 'N32', 'N33', 'NAR', 'OCO', 'NP1', 'OH', 'O3', 'CL', 'F', 'NAM', 'N1', 'O2', 'OP', 'SH']
lgroups = ['CG', 'C2N', 'N30', 'N31', 'N32', 'N33', 'NAR', 'OCO', 'NP1', 'OH', 'O3', 'CL', 'F', 'NAM', 'N1', 'O2', 'OP', 'SH']
@@ -213,21 +214,21 @@ class Parameters:
if len(map[g2])==0 and (self.sidechain_cutoffs.get_value(g1,g2)[0] !=3 or self.sidechain_cutoffs.get_value(g1,g2)[1] != 4):
map_interaction += '? '
print(interaction,map_interaction )
info(interaction, map_interaction)
if g1==g2:
break
print('-')
info('-')
print('--------------- Exceptions ----------------------------')
print('COO-HIS',self.COO_HIS_exception)
print('OCO-HIS',self.OCO_HIS_exception)
print('CYS-HIS',self.CYS_HIS_exception)
print('CYS-CYS',self.CYS_CYS_exception)
info('--------------- Exceptions ----------------------------')
info('COO-HIS', self.COO_HIS_exception)
info('OCO-HIS', self.OCO_HIS_exception)
info('CYS-HIS', self.CYS_HIS_exception)
info('CYS-CYS', self.CYS_CYS_exception)
print('--------------- Mapping -------------------------------')
print("""
info('--------------- Mapping -------------------------------')
info("""
Titratable:
CG ARG
C2N ARG
@@ -258,12 +259,12 @@ O2
def print_interaction_parameters_latex(self):
# print('--------------- Model pKa values ----------------------')
# info('--------------- Model pKa values ----------------------')
# for k in self.model_pkas.keys():
# print('%3s %8.2f'%(k,self.model_pkas[k]))
# info('%3s %8.2f'%(k,self.model_pkas[k]))
# print('')
# print('--------------- Interactions --------------------------')
# info('')
# info('--------------- Interactions --------------------------')
agroups = ['COO', 'HIS', 'CYS', 'TYR', 'SER', 'N+', 'LYS', 'AMD', 'ARG', 'TRP', 'ROH', 'CG', 'C2N', 'N30', 'N31', 'N32', 'N33', 'NAR', 'OCO', 'NP1', 'OH', 'O3', 'CL', 'F', 'NAM', 'N1', 'O2', 'OP', 'SH']
lgroups = ['CG', 'C2N', 'N30', 'N31', 'N32', 'N33', 'NAR', 'OCO', 'NP1', 'OH', 'O3', 'CL', 'F', 'NAM', 'N1', 'O2', 'OP', 'SH']
@@ -329,7 +330,7 @@ Group1 & Group2 & Interaction & c1 &c2 \\\\
break
s += ' \\end{longtable}\n'
print(s)
info(s)
return
def print_interactions_latex(self):
@@ -373,7 +374,7 @@ Group1 & Group2 & Interaction & c1 &c2 \\\\
break
s += ' \\end{longtable}\n'
print(s)
info(s)
return
@@ -444,7 +445,7 @@ class Interaction_matrix:
# p+='sidechain_cutoff %3s %3s %s\n'%(ks[i],ks[j],self[ks[i]][ks[j]])
# n+=1
# print('total',n,len(ks))
# info('total',n,len(ks))
# return p
@@ -476,7 +477,7 @@ class Pair_wise_matrix:
if k1 in self.dictionary.keys() and k2 in self.dictionary[k1].keys():
if k1!=k2:
print ('Warning: Paramter value for %s, %s defined more than once'%(k1,k2))
warning('Parameter value for %s, %s defined more than once' % (k1, k2))
if not k1 in self.dictionary:
self.dictionary[k1] = {}