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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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21
propka/iterative.py
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@@ -7,6 +7,7 @@ import math, time
import propka.lib as lib
from propka.determinant import Determinant
import propka.calculations
from propka.lib import info, warning, debug
# Some library functions for the interative pKa determinants
@@ -186,8 +187,8 @@ def addDeterminants(iterative_interactions, version, options=None):
done_group.append(group)
# Initialize iterative scheme
if options.verbose == True:
print("\n --- pKa iterations (%d groups, %d interactions) ---" % ( len(iteratives), len(iterative_interactions) ))
debug("\n --- pKa iterations (%d groups, %d interactions) ---" %
(len(iteratives), len(iterative_interactions)))
converged = False
iteration = 0
# set non-iterative pka values as first step
@@ -246,30 +247,30 @@ def addDeterminants(iterative_interactions, version, options=None):
itres.pKa_iter.append(itres.pKa_new)
if iteration == 10:
print("did not converge in %d iterations" % (iteration))
info("did not converge in %d iterations" % (iteration))
break
# --- Iterations finished ---
# printing pKa iterations
if options.verbose == True:
str = "%12s" % (" ")
for index in range(0, iteration+1 ):
# formerly was conditioned on if options.verbosity >= 2 - now unnecessary
str = "%12s" % (" ")
for index in range(0, iteration+1 ):
str += "%8d" % (index)
print(str)
for itres in iteratives:
debug(str)
for itres in iteratives:
str = "%s " % (itres.label)
for pKa in itres.pKa_iter:
str += "%8.2lf" % (pKa)
if itres.converged == False:
str += " *"
print(str)
debug(str)
# creating real determinants and adding them to group object
for itres in iteratives:
for type in ['sidechain','backbone','coulomb']:
for interaction in itres.determinants[type]:
#print('done',itres.group.label,interaction[0],interaction[1])
#info('done',itres.group.label,interaction[0],interaction[1])
value = interaction[1]
if value > 0.005 or value < -0.005:
g = interaction[0]