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# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
SimulatorParameters.py
Read the sim-params.txt file, and extract information needed on the
NE1 side. This currently consists of parameters controlling the
Yukawa non-bonded potential function for PAM3 and PAM5 DNA models.
NE1 generates the tables which define a user-defined potential
function for GROMACS.
@author: Eric M
@version: $Id$
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
"""
import os
import foundation.env as env
from platform_dependent.PlatformDependent import find_plugin_dir
from utilities.debug import print_compact_traceback
class SimulatorParameters(object):
def __init__(self):
ok, nd1_plugin_path = find_plugin_dir("NanoDynamics-1")
if (not ok):
env.history.redmsg("Error: can't find " + nd1_plugin_path)
nd1_plugin_path = "."
fileName = os.path.join(nd1_plugin_path, "sim-params.txt")
self._parameterValues = {}
try:
print "sim parameters used by NE1 read from: [%s]" % fileName
parametersFile = open(fileName)
for line in parametersFile:
s = line.split()
if (len(s) > 0 and s[0] == "ne1"):
if (len(s) > 1):
key = s[1]
if (len(s) > 2):
value = " ".join(s[2:])
else:
value = True
self._parameterValues[key] = value
except IOError:
msg = "Error reading [%s]" % fileName
print_compact_traceback(msg + ": ")
env.history.redmsg(msg)
self._parameterValues = {}
def _getFloatParameter(self, parameterName, defaultValue = 0.0):
if (self._parameterValues.has_key(parameterName)):
try:
value = float(self._parameterValues[parameterName])
return value
except:
print_compact_traceback()
env.history.redmsg("malformed float parameter %s in sim-params.txt" % parameterName)
return defaultValue
def _getBooleanParameter(self, parameterName, defaultValue = False):
if (self._parameterValues.has_key(parameterName)):
if (self._parameterValues[parameterName]):
return True
return False
return defaultValue
def getYukawaRSwitch(self):
return self._getFloatParameter("YukawaRSwitch", 2.0)
def getYukawaRCutoff(self):
return self._getFloatParameter("YukawaRCutoff", 3.0)
def getYukawaShift(self):
return self._getBooleanParameter("YukawaShift", True)
def getYukawaCounterionCharge(self):
return self._getFloatParameter("YukawaCounterionCharge", 2.0)
def getYukawaCounterionMolarity(self):
return self._getFloatParameter("YukawaCounterionMolarity", 0.02)
def getYukawaTemperatureKelvin(self):
return self._getFloatParameter("YukawaTemperatureKelvin", 298.0)
def getYukawaDielectric(self):
return self._getFloatParameter("YukawaDielectric", 78.5)
def getYukawaConstantMultiple(self):
return self._getFloatParameter("YukawaConstantMultiple", 1.0)
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