import sys, re
from lnx_util import parseInput, print_help
import subprocess
inputP= parseInput(sys.argv[1:])
paraOpt = '-flog -h'.split()
helpdoc=\
'''
Usage! ./prog.py
-flog run1_0.log ; log file from any replica
-h ; print help information
'''
print_help(inputP, paraOpt, helpdoc)
finm = inputP['-flog']
rate = 0.25
exe = 'grep \'Repl fake T\' run1_0.log '
p= subprocess.Popen( exe, shell=True, stdout=subprocess.PIPE)
temperature = [ float(i) for i in re.findall('\d*\.*\d*', p.stdout.readline() ) if len(i) >0 ]
exe = 'grep -A 2 \'Repl average probabilities:\' run1_0.log | tail -n 1 '
p= subprocess.Popen( exe, shell=True, stdout=subprocess.PIPE)
prob = [ float(i) for i in re.findall('\d*\.*\d*', p.stdout.readline() ) if len(i) >0 ]
new_temp = [ 0 for i in range(len(temperature)) ]
new_temp[0]= 323.0
"Usage! ./prog.py \n"
" -top top1 ; topology file for solutes that need rescale\n"
" -bondedTop top2 ; force field file that contains bonded and non_boned interactions\n"
" -nonbondedTop top3 ;\n"
" -otop outTop1 ; topology modified from top1\n"
" -obonded outTopbonded ; topology modified for bonded\n"
" -ononbonded outTopnonbonded ; topology modified for nonbonded\n"
" -T1 323 k ; \n"
" -T2 600 k ; gamma = beta_2 / beta_1 \n"
" ; charge: q_i = sqrt(gamma) *q_i ;\n"
" ; vdw : epsilon_i = epsilon_i * gamma ; i belongs to solute ;\n"
" -sep ; when sep flag is set, we print the topology as an individual top rather than free energy format \n"
" -h ; print help doc \n"
)
lnx_util.print_help(inputP, paraOpt, helpdoc)
t1 = float(inputP["-T1"])
t2 = float(inputP["-T2"])
gamma = t1 / t2
print "gamma: %5.3f" % gamma
solute_top = rest_lipid_top.Topology(inputP["-top"], gamma)
bondedff = rest_force_field_top.BondedForceField(inputP["-bondedTop"], solute_top.bondMap, gamma)
nonbondedff = rest_force_field_top.NoneBondedForceField(inputP["-nonbondedTop"], solute_top.nameMap, gamma)
if inputP.has_key("-sep"):
solute_top.lambda_display(open(inputP["-otop"], "w"))
else:
solute_top.display(open(inputP["-otop"], "w"))