import os
path = os.getcwd() + "/"
sys.path.append('../..')
from ctools.System import System
System._sys = System("Redone Sample")
print "System initialized\n"
f = open("DesmondToGromacsErrors.txt", "w")
for dir in os.listdir(path):
if os.path.isdir("%s" % (dir)):
for file in os.listdir("%s" % (dir)):
if ".cms" in file:
filename = string.rstrip(file, ".cms")
print "\nReading in Desmond structure %s" % (filename)
sys.path.append('../../ParserFiles')
from ctools.DesmondExt.DesmondParser import DesmondParser
DesmondParser = DesmondParser()
try:
DesmondParser.readFile(path + filename + "/" + filename +
".cms")
except Exception, e:
f.write("\nError reading %s -- %s" % (filename, e))
filename_out = filename + "_OUT"
try:
if not (os.path.exists('%sDesmondToGromacsInputs/%s' %
(path, filename))):
os.makedirs('%sDesmondToGromacsInputs/%s' %
(path, filename))
filename_out = os.path.abspath(
'%sDesmondToGromacsInputs/%s/%s' %
(path, filename, filename_out))
print "\nWriting out Gromacs topology %s.top" % (
path = os.getcwd()+"/"
sys.path.append('../../..')
from ctools.System import *
System._sys = System("Redone Sample")
print "System initialized\n"
f = open("DesmondToDesmondErrors.txt", "w")
for dir in os.listdir(path+"/"):
if os.path.isdir("%s" % (dir)):
for file in os.listdir("%s" %(dir)):
if (( ".cms" in file)):
filename = string.rstrip(file,".cms")
print "\nReading in Desmond structure %s"%(filename)
sys.path.append('../../ParserFiles')
from ctools.DesmondExt.DesmondParser import DesmondParser
DesmondParser = DesmondParser()
try:
DesmondParser.readFile(path+filename+"/"+filename+".cms")
except Exception,e:
print "%s" %(e)
f.write("\nError reading %s.cms -- %s" %(filename, e))
filename_out = filename + "_OUT"
try:
if not (os.path.exists('%sDesmondToDesmondInputs/%s' %(path,filename))):
os.makedirs('%sDesmondToDesmondInputs/%s' %(path, filename))
filename_out = os.path.abspath('%sDesmondToDesmondInputs/%s/%s' %(path, filename, filename_out))
DesmondParser.writeFile(filename_out+".cms")
except Exception,e:
print "%s" %(e)
sys.path.append('../..')
from ctools.System import System
System._sys = System("Redone Sample")
print "System initialized\n"
f = open( "DesmondToGromacsErrors.txt", "w")
for dir in os.listdir(path):
if os.path.isdir("%s" % (dir)):
for file in os.listdir("%s" %(dir)):
if ".cms" in file:
filename = string.rstrip(file,".cms")
print "\nReading in Desmond structure %s"%(filename)
sys.path.append('../../ParserFiles')
from ctools.DesmondExt.DesmondParser import DesmondParser
DesmondParser = DesmondParser()
try:
DesmondParser.readFile(path+filename+"/"+filename+".cms")
except Exception,e:
f.write("\nError reading %s -- %s" %(filename, e))
filename_out = filename + "_OUT"
try:
if not (os.path.exists('%sDesmondToGromacsInputs/%s' %(path,filename))):
os.makedirs('%sDesmondToGromacsInputs/%s' %(path,filename))
filename_out = os.path.abspath('%sDesmondToGromacsInputs/%s/%s' %(path,filename, filename_out))
print "\nWriting out Gromacs topology %s.top"%(filename_out)
from ctools.GromacsExt.GromacsTopologyParser import GromacsTopologyParser
GromacsTopologyParser = GromacsTopologyParser()
GromacsTopologyParser.writeTopology(filename_out+".top")
except Exception, e:
f.write("\nError writing %s.top -- %s" %(filename_out,e))
print "\nWriting in Gromacs Stucture as %s"%(filename_out+".gro")
from ctools.GromacsExt.GromacsStructurParser import GromacsStructureParser