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