def loadStructure(*files):
for file in files:
try:
filename = str(file)
except:
sys.stderr.write("ERROR(loadStructure): Invalid argument! Arguments should be string filenames\n")
extension = file.split(".")[-1]
if extension.lower() == 'gro':
import ctools.GromacsExt.GromacsStructureParser as GromacsStructureParser
print 'Reading in Gromacs structure "%s"...' %(filename)
GromacsStructureParser.readStructure(filename)
elif extension.lower() == '':
pass
else:
sys.stderr.write(" Error: '%s' is not a supported structure file format\n" %(extension.lower()))
print "Structure loaded\n"
import sys
import os.path
from ctools.System import System
System._sys = System("Redone Sample")
print "System initialized\n"
print "ENTER FILENAME?\n"
filename = raw_input("")
while not (os.path.isfile(filename+".gro") or os.path.isfile(filename+".top")):
print "File doesn't exit, try again\n"
filename = raw_input("")
filename_out = filename + "_OUT"
from ctools.GromacsExt.GromacsTopologyParser import GromacsTopologyParser
print 'Reading in Gromacs topology "%s"...' %(filename)
if not GromacsTopologyParser._GroTopParser:
GromacsTopologyParser._GroTopParser = GromacsTopologyParser()
GromacsTopologyParser._GroTopParser.parseTopology(filename + '.top')
import ctools.GromacsExt.GromacsStructureParser as GromacsStructureParser
print 'Reading in Gromacs structure "%s"...' %(filename)
GromacsStructureParser.readStructure(filename + '.gro')
print "\nWriting out Gromacs topology %s"%(filename_out+".top")
import ctools.GromacsExt.GromacsTopologyParser as GromacsTopologyParser
GromacsTopologyParser = GromacsTopologyParser()
GromacsTopologyParser.writeTopology(filename_out+".top")
print "\nWriting in Gromacs structure %s"%(filename_out+".gro")
import ctools.GromacsExt.GromacsStructureParser as GromacsStructureParser
GromacsStructureParser.writeStructure(filename_out+".gro")
print "\nWriting out Desmond structure %s" % (filename_out)
DesmondParser.writeFile(filename_out + ".cms")
elif num == 2:
print "\nReading in Desmond structure %s" % (filename)
import ctools.DesmondExt.DesmondParser as DesmondParser
DesmondParser = DesmondParser()
DesmondParser.readFile(filename + ".cms")
elif num == 3:
from ctools.GromacsExt.GromacsTopologyParser import GromacsTopologyParser
print 'Reading in Gromacs topology "%s"...' % (filename)
if not GromacsTopologyParser._GroTopParser:
GromacsTopologyParser._GroTopParser = GromacsTopologyParser()
GromacsTopologyParser._GroTopParser.parseTopology(filename + '.top')
import ctools.GromacsExt.GromacsStructureParser as GromacsStructureParser
print 'Reading in Gromacs structure "%s"...' % (filename)
GromacsStructureParser.readStructure(filename + '.gro')
print "Writing out Desmond structure %s" % (filename_out)
import ctools.DesmondExt.DesmondParser as DesmondParser
DesmondParser = DesmondParser()
DesmondParser.writeFile(filename_out)
elif num == 4:
from ctools.GromacsExt.GromacsTopologyParser import GromacsTopologyParser
print 'Reading in Gromacs topology "%s"...' % (filename)
if not GromacsTopologyParser._GroTopParser:
GromacsTopologyParser._GroTopParser = GromacsTopologyParser()
GromacsTopologyParser._GroTopParser.parseTopology(filename + '.top')
import ctools.GromacsExt.GromacsStructureParser as GromacsStructureParser
print 'Reading in Gromacs structure "%s"...' % (filename)
GromacsStructureParser.readStructure(filename + '.gro')
print "\nWriting out Gromacs topology %s" % (filename_out + ".top")
import ctools.GromacsExt.GromacsTopologyParser as GromacsTopologyParser