def load(*files):
"""
"""
for f in files:
try:
filename = str(f)
except:
raise Exception("Arguments should be string filenames")
extension = splitext(filename)[1].lower()
if extension == '.gro':
import intermol.GromacsExt.GromacsStructureParser as GromacsStructureParser
print "Reading in Gromacs structure '{0}'...".format(filename)
GromacsStructureParser.readStructure(filename)
print "Structure loaded\n"
elif extension == '.top':
from intermol.GromacsExt.GromacsTopologyParser import GromacsTopologyParser
print "Reading in Gromacs topology '{0}'...".format(filename)
if not GromacsTopologyParser._GroTopParser:
GromacsTopologyParser._GroTopParser = GromacsTopologyParser()
GromacsTopologyParser._GroTopParser.parseTopology(filename)
print "Topology loaded\n"
elif extension == '.cms':
from intermol.DesmondExt.DesmondParser import DesmondParser as DesmondParser
DesmondParser = DesmondParser()
print "Reading in Desmond structure '{0}'..."
DesmondParser.readFile(filename)
print "Sructure loaded\n"
elif extension == '.lmp':
input_name = splitext(filename)[0] + '.input'
from intermol.lammps_extension.lammps_parser import LammpsParser
print "Reading LAMMPS data & input files..."
lammps_parser = LammpsParser()
lammps_parser.read_input(input_name)
lammps_parser.read_data(filename)
print "Data loaded\n"
else:
raise Exception("{0} is not a supported file format".format(extension))
def write(*files):
"""
"""
for f in files:
try:
filename = str(f)
except:
raise Exception("Arguments should be string filenames")
extension = splitext(filename)[1].lower()
if extension == '.gro':
import intermol.GromacsExt.GromacsStructureParser as GromacsStructureParser
print "Writing Gromacs structure file..."
GromacsStructureParser.writeStructure(filename)
elif extension == '.top':
from intermol.GromacsExt.GromacsTopologyParser import GromacsTopologyParser
print "Writing Gromacs topology file..."
if not GromacsTopologyParser._GroTopParser:
GromacsTopologyParser._GroTopParser = GromacsTopologyParser()
GromacsTopologyParser._GroTopParser.writeTopology(filename)
elif extension == '.cms':
from intermol.DesmondExt.DesmondParser import DesmondParser
print "Writing Desmond topology file..."
DesmondParser = DesmondParser()
DesmondParser.writeFile(filename)
elif extension == '.lmp':
input_name = splitext(filename)[0] + '.input'
from intermol.lammps_extension.lammps_parser import LammpsParser
print "Writing LAMMPS data & input files..."
lammps_parser = LammpsParser()
lammps_parser.write(filename)
print "Finished writing '{0}'".format(input_name)
else:
raise Exception("{0} is not a supported file format".format(extension))
print "Finished writing '{0}'".format(filename)
def readFile(infile):
logger.info('Reading LAMMPS files {0}'.format(infile))
parser = LammpsParser()
parser.read_system(infile)
logger.info('Structure loaded')
def writeFile(outfile):
logger.info('Writing LAMMPS file {0}'.format(outfile))
parser = LammpsParser()
parser.write(outfile)
logger.info('Write complete')
def readFile(infile):
logger.info('Reading LAMMPS files {0}'.format(infile))
parser = LammpsParser()
parser.read_system(infile)
logger.info('Structure loaded')
def writeFile(outfile):
logger.info('Writing LAMMPS file {0}'.format(outfile))
parser = LammpsParser()
parser.write(outfile)
logger.info('Write complete')
