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')