def extra_info(self): for state in self.state_list: try: state['lam'] = units.energy['nm'] / (state['exc_en'] / units.energy['eV']) except ZeroDivisionError: pass if 'coor_file' in self.ioptions: self.struc = lib_struc.structure() self.struc.read_file(self.ioptions['coor_file'], self.ioptions['coor_format']) elif 'mo_file' in self.ioptions: self.struc = lib_struc.structure() self.struc.read_file(self.ioptions['mo_file'], 'molden') else: self.struc = None
def file_at_lists(self): print("Automatic generation of at_lists partitioning ...") self.coor_file() struc = lib_struc.structure() struc.read_file(file_path=self['coor_file'], file_type=self['coor_format']) return struc.ret_partition()
Syntax: babel.py <intype> <infile> <outtype> <outfile> e.g. babel.py tmol coord xyz coord.xyz """) if len(sys.argv) < 4+1: print(""" Supported file types: col -- Columbus and Newton-X format colr -- Columbus format, atoms reordered txyz2 -- Tinker format with reading possibility (verify the atom types in the output) vnx -- veloctiy (Newton-X format) ntxyz -- velocity (Tinker format) additionally all formats from openbabel are included type 'babel -H' for a complete list""") print('\nFour arguments required.') sys.exit() (intype,infile,outtype,outfile) = sys.argv[1:] if intype in lib_struc.veloc_types: # special treatment of velocities veloc = struc_linalg.veloc() veloc.read_file(file_path=infile, file_type=intype) veloc.write_veloc(file_path=outfile,file_type=outtype) else: struc = lib_struc.structure() struc.read_file(file_path=infile, file_type=intype) struc.make_coord_file(file_path=outfile,file_type=outtype) print("Finished: file %s written."%outfile)
Syntax: babel.py <intype> <infile> <outtype> <outfile> e.g. babel.py tmol coord xyz coord.xyz """) if len(sys.argv) < 4 + 1: print(""" Supported file types: col -- Columbus and Newton-X format colr -- Columbus format, atoms reordered txyz2 -- Tinker format with reading possibility (verify the atom types in the output) vnx -- veloctiy (Newton-X format) ntxyz -- velocity (Tinker format) additionally all formats from openbabel are included type 'babel -H' for a complete list""") print('\nFour arguments required.') sys.exit() (intype, infile, outtype, outfile) = sys.argv[1:] if intype in lib_struc.veloc_types: # special treatment of velocities veloc = struc_linalg.veloc() veloc.read_file(file_path=infile, file_type=intype) veloc.write_veloc(file_path=outfile, file_type=outtype) else: struc = lib_struc.structure() struc.read_file(file_path=infile, file_type=intype) struc.make_coord_file(file_path=outfile, file_type=outtype) print("Finished: file %s written." % outfile)