removed

parser/parser-atk/parser_configurations2.py

-from periodic_table import things as ptab_ns
-from physical_quantities import things as physquan_ns
-from configurations import conf_types, things as confs_ns
-
-
-def parse_configuration(fd, name, verbose=False):
-    """ convert a nanolanguage python script into
-    ASE list of atoms.
-
-    Parameters:
-
-        fd: netcdf_file handle
-        name: str (i.e "BulkConfiguration_gID000")
-
-    """
-    code = fd.variables[name].data[:].copy()
-    code = code.tostring().decode("utf-8")
-    if verbose:
-        print('parsing code:\n------------')
-        print(code)
-
-    things = ptab_ns.copy()
-    things.update(physquan_ns)
-    things.update(confs_ns)
-    exec(code, {}, things)
-    for obj in things.values():
-        for conf_type in conf_types:
-            if isinstance(obj, confs_ns[conf_type]):
-                return obj.atoms
-    return -1
-
-
-if __name__ == '__main__':
-    from ase.visualize import view
-    from scipy.io.netcdf import netcdf_file
-    import sys
-    fd = netcdf_file(sys.argv[1], 'r')
-    name = 'BulkConfiguration_gID000'
-    atoms = parse_configuration(fd, name)
-    view(atoms)
-#    configurations = {}
-#    fp_gids = fd.fingerprint_table[:].decode('utf-8').split('#')
-#    for c in fp_gids:
-#        if len(c) > 0:
-#            fingerprint, gID = c.split(':')[:2]
-#            gID.strip()
-#            for name in ['BulkConfiguration_' + gID,
-#                         'MoleculeConfiguration_' + gID]:
-#                if name in fd.variables.keys():
-#                    configurations[name] = fingerprint
-#
-#    for name, fingerprint in configurations.items():
-#        print(name+',', fingerprint)
-#        atoms = parse_configuration(fd, name)
-#        view(atoms)