def test_conv_kurucz(tmpdir):
pass
os.chdir(str(tmpdir))
db = pyfant.FileMolDB()
db.init_default()
# conn = db.get_conn()
molconsts = pyfant.MolConsts()
molconsts.populate_all_using_str(db, "OH [A 2 Sigma - X 2 Pi]")
molconsts.None_to_zero()
h = _fake_file()
fileobj = pyfant.FileKuruczMolecule()
fileobj._do_load_h(h, "_fake_file")
conv = pyfant.ConvKurucz(molconsts=molconsts,
flag_hlf=True,
flag_normhlf=True,
flag_fcf=False,
flag_quiet=False,
fcfs=None,
iso=None)
f, log = conv.make_file_molecules(fileobj)
assert f.num_lines == 5
assert f[0].s == 0.5
def test_populate_all_using_str(tmpdir):
os.chdir(str(tmpdir))
db = pyfant.FileMolDB()
db.init_default()
consts = pyfant.MolConsts()
consts.populate_all_using_str(db, "OH [A 2 SIGMA - X 2 PI]")
def test_molconsts_to_molecule(tmpdir):
os.chdir(str(tmpdir))
db = pyfant.FileMolDB()
db.init_default()
mc = pyfant.some_molconsts(db)
mm = pyfant.molconsts_to_molecule(mc)
def test_parse_pfantmol_descriptions(tmpdir):
os.chdir(str(tmpdir))
db = pyfant.FileMolDB()
db.init_default()
cursor = db.get_conn().execute("select * from pfantmol")
for row in cursor:
mc = pyfant.MolConsts()
mc.populate_parse_str(row["description"])
def test_populate_all_using_ids(tmpdir):
os.chdir(str(tmpdir))
db = pyfant.FileMolDB()
db.init_default()
consts = pyfant.MolConsts()
consts.populate_all_using_ids(db,
id_molecule=7,
id_system=6,
id_pfantmol=12,
id_statel=96,
id_state2l=97)
def _do_load_moldb(self):
"""Loads FileMolDB and updates part of GUI accordingly.
This is an intermediate GUI updating stage."""
moldb, flag_valid = pyfant.FileMolDB(), False
fn_moldb = self.w_fn_moldb.value
try:
moldb.load(fn_moldb)
flag_valid = True
except Exception as e:
self.add_log_error("Error loading file '{}'".format(fn_moldb), True, e)
self.w_fn_moldb.flag_valid = flag_valid
self.w_molconsts.set_moldb(moldb if flag_valid else None)
def test_populate_all_using_ids_raises(tmpdir):
"""Uses invalid ids to see method raising ValueError"""
os.chdir(str(tmpdir))
db = pyfant.FileMolDB()
db.init_default()
consts = pyfant.MolConsts()
with pytest.raises(ValueError):
consts.populate_all_using_ids(db,
id_molecule=111,
id_system=11116,
id_pfantmol=11112,
id_statel=111196,
id_state2l=111197)
def test_some_molconsts(tmpdir):
"""Reproduces all the steps in some_molconsts()"""
os.chdir(str(tmpdir))
db = pyfant.FileMolDB()
db.init_default()
s = "OH [A 2 SIGMA - X 2 PI]"
ret = pyfant.MolConsts()
ret.populate_all_using_str(db, s)
ret.populate_parse_str(s)
db.get_conn().close()
os.unlink(db.filename)
ret.None_to_zero()
return ret
def test_adds_to_one0(tmpdir):
os.chdir(str(tmpdir))
db = pyfant.FileMolDB()
db.init_default()
consts = pyfant.MolConsts()
consts.populate_all_using_str(db, "OH [A 2 sigma - X 2 pi]")
consts.None_to_zero()
mtools = pyfant.kovacs_toolbox(consts)
for J2l in range(30):
try:
k = 2. / ((2 * consts.get_S2l() + 1) * (2 * J2l + 1) *
(2 - consts["cro"]))
mtools.populate(0, 0, J2l)
sum_ = sum([x * k for x in mtools._dict_sj.values() if x > 0])
print("J2l={:2}: sum={}".format(J2l, sum_))
except ZeroDivisionError:
print("ZeroDivisionError for J2l={}".format(J2l))
if __name__ == "__main__":
deffn = pyfant.FileMolDB.default_filename
parser = argparse.ArgumentParser(
description=__doc__,
formatter_class=a99.SmartFormatter
)
parser.add_argument('fn', type=str, help='Molecules database file name',
default=deffn, nargs='?')
args = parser.parse_args()
if args.fn == deffn and not os.path.isfile(deffn):
args.fn = None
m = None
if args.fn is not None:
m = pyfant.FileMolDB()
m.load(args.fn)
app = a99.get_QApplication([])
form = pyfant.XFileMolDB(None, [m,])
form.showMaximized()
sys.exit(app.exec_())
def test_FileMolDB(tmpdir):
os.chdir(str(tmpdir))
obj = pyfant.FileMolDB()
obj.init_default()
obj.save_as("another")
"""Converts Plez's Turbospectrum file to PFANT format.
Requires Turbospectrum linelist file 'N14H-AX-2011.bsyn.list' (system 'NH A-X PGopher').
"""
import pyfant
fmoldb = pyfant.FileMolDB()
fmoldb.init_default()
molconsts = fmoldb.get_molconsts("NH [A 3 Pi - X 3 Sigma]")
molconsts.None_to_zero()
fplez = pyfant.FilePlezLinelist()
fplez.load("N14H-AX-2011.bsyn.list")
converter = pyfant.ConvPlez(name="NH A-X PGopher", molconsts=molconsts)
fmol, log = converter.make_file_molecules(fplez)
fmol.save_as("nh-converted.dat")
