fixed HITRAN exact name

src/exojax/spec/api.py

@@ -457,7 +457,7 @@ def exact_isotope_name(self, isotope):
         Returns:
             str: exact isotope name such as (12C)(16O)
         """
-        from exojax.utils.isotopes import exact_hitran_isotope_name_from_isotope
+        from exojax.utils.molname import exact_hitran_isotope_name_from_isotope
         return exact_hitran_isotope_name_from_isotope(self.simple_molecule_name,
                                                isotope)
 

src/exojax/spec/molinfo.py

@@ -1,7 +1,8 @@
 import warnings
 from exojax.utils.isotopes import molmass_hitran
-from exojax.utils.molname import e2s
-from exojax.utils.isotopes import exact_molecule_name_to_isotope_number
+from exojax.utils.molname import exact_molname_exomol_to_simple_molname
+from exojax.utils.molname import exact_molecule_name_to_isotope_number
+from exojax.utils.molname import exact_molname_hitran_to_simple_molname
 
 def isotope_molmass(exact_molecule_name):
     """isotope molecular mass 
@@ -13,11 +14,18 @@ def isotope_molmass(exact_molecule_name):
         float or None: molecular mass g/mol
     """
     molmass_isotope, abundance_isotope = molmass_hitran()
-    isotope_number = exact_molecule_name_to_isotope_number(exact_molecule_name)
-    if isotope_number is not None:
-        simple_molecule_name = e2s(exact_molecule_name)
+    molnumber, isotope_number = exact_molecule_name_to_isotope_number(exact_molecule_name)
+    try:
+        simple_molecule_name = exact_molname_exomol_to_simple_molname(exact_molecule_name)
         return molmass_isotope[simple_molecule_name][isotope_number]
-    else:
+    except:
+        pass
+
+    try:
+        simple_molecule_name = exact_molname_hitran_to_simple_molname(exact_molecule_name)
+        return molmass_isotope[simple_molecule_name][isotope_number]
+    except:
+        warnings.warn("exact molecule name is not Exomol nor HITRAN form.")
         warnings.warn("No molmass available", UserWarning)
         return None
 

src/exojax/utils/isotopes.py

@@ -15,55 +15,10 @@
 
 import numpy as np
 from exojax.utils import isodata
-from exojax.utils import molname
 import pkgutil
 from io import BytesIO
 import pandas as pd
-
-
-def exact_molecule_name_to_isotope_number(exact_molecule_name):
-    """Convert exact molecule name to isotope number
-
-    Args:
-        exact_molecule_name (str): exact exomol, hitran, molecule name such as 12C-16O,  (12C)(16O)
-
-    Returns:
-        int: isotope number 
-    """
-    from radis.db.molparam import isotope_name_dict
-
-    #check exomol exact name
-    keys = [
-        k for k, v in isotope_name_dict.items() if v == exact_molecule_name
-    ]
-    if len(keys) == 0:
-        #check hitran exact name
-        exact_hitran_molecule_name = exact_molname_exomol_to_hitran(
-            exact_molecule_name)
-        keys = [
-            k for k, v in isotope_name_dict.items()
-            if v == exact_hitran_molecule_name
-        ]
-    if len(keys) == 1:
-        isotope_number = keys[0][1]
-    else:
-        print("No isotope number identified")
-        print("Report at https://github.com/HajimeKawahara/exojax/issues.")
-        return None
-
-    return isotope_number
-
-
-def exact_molname_exomol_to_hitran(exact_exomol_molecule_name):
-    """Convert exact_molname used in ExoMol to those in HITRAN
-
-    Args:
-        exact_exomol_molecule_name (str): exact exomol molecule name such as 12C-16O
-
-    Returns:
-        str: exact exomol molecule name such as (12C)(16O)
-    """
-    return "(" + exact_exomol_molecule_name.replace("-", ")(") + ")"
+from exojax.utils.molname import exact_molname_exomol_to_simple_molname
 
 
 def molmass_hitran():
@@ -104,20 +59,6 @@ def molmass_hitran():
     return molmass_isotope, abundance_isotope
 
 
-def exact_hitran_isotope_name_from_isotope(simple_molecule_name, isotope):
-    """exact isotope name from isotope (number)
-
-    Args:
-        simple_molecular_name (str): simple molecular name such as CO
-        isotope (int): isotope number starting from 1
-
-    Returns:
-        str: HITRAN exact isotope name such as (12C)(16O)
-    """
-    from radis.db.molparam import MolParams
-    mp = MolParams()
-    return mp.get(simple_molecule_name, isotope, "isotope_name")
-
 
 def get_isotope(atom, isolist):
     """get isotope info.
@@ -135,7 +76,7 @@ def get_isotope(atom, isolist):
     mass_number = []
     abundance = []
     for j, isol in enumerate(isolist['isotope']):
-        if molname.e2s(isol) == atom:
+        if exact_molname_exomol_to_simple_molname(isol) == atom:
             iso.append(isolist['isotope'][j])
             mass_number.append(isolist['mass_number'][j])
             abundance.append(float(isolist['abundance'][j]))

src/exojax/utils/molname.py

@@ -1,29 +1,80 @@
+from radis.db.classes import get_molecule
 import re
+import warnings
 
 
-def e2s(molname_exact):
+def exact_hitran_isotope_name_from_isotope(simple_molecule_name, isotope):
+    """exact isotope name from isotope (number)
+
+    Args:
+        simple_molecular_name (str): simple molecular name such as CO
+        isotope (int): isotope number starting from 1
+
+    Returns:
+        str: HITRAN exact isotope name such as (12C)(16O)
+    """
+    from radis.db.molparam import MolParams
+    mp = MolParams()
+    return mp.get(simple_molecule_name, isotope, "isotope_name")
+
+
+def exact_molecule_name_to_isotope_number(exact_molecule_name):
+    """Convert exact molecule name to isotope number
+
+    Args:
+        exact_molecule_name (str): exact exomol, hitran, molecule name such as 12C-16O,  (12C)(16O)
+
+    Returns:
+        int: molecular number, isotope number 
+    """
+    from radis.db.molparam import isotope_name_dict
+
+    #check exomol exact name
+    keys = [
+        k for k, v in isotope_name_dict.items() if v == exact_molecule_name
+    ]
+    if len(keys) == 0:
+        #check hitran exact name
+        exact_hitran_molecule_name = exact_molname_exomol_to_hitran(
+            exact_molecule_name)
+        keys = [
+            k for k, v in isotope_name_dict.items()
+            if v == exact_hitran_molecule_name
+        ]
+    if len(keys) == 1:
+        molnumber = keys[0][0]
+        isotope_number = keys[0][1]
+    else:
+        print("No isotope number identified")
+        print("Report at https://github.com/HajimeKawahara/exojax/issues.")
+        return None
+
+    return molnumber, isotope_number
+
+
+def exact_molname_exomol_to_simple_molname(exact_exomol_molecule_name):
     """convert the exact molname (used in ExoMol) to the simple molname.
 
     Args:
-       molname_exact: the exact molname
+       exact_exomol_molecule_name: the exact exomol molecule name
 
     Returns:
        simple molname
 
     Examples:
-       >>> print(e2s("12C-1H4"))
+       >>> print(exact_molname_exomol_to_simple_molname("12C-1H4"))
        >>> CH4
-       >>> print(e2s("23Na-16O-1H"))
+       >>> print(exact_molname_exomol_to_simple_molname("23Na-16O-1H"))
        >>> NaOH
-       >>> print(e2s("HeH_p"))
+       >>> print(exact_molname_exomol_to_simple_molname("HeH_p"))
        >>> HeH_p
-       >>> print(e2s("trans-31P2-1H-2H")) #not working 
+       >>> print(exact_molname_exomol_to_simple_molname("trans-31P2-1H-2H")) #not working 
        >>> Warning: Exact molname  trans-31P2-1H-2H cannot be converted to simple molname
        >>> trans-31P2-1H-2H
     """
 
     try:
-        t = molname_exact.split('-')
+        t = exact_exomol_molecule_name.split('-')
         molname_simple = ''
         for ele in t:
             alp = ''.join(re.findall(r'\D', ele))
@@ -32,12 +83,46 @@ def e2s(molname_exact):
                 num = num0
             else:
                 num = ''
-            molname_simple = molname_simple+alp+num
+            molname_simple = molname_simple + alp + num
         return molname_simple
     except:
-        print('Warning: Exact molname ', molname_exact,
+        print('Warning: Exact molname ', exact_exomol_molecule_name,
               'cannot be converted to simple molname')
-        return molname_exact
+        return exact_exomol_molecule_name
+
+
+def exact_molname_hitran_to_simple_molname(exact_hitran_molecule_name):
+    """convert exact hitran molname (16C)(13C)(17O) to simple molname, CO2.
+
+    Args:
+        exact_hitran_molecule_name (str): exact_hitran_molecule_name, such as (16C)(13C)(17O) 
+
+    Returns:
+        str: simple molecue name, such as CO2
+    """
+    molnum, isonum = exact_molecule_name_to_isotope_number(
+        exact_hitran_molecule_name)
+    return get_molecule(molnum)
+
+
+def exact_molname_exomol_to_hitran(exact_exomol_molecule_name):
+    """Convert exact_molname used in ExoMol to those in HITRAN
+
+    Args:
+        exact_exomol_molecule_name (str): exact exomol molecule name such as 12C-16O
+
+    Returns:
+        str: exact exomol molecule name such as (12C)(16O)
+    """
+    return "(" + exact_exomol_molecule_name.replace("-", ")(") + ")"
+
+
+def e2s(exact_exomol_molecule_name):
+
+    warnings.warn(
+        "e2s will be replaced to exact_molname_exomol_to_simple_molname.",
+        DeprecationWarning)
+    return exact_molname_exomol_to_simple_molname(exact_exomol_molecule_name)
 
 
 def split_simple(molname_simple):
@@ -68,7 +153,7 @@ def split_simple(molname_simple):
                 num = ''
             tmp = ch
         elif ch.islower():
-            tmp = tmp+ch
+            tmp = tmp + ch
         elif ch.isdigit():
             num = ch
 
@@ -98,9 +183,9 @@ def s2e_stable(molname_simple):
     molname_exact = ''
     for j, atm in enumerate(atom_list):
         iso = isotopes.get_stable_isotope(atm, isolist)
-        molname_exact = molname_exact+iso[0]+num_list[j]
-        if j < len(atom_list)-1:
-            molname_exact = molname_exact+'-'
+        molname_exact = molname_exact + iso[0] + num_list[j]
+        if j < len(atom_list) - 1:
+            molname_exact = molname_exact + '-'
     return molname_exact
 
 

tests/unittests/atom/molmass_test.py

@@ -6,9 +6,9 @@
 
 def test_molmass():
     assert molmass_isotope('air')==28.97
-    assert molmass_isotope('CO2')==pytest.approx(44.00974325129166)
+    assert molmass_isotope('CO2')==pytest.approx(43.98983)
     assert molmass_isotope('He')==4.002602
-    assert molmass_isotope('CO2',db_HIT=True)==44.00974325129166
+    assert molmass_isotope('CO2',db_HIT=True)==43.98983
     assert molmass_isotope('He',db_HIT=True)==4.002602
 
 

tests/unittests/spec/api/molinfo_test.py

@@ -4,10 +4,11 @@
 
 
 def test_isotope_molmass():
+    assert isotope_molmass("(12C)(16O)") == pytest.approx(27.994915)
     assert isotope_molmass("12C-16O") == pytest.approx(27.994915)
 
 def test_mean_molmass():
-    assert molmass_isotope("CO") == pytest.approx(28.01044518292034)
+    assert molmass_isotope("CO") == pytest.approx(27.994915)
 
 if __name__ == "__main__":
     test_isotope_molmass()

tests/unittests/utils/isotopes_test.py

@@ -1,49 +1,18 @@
 from exojax.utils.isotopes import get_isotope
 from exojax.utils.isotopes import get_stable_isotope
 from exojax.utils.isotopes import isodata
-from exojax.utils.isotopes import exact_hitran_isotope_name_from_isotope
 from exojax.utils.isotopes import molmass_hitran
-from exojax.utils.isotopes import exact_molecule_name_to_isotope_number
-from exojax.utils.isotopes import exact_molname_exomol_to_hitran
 import numpy as np
 import pytest
 
 
-
-def test_exact_molecule_name_to_isotope_number():
-    eemn = "12C-16O"
-    isonum = exact_molecule_name_to_isotope_number(eemn)
-    assert isonum == 1
-    eemn = "16O-13C-17O"
-    isonum = exact_molecule_name_to_isotope_number(eemn)
-    assert isonum == 6
-
-
-def test_exact_molname_exomol_to_hitran():
-    eemn = "16O-13C-17O"
-    ehmn = exact_molname_exomol_to_hitran(eemn)
-    assert ehmn == "(16O)(13C)(17O)"
-
-
 def test_molarmass_hitran():
     molmass_isotope, abundance_isotope = molmass_hitran()
     assert molmass_isotope["CO"][1] == 27.994915
     assert molmass_isotope["CO"][0] == pytest.approx(28.01044518292034)  #mean
     assert abundance_isotope["CO"][1] == pytest.approx(9.86544E-01)
 
 
-def test_exact_isotope_name_from_isotope():
-    simple_molecule_name = "CO"
-    isotope = 1
-    assert exact_hitran_isotope_name_from_isotope(simple_molecule_name,
-                                                  isotope) == "(12C)(16O)"
-
-    simple_molecule_name = "H2O"
-    isotope = 5
-    assert exact_hitran_isotope_name_from_isotope(simple_molecule_name,
-                                                  isotope) == "HD(18O)"
-
-
 def test_get_isotope():
     isolist = isodata.read_mnlist()
     ref = (['1H', '2H', '3H'], [1.007825, 2.014102,
@@ -62,7 +31,5 @@ def test_get_stable_isotope():
 if __name__ == "__main__":
     test_get_isotope()
     test_get_stable_isotope()
-    test_exact_isotope_name_from_isotope()
     test_molarmass_hitran()
-    test_exact_molname_exomol_to_hitran()
-    test_exact_molecule_name_to_isotope_number()
+