Update variables names for NIST database

Author: RJMW

beams/annotation.py

@@ -31,9 +31,9 @@ def calculate_ppm_error(mass, theo_mass):
 def _remove_elements_from_compositions(records, keep):
 
     path_nist_database = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'data', 'nist_database.txt')
-    nist_mass = nist_database_to_pyteomics(path_nist_database)
+    nist_database = nist_database_to_pyteomics(path_nist_database)
 
-    elements = [e for e in nist_mass if e not in keep]
+    elements = [e for e in nist_database if e not in keep]
     for record in records:
         for e in elements:
             if "composition" in record:
@@ -616,7 +616,7 @@ def annotate_molecular_formulae(peaklist, lib_adducts, ppm, db_out, db_in="http:
             r.raise_for_status()
 
     path_nist_database = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'data', 'nist_database.txt')
-    nist_mass = nist_database_to_pyteomics(path_nist_database)
+    nist_database = nist_database_to_pyteomics(path_nist_database)
 
     for i in range(len(peaklist.iloc[:, 0])):
         mz = float(peaklist["mz"].iloc[i])
@@ -652,7 +652,7 @@ def annotate_molecular_formulae(peaklist, lib_adducts, ppm, db_out, db_in="http:
                         del record["DoubleBondEquivalents"]
                     record["mz"] = mz
                     record["ppm_error"] = calculate_ppm_error(mz, record["exact_mass"])
-                    comp = OrderedDict([(item, record[item]) for item in record if item in nist_mass.keys()])
+                    comp = OrderedDict([(item, record[item]) for item in record if item in nist_database.keys()])
                     record["molecular_formula"] = composition_to_string(comp)
                     record["adduct"] = adduct
                 records = _remove_elements_from_compositions(records, keep=["C", "H", "N", "O", "P", "S"])
@@ -858,7 +858,7 @@ def annotate_drug_products(peaklist, db_out, list_smiles, lib_adducts, ppm, phas
                    );""")
 
     path_nist_database = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'data', 'nist_database.txt')
-    nist_db = nist_database_to_pyteomics(path_nist_database)
+    nist_database = nist_database_to_pyteomics(path_nist_database)
 
     records = []
     for smiles_parent in list_smiles:

beams/in_out.py

@@ -48,7 +48,7 @@ def read_molecular_formulae(filename, separator="\t", calculate=True, filename_a
 
     if calculate:
         path_nist_database = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'data', 'nist_database.txt')
-        nist_db = nist_database_to_pyteomics(path_nist_database)
+        nist_database = nist_database_to_pyteomics(path_nist_database)
 
     df = read_csv(filename, sep=separator, float_precision="round_trip")
     records = []
@@ -60,7 +60,7 @@ def read_molecular_formulae(filename, separator="\t", calculate=True, filename_a
             sum_CHNOPS = sum([comp[e] for e in comp if e in ["C", "H", "N", "O", "P", "S"]])
             record["CHNOPS"] = sum_CHNOPS == sum(list(comp.values()))
             if calculate:
-                record["exact_mass"] = round(pyteomics_mass.mass.calculate_mass(formula=str(row.molecular_formula), mass_data=nist_db), 6)
+                record["exact_mass"] = round(pyteomics_mass.mass.calculate_mass(formula=str(row.molecular_formula), mass_data=nist_database), 6)
             else:
                 record["exact_mass"] = float(row.exact_mass)
             record.update(HC_HNOPS_rules(str(row.molecular_formula)))
@@ -77,7 +77,7 @@ def read_compounds(filename, separator="\t", calculate=True, filename_atoms=""):
 
     if calculate:
         path_nist_database = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'data', 'nist_database.txt')
-        nist_db = nist_database_to_pyteomics(path_nist_database)
+        nist_database = nist_database_to_pyteomics(path_nist_database)
 
     df = read_csv(filename, sep=separator, float_precision="round_trip")
     records = []
@@ -89,7 +89,7 @@ def read_compounds(filename, separator="\t", calculate=True, filename_atoms=""):
             sum_CHNOPS = sum([comp[e] for e in comp if e in ["C", "H", "N", "O", "P", "S"]])
             record["CHNOPS"] = sum_CHNOPS == sum(list(comp.values()))
             if calculate:
-                record["exact_mass"] = round(pyteomics_mass.calculate_mass(formula=str(str(row.molecular_formula)), mass_data=nist_db),6)
+                record["exact_mass"] = round(pyteomics_mass.calculate_mass(formula=str(str(row.molecular_formula)), mass_data=nist_database),6)
             else:
                 record["exact_mass"] = float(row.exact_mass)
             record["compound_id"] = row.compound_id

tests/test_libraries.py

@@ -41,13 +41,13 @@ def test_mass_differences(self):
         self.assertEqual(lib_differences.lib, [])
 
     def test_nist_database_to_pyteomics(self):
-        nist_mass = nist_database_to_pyteomics(os.path.join(self.path, "beams", "data", "nist_database.txt"))
-        self.assertEqual(nist_mass["C"][0], (12.0, 1.0))
-        self.assertEqual(nist_mass["H"][0], (1.00782503223, 1.0))
-        self.assertEqual(nist_mass["N"][0], (14.00307400443, 1.0))
-        self.assertEqual(nist_mass["O"][0], (15.99491461957, 1.0))
-        self.assertEqual(nist_mass["P"][0], (30.97376199842, 1.0))
-        self.assertEqual(nist_mass["S"][0], (31.9720711744, 1.0))
+        nist_database = nist_database_to_pyteomics(os.path.join(self.path, "beams", "data", "nist_database.txt"))
+        self.assertEqual(nist_database["C"][0], (12.0, 1.0))
+        self.assertEqual(nist_database["H"][0], (1.00782503223, 1.0))
+        self.assertEqual(nist_database["N"][0], (14.00307400443, 1.0))
+        self.assertEqual(nist_database["O"][0], (15.99491461957, 1.0))
+        self.assertEqual(nist_database["P"][0], (30.97376199842, 1.0))
+        self.assertEqual(nist_database["S"][0], (31.9720711744, 1.0))
 
 
 if __name__ == '__main__':