Minor changes and added missing tests for the RSA functions.

prointvar/dssp.py

@@ -20,7 +20,7 @@
 from prointvar.pdbx import PDBXreader
 from prointvar.pdbx import PDBXwriter
 
-from prointvar.utils import compute_rsa
+from prointvar.utils import get_rsa
 from prointvar.utils import get_rsa_class
 from prointvar.utils import row_selector
 from prointvar.utils import lazy_file_remover
@@ -272,8 +272,8 @@ def add_dssp_rsa(data, method="Sander"):
     table = data
     rsas = []
     for i in table.index:
-        rsas.append(compute_rsa(table.loc[i, "ACC"], table.loc[i, "AA"],
-                                method=method))
+        rsas.append(get_rsa(table.loc[i, "ACC"], table.loc[i, "AA"],
+                            method=method))
     table["RSA"] = rsas
     return table
 

prointvar/utils.py

@@ -435,7 +435,7 @@ def get_rsa_class(rsa):
     return rsa_class
 
 
-def compute_rsa(acc, resname, method="Sander"):
+def get_rsa(acc, resname, method="Sander"):
     """
     Computes Relative Solvent Accessibility (RSA) from an input
     DSSP ACC value, and according to ASA standard values.

tests/test_utils.py

@@ -43,6 +43,8 @@
 from prointvar.utils import get_start_end_ranges_consecutive_ints
 from prointvar.utils import constrain_column_types
 from prointvar.utils import exclude_columns
+from prointvar.utils import get_rsa
+from prointvar.utils import get_rsa_class
 
 from prointvar.config import config as c
 
@@ -159,6 +161,8 @@ def setUp(self):
              {'label': '5', 'value': 5, 'type': 0.32}])
         self.constrain_column_types = constrain_column_types
         self.exclude_columns = exclude_columns
+        self.get_rsa = get_rsa
+        self.get_rsa_class = get_rsa_class
 
         logging.disable(logging.DEBUG)
 
@@ -194,6 +198,8 @@ def tearDown(self):
         self.mock_df = None
         self.constrain_column_types = None
         self.exclude_columns = None
+        self.get_rsa = None
+        self.get_rsa_class = None
 
         logging.disable(logging.NOTSET)
 
@@ -542,6 +548,22 @@ def test_exclude_columns(self):
         self.assertEqual(len(self.mock_df.columns), 2)
         self.assertNotIn("type", self.mock_df)
 
+    def test_get_rsa(self):
+        rsa = self.get_rsa(10.0, "A", method="Sander")
+        self.assertEqual(9.434, rsa)
+        rsa = self.get_rsa(20.0, "A", method="Miller")
+        self.assertEqual(17.699, rsa)
+        rsa = self.get_rsa(30.0, "A", method="Wilke")
+        self.assertEqual(23.256, rsa)
+
+    def test_get_rsa_class(self):
+        rsa_class = self.get_rsa_class(25.5)
+        self.assertEqual('Surface', rsa_class)
+        rsa_class = self.get_rsa_class(7.5)
+        self.assertEqual('Part. Exposed', rsa_class)
+        rsa_class = self.get_rsa_class(1.5)
+        self.assertEqual('Core', rsa_class)
+
 
 if __name__ == '__main__':
     logging.basicConfig(stream=sys.stderr)