add exception test for pdb writer

GOMC-WSU · Aug 19, 2024 · dea1acd · dea1acd
1 parent 0dd052b
commit dea1acd
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Showing 3 changed files with 27 additions and 16 deletions.
diff --git a/mosdef_dihedral_fit/tests/files/with_errors/CT_CT_C_3_OH_with_errors.pdb b/mosdef_dihedral_fit/tests/files/with_errors/CT_CT_C_3_OH_with_errors.pdb
@@ -1,13 +1,13 @@
-CRYST1    9.879    8.003    6.628  90.00  90.00  90.00 P 1            
-HETATM    1  C1  RES     1       0.000   0.000   0.000  0.00  0.00           C  
-HETATM    2  C2  RES     1      -1.500   0.000   0.000  0.00  0.00           C  
-HETATM    3  C3  RES     1      -2.200   1.212   0.000  0.00  0.00           C  
-HETATM    4  O1  RES     1       0.700  -1.212  -0.000  0.00  0.00           O  
-HETATM    5  O2  RES     1       0.771   1.169   0.000  0.00  0.00           O  
-HETATM    6  H1  RES     1      -1.813   1.790   0.713  0.00  0.00           H  
-HETATM    7  H2  RES     1      -1.967   1.754  -0.813  0.00  0.00           H  
-HETATM    8  H3  RES     1      -1.820  -0.485  -0.814  0.00  0.00           H  
-HETATM    9  H4  RES     1      -1.820  -0.485   0.814  0.00  0.00           H  
-HETATM   10  H5  RES     1      -3.197   1.252   0.096  0.00  0.00           H  
-HETATM   11  H6  RES     1       1.682  -1.022  -0.000  0.00  0.00           H  
-END                                                                             
+CRYST1    9.879    8.003    6.628  90.00  90.00  90.00 P 1
+HETATM    1  C1  RES     1       0.000   0.000   0.000  0.00  0.00
+HETATM    2  C2  RES     1      -1.500   0.000   0.000  0.00  0.00
+HETATM    3  C3  RES     1      -2.200   1.212   0.000  0.00  0.00
+HETATM    4  O1  RES     1       0.700  -1.212  -0.000  0.00  0.00
+HETATM    5  O2  RES     1       0.771   1.169   0.000  0.00  0.00
+HETATM    6  H1  RES     1      -1.813   1.790   0.713  0.00  0.00
+HETATM    7  H2  RES     1      -1.967   1.754  -0.813  0.00  0.00
+HETATM    8  H3  RES     1      -1.820  -0.485  -0.814  0.00  0.00
+HETATM    9  H4  RES     1      -1.820  -0.485   0.814  0.00  0.00
+HETATM   10  H5  RES     1      -3.197   1.252   0.096  0.00  0.00
+HETATM   11  H6  RES     1       1.682  -1.022  -0.000  0.00  0.00
+END
diff --git a/mosdef_dihedral_fit/tests/test_file_read_write.py b/mosdef_dihedral_fit/tests/test_file_read_write.py
@@ -107,6 +107,14 @@ def test_get_from_pdb(self):
             "H",
             "H",
         ]
+        error_fn = "with_errors/CT_CT_C_3_OH_with_errors.pdb"
+        full_error_fn = self.get_fn(error_fn)
+        error_msg = (
+            "ERROR: The provided pdb format is not the required PDB format "
+            "or the pdb file has zero \(0\) atoms or beads in it."
+        )
+        with pytest.raises(TypeError, match=error_msg):
+            get_atom_names_and_elements_from_pdb(full_error_fn)
 
     def test_write_xyz_file_from_gaussian(self):
         atom_namesList = [

diff --git a/mosdef_dihedral_fit/utils/file_read_and_write.py b/mosdef_dihedral_fit/utils/file_read_and_write.py
@@ -109,13 +109,16 @@ def get_atom_names_and_elements_from_pdb(pdb_directory_and_filename):
                     if element_name_str_space_iter != " ":
                         element_name_j += element_name_str_space_iter
 
-                atom_name_list.append(atom_name_j)
-                element_name_list.append(element_name_j)
+                if atom_name_j != "":
+                    atom_name_list.append(atom_name_j)
+                if element_name_j != "":
+                    element_name_list.append(element_name_j)
 
             if len(split_line_m) > 0 and str(split_line_m[0]) in ["CRYST1"]:
                 get_atom_type_bool = True
 
-    if len(atom_name_list) == 0:
+    print(element_name_list)
+    if len(element_name_list) == 0:
         raise TypeError(
             "ERROR: The provided pdb format is not the required PDB format "
             "or the pdb file has zero (0) atoms or beads in it."