added all the functions, but with warnings, saying input tests correc…

…tness is not checked.

docs/index.rst

@@ -117,6 +117,7 @@ The official VMD web page is http://www.ks.uiuc.edu/Research/vmd
     	:maxdepth: 2
 
     	topic_guides/data_structures
+	topic_guides/secondary_structures
 
 .. toctree::
     	:caption: Reference

docs/topic_guides/data_structures.rst

@@ -10,10 +10,13 @@ Calculate a Dihedral Angle
 
 	.. automodule:: mosdef_dihedral_fit.utils.math_operations
         	:members: dihedral_angle
-
+			
 
 Fit a Dihedral
 --------------
 
 	.. automodule:: mosdef_dihedral_fit.dihedral_fit.fit_dihedral_with_gomc
 		:members: fit_dihedral_with_gomc
+
+
+

docs/topic_guides/secondary_structures.rst

@@ -0,0 +1,50 @@
+.. _secondary_data_structures:
+
+=========================
+Secondary Data Structures
+=========================
+
+.. warning::
+	These secondary functions, mostly from the **utils** folder,= 
+	**do not contain Type or Value Input Checks**.  Therefore, they are being
+	listed with a warning that only advanced users should use these functions, as  
+	they were not designed with input error checks.  
+
+	Advanced users who wish to use these functions can find them 
+	`here <https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/tree/main/mosdef_dihedral_fit/utils>`_. 
+
+
+Read and Write Functions (For Advanded Users)
+---------------------------------------------
+
+.. warning::
+	These secondary functions, mostly from the **utils** folder,= 
+	**do not contain Type or Value Input Checks**.  Therefore, they are being
+	listed with a warning that only advanced users should use these functions, as  
+	they were not designed with input error checks.  
+
+	Advanced users who wish to use these functions can find them 
+	`here <https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/tree/main/mosdef_dihedral_fit/utils>`_. 
+
+
+.. automodule:: mosdef_dihedral_fit.utils.file_read_and_write
+	:members: get_atom_names_and_elements_from_mol2, get_atom_names_and_elements_from_pdb, write_xyz_file_from_gaussian_coordinates, write_restart_coor_from_xyz_file, check_gaussian_angle_energy_file_correct, check_gaussian_optimized_coordinate_file_correct, get_final_gaussian_output_file_data, get_gaussian_log_file_data, write_qm_data_files, get_matching_dihedral_info_and_opls_fitting_data
+
+
+Math and Operation Functions (For Advanded Users)
+-------------------------------------------------
+
+.. warning::
+	These secondary functions, mostly from the **utils** folder,= 
+	**do not contain Type or Value Input Checks**.  Therefore, they are being
+	listed with a warning that only advanced users should use these functions, as  
+	they were not designed with input error checks.  
+
+	Advanced users who wish to use these functions can find them 
+	`here <https://github.com/GOMC-WSU/MoSDeF-dihedral-fit/tree/main/mosdef_dihedral_fit/utils>`_. 
+
+
+.. automodule:: mosdef_dihedral_fit.utils.math_operations
+	:noindex: dihedral_angle
+	:members: round_to_sig_figs, normalize_vector, angle_between_2_vectors, check_previous_qm_values_match, sum_opls_const_1_plus_or_minus_cos_n_values, periodic_dihedral_n_1_2_3_4_5, RB_torsion_n_1_2_3_4_5, opls_dihedral_n_1_2_3_4
+

mosdef_dihedral_fit/tests/files/gaussian/HC_CT_CT_HC/output/GOMC_pdb_psf_ff_files_dihedrals_zeroed.inp

@@ -57,7 +57,7 @@ DIHEDRALS * CHARMM
 ! Boltzmann = 0.0019872041 kcal / (mol * K)
 !
 ! type_1   type_2     type_3     type_4     Kchi            n          delta           ! extended_type_1      extended_type_2      extended_type_3      extended_type_4
-HC         CT         CT         HC         0.5             0          90.0            ! TMP_opls_140         TMP_opls_135         TMP_opls_135         TMP_opls_140
+HC         CT         CT         HC         0.5             0          90.0            ! TMP_opls_140         TMP_opls_135         TMP_opls_135         TMP_opls_140        
 ! The input dihedral to periodic dihedral conversion error is OK [error <= 10^(-10)]
 ! Maximum( |(input dihedral calc)-(periodic dihedral calc)| ) =  3.608224830031759e-16
 

mosdef_dihedral_fit/tests/test_file_read_write.py

@@ -276,7 +276,7 @@ def test_write_qm_data_files(self):
         out_indices = []
         write_qm_data_files({full_path: out_indices})
         assert os.path.exists("extracted_gaussian_data/dihedral.txt")
-
+    
     def test_get_matching_dihedral_info_and_opls_fitting_data(self):
         out = get_matching_dihedral_info_and_opls_fitting_data(
             fit_dihedral_atom_types=["HC", "CT", "CT", "HC"],
@@ -304,7 +304,7 @@ def test_get_matching_dihedral_info_and_opls_fitting_data(self):
             [4, 1, 2, 8],
             [5, 1, 2, 6],
             [5, 1, 2, 7],
-            [5, 1, 2, 8],
+            [5, 1, 2, 8]
         ]
         assert dihedral_numsList == expected_dihedralnumsList
 
@@ -327,7 +327,7 @@ def test_get_matching_dihedral_info_and_opls_fitting_data(self):
             [-1.012159, 1.156346, 0.0],
             [0.0, 0.76376, 0.0],
             [-0.0, -0.76376, 0.0],
-            [1.012159, -1.156346, 0.0],
+            [1.012159, -1.156346, 0.0]
         ]
         assert np.allclose(coordsList[0][0], expected_coords)
         assert np.shape(coordsList) == (37, 9, 4, 3)
@@ -351,10 +351,10 @@ def test_get_matching_dihedral_info_and_opls_fitting_data(self):
             8.999999999999845,
             8.99999999999938,
             2.780442542871242e-12,
-            8.99999999999753,
+            8.99999999999753
         ]
         assert np.allclose(opls_paramsList[0], expected_opls_params)
-
+    
     def test_change_gomc_ff_file_dihedral_values(self):
         new_file = self.get_fn(
             "gaussian/HC_CT_CT_HC/output/GOMC_pdb_psf_ff_files_dihedrals_zeroed.inp"
@@ -379,3 +379,4 @@ def test_change_gomc_ff_file_dihedral_values(self):
                     break
 
         assert checkFile
+