Merge pull request #112 from bc118/add_test_dih_angle_calc

Added better input tests for dihedral angle calc added all the functions with a warning

docs/index.rst

@@ -110,13 +110,14 @@ The official VMD web page is http://www.ks.uiuc.edu/Research/vmd
     	:maxdepth: 2
 
 	getting_started/installation/installation
-        getting_started/quick_start/quick_start
+	getting_started/quick_start/quick_start
 
 .. toctree::
 	:caption: Topic Guides
     	:maxdepth: 2
 
-    	topic_guides/data_structures
+	topic_guides/data_structures
+	topic_guides/additional_utilities
 
 .. toctree::
     	:caption: Reference

docs/topic_guides/additional_utilities.rst

@@ -0,0 +1,50 @@
+.. _additional_utilities:
+
+====================
+Additional Utilities
+====================
+
+.. warning::
+	These additional utilities, 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 additional utilities, 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 additional utilities, 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
+

docs/topic_guides/data_structures.rst

@@ -10,10 +10,12 @@ 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
+
+

mosdef_dihedral_fit/tests/test_file_read_write.py

@@ -2,12 +2,8 @@
 
 import numpy as np
 import pytest
-import unyt as u
 
 import mosdef_dihedral_fit.utils.math_operations as mdf_math
-from mosdef_dihedral_fit.dihedral_fit.fit_dihedral_with_gomc import (
-    fit_dihedral_with_gomc,
-)
 from mosdef_dihedral_fit.tests.base_test import BaseTest
 from mosdef_dihedral_fit.utils.file_read_and_write import (
     change_gomc_ff_file_dihedral_values,