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docs/_images/mosdef_dihedral_fit_license

@@ -31,4 +31,4 @@ The **vmd-python** software is licensed by the Theoretical and Computational Bio
 
 The vmd-python website is https://github.com/Eigenstate/vmd-python
 
-The official VMD web page is http://www.ks.uiuc.edu/Research/vmd
+The official VMD web page is http://www.ks.uiuc.edu/Research/vmd

docs/environment_docs.yml

@@ -21,4 +21,3 @@ dependencies:
       - sphinxcontrib-svg2pdfconverter
       - sphinxcontrib-video
       - sphinxcontrib-serializinghtml
-

docs/getting_started/quick_start/fit_a_dihedral_with_Gaussian_and_write_all_files.rst

@@ -169,4 +169,3 @@ Run the dihedral fit to fit to the MM simulations:
     	fit_min_validated_r_squared=0.99,
     	fit_validation_r_squared_rtol=5e-03
     )
-

docs/getting_started/quick_start/gomc_examples_repository.rst

@@ -9,4 +9,3 @@ Simple Examples
     with it's directory/path specified in the dihedral fit function.
 
 `Simple MoSDeF-dihedral-fit examples <https://github.com/GOMC-WSU/GOMC_Examples/tree/main/MoSDeF-dihedral-fit>`_ are provided on the **GOMC** Github page.
-

docs/reference/citing_mosdef_dihedral_fit_python.rst

@@ -59,4 +59,3 @@ Please also cite the following software:
 	* `Visual Molecular Dynamics (VMD) <https://www.ks.uiuc.edu/Research/vmd/>`_
 
 	* `vmd-python <https://github.com/Eigenstate/vmd-python>`_
-

docs/reference/user_notices.rst

@@ -12,4 +12,4 @@ There are some critical items to complete and consider when using the **MoSDeF-d
 
     #. The mixing/combining rules and 1-4 non-bonded dihedral interactions are in the **MoSDeF** XML file and will automatically be input into **GOMC**, the Molecular Mechanics (MM) engine, so please be sure these are entered properly in the XML file or it may set the default parameters, which will produce a wrong result.
 
-    #. The atomic order and molecule must exactly match for the user inputted `Gaussian <https://gaussian.com>`_ log files and the **mol2** file.  There are checks to ensure that the same elements and the number of atoms are used, but there is no simple way to determine if the atoms are out of order when these criteria match.  Therefore, it is up to the user to ensure these are the same.  It is recommended that the user create the **mol2** and use its elements and coordinates to set up the **Gaussian** simulation, as this will reduce the chance of errors.
+    #. The atomic order and molecule must exactly match for the user inputted `Gaussian <https://gaussian.com>`_ log files and the **mol2** file.  There are checks to ensure that the same elements and the number of atoms are used, but there is no simple way to determine if the atoms are out of order when these criteria match.  Therefore, it is up to the user to ensure these are the same.  It is recommended that the user create the **mol2** and use its elements and coordinates to set up the **Gaussian** simulation, as this will reduce the chance of errors.

mosdef_dihedral_fit/__init__.py

@@ -1,5 +1,6 @@
 """ MoSDeF-dihedral-fit: A simple software package to fit dihedrals using the MoSDeF."""
-from mosdef_dihedral_fit.dihedral_fit.fit_dihedral_with_gomc import fit_dihedral_with_gomc
-
+from mosdef_dihedral_fit.dihedral_fit.fit_dihedral_with_gomc import (
+    fit_dihedral_with_gomc,
+)
 
 __version__ = "0.0.0"