[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

docs/Makefile

@@ -175,4 +175,3 @@ pseudoxml:
 	$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
 	@echo
 	@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."
-

docs/_images/pyMDMC_GITHUB_2021.bib

@@ -4,4 +4,3 @@ @Inbook{pyMDMC_GITHUB_2021
     year        = "2021",
     url         = "https://github.com/GOMC-WSU/py-MCMD"
 }
-

docs/_images/pyMDMC_GITHUB_2021.ris

@@ -1,7 +1,7 @@
 TY  -
 AU  - Crawford, B.
 AU  - Potoff J.
-AU  - 
+AU  -
 AU  -
 AU  -
 AU  -

docs/_images/pyMDMC_PAPER_2022.bib

@@ -5,4 +5,3 @@ @article{pyMDMC_PAPER_2021
     doi         = "https://doi.org/10.1021/acs.jctc.1c00911"
     url         = "https://pubs.acs.org/doi/10.1021/acs.jctc.1c00911"
 }
-

docs/_images/pyMDMC_ZENODO_2021.bib

@@ -5,4 +5,3 @@ @Inbook{pyMDMC_ZENODO_2021
     url         = "https://doi.org/10.5281/zenodo.5142483"
     doi         = "10.5281/zenodo.5142483"
 }
-

docs/_images/pyMDMC_ZENODO_2021.ris

@@ -1,7 +1,7 @@
 TY  -
 AU  - Crawford, B.
 AU  - Potoff J.
-AU  - 
+AU  -
 AU  -
 AU  -
 AU  -

docs/citing_MDMC_PYTHON.rst

@@ -73,4 +73,3 @@ We also recommend citing the `Concatenate DCD files (CatDCD) <https://www.ks.uiu
         year        = "2009",
         url         = "https://www.ks.uiuc.edu/Development/MDTools/catdcd/"
     }
-

docs/docs-env.yml

@@ -16,4 +16,3 @@ dependencies:
     - sphinxcontrib-svg2pdfconverter
 sphinx:
   fail_on_warning: true
-

docs/example_simulation.rst

@@ -13,4 +13,3 @@ The **green** protein and waters (spheres) represent the crystallography data.
 
 	<iframe src="_static/Hybrid_MC_MD_BPTI.mp4" width="100%" height="410" style="border:1px solid black;">
 </iframe>
-

docs/generating_systems.rst

@@ -26,4 +26,3 @@ Non-Traditional Chemical Engineering Systems
 -------
 
 Non-Traditional chemical engineering systems are proteins or other molecules requiring multiple residue names per molecule. Currently, the GOMC-MoSDeF software is not compatible with these systems.  Therefore, these systems should be constructed using different software, such as `Visual Molecular Dynamics (VMD) <https://www.ks.uiuc.edu/Research/vmd/>`_, or other similar software.
-

docs/index.rst

@@ -32,4 +32,3 @@ The py-MCMD Python package consists of two (2) different licenses (:download:`Co
 	CatDCD_instructions_license
 	generating_systems
 	citing_MDMC_PYTHON
-

docs/installation.rst

@@ -30,4 +30,3 @@ This Python code is currently compatible only with `NAMD version 2.14 <https://w
 **NOTE: ONLY run NAMD in the NVT ensemble, as running NAMD in the NPT ensemble will cause errors in the box positioning since NAMD and GOMC have different box centering algorithms when centering the box during box size changes.**
 
 **NOTE:**  GOMC does not currently use improper or Urey—Bradley potentials, so if the hybrid simulations contain impropers or Urey—Bradleys, the NAMD simulation energies will be different.  In a protein simulation, it should be OK not to use impropers or Urey-Bradleys in GOMC and utilize them in NAMD since the protein will not move in the GOMC simulation due to its size.  Each simulation will need to be individually evaluated to determine if not having the impropers or Urey-Bradleys in GOMC is irrelevant or significant to the simulation results.**
-

docs/make.bat

@@ -240,4 +240,3 @@ if "%1" == "pseudoxml" (
 )
 
 :end
-

docs/requirements.txt

@@ -8,4 +8,3 @@ ipykernel
 nbsphinx
 mock
 ele
-

docs/running_analysis_code.rst

@@ -32,4 +32,3 @@ Flags for Combining Data Code
 
 	* **-o** *or* **--overwrite** flag : (True, true, T, t, False, false, F, or f), default = False
 		Determines whether to overwrite an exiting combined data folder and data, if they exist.
-

docs/running_the_simulation.rst

@@ -44,4 +44,3 @@ The flags for running the *run_NAMD_GOMC.py* file user_input_variables_NAMD_GOMC
 
 	-namd_sims_order *or* --namd_simulation_order : default='series',  (options: 'series' or 'parallel')
 		This sets the NAMD simulation to be run in series or parallel. The data is entered only as series or parallel (default = series). This is only relevant for the GEMC ensemble when utilizing two (2) NAMD simulation boxes (i.e., only_use_box_0_for_namd_for_gemc = False  --> both box 0 and box 1). The GCMC, NVT, NPT, or the GEMC ensembles when using only one (1) NAMD simulation box (i.e., only_use_box_0_for_namd_for_gemc = True --> only box 0) are always run in series, since there is nothing to run in parallel. Note: This feature was added so the user can minimize the load on the GPU by running both NAMD simulations in parallel.
-

docs/simulation_analysis.rst

@@ -154,4 +154,3 @@ The variables below are contained in the *"user_input_combine_data_NAMD_GOMC.jso
 		This input is used when combining the 'Hybrid' data.
 		This is required when combining the
 		'GOMC-only', or 'NAMD-only' data, but is not used.
-

docs/simulation_output.rst

@@ -26,4 +26,3 @@ The hybrid simulation Python code outputs the main NAMD and GOMC folders, each c
 
 
 Retaining all the individual simulation runs can add up to considerable storage requirements. Therefore, we recommended optimizing the number of steps and moves for each simulation engine and calculating the entire run's storage requirements before starting the production runs. *In the future, we plan on programming an auto-cleanup and that will combine all the individual runs on the fly and minimize the storage requirement.*
-

docs/simulation_parameters_files.rst

@@ -260,4 +260,3 @@ The MD/MC Hybrid input file is in the `json <https://developer.mozilla.org/en-US
 		SO IT MAY NOT WORK ON OTHER GOMC VERSIONS WITHOUT SOME CODE MODIFICATION,
 		AND SOME ADDITIONAL FUNCTIONALLITY IS NOT IN PREVIOUS GOMC VERSIONS.
 		Example: "required_data/bin"
-