diff --git a/.github/workflows/check_acpype.yml b/.github/workflows/check_acpype.yml
index 46ef6839..6b7b2f23 100644
--- a/.github/workflows/check_acpype.yml
+++ b/.github/workflows/check_acpype.yml
@@ -1,114 +1,120 @@
 # This workflow will install Python dependencies, run tests and lint with a single version of Python
 # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
 name: check_acpype
+
 on:
-   push:
-      branches:
-         - master
-   pull_request:
-      branches:
-         - master
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+    paths:
+      - "acpype/**"
+      - "tests/**"
+
 jobs:
-   check-test:
-      runs-on: ubuntu-latest
-      strategy:
-         matrix:
-            python-version: ["3.6", "3.7", "3.8", "3.9", "3.10"]
-
-      steps:
-         - uses: actions/checkout@v2
-
-         - name: Set up Python ${{ matrix.python-version }}
-           uses: actions/setup-python@v2
-           with:
-              python-version: ${{ matrix.python-version }}
-
-         # - name: Python Poetry Action
-         #   uses: abatilo/actions-poetry@v2.1.3
-
-         - name: Cache pip
-           uses: actions/cache@v2
-           with:
-              # This path is specific to Ubuntu
-              path: ~/.cache/pip
-              # Look to see if there is a cache hit for the corresponding requirements file
-              key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}
-              restore-keys: |
-                 ${{ runner.os }}-pip-
-                 ${{ runner.os }}-
-
-         - name: Set Env
-           run: |
-              echo "DEBIAN_FRONTEND=noninteractive" >> $GITHUB_ENV
-              echo "AMBERHOME=$PWD/acpype/amber21-11_linux" >> $GITHUB_ENV
-              echo "$PWD/acpype/amber21-11_linux/bin" >> $GITHUB_PATH
-
-         - name: Install dependencies
-           run: |
-              sudo apt-get update
-              sudo apt-get install -y --no-install-recommends tzdata libarpack++2-dev
-
-         - name: Install OpenBabel
-           run: |
-              sudo apt-get install --no-install-recommends -y openbabel
-
-         - name: Poetry install dependencies
-           run: |
-              pip3 install poetry
-              poetry add openbabel-wheel
-              poetry install
-
-         - name: Lint with flake8
-           run: poetry run flake8 -v --count
-
-         - name: Check format with black
-           run: poetry run black --diff --check .
-
-         - name: Run isort
-           run: poetry run isort . --check-only --profile black
-
-         - name: Test with PyTest
-           run: |
-              poetry run pytest --color=yes --cov=./ --cov-report=xml
-
-         - name: Upload coverage to Codecov
-           if: matrix.python-version == 3.6
-           uses: codecov/codecov-action@v2
-           with:
-              fail_ci_if_error: true
-
-   release:
-      needs: check-test
-      runs-on: ubuntu-latest
-      steps:
-         - name: Get current date
-           id: date
-           run: echo "::set-output name=date::$(date +'%Y.%-m.%-d')"
-
-         - name: Create tag
-           # will only create a new release if the commit message is 'new_release' to master branch
-           if: github.ref == 'refs/heads/master' && contains(github.event.head_commit.message, 'new_tag')
-           uses: actions/github-script@v3
-           with:
-              # github-token: ${{ github.token }} # optional
-              script: |
-                 github.git.createRef({
-                 owner: context.repo.owner,
-                 repo: context.repo.repo,
-                 ref: "refs/tags/${{ steps.date.outputs.date }}",
-                 sha: context.sha
-                 })
-
-         - name: Create Release
-           # will only create a new release if the commit message is 'new_release' to master branch
-           if: github.ref == 'refs/heads/master' && contains(github.event.head_commit.message, 'new_release')
-           id: create_release
-           uses: actions/create-release@v1
-           env:
-              # This token is provided by Actions, you do not need to create your own token
-              GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-           with:
-              tag_name: ${{ steps.date.outputs.date }}
-              release_name: Release ${{ steps.date.outputs.date }}
-              draft: false
-              prerelease: false
+  check-test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.6", "3.7", "3.8", "3.9", "3.10"]
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      # - name: Python Poetry Action
+      #   uses: abatilo/actions-poetry@v2.1.3
+
+      - name: Cache pip
+        uses: actions/cache@v2
+        with:
+          # This path is specific to Ubuntu
+          path: ~/.cache/pip
+          # Look to see if there is a cache hit for the corresponding requirements file
+          key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+            ${{ runner.os }}-
+
+      - name: Set Env
+        run: |
+          echo "PYTEST_ADDOPTS=--random-order" >> $GITHUB_ENV
+          echo "DEBIAN_FRONTEND=noninteractive" >> $GITHUB_ENV
+          echo "AMBERHOME=$PWD/acpype/amber21-11_linux" >> $GITHUB_ENV
+          echo "$PWD/acpype/amber21-11_linux/bin" >> $GITHUB_PATH
+
+      - name: Install dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y --no-install-recommends tzdata libarpack++2-dev
+
+      - name: Install OpenBabel
+        run: |
+          sudo apt-get install --no-install-recommends -y openbabel
+
+      - name: Poetry install dependencies
+        run: |
+          pip3 install poetry
+          poetry add openbabel-wheel
+          poetry install
+
+      - name: Lint with flake8
+        run: poetry run flake8 -v --count
+
+      - name: Check format with black
+        run: poetry run black --diff --check .
+
+      - name: Run isort
+        run: poetry run isort . --check-only --profile black
+
+      - name: Test with PyTest
+        run: |
+          poetry run pytest --color=yes --cov=acpype --cov=tests --cov-report=xml
+
+      - name: Upload coverage to Codecov
+        if: matrix.python-version == 3.6
+        uses: codecov/codecov-action@v2
+        with:
+          fail_ci_if_error: true
+
+  release:
+    needs: check-test
+    runs-on: ubuntu-latest
+    steps:
+      - name: Get current date
+        id: date
+        run: echo "::set-output name=date::$(date +'%Y.%-m.%-d')"
+
+      - name: Create tag
+        # will only create a new release if the commit message is 'new_release' to master branch
+        if: github.ref == 'refs/heads/master' && contains(github.event.head_commit.message, 'new_tag')
+        uses: actions/github-script@v3
+        with:
+          # github-token: ${{ github.token }} # optional
+          script: |
+            github.git.createRef({
+            owner: context.repo.owner,
+            repo: context.repo.repo,
+            ref: "refs/tags/${{ steps.date.outputs.date }}",
+            sha: context.sha
+            })
+
+      - name: Create Release
+        # will only create a new release if the commit message is 'new_release' to master branch
+        if: github.ref == 'refs/heads/master' && contains(github.event.head_commit.message, 'new_release')
+        id: create_release
+        uses: actions/create-release@v1
+        env:
+          # This token is provided by Actions, you do not need to create your own token
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          tag_name: ${{ steps.date.outputs.date }}
+          release_name: Release ${{ steps.date.outputs.date }}
+          draft: false
+          prerelease: false
diff --git a/.github/workflows/codeql-analysis.yml b/.github/workflows/codeql-analysis.yml
index 9c86176d..1204eda2 100644
--- a/.github/workflows/codeql-analysis.yml
+++ b/.github/workflows/codeql-analysis.yml
@@ -1,7 +1,7 @@
 # For most projects, this workflow file will not need changing; you simply need
 # to commit it to your repository.
 #
-# You may wish to alter this file to override the set of languages analyzed,
+# You may wish to alter this file to override the set of languages analysed,
 # or to provide custom queries or build logic.
 #
 # ******** NOTE ********
@@ -13,10 +13,14 @@ name: "CodeQL"
 
 on:
   push:
-    branches: [master]
+    branches:
+      - master
   pull_request:
-    # The branches below must be a subset of the branches above
-    branches: [master]
+    branches:
+      - master
+    paths:
+      - "acpype/**"
+      - "tests/**"
   schedule:
     - cron: "15 0 * * *"
 
diff --git a/.gitignore b/.gitignore
index e280b939..18739599 100644
--- a/.gitignore
+++ b/.gitignore
@@ -55,6 +55,7 @@ coverage.xml
 
 # Sphinx documentation
 docs/_build/
+docs/_autosummary
 
 pip-selfcheck.json
 *.acpype
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index dbc88bd7..b7a26aa4 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,4 +1,12 @@
 repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.1.0
+    hooks:
+      # - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-added-large-files
+      - id: debug-statements
+
   - repo: local
     hooks:
       - id: flake8
@@ -19,6 +27,12 @@ repos:
         language: system
         types: [python]
         require_serial: true
+      - id: pyupgrade
+        name: pyupgrade
+        entry: poetry run pyupgrade --py36-plus
+        language: system
+        types: [python]
+        require_serial: true
       - id: ver_today
         name: ver_today
         entry: ./scripts/ver_today.sh
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
new file mode 100644
index 00000000..f121fab0
--- /dev/null
+++ b/CONTRIBUTING.md
@@ -0,0 +1,71 @@
+# Instructions for setting up a development environment
+
+## For Coding
+
+For `Linux` (Ubuntu 20 recommended) and `macOS`. Anyway, `CONDA` is strongly recommended.
+Also recommended is GPG key, so do accordingly in [GitHub](https://docs.github.com/articles/generating-a-gpg-key/).
+
+```bash
+curl -sSL https://install.python-poetry.org | python3 -
+
+conda create -n acpype python=3.9 ambertools openbabel ocl-icd-system ipython gromacs=2019.1 -y
+# ocl-icd-system: case you have GPU
+
+conda activate acpype
+
+git clone https://github.com/alanwilter/acpype.git
+
+cd acpype
+
+poetry install
+
+pre-commit install
+
+pre-commit run -a
+
+sys=$(perl -e '`uname` eq "Darwin\n" ? print "os" : print "linux"')
+
+cp ./acpype/amber21-11_${sys}/bin/charmmgen $(dirname $(which antechamber))
+
+git config user.email _email_ # as seen in 'gpg --list-secret-keys --keyid-format=long'
+
+git config user.signingkey _singing_key_ # as seen in 'gpg --list-secret-keys --keyid-format=long'
+
+git config commit.gpgsign true
+
+pytest --cov=tests --cov=acpype --cov-report=term-missing:skip-covered --cov-report=xml
+```
+
+If using `VSCode`:
+
+- Enable `enableCommitSigning` in `settings.json` (***Workspace*** recommended):
+
+    ```yml
+    "git.enableCommitSigning": true,
+    ```
+
+- Another `VSCode` nuisance, if using its graphic buttons for commit etc.: its environment won't necessarily recognise the dependencies installed via `poetry` under `conda` environment named `acpype` (unless you have started `VSCode` from folder repository with command `code .`). To avoid troubles do:
+
+    ```bash
+    conda deactivate
+    poetry install # it will create its own virtualenv
+    ```
+
+    You could use this `poetry virtualenv` as the `Python Interpreter` for `VSCode`, however `ambertools`, `gromacs` and `openbabel` won't be available (unless you've had installed them system wide by other means rather than `conda`).
+    To avoid further troubles, go back to `conda activate acpype` and remember to do the instructions above if you add new dependencies to the project via `poetry`.
+
+## For Documenting
+
+Using [Sphinx](https://www.sphinx-doc.org) with theme from `pip install sphinx-rtd-theme`.
+
+Online documentation provided by [Read the Docs](http://acpype.readthedocs.io).
+
+To test it locally:
+
+```bash
+cd docs/
+make clean
+make html
+```
+
+Then open `_build/html/index.html` in a browser.
diff --git a/FUNDING.yml b/FUNDING.yml
index a7904ca3..c2d27bf7 100644
--- a/FUNDING.yml
+++ b/FUNDING.yml
@@ -1,2 +1,2 @@
 github: [alanwilter]
-custom: ["https://www.paypal.me/alanwilter"]
\ No newline at end of file
+custom: ["https://www.paypal.me/alanwilter"]
diff --git a/README.md b/README.md
index 683250ca..f450986d 100644
--- a/README.md
+++ b/README.md
@@ -15,7 +15,10 @@
 [![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white&style=plastic)](https://github.com/pre-commit/pre-commit)
 [![Commits since release](https://img.shields.io/github/commits-since/alanwilter/acpype/2021.12.24/master?style=plastic)](https://github.com/alanwilter/acpype/commits/master)
 [![Codecov](https://img.shields.io/codecov/c/github/alanwilter/acpype?style=plastic)](https://app.codecov.io/gh/alanwilter/acpype)
-
+[![Documentation Status](https://readthedocs.org/projects/acpype/badge/?version=latest&style=plastic)](https://acpype.readthedocs.io/en/latest/?badge=latest)
+[![Citations](https://img.shields.io/static/v1?label=Citations&message=1040&color=orange&style=plastic)](https://scholar.google.com/scholar?hl=en&as_sdt=2005&sciodt=0%2C5&cites=15065215520855508960&scipsc=&q=ACPYPE-Antechamber+python+parser+interface&btnG=)
+<!-- [![DOI:doi.org/10.1186/1756-0500-5-367](https://img.shields.io/badge/DOI-10.1186%2F1756--0500--5--367-blue?style=plastic)](https://doi.org/10.1186/1756-0500-5-367) -->
+<!-- [![Google Scholar Citations](https://openbabel.org/citations.svg?maxAge=86400)](https://scholar.google.com/scholar?cites=15065215520855508960&as_sdt=2005&sciodt=0,5&hl=en) -->
 <!-- [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5601736.svg)](https://doi.org/10.1186/1756-0500-5-367)
 ![DOI](https://doi.org/10.1186/1756-0500-5-367) -->
 <!-- ![Scrutinizer code quality (GitHub/Bitbucket)](https://img.shields.io/scrutinizer/quality/g/alanwilter/acpype) -->
@@ -38,6 +41,8 @@ Several flavours of AMBER FF are ported already for GROMACS (see [ffamber](http:
 
 This code is released under **[GNU General Public License V3](https://www.gnu.org/licenses/gpl-3.0.en.html)**.
 
+See online [documentation](https://acpype.readthedocs.io/) for more.
+
 ### **NO WARRANTY AT ALL**
 
 It was inspired by:
diff --git a/_config.yml b/_config.yml
index ddeb671b..f93e2583 100644
--- a/_config.yml
+++ b/_config.yml
@@ -1 +1 @@
-theme: jekyll-theme-time-machine
\ No newline at end of file
+theme: jekyll-theme-time-machine
diff --git a/acpype/__init__.py b/acpype/__init__.py
index 8aac1a7f..7ec0a758 100644
--- a/acpype/__init__.py
+++ b/acpype/__init__.py
@@ -1,4 +1,58 @@
+"""
+    The Package
+
+    Requirements:
+        - ``Python 3.6`` or higher
+        - ``Antechamber`` (from ``AmberTools`` preferably)
+        - ``OpenBabel`` (optional, but strongly recommended)
+
+    This code is released under **GNU General Public License V3**.
+
+        **<<<  NO WARRANTY AT ALL!!!  >>>**
+
+    It was inspired by:
+
+        - ``amb2gmx.pl`` (Eric Sorin, David Mobley and John Chodera) and depends on Antechamber and Openbabel
+        - `YASARA Autosmiles <http://www.yasara.org/autosmiles.htm>`_ (Elmar Krieger)
+        - ``topolbuild`` (Bruce Ray)
+        - ``xplo2d`` (G.J. Kleywegt)
+
+    For Non-uniform 1-4 scale factor conversion (e.g. if using ``GLYCAM06``), please cite:
+
+        BERNARDI, A., FALLER, R., REITH, D., and KIRSCHNER, K. N. ACPYPE update for
+        nonuniform 1-4 scale factors: Conversion of the GLYCAM06 force field from AMBER
+        to GROMACS. SoftwareX 10 (2019), 100241.
+        doi: `10.1016/j.softx.2019.100241 <https://doi.org/10.1016/j.softx.2019.100241>`_
+
+    For Antechamber, please cite:
+
+        1.  WANG, J., WANG, W., KOLLMAN, P. A., and CASE, D. A. Automatic atom type and
+            bond type perception in molecular mechanical calculations. Journal of Molecular
+            Graphics and Modelling 25, 2 (2006), 247-260.
+            doi: `10.1016/j.jmgm.2005.12.005 <https://doi.org/10.1016/j.jmgm.2005.12.005>`_
+        2.  WANG, J., WOLF, R. M., CALDWELL, J. W., KOLLMAN, P. A., and CASE, D. A.
+            Development and testing of a General Amber Force Field. Journal of Computational
+            Chemistry 25, 9 (2004), 1157-1174.
+            doi: `10.1002/jcc.20035 <https://doi.org/10.1002/jcc.20035>`_
+
+    If you use this code, I am glad if you cite:
+
+        SOUSA DA SILVA, A. W. & VRANKEN, W. F.
+        ACPYPE - AnteChamber PYthon Parser interfacE.
+        BMC Research Notes 5 (2012), 367
+        doi: `10.1186/1756-0500-5-367 <http://www.biomedcentral.com/1756-0500/5/367>`_
+
+    and (optionally)
+
+        BATISTA, P. R.; WILTER, A.; DURHAM, E. H. A. B. & PASCUTTI, P. G. Molecular
+        Dynamics Simulations Applied to the Study of Subtypes of HIV-1 Protease.
+        Cell Biochemistry and Biophysics 44 (2006), 395-404.
+        doi: `10.1385/CBB:44:3:395 <https://doi.org/10.1385/CBB:44:3:395>`_
+
+    Alan Silva, D.Sc. <alanwilter _at_ gmail _dot_ com>
+"""
+
 # from https://packaging.python.org/guides/single-sourcing-package-version/
 # using option 2
 # updated automatically via pre-commit git-hook
-__version__ = "2021.12.25"
+__version__ = "2022.1.3"
diff --git a/acpype/acs_api.py b/acpype/acs_api.py
index 35d0a9c8..cd3d82dd 100644
--- a/acpype/acs_api.py
+++ b/acpype/acs_api.py
@@ -67,7 +67,7 @@ def readFiles(basename, chargeType, atomType):
             filename = basename + "_" + chargeType + "_" + atomType + files[1]
         else:
             filename = basename + files[1]
-        readfile = tuple(open(filename, "r"))
+        readfile = tuple(open(filename))
         for line in readfile:
             files[0].write(line)
 
@@ -171,5 +171,5 @@ def acpype_api(
     try:
         shutil.rmtree(molecule.absHomeDir)
     except Exception:
-        pass
+        print("DEBUG: No folder left to be removed")
     return json.dumps(output)
diff --git a/acpype/amber21-11_linux/bin/am1bcc b/acpype/amber21-11_linux/bin/am1bcc
index 7aff7250..6ec88848 100755
--- a/acpype/amber21-11_linux/bin/am1bcc
+++ b/acpype/amber21-11_linux/bin/am1bcc
@@ -6,4 +6,4 @@
 this_script_dir="$(cd "$(dirname "$0")" && pwd)"
 source $this_script_dir/../amber.sh
 
-$AMBERHOME/bin/wrapped_progs/am1bcc "$@"
\ No newline at end of file
+$AMBERHOME/bin/wrapped_progs/am1bcc "$@"
diff --git a/acpype/amber21-11_linux/bin/antechamber b/acpype/amber21-11_linux/bin/antechamber
index 89285850..e14a11b7 100755
--- a/acpype/amber21-11_linux/bin/antechamber
+++ b/acpype/amber21-11_linux/bin/antechamber
@@ -6,4 +6,4 @@
 this_script_dir="$(cd "$(dirname "$0")" && pwd)"
 source $this_script_dir/../amber.sh
 
-$AMBERHOME/bin/wrapped_progs/antechamber "$@"
\ No newline at end of file
+$AMBERHOME/bin/wrapped_progs/antechamber "$@"
diff --git a/acpype/amber21-11_linux/bin/atomtype b/acpype/amber21-11_linux/bin/atomtype
index b3e17770..abe002e8 100755
--- a/acpype/amber21-11_linux/bin/atomtype
+++ b/acpype/amber21-11_linux/bin/atomtype
@@ -6,4 +6,4 @@
 this_script_dir="$(cd "$(dirname "$0")" && pwd)"
 source $this_script_dir/../amber.sh
 
-$AMBERHOME/bin/wrapped_progs/atomtype "$@"
\ No newline at end of file
+$AMBERHOME/bin/wrapped_progs/atomtype "$@"
diff --git a/acpype/amber21-11_linux/bin/bondtype b/acpype/amber21-11_linux/bin/bondtype
index 0efcaba2..41bfdaa2 100755
--- a/acpype/amber21-11_linux/bin/bondtype
+++ b/acpype/amber21-11_linux/bin/bondtype
@@ -6,4 +6,4 @@
 this_script_dir="$(cd "$(dirname "$0")" && pwd)"
 source $this_script_dir/../amber.sh
 
-$AMBERHOME/bin/wrapped_progs/bondtype "$@"
\ No newline at end of file
+$AMBERHOME/bin/wrapped_progs/bondtype "$@"
diff --git a/acpype/amber21-11_linux/bin/parmchk2 b/acpype/amber21-11_linux/bin/parmchk2
index 1d1a9ddb..aea6c466 100755
--- a/acpype/amber21-11_linux/bin/parmchk2
+++ b/acpype/amber21-11_linux/bin/parmchk2
@@ -6,4 +6,4 @@
 this_script_dir="$(cd "$(dirname "$0")" && pwd)"
 source $this_script_dir/../amber.sh
 
-$AMBERHOME/bin/wrapped_progs/parmchk2 "$@"
\ No newline at end of file
+$AMBERHOME/bin/wrapped_progs/parmchk2 "$@"
diff --git a/acpype/amber21-11_linux/dat/chamber/par_all36_carb.prm b/acpype/amber21-11_linux/dat/chamber/par_all36_carb.prm
index 275a5613..83ea2f00 100644
--- a/acpype/amber21-11_linux/dat/chamber/par_all36_carb.prm
+++ b/acpype/amber21-11_linux/dat/chamber/par_all36_carb.prm
@@ -2494,4 +2494,3 @@ OC303     0.0  -0.1000   1.6500              ! OC301
 !                   ! S. Marchand and B. Roux, dA = -384.8 kcal/mol
 
 END
-
diff --git a/acpype/amber21-11_linux/dat/chamber/top_all22_prot.inp b/acpype/amber21-11_linux/dat/chamber/top_all22_prot.inp
index 31e07a62..ec4a0aab 100644
--- a/acpype/amber21-11_linux/dat/chamber/top_all22_prot.inp
+++ b/acpype/amber21-11_linux/dat/chamber/top_all22_prot.inp
@@ -1798,4 +1798,3 @@ IC 1C   2N   2CA  2C    0.0000  0.0000 180.0000  0.0000  0.0000
 IC 1C   2CA  *2N  2HN   0.0000  0.0000 180.0000  0.0000  0.0000
 
 END
-
diff --git a/acpype/amber21-11_linux/dat/chamber/top_all27_prot_na.rtf b/acpype/amber21-11_linux/dat/chamber/top_all27_prot_na.rtf
index fa069cda..5f362fdb 100644
--- a/acpype/amber21-11_linux/dat/chamber/top_all27_prot_na.rtf
+++ b/acpype/amber21-11_linux/dat/chamber/top_all27_prot_na.rtf
@@ -2572,4 +2572,3 @@ IC  1C4'  1C3'  1O3' 2P     1.5284  111.92  159.13  119.05   1.6001
 IC  1C3'  1O3'  2P   2O5'   1.4212  119.05  -98.86  101.45   1.5996
 
 END
-
diff --git a/acpype/amber21-11_linux/dat/chamber/top_all36_carb.rtf b/acpype/amber21-11_linux/dat/chamber/top_all36_carb.rtf
index 69bac408..39539151 100644
--- a/acpype/amber21-11_linux/dat/chamber/top_all36_carb.rtf
+++ b/acpype/amber21-11_linux/dat/chamber/top_all36_carb.rtf
@@ -5602,4 +5602,3 @@ IC  O5   OP52 *P5  OP53       1.5968  102.94  113.03  118.81   1.5471
 IC  O5   OP52 *P5  OP54       1.5968  102.94 -113.60  109.37   1.4811
 
 END
-
diff --git a/acpype/amber21-11_linux/dat/chamber/top_all36_prot.rtf b/acpype/amber21-11_linux/dat/chamber/top_all36_prot.rtf
index ab8ec747..e4a9ce58 100644
--- a/acpype/amber21-11_linux/dat/chamber/top_all36_prot.rtf
+++ b/acpype/amber21-11_linux/dat/chamber/top_all36_prot.rtf
@@ -1704,4 +1704,3 @@ IC 1C   2N   2CA  2C    0.0000  0.0000 180.0000  0.0000  0.0000
 IC 1C   2CA  *2N  2HN   0.0000  0.0000 180.0000  0.0000  0.0000
 
 END
-
diff --git a/acpype/amber21-11_linux/dat/chamber/toppar_water_ions.str b/acpype/amber21-11_linux/dat/chamber/toppar_water_ions.str
index d0ab01f8..9096dd0b 100644
--- a/acpype/amber21-11_linux/dat/chamber/toppar_water_ions.str
+++ b/acpype/amber21-11_linux/dat/chamber/toppar_water_ions.str
@@ -306,4 +306,3 @@ BOMLEV @bom @PARA
 WRNLEV @wrn @PARA
 
 return
-
diff --git a/acpype/amber21-11_linux/dat/leap/cmd/leaprc.RNA.OL3 b/acpype/amber21-11_linux/dat/leap/cmd/leaprc.RNA.OL3
index af6ab238..de49b9ea 100644
--- a/acpype/amber21-11_linux/dat/leap/cmd/leaprc.RNA.OL3
+++ b/acpype/amber21-11_linux/dat/leap/cmd/leaprc.RNA.OL3
@@ -134,4 +134,3 @@ addPdbAtomMap {
   { "O2P" "OP2" }
   { "O3P" "OP3" }
 }
-
diff --git a/acpype/amber21-11_linux/dat/leap/cmd/leaprc.RNA.ROC b/acpype/amber21-11_linux/dat/leap/cmd/leaprc.RNA.ROC
index 83478d8c..ea4c4243 100644
--- a/acpype/amber21-11_linux/dat/leap/cmd/leaprc.RNA.ROC
+++ b/acpype/amber21-11_linux/dat/leap/cmd/leaprc.RNA.ROC
@@ -134,4 +134,3 @@ addPdbAtomMap {
   { "O1P" "OP1" }
   { "O2P" "OP2" }
 }
-
diff --git a/acpype/amber21-11_linux/dat/leap/cmd/leaprc.RNA.Shaw b/acpype/amber21-11_linux/dat/leap/cmd/leaprc.RNA.Shaw
index 29e229d1..d95015b6 100644
--- a/acpype/amber21-11_linux/dat/leap/cmd/leaprc.RNA.Shaw
+++ b/acpype/amber21-11_linux/dat/leap/cmd/leaprc.RNA.Shaw
@@ -142,4 +142,3 @@ addPdbAtomMap {
   { "O1P" "OP1" }
   { "O2P" "OP2" }
 }
-
diff --git a/acpype/amber21-11_linux/dat/leap/cmd/leaprc.amberdyes b/acpype/amber21-11_linux/dat/leap/cmd/leaprc.amberdyes
index 088d852c..9aeb7524 100644
--- a/acpype/amber21-11_linux/dat/leap/cmd/leaprc.amberdyes
+++ b/acpype/amber21-11_linux/dat/leap/cmd/leaprc.amberdyes
@@ -45,5 +45,3 @@ dyeparams = loadamberparams amberdyes.dat
 # Load the AmberDyes lib files
 #
 loadoff amberdyes.lib
-
-
diff --git a/acpype/amber21-11_linux/dat/leap/cmd/leaprc.lipid14 b/acpype/amber21-11_linux/dat/leap/cmd/leaprc.lipid14
index 3052988a..03b05f83 100644
--- a/acpype/amber21-11_linux/dat/leap/cmd/leaprc.lipid14
+++ b/acpype/amber21-11_linux/dat/leap/cmd/leaprc.lipid14
@@ -47,4 +47,3 @@ lipid14 = loadamberparams lipid14.dat
 #       Load the Lipid14 master lib file.
 #       Note that other residues are stored in the lipid14_supp.lib file and will be released at a later date.
 loadoff lipid14.lib
-
diff --git a/acpype/amber21-11_linux/dat/leap/cmd/leaprc.lipid17 b/acpype/amber21-11_linux/dat/leap/cmd/leaprc.lipid17
index cdb75a74..6c0821fd 100644
--- a/acpype/amber21-11_linux/dat/leap/cmd/leaprc.lipid17
+++ b/acpype/amber21-11_linux/dat/leap/cmd/leaprc.lipid17
@@ -42,4 +42,3 @@ lipid17 = loadamberparams lipid17.dat
 # Load the Lipid17 master lib file.
 #
 loadoff lipid17.lib
-
diff --git a/acpype/amber21-11_linux/dat/leap/cmd/leaprc.music b/acpype/amber21-11_linux/dat/leap/cmd/leaprc.music
index 9b3e17d4..bce07722 100644
--- a/acpype/amber21-11_linux/dat/leap/cmd/leaprc.music
+++ b/acpype/amber21-11_linux/dat/leap/cmd/leaprc.music
@@ -17,4 +17,3 @@ addAtomTypes {
 #
 loadOff music.lib
 music = loadamberparams music.dat
-
diff --git a/acpype/amber21-11_linux/dat/leap/cmd/leaprc.protein.fb15 b/acpype/amber21-11_linux/dat/leap/cmd/leaprc.protein.fb15
index a2d52f0d..fcb6ed5f 100644
--- a/acpype/amber21-11_linux/dat/leap/cmd/leaprc.protein.fb15
+++ b/acpype/amber21-11_linux/dat/leap/cmd/leaprc.protein.fb15
@@ -159,4 +159,3 @@ addPdbResMap {
 NHIS = NHIE
 HIS = HIE
 CHIS = CHIE
-
diff --git a/acpype/amber21-11_linux/dat/leap/cmd/leaprc.water.fb3 b/acpype/amber21-11_linux/dat/leap/cmd/leaprc.water.fb3
index 8850b444..eb324fac 100644
--- a/acpype/amber21-11_linux/dat/leap/cmd/leaprc.water.fb3
+++ b/acpype/amber21-11_linux/dat/leap/cmd/leaprc.water.fb3
@@ -73,4 +73,3 @@ HOH = FB3
 WAT = FB3
 mods2 = loadamberparams frcmod.tip3pfb
 loadAmberParams frcmod.ionslm_126_fb3
-
diff --git a/acpype/amber21-11_linux/dat/leap/cmd/leaprc.water.fb4 b/acpype/amber21-11_linux/dat/leap/cmd/leaprc.water.fb4
index a81a0e01..d7d66f0d 100644
--- a/acpype/amber21-11_linux/dat/leap/cmd/leaprc.water.fb4
+++ b/acpype/amber21-11_linux/dat/leap/cmd/leaprc.water.fb4
@@ -74,4 +74,3 @@ HOH = FB4
 WAT = FB4
 mods2 = loadamberparams frcmod.tip4pfb
 loadAmberParams frcmod.ionslm_126_fb4
-
diff --git a/acpype/amber21-11_linux/dat/leap/cmd/leaprc.water.opc b/acpype/amber21-11_linux/dat/leap/cmd/leaprc.water.opc
index d8ce23bd..b4937f12 100644
--- a/acpype/amber21-11_linux/dat/leap/cmd/leaprc.water.opc
+++ b/acpype/amber21-11_linux/dat/leap/cmd/leaprc.water.opc
@@ -74,4 +74,3 @@ HOH = OPC
 WAT = OPC
 loadAmberParams frcmod.opc
 loadAmberParams frcmod.ionslm_126_opc
-
diff --git a/acpype/amber21-11_linux/dat/leap/cmd/leaprc.water.opc3 b/acpype/amber21-11_linux/dat/leap/cmd/leaprc.water.opc3
index ef16ab99..162dee53 100644
--- a/acpype/amber21-11_linux/dat/leap/cmd/leaprc.water.opc3
+++ b/acpype/amber21-11_linux/dat/leap/cmd/leaprc.water.opc3
@@ -73,4 +73,3 @@ HOH = OP3
 WAT = OP3
 loadAmberParams frcmod.opc3
 loadAmberParams frcmod.ionslm_126_opc3
-
diff --git a/acpype/amber21-11_linux/dat/leap/cmd/leaprc.water.spce b/acpype/amber21-11_linux/dat/leap/cmd/leaprc.water.spce
index 1925eeae..4cda39aa 100644
--- a/acpype/amber21-11_linux/dat/leap/cmd/leaprc.water.spce
+++ b/acpype/amber21-11_linux/dat/leap/cmd/leaprc.water.spce
@@ -74,4 +74,3 @@ WAT = SPC
 loadAmberParams frcmod.spce
 loadAmberParams frcmod.ionsjc_spce
 loadAmberParams frcmod.ions234lm_126_spce
-
diff --git a/acpype/amber21-11_linux/dat/leap/cmd/leaprc.water.spceb b/acpype/amber21-11_linux/dat/leap/cmd/leaprc.water.spceb
index 33d58d6d..3b694441 100644
--- a/acpype/amber21-11_linux/dat/leap/cmd/leaprc.water.spceb
+++ b/acpype/amber21-11_linux/dat/leap/cmd/leaprc.water.spceb
@@ -21,4 +21,3 @@ WAT = SPC
 loadAmberParams frcmod.spceb
 loadAmberParams frcmod.ionsjc_spce
 loadAmberParams frcmod.ions234lm_126_spce
-
diff --git a/acpype/amber21-11_linux/dat/leap/cmd/leaprc.water.tip3p b/acpype/amber21-11_linux/dat/leap/cmd/leaprc.water.tip3p
index 19cf3d48..cf1ead74 100644
--- a/acpype/amber21-11_linux/dat/leap/cmd/leaprc.water.tip3p
+++ b/acpype/amber21-11_linux/dat/leap/cmd/leaprc.water.tip3p
@@ -82,4 +82,3 @@ loadAmberParams frcmod.tip3p
 loadAmberParams frcmod.ions1lm_126_tip3p
 loadAmberParams frcmod.ionsjc_tip3p
 loadAmberParams frcmod.ions234lm_126_tip3p
-
diff --git a/acpype/amber21-11_linux/dat/leap/cmd/leaprc.water.tip4pd b/acpype/amber21-11_linux/dat/leap/cmd/leaprc.water.tip4pd
index d09dc07f..2431c67b 100644
--- a/acpype/amber21-11_linux/dat/leap/cmd/leaprc.water.tip4pd
+++ b/acpype/amber21-11_linux/dat/leap/cmd/leaprc.water.tip4pd
@@ -72,4 +72,3 @@ HOH = T4D
 WAT = T4D
 loadAmberParams frcmod.tip4pd
 loadAmberParams frcmod.ions_charmm22
-
diff --git a/acpype/amber21-11_linux/dat/leap/cmd/leaprc.water.tip4pew b/acpype/amber21-11_linux/dat/leap/cmd/leaprc.water.tip4pew
index a6fcfc25..db5ffea9 100644
--- a/acpype/amber21-11_linux/dat/leap/cmd/leaprc.water.tip4pew
+++ b/acpype/amber21-11_linux/dat/leap/cmd/leaprc.water.tip4pew
@@ -75,4 +75,3 @@ WAT = T4E
 loadAmberParams frcmod.tip4pew
 loadAmberParams frcmod.ionsjc_tip4pew
 loadAmberParams frcmod.ions234lm_126_tip4pew
-
diff --git a/acpype/amber21-11_linux/dat/leap/cmd/leaprc.xFPchromophores b/acpype/amber21-11_linux/dat/leap/cmd/leaprc.xFPchromophores
index 82fce3a0..fb1a9af2 100644
--- a/acpype/amber21-11_linux/dat/leap/cmd/leaprc.xFPchromophores
+++ b/acpype/amber21-11_linux/dat/leap/cmd/leaprc.xFPchromophores
@@ -17,4 +17,3 @@ xFPparams = loadamberparams frcmod.xFPchromophores
 #
 
 loadOff xFPchromophores.lib
-
diff --git a/acpype/amber21-11_linux/dat/leap/cmd/oldff/leaprc.ff02 b/acpype/amber21-11_linux/dat/leap/cmd/oldff/leaprc.ff02
index 47fd1641..9a06ac0b 100644
--- a/acpype/amber21-11_linux/dat/leap/cmd/oldff/leaprc.ff02
+++ b/acpype/amber21-11_linux/dat/leap/cmd/oldff/leaprc.ff02
@@ -167,4 +167,3 @@ addPdbAtomMap {
 NHIS = NHIE
 HIS = HIE
 CHIS = CHIE
-
diff --git a/acpype/amber21-11_linux/dat/leap/cmd/oldff/leaprc.ff02pol.r0 b/acpype/amber21-11_linux/dat/leap/cmd/oldff/leaprc.ff02pol.r0
index 732b376c..32441dc2 100644
--- a/acpype/amber21-11_linux/dat/leap/cmd/oldff/leaprc.ff02pol.r0
+++ b/acpype/amber21-11_linux/dat/leap/cmd/oldff/leaprc.ff02pol.r0
@@ -169,4 +169,3 @@ addPdbAtomMap {
 NHIS = NHIE
 HIS = HIE
 CHIS = CHIE
-
diff --git a/acpype/amber21-11_linux/dat/leap/cmd/oldff/leaprc.ff02pol.r1 b/acpype/amber21-11_linux/dat/leap/cmd/oldff/leaprc.ff02pol.r1
index c6d9f3d1..c88a40a1 100644
--- a/acpype/amber21-11_linux/dat/leap/cmd/oldff/leaprc.ff02pol.r1
+++ b/acpype/amber21-11_linux/dat/leap/cmd/oldff/leaprc.ff02pol.r1
@@ -183,4 +183,3 @@ addPdbAtomMap {
 NHIS = NHIE
 HIS = HIE
 CHIS = CHIE
-
diff --git a/acpype/amber21-11_linux/dat/leap/cmd/oldff/leaprc.ff14SB b/acpype/amber21-11_linux/dat/leap/cmd/oldff/leaprc.ff14SB
index 38c3ee16..48a06105 100644
--- a/acpype/amber21-11_linux/dat/leap/cmd/oldff/leaprc.ff14SB
+++ b/acpype/amber21-11_linux/dat/leap/cmd/oldff/leaprc.ff14SB
@@ -206,4 +206,3 @@ addPdbAtomMap {
 NHIS = NHIE
 HIS = HIE
 CHIS = CHIE
-
diff --git a/acpype/amber21-11_linux/dat/leap/cmd/oldff/leaprc.ff86 b/acpype/amber21-11_linux/dat/leap/cmd/oldff/leaprc.ff86
index 0204b6fa..bf6d8e6a 100644
--- a/acpype/amber21-11_linux/dat/leap/cmd/oldff/leaprc.ff86
+++ b/acpype/amber21-11_linux/dat/leap/cmd/oldff/leaprc.ff86
@@ -218,4 +218,3 @@ CM = CMET
 CS = CSER
 CT = CTHR
 CP = CPRO
-
diff --git a/acpype/amber21-11_linux/dat/leap/cmd/oldff/leaprc.lipid11 b/acpype/amber21-11_linux/dat/leap/cmd/oldff/leaprc.lipid11
index 521b5e03..e30b9b49 100644
--- a/acpype/amber21-11_linux/dat/leap/cmd/oldff/leaprc.lipid11
+++ b/acpype/amber21-11_linux/dat/leap/cmd/oldff/leaprc.lipid11
@@ -44,4 +44,3 @@ lipid11 = loadamberparams lipid11.dat
 
 #       Load the Lipid 11 master lib file.
 loadoff lipid11.lib
-
diff --git a/acpype/amber21-11_linux/dat/leap/cmd/oldff/leaprc.parmbsc0_chiOL4_ezOL1 b/acpype/amber21-11_linux/dat/leap/cmd/oldff/leaprc.parmbsc0_chiOL4_ezOL1
index 5b6608fd..3f88d02a 100644
--- a/acpype/amber21-11_linux/dat/leap/cmd/oldff/leaprc.parmbsc0_chiOL4_ezOL1
+++ b/acpype/amber21-11_linux/dat/leap/cmd/oldff/leaprc.parmbsc0_chiOL4_ezOL1
@@ -23,4 +23,3 @@ addPdbAtomMap {
 loadamberprep dna_nuc94-bsc0_chiOl4-ezOL1.in
 ez = loadamberparams frcmod.parmbsc0_ezOL1
 chi = loadamberparams frcmod.chiOL4
-
diff --git a/acpype/amber21-11_linux/dat/leap/lib/Makefile b/acpype/amber21-11_linux/dat/leap/lib/Makefile
index 4191e69f..973b69c9 100644
--- a/acpype/amber21-11_linux/dat/leap/lib/Makefile
+++ b/acpype/amber21-11_linux/dat/leap/lib/Makefile
@@ -51,4 +51,3 @@ ff12polL:
 ff12polA:
 	/bin/rm -f ff12polA.log
 	../../../bin/teLeap -s -f ff12polA.cmd
-
diff --git a/acpype/amber21-11_linux/dat/leap/lib/oldff/phosphoaa10.lib b/acpype/amber21-11_linux/dat/leap/lib/oldff/phosphoaa10.lib
index b461fd86..e64d8d03 100644
--- a/acpype/amber21-11_linux/dat/leap/lib/oldff/phosphoaa10.lib
+++ b/acpype/amber21-11_linux/dat/leap/lib/oldff/phosphoaa10.lib
@@ -1030,4 +1030,3 @@
  0.0 0.0 0.0
  0.0 0.0 0.0
  0.0 0.0 0.0
-
diff --git a/acpype/amber21-11_linux/dat/leap/lib/oldff/phosphoaa10.readme b/acpype/amber21-11_linux/dat/leap/lib/oldff/phosphoaa10.readme
index f0cac2c8..70409c86 100644
--- a/acpype/amber21-11_linux/dat/leap/lib/oldff/phosphoaa10.readme
+++ b/acpype/amber21-11_linux/dat/leap/lib/oldff/phosphoaa10.readme
@@ -23,5 +23,3 @@ phosphohistidine
 %V 12
 %P 281-289
 %D 2006
-
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/GLYCAM_06EPb.dat b/acpype/amber21-11_linux/dat/leap/parm/GLYCAM_06EPb.dat
index a376165d..6d2c7872 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/GLYCAM_06EPb.dat
+++ b/acpype/amber21-11_linux/dat/leap/parm/GLYCAM_06EPb.dat
@@ -186,4 +186,3 @@ MOD4      RE
 
 END
 END
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ROC-RNA b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ROC-RNA
index 59e64b69..580b5231 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ROC-RNA
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ROC-RNA
@@ -45,4 +45,3 @@ OS-CT-N*-CS   1           0.315000     186.8           -4.0     CHI_URACIL
 OS-CT-N*-CS   1           0.950000     189.5           -3.0     CHI_URACIL
 OS-CT-N*-CS   1           1.165000      33.9           -2.0     CHI_URACIL
 OS-CT-N*-CS   1           0.329000     132.7            1.0     CHI_URACIL
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ROC-RNA_const b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ROC-RNA_const
index 8fbbb32d..e9a3cb0e 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ROC-RNA_const
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ROC-RNA_const
@@ -84,5 +84,3 @@ P -OS-CI-CF   1           0.383000       0.0            3.0
 
 NONB
 CF          1.9080  0.1094
-
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.chcl3 b/acpype/amber21-11_linux/dat/leap/parm/frcmod.chcl3
index 2f1c0819..a7367733 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.chcl3
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.chcl3
@@ -16,4 +16,3 @@ NONB
   CZ       1.9080     0.1094
   CL       2.0000     0.3250
   HZ       1.1870     0.0157
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.conste b/acpype/amber21-11_linux/dat/leap/parm/frcmod.conste
index cd115f95..47b483e0 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.conste
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.conste
@@ -109,4 +109,3 @@ NONBON
   LC         1.85      0.12      0.0
   NP         1.8240    0.1700    0.0
   NO         1.8240    0.1700    0.0
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.dc4 b/acpype/amber21-11_linux/dat/leap/parm/frcmod.dc4
index afa13492..466dfc6e 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.dc4
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.dc4
@@ -17,4 +17,3 @@ NONBON
   OW       1.8150    0.1825
   HW       0.0000    0.0000
   EP       0.0       0.0
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.fb15 b/acpype/amber21-11_linux/dat/leap/parm/frcmod.fb15
index a294dc5e..406133b4 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.fb15
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.fb15
@@ -2011,4 +2011,3 @@ NONB
 6V    1.9080   0.1094
 6W    1.9080   0.1094
 6Y    1.9080   0.1094
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ff02pol.r1 b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ff02pol.r1
index 0bbed679..9fba84a4 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ff02pol.r1
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ff02pol.r1
@@ -32,7 +32,3 @@ H0-CT-C -N    1    1.0607        180.00        1.           Wang 2006
 
 NONBON
   H0       1.3870   0.0157             Veenstra et al JCC,8,(1992),963
-
-
-
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ff03 b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ff03
index 0525cad0..7af9025a 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ff03
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ff03
@@ -32,4 +32,3 @@ H0-CT-C -N    1    1.0607      180.00            1.
 
 NONBON
   H0       1.3870   0.0157             Veenstra et al JCC,8,(1992),963 
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ff03ua b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ff03ua
index 7ceda199..bed41e3f 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ff03ua
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ff03ua
@@ -149,4 +149,3 @@ NONBON
   C1          1.9580  0.0994             sp3 aliphetic carbon (UA model CH )
   C2          2.0580  0.1094             sp3 aliphetic carbon (UA model CH2)
   C3          2.0580  0.1494             sp3 aliphetic carbon (UA model CH3)
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ff12SB b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ff12SB
index 21560bbc..29efa587 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ff12SB
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ff12SB
@@ -529,4 +529,3 @@ NONB
   3C          1.9080  0.1094             Spellmeyer
   C8          1.9080  0.1094             Spellmeyer
   CO          1.9080  0.0860             OPLS
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ff14SB b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ff14SB
index 5fee412e..895e9d46 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ff14SB
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ff14SB
@@ -510,5 +510,3 @@ NONB
   3C          1.9080  0.1094             Spellmeyer
   C8          1.9080  0.1094             Spellmeyer
   CO          1.9080  0.0860             OPLS
-
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ff14SBmodAA b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ff14SBmodAA
index 554e7294..eec2a29d 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ff14SBmodAA
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ff14SBmodAA
@@ -292,4 +292,3 @@ NF    1.83720000   0.10980000
 8C    1.90800000   0.10940000
 SC    1.90800000   0.10940000
 SE    2.18000000   0.22000000
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ff99SB b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ff99SB
index 33921d76..d5de3be1 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ff99SB
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ff99SB
@@ -24,4 +24,3 @@ CT-CT-C -N    1    0.20          0.0            -2.
 CT-CT-C -N    1    0.20          0.0             1.
 
 NONB
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ff99SB14 b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ff99SB14
index 2ef22ff2..c064b309 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ff99SB14
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ff99SB14
@@ -48,4 +48,3 @@ C8-CX-C -N    1    0.20          0.0            -2.
 C8-CX-C -N    1    0.20          0.0             1.
 
 NONB
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ff99SBildn b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ff99SBildn
index 8a67c25a..9e87e2e3 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ff99SBildn
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ff99SBildn
@@ -115,4 +115,3 @@ NONB
   C4          1.9080  0.1094             Spellmeyer
   C5          1.9080  0.0860             OPLS
   C6          1.9080  0.0860             OPLS
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ff99SBnmr b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ff99SBnmr
index 48975d59..831ac1f9 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ff99SBnmr
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ff99SBnmr
@@ -24,4 +24,3 @@ CT-CT-C -N    1    0.31          0.0            -2.
 CT-CT-C -N    1    0.41        180.0             1.
 
 NONB
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ff99SP b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ff99SP
index 42c333db..bd7face1 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ff99SP
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ff99SP
@@ -10,4 +10,3 @@ C -N -CT-C    1    0.200       180.000          -2.
 C -N -CT-C    1    0.000         0.000           1.
 
 NONB
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ff99bsc0CG b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ff99bsc0CG
index c0f64ee8..6bd9fc3b 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ff99bsc0CG
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ff99bsc0CG
@@ -4,4 +4,3 @@ DIHE
 OS-CT-N*-CK    1       0.760994   50.0         1.0
 OS-CT-N*-CM    1       0.760994   50.0        -1.0
 OS-CT-N*-CM    1       0.505314   74.0         2.0
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions1lm_1264_spce b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions1lm_1264_spce
index e959479b..e166e835 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions1lm_1264_spce
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions1lm_1264_spce
@@ -34,4 +34,3 @@ F-    1.726  0.15629366    12-6-4 set for SPC\E water from Li et al., JCTC, 2015
 Cl-   2.153  0.52404590    12-6-4 set for SPC\E water from Li et al., JCTC, 2015, 11, 1645
 Br-   2.324  0.65475744    12-6-4 set for SPC\E water from Li et al., JCTC, 2015, 11, 1645
 I-    2.579  0.79809803    12-6-4 set for SPC\E water from Li et al., JCTC, 2015, 11, 1645
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions1lm_1264_tip3p b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions1lm_1264_tip3p
index a1d57cc0..6c1e5528 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions1lm_1264_tip3p
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions1lm_1264_tip3p
@@ -34,4 +34,3 @@ F-    1.725  0.15557763    12-6-4 set for TIP3P water from Li et al., JCTC, 2015
 Cl-   2.150  0.52153239    12-6-4 set for TIP3P water from Li et al., JCTC, 2015, 11, 1645
 Br-   2.314  0.64785703    12-6-4 set for TIP3P water from Li et al., JCTC, 2015, 11, 1645
 I-    2.567  0.79269938    12-6-4 set for TIP3P water from Li et al., JCTC, 2015, 11, 1645
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions1lm_1264_tip4pew b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions1lm_1264_tip4pew
index 29d8418d..39c70673 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions1lm_1264_tip4pew
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions1lm_1264_tip4pew
@@ -34,4 +34,3 @@ F-    1.728  0.15773029    12-6-4 set for TIP4P\EW water from Li et al., JCTC, 2
 Cl-   2.154  0.52488228    12-6-4 set for TIP4P\EW water from Li et al., JCTC, 2015, 11, 1645
 Br-   2.326  0.65612582    12-6-4 set for TIP4P\EW water from Li et al., JCTC, 2015, 11, 1645
 I-    2.585  0.80075128    12-6-4 set for TIP4P\EW water from Li et al., JCTC, 2015, 11, 1645
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions1lm_126_spce b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions1lm_126_spce
index bdb4eee7..153a6930 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions1lm_126_spce
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions1lm_126_spce
@@ -30,4 +30,3 @@ F-    1.819  0.22878796    HFE set for SPC\E water from Li et al., JCTC, 2015, 1
 Cl-   2.308  0.64367011    HFE set for SPC\E water from Li et al., JCTC, 2015, 11, 1645
 Br-   2.470  0.74435812    HFE set for SPC\E water from Li et al., JCTC, 2015, 11, 1645
 I-    2.770  0.86877007    HFE set for SPC\E water from Li et al., JCTC, 2015, 11, 1645
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions1lm_126_tip3p b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions1lm_126_tip3p
index 965cb307..ab93cc30 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions1lm_126_tip3p
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions1lm_126_tip3p
@@ -30,4 +30,3 @@ F-    1.783  0.19945255    HFE set for TIP3P water from Li et al., JCTC, 2015, 1
 Cl-   2.252  0.60293097    HFE set for TIP3P water from Li et al., JCTC, 2015, 11, 1645
 Br-   2.428  0.72070940    HFE set for TIP3P water from Li et al., JCTC, 2015, 11, 1645
 I-    2.724  0.85418187    HFE set for TIP3P water from Li et al., JCTC, 2015, 11, 1645
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions1lm_126_tip4pew b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions1lm_126_tip4pew
index abc3db9d..e6090ebb 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions1lm_126_tip4pew
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions1lm_126_tip4pew
@@ -30,4 +30,3 @@ F-    1.842  0.24821230    HFE set for TIP4P\EW water from Li et al., JCTC, 2015
 Cl-   2.321  0.65269755    HFE set for TIP4P\EW water from Li et al., JCTC, 2015, 11, 1645
 Br-   2.520  0.77034233    HFE set for TIP4P\EW water from Li et al., JCTC, 2015, 11, 1645
 I-    2.819  0.88281946    HFE set for TIP4P\EW water from Li et al., JCTC, 2015, 11, 1645
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions1lm_iod b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions1lm_iod
index b883dcec..6512ca86 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions1lm_iod
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions1lm_iod
@@ -34,4 +34,3 @@ F-    1.739  0.16573832    IOD set from Li et al., JCTC, 2015, 11, 1645
 Cl-   2.162  0.53154665    IOD set from Li et al., JCTC, 2015, 11, 1645
 Br-   2.331  0.65952968    IOD set from Li et al., JCTC, 2015, 11, 1645
 I-    2.590  0.80293907    IOD set from Li et al., JCTC, 2015, 11, 1645
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions234lm_1264_spce b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions234lm_1264_spce
index 679ab652..a960fd62 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions234lm_1264_spce
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions234lm_1264_spce
@@ -82,4 +82,3 @@ Ce4+  1.761  0.18227365    12-6-4 set for SPC\E water from Li et al., JPCB, 2015
 U4+   1.791  0.20584696    12-6-4 set for SPC\E water from Li et al., JPCB, 2015, 119, 883
 Pu4+  1.750  0.17392181    12-6-4 set for SPC\E water from Li et al., JPCB, 2015, 119, 883
 Th4+  1.773  0.19156806    12-6-4 set for SPC\E water from Li et al., JPCB, 2015, 119, 883
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions234lm_1264_tip3p b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions234lm_1264_tip3p
index cf872751..05115b74 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions234lm_1264_tip3p
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions234lm_1264_tip3p
@@ -82,4 +82,3 @@ Ce4+  1.766  0.18612361    12-6-4 set for TIP3P water from Li et al., JPCB, 2015
 U4+   1.792  0.20665151    12-6-4 set for TIP3P water from Li et al., JPCB, 2015, 119, 883
 Pu4+  1.752  0.17542802    12-6-4 set for TIP3P water from Li et al., JPCB, 2015, 119, 883
 Th4+  1.770  0.18922704    12-6-4 set for TIP3P water from Li et al., JPCB, 2015, 119, 883
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions234lm_1264_tip4pew b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions234lm_1264_tip4pew
index bfce1bf4..1538b8fa 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions234lm_1264_tip4pew
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions234lm_1264_tip4pew
@@ -82,4 +82,3 @@ Ce4+  1.761  0.18227365    12-6-4 set for TIP4P\EW water from Li et al., JPCB, 2
 U4+   1.791  0.20584696    12-6-4 set for TIP4P\EW water from Li et al., JPCB, 2015, 119, 883
 Pu4+  1.753  0.17618319    12-6-4 set for TIP4P\EW water from Li et al., JPCB, 2015, 119, 883
 Th4+  1.758  0.17997960    12-6-4 set for TIP4P\EW water from Li et al., JPCB, 2015, 119, 883
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions234lm_126_spce b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions234lm_126_spce
index aeee367d..81e8b614 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions234lm_126_spce
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions234lm_126_spce
@@ -98,4 +98,3 @@ Ce4+  1.689  0.13084945    IOD set for SPC\E water from Li et al., JPCB, 2015, 1
 U4+   1.689  0.13084945    IOD set for SPC\E water from Li et al., JPCB, 2015, 119, 883
 Pu4+  1.666  0.11617738    IOD set for SPC\E water from Li et al., JPCB, 2015, 119, 883
 Th4+  1.713  0.14710519    IOD set for SPC\E water from Li et al., JPCB, 2015, 119, 883
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions234lm_126_tip3p b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions234lm_126_tip3p
index 66012ed2..b6f43ab9 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions234lm_126_tip3p
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions234lm_126_tip3p
@@ -98,4 +98,3 @@ Ce4+  1.684  0.12758274    IOD set for TIP3P water from Li et al., JPCB, 2015, 1
 U4+   1.684  0.12758274    IOD set for TIP3P water from Li et al., JPCB, 2015, 119, 883
 Pu4+  1.662  0.11371963    IOD set for TIP3P water from Li et al., JPCB, 2015, 119, 883
 Th4+  1.708  0.14364160    IOD set for TIP3P water from Li et al., JPCB, 2015, 119, 883
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions234lm_126_tip4pew b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions234lm_126_tip4pew
index 2cddb4c7..3e788aa9 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions234lm_126_tip4pew
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions234lm_126_tip4pew
@@ -98,4 +98,3 @@ Ce4+  1.667  0.11679623    IOD set for TIP4P\EW water from Li et al., JPCB, 2015
 U4+   1.667  0.11679623    IOD set for TIP4P\EW water from Li et al., JPCB, 2015, 119, 883
 Pu4+  1.645  0.10359269    IOD set for TIP4P\EW water from Li et al., JPCB, 2015, 119, 883
 Th4+  1.690  0.13150785    IOD set for TIP4P\EW water from Li et al., JPCB, 2015, 119, 883
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions234lm_hfe_spce b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions234lm_hfe_spce
index a7221023..aaf5ce6f 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions234lm_hfe_spce
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions234lm_hfe_spce
@@ -98,4 +98,3 @@ Ce4+  1.360  0.01020237    HFE set for SPC\E water from Li et al., JPCB, 2015, 1
 U4+   1.218  0.00148497    HFE set for SPC\E water from Li et al., JPCB, 2015, 119, 883
 Pu4+  1.281  0.00379705    HFE set for SPC\E water from Li et al., JPCB, 2015, 119, 883
 Th4+  1.468  0.02986171    HFE set for SPC\E water from Li et al., JPCB, 2015, 119, 883
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions234lm_hfe_tip3p b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions234lm_hfe_tip3p
index 5cfc2bf6..32e7b4a0 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions234lm_hfe_tip3p
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions234lm_hfe_tip3p
@@ -98,4 +98,3 @@ Ce4+  1.353  0.00941798    HFE set for TIP3P water from Li et al., JPCB, 2015, 1
 U4+   1.209  0.00128267    HFE set for TIP3P water from Li et al., JPCB, 2015, 119, 883
 Pu4+  1.273  0.00339720    HFE set for TIP3P water from Li et al., JPCB, 2015, 119, 883
 Th4+  1.463  0.02858630    HFE set for TIP3P water from Li et al., JPCB, 2015, 119, 883
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions234lm_hfe_tip4pew b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions234lm_hfe_tip4pew
index 82472082..7742bd5d 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions234lm_hfe_tip4pew
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions234lm_hfe_tip4pew
@@ -98,4 +98,3 @@ Ce4+  1.257  0.00270120    HFE set for TIP4P\EW water from Li et al., JPCB, 2015
 U4+   1.105  0.00018227    HFE set for TIP4P\EW water from Li et al., JPCB, 2015, 119, 883
 Pu4+  1.172  0.00067804    HFE set for TIP4P\EW water from Li et al., JPCB, 2015, 119, 883
 Th4+  1.370  0.01141046    HFE set for TIP4P\EW water from Li et al., JPCB, 2015, 119, 883
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions234lm_iod_spce b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions234lm_iod_spce
index 4f8c06ea..f68fb188 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions234lm_iod_spce
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions234lm_iod_spce
@@ -82,4 +82,3 @@ Ce4+  1.689  0.13084945    IOD set for SPC\E water from Li et al., JPCB, 2015, 1
 U4+   1.689  0.13084945    IOD set for SPC\E water from Li et al., JPCB, 2015, 119, 883
 Pu4+  1.666  0.11617738    IOD set for SPC\E water from Li et al., JPCB, 2015, 119, 883
 Th4+  1.713  0.14710519    IOD set for SPC\E water from Li et al., JPCB, 2015, 119, 883
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions234lm_iod_tip3p b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions234lm_iod_tip3p
index 561edd2b..ac3a4008 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions234lm_iod_tip3p
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions234lm_iod_tip3p
@@ -82,4 +82,3 @@ Ce4+  1.684  0.12758274    IOD set for TIP3P water from Li et al., JPCB, 2015, 1
 U4+   1.684  0.12758274    IOD set for TIP3P water from Li et al., JPCB, 2015, 119, 883
 Pu4+  1.662  0.11371963    IOD set for TIP3P water from Li et al., JPCB, 2015, 119, 883
 Th4+  1.708  0.14364160    IOD set for TIP3P water from Li et al., JPCB, 2015, 119, 883
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions234lm_iod_tip4pew b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions234lm_iod_tip4pew
index 651ef977..fc8614d1 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions234lm_iod_tip4pew
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ions234lm_iod_tip4pew
@@ -82,4 +82,3 @@ Ce4+  1.667  0.11679623    IOD set for TIP4P\EW water from Li et al., JPCB, 2015
 U4+   1.667  0.11679623    IOD set for TIP4P\EW water from Li et al., JPCB, 2015, 119, 883
 Pu4+  1.645  0.10359269    IOD set for TIP4P\EW water from Li et al., JPCB, 2015, 119, 883
 Th4+  1.690  0.13150785    IOD set for TIP4P\EW water from Li et al., JPCB, 2015, 119, 883
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionsjc_spce b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionsjc_spce
index a5acf83e..d6c3763a 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionsjc_spce
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionsjc_spce
@@ -20,4 +20,3 @@ NONBON
   Cl-      2.711     0.0127850
   Br-      2.751     0.0269586
   I-       2.919     0.0427845
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_1264_fb3 b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_1264_fb3
index 15849237..6c54e5a7 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_1264_fb3
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_1264_fb3
@@ -106,5 +106,3 @@ Ce4+  1.760  0.18150763    12-6-4 set for the TIP3P-FB water model from Li et al
 U4+   1.788  0.20344023    12-6-4 set for the TIP3P-FB water model from Li et al., JCTC, 2021, 17, 2342
 Pu4+  1.744  0.16943676    12-6-4 set for the TIP3P-FB water model from Li et al., JCTC, 2021, 17, 2342
 Th4+  1.763  0.18380968    12-6-4 set for the TIP3P-FB water model from Li et al., JCTC, 2021, 17, 2342
-
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_1264_fb4 b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_1264_fb4
index 1a361eb3..8c3fdeb8 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_1264_fb4
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_1264_fb4
@@ -106,5 +106,3 @@ Ce4+  1.750  0.17392181    12-6-4 set for the TIP4P-FB water model from Li et al
 U4+   1.787  0.20264033    12-6-4 set for the TIP4P-FB water model from Li et al., JCTC, 2021, 17, 2342
 Pu4+  1.744  0.16943676    12-6-4 set for the TIP4P-FB water model from Li et al., JCTC, 2021, 17, 2342
 Th4+  1.761  0.18227365    12-6-4 set for the TIP4P-FB water model from Li et al., JCTC, 2021, 17, 2342
-
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_1264_opc b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_1264_opc
index 0a957133..3345d8ff 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_1264_opc
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_1264_opc
@@ -106,5 +106,3 @@ Ce4+  1.747  0.17167295    12-6-4 set for the OPC water model from Li et al., JC
 U4+   1.767  0.18689752    12-6-4 set for the OPC water model from Li et al., JCTC, 2021, 17, 2342
 Pu4+  1.745  0.17018074    12-6-4 set for the OPC water model from Li et al., JCTC, 2021, 17, 2342
 Th4+  1.755  0.17769767    12-6-4 set for the OPC water model from Li et al., JCTC, 2021, 17, 2342
-
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_1264_opc3 b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_1264_opc3
index 0697f666..3de1be81 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_1264_opc3
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_1264_opc3
@@ -106,5 +106,3 @@ Ce4+  1.752  0.17542802    12-6-4 set for the OPC3 water model from Li et al., J
 U4+   1.770  0.18922704    12-6-4 set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342
 Pu4+  1.755  0.17769767    12-6-4 set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342
 Th4+  1.755  0.17769767    12-6-4 set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342
-
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_126_fb3 b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_126_fb3
index 92c2a373..fb6595dd 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_126_fb3
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_126_fb3
@@ -122,4 +122,3 @@ Ce4+  1.705  0.14158262    IOD set for the TIP3P-FB water model from Li et al.,
 U4+   1.705  0.14158262    IOD set for the TIP3P-FB water model from Li et al., JCTC, 2021, 17, 2342
 Pu4+  1.682  0.12628793    IOD set for the TIP3P-FB water model from Li et al., JCTC, 2021, 17, 2342
 Th4+  1.718  0.15060822    IOD set for the TIP3P-FB water model from Li et al., JCTC, 2021, 17, 2342
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_126_fb4 b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_126_fb4
index 16987d53..0565b1be 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_126_fb4
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_126_fb4
@@ -122,4 +122,3 @@ Ce4+  1.692  0.13282966    IOD set for the TIP4P-FB water model from Li et al.,
 U4+   1.692  0.13282966    IOD set for the TIP4P-FB water model from Li et al., JCTC, 2021, 17, 2342
 Pu4+  1.667  0.11679623    IOD set for the TIP4P-FB water model from Li et al., JCTC, 2021, 17, 2342
 Th4+  1.709  0.14433113    IOD set for the TIP4P-FB water model from Li et al., JCTC, 2021, 17, 2342
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_126_opc b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_126_opc
index 9088f4ef..dbdc433f 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_126_opc
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_126_opc
@@ -122,4 +122,3 @@ Ce4+  1.683  0.12693448    IOD set for the OPC water model from Li et al., JCTC,
 U4+   1.683  0.12693448    IOD set for the OPC water model from Li et al., JCTC, 2021, 17, 2342
 Pu4+  1.658  0.11129023    IOD set for the OPC water model from Li et al., JCTC, 2021, 17, 2342
 Th4+  1.704  0.14089951    IOD set for the OPC water model from Li et al., JCTC, 2021, 17, 2342
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_126_opc3 b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_126_opc3
index 1c8c3c64..469b0226 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_126_opc3
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_126_opc3
@@ -122,4 +122,3 @@ Ce4+  1.708  0.14364160    IOD set for the OPC3 water model from Li et al., JCTC
 U4+   1.708  0.14364160    IOD set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342
 Pu4+  1.682  0.12628793    IOD set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342
 Th4+  1.721  0.15272873    IOD set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_hfe_fb3 b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_hfe_fb3
index 870456b3..8d71f241 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_hfe_fb3
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_hfe_fb3
@@ -122,5 +122,3 @@ Ce4+  1.352  0.00930991    HFE set for the TIP3P-FB water model from Li et al.,
 U4+   1.223  0.00160860    HFE set for the TIP3P-FB water model from Li et al., JCTC, 2021, 17, 2342
 Pu4+  1.285  0.00401101    HFE set for the TIP3P-FB water model from Li et al., JCTC, 2021, 17, 2342
 Th4+  1.454  0.02639002    HFE set for the TIP3P-FB water model from Li et al., JCTC, 2021, 17, 2342
-
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_hfe_fb4 b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_hfe_fb4
index 061da026..eeb84e14 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_hfe_fb4
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_hfe_fb4
@@ -122,5 +122,3 @@ Ce4+  1.301  0.00496778    HFE set for the TIP4P-FB water model from Li et al.,
 U4+   1.148  0.00043416    HFE set for the TIP4P-FB water model from Li et al., JCTC, 2021, 17, 2342
 Pu4+  1.215  0.00141473    HFE set for the TIP4P-FB water model from Li et al., JCTC, 2021, 17, 2342
 Th4+  1.388  0.01386171    HFE set for the TIP4P-FB water model from Li et al., JCTC, 2021, 17, 2342
-
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_hfe_opc b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_hfe_opc
index ed995fb8..1978346b 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_hfe_opc
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_hfe_opc
@@ -122,5 +122,3 @@ Ce4+  1.306  0.00530214    HFE set for the OPC water model from Li et al., JCTC,
 U4+   1.155  0.00049581    HFE set for the OPC water model from Li et al., JCTC, 2021, 17, 2342
 Pu4+  1.221  0.00155814    HFE set for the OPC water model from Li et al., JCTC, 2021, 17, 2342
 Th4+  1.393  0.01460944    HFE set for the OPC water model from Li et al., JCTC, 2021, 17, 2342
-
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_hfe_opc3 b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_hfe_opc3
index 20061d07..66fac800 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_hfe_opc3
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_hfe_opc3
@@ -122,5 +122,3 @@ Ce4+  1.370  0.01141046    HFE set for the OPC3 water model from Li et al., JCTC
 U4+   1.247  0.00232970    HFE set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342
 Pu4+  1.308  0.00544088    HFE set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342
 Th4+  1.475  0.03171494    HFE set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342
-
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_iod_fb3 b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_iod_fb3
index ec901d51..26c933e8 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_iod_fb3
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_iod_fb3
@@ -106,5 +106,3 @@ Ce4+  1.705  0.14158262    IOD set for the TIP3P-FB water model from Li et al.,
 U4+   1.705  0.14158262    IOD set for the TIP3P-FB water model from Li et al., JCTC, 2021, 17, 2342
 Pu4+  1.682  0.12628793    IOD set for the TIP3P-FB water model from Li et al., JCTC, 2021, 17, 2342
 Th4+  1.718  0.15060822    IOD set for the TIP3P-FB water model from Li et al., JCTC, 2021, 17, 2342
-
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_iod_fb4 b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_iod_fb4
index 25a91258..db31f8a1 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_iod_fb4
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_iod_fb4
@@ -106,5 +106,3 @@ Ce4+  1.692  0.13282966    IOD set for the TIP4P-FB water model from Li et al.,
 U4+   1.692  0.13282966    IOD set for the TIP4P-FB water model from Li et al., JCTC, 2021, 17, 2342
 Pu4+  1.667  0.11679623    IOD set for the TIP4P-FB water model from Li et al., JCTC, 2021, 17, 2342
 Th4+  1.709  0.14433113    IOD set for the TIP4P-FB water model from Li et al., JCTC, 2021, 17, 2342
-
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_iod_opc b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_iod_opc
index 8287726c..63e97d60 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_iod_opc
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_iod_opc
@@ -106,4 +106,3 @@ Ce4+  1.683  0.12693448    IOD set for the OPC water model from Li et al., JCTC,
 U4+   1.683  0.12693448    IOD set for the OPC water model from Li et al., JCTC, 2021, 17, 2342
 Pu4+  1.658  0.11129023    IOD set for the OPC water model from Li et al., JCTC, 2021, 17, 2342
 Th4+  1.704  0.14089951    IOD set for the OPC water model from Li et al., JCTC, 2021, 17, 2342
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_iod_opc3 b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_iod_opc3
index 9e0dd4e1..198c7663 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_iod_opc3
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.ionslm_iod_opc3
@@ -106,8 +106,3 @@ Ce4+  1.708  0.14364160    IOD set for the OPC3 water model from Li et al., JCTC
 U4+   1.708  0.14364160    IOD set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342
 Pu4+  1.682  0.12628793    IOD set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342
 Th4+  1.721  0.15272873    IOD set for the OPC3 water model from Li et al., JCTC, 2021, 17, 2342
-
-
-
-
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.opc b/acpype/amber21-11_linux/dat/leap/parm/frcmod.opc
index a349b9e0..937cf947 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.opc
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.opc
@@ -22,4 +22,3 @@ NONBON
   OW       1.777167268 0.2128008130
   HW          0.0000  0.0000
   EP       1.0         0.0
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.parmCHI_YIL b/acpype/amber21-11_linux/dat/leap/parm/frcmod.parmCHI_YIL
index eba978ae..f1481a58 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.parmCHI_YIL
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.parmCHI_YIL
@@ -110,5 +110,3 @@ Q1          1.9080  0.0860
 Q2          1.9080  0.0860                         
 Q3          1.9080  0.0860                         
 Q4          1.9080  0.0860                         
-
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.parmbsc0 b/acpype/amber21-11_linux/dat/leap/parm/frcmod.parmbsc0
index 3ffb632f..9041a700 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.parmbsc0
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.parmbsc0
@@ -49,4 +49,3 @@ CT-CT-CI-OH    1       0.962830  348.09535     3.0  gamma
 
 NONB
 CI          1.9080  0.1094
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.parmbsc0_ezOL1 b/acpype/amber21-11_linux/dat/leap/parm/frcmod.parmbsc0_ezOL1
index 6f357939..5bfaf0c0 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.parmbsc0_ezOL1
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.parmbsc0_ezOL1
@@ -82,5 +82,3 @@ C3-CT-CI-OH   1    0.962830    348.09535         3.0  gamma
 NONBOND
 C3          1.9080  0.1094             Spellmeyer
  
-
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.parmbsc1 b/acpype/amber21-11_linux/dat/leap/parm/frcmod.parmbsc1
index 15b34f96..dd644755 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.parmbsc1
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.parmbsc1
@@ -122,4 +122,3 @@ NONBONDED
 CE          1.9080  0.1094
 C1          1.9080  0.0860             Spellmeyer 
 C2          1.9080  0.0860             Spellmeyer 
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.phmd b/acpype/amber21-11_linux/dat/leap/parm/frcmod.phmd
index cdbca4fa..17e90685 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.phmd
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.phmd
@@ -13,4 +13,3 @@ HO-O2-CO-O2    1       6.0         0.0          1 ! modified from HO-OH-C -O
 2C-CO-O2-HO   1    0.479         0.0            -3. ! copied from 2C-C -OH-HO in frcmod.ff14s
 2C-CO-O2-HO   1    6.000       180.0            -2. ! copied from 2C-C -OH-HO in frcmod.ff14s and increased barrier
 2C-CO-O2-HO   1    0.448       180.0             1. ! copied from 2C-C -OH-HO in frcmod.ff14sb
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.phosaa14SB b/acpype/amber21-11_linux/dat/leap/parm/frcmod.phosaa14SB
index 2c8ef1bd..5c74ee0d 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.phosaa14SB
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.phosaa14SB
@@ -219,4 +219,3 @@ OV      1.6562  0.1700          a uniform radius increase of -0.0275 A was appli
 OX      1.8401  0.2100          modified acc. to FEP solvation energies for SER/THR 2-
 OZ      1.8626  0.1700          a uniform radius increase of 0.1789 A was applied
 CG      1.9080  0.0860          Y1P/PTR C Gamma (CA) from parm14ipq.dat
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.pol3 b/acpype/amber21-11_linux/dat/leap/parm/frcmod.pol3
index 7e8d3b03..7fea832b 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.pol3
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.pol3
@@ -14,4 +14,3 @@ DIHE
 NONBON
   OW       1.798    0.156
   HW       0.0      0.0
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.qspcfw b/acpype/amber21-11_linux/dat/leap/parm/frcmod.qspcfw
index feef336f..829a0da4 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.qspcfw
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.qspcfw
@@ -15,4 +15,3 @@ DIHE
 NONBON
   OW       1.7767    0.1554
   HW          0.0000  0.0000
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.shaw b/acpype/amber21-11_linux/dat/leap/parm/frcmod.shaw
index f1b434fe..9c4b288a 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.shaw
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.shaw
@@ -162,4 +162,3 @@ NONBON
   CE          1.85229  0.0636             Tan et al.
   CF          1.85229  0.0636             Tan et al.
   CQ          1.85229  0.0636             Tan et al.
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.spce b/acpype/amber21-11_linux/dat/leap/parm/frcmod.spce
index 60b29a87..318815d1 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.spce
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.spce
@@ -14,4 +14,3 @@ DIHE
 NONBON
   OW       1.7767    0.1553
   HW          0.0000  0.0000
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.spceb b/acpype/amber21-11_linux/dat/leap/parm/frcmod.spceb
index 2551621a..d0e5e31d 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.spceb
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.spceb
@@ -14,4 +14,3 @@ DIHE
 NONBON
   OW       1.7767    0.1553
   HW          0.0000  0.0000
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.spcfw b/acpype/amber21-11_linux/dat/leap/parm/frcmod.spcfw
index 947f69f8..0575c505 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.spcfw
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.spcfw
@@ -15,4 +15,3 @@ DIHE
 NONBON
   OW       1.7767    0.1554
   HW          0.0000  0.0000
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.tip3p b/acpype/amber21-11_linux/dat/leap/parm/frcmod.tip3p
index 48b3152f..7be2ffa7 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.tip3p
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.tip3p
@@ -14,4 +14,3 @@ DIHE
 NONBON
   OW          1.7683  0.1520             TIP3P water model
   HW          0.0000  0.0000             TIP3P water model
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.tip3pf b/acpype/amber21-11_linux/dat/leap/parm/frcmod.tip3pf
index 71695ee7..af375eea 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.tip3pf
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.tip3pf
@@ -14,4 +14,3 @@ DIHE
 NONBON
   OW       1.7926    0.098 
   HW          0.0000  0.0000
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.tip3pfb b/acpype/amber21-11_linux/dat/leap/parm/frcmod.tip3pfb
index efd6fcf2..49c4e52f 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.tip3pfb
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.tip3pfb
@@ -14,4 +14,3 @@ DIHE
 NONBON
   OW       1.7835723    0.155866
   HW          0.0000  0.0000
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.tip4p b/acpype/amber21-11_linux/dat/leap/parm/frcmod.tip4p
index b06cfb5e..5da44d2a 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.tip4p
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.tip4p
@@ -17,4 +17,3 @@ NONBON
   OW       1.7699    0.1550
   HW          0.0000  0.0000
   EP       1.0       0.0
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.tip4pd b/acpype/amber21-11_linux/dat/leap/parm/frcmod.tip4pd
index a0c25134..af611c8e 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.tip4pd
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.tip4pd
@@ -19,4 +19,3 @@ X -HW-OW-X    2       0.0         0.0         1.0
 NONBON
   OW       1.776296  0.22384
   EP       1.0       0.0
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.tip4pew b/acpype/amber21-11_linux/dat/leap/parm/frcmod.tip4pew
index f356f24b..cdc1faab 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.tip4pew
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.tip4pew
@@ -21,4 +21,3 @@ NONBON
   OW       1.775931  0.16275
   HW          0.0000  0.0000
   EP       1.0       0.0
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.tip4pfb b/acpype/amber21-11_linux/dat/leap/parm/frcmod.tip4pfb
index 97249d0b..585e7b0a 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.tip4pfb
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.tip4pfb
@@ -21,4 +21,3 @@ NONBON
   OW       1.77660486  0.179082
   HW          0.0000  0.0000
   EP       1.0       0.0
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/frcmod.tip5p b/acpype/amber21-11_linux/dat/leap/parm/frcmod.tip5p
index c5f6557b..a98c8e24 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/frcmod.tip5p
+++ b/acpype/amber21-11_linux/dat/leap/parm/frcmod.tip5p
@@ -17,4 +17,3 @@ NONBON
   OW       1.7510    0.1600
   HW          0.0000  0.0000
   EP       1.0       0.0
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/gaff.dat b/acpype/amber21-11_linux/dat/leap/parm/gaff.dat
index e105bead..e0834025 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/gaff.dat
+++ b/acpype/amber21-11_linux/dat/leap/parm/gaff.dat
@@ -7308,5 +7308,3 @@ Updates to GAFF 1.81, May, 2017:
    added new atom types for n3/n4/n/nh/os/ss in RG3 and RG4
    updated bond length/angle parameters involved by the newly introduced atom types
 ---------------------------------------------------------------------------
-
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/gaff2.dat b/acpype/amber21-11_linux/dat/leap/parm/gaff2.dat
index e40965b5..0fbafe33 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/gaff2.dat
+++ b/acpype/amber21-11_linux/dat/leap/parm/gaff2.dat
@@ -7680,4 +7680,3 @@ Updates to GAFF 2.11, May, 2017:
    added new atom types for n3/n4/n/nh/os/ss in RG3 and RG4
    updated bond length/angle parameters involved by the newly introduced atom types
 ----------------------------------------------------------------------------
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/lipid11.dat b/acpype/amber21-11_linux/dat/leap/parm/lipid11.dat
index 9c25f35c..76e95ba1 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/lipid11.dat
+++ b/acpype/amber21-11_linux/dat/leap/parm/lipid11.dat
@@ -348,4 +348,3 @@ GLYCAM   LIPID11    Description
  OS        oS       O ether
  P         pA       phosphor in phosphates
  O2        oC       O carboxyl group
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/lipid14.dat b/acpype/amber21-11_linux/dat/leap/parm/lipid14.dat
index aa144bcb..7537d3c1 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/lipid14.dat
+++ b/acpype/amber21-11_linux/dat/leap/parm/lipid14.dat
@@ -346,4 +346,3 @@ GAFFlipid Lipid14   Description
 --------- -------   -----------
  a3        cD       sp3 carbon (See GAFFlipid paper)
  hl        hL       H bonded to aliphatic carbon without electrwd. group (See GAFFlipid paper)
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/nucgen.dat b/acpype/amber21-11_linux/dat/leap/parm/nucgen.dat
index 52c9d051..5bd3499d 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/nucgen.dat
+++ b/acpype/amber21-11_linux/dat/leap/parm/nucgen.dat
@@ -372,7 +372,3 @@ O2     7.61     19.2      -1.17
 N1     7.16     36.1      -1.62
 C6     6.55     46.3      -1.66
 C5     5.28     49.1      -1.29
-
-
-
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/opls.info b/acpype/amber21-11_linux/dat/leap/parm/opls.info
index c003dd90..d9c25ea0 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/opls.info
+++ b/acpype/amber21-11_linux/dat/leap/parm/opls.info
@@ -393,5 +393,3 @@ Type    V0        V1    f   V2    f   V3    f      Description
  Department of Chemistry, Yale University
        bill@doctor.chem.yale.edu
 ------------------------------------------
-
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/parm10.dat b/acpype/amber21-11_linux/dat/leap/parm/parm10.dat
index cb5815c9..a5dffe8f 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/parm10.dat
+++ b/acpype/amber21-11_linux/dat/leap/parm/parm10.dat
@@ -1002,4 +1002,3 @@ MOD4      RE
   I           2.35    0.40               JCC,7,(1986),230;  
  
 END
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/parm19.dat b/acpype/amber21-11_linux/dat/leap/parm/parm19.dat
index 59aad2e1..ef4d82ed 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/parm19.dat
+++ b/acpype/amber21-11_linux/dat/leap/parm/parm19.dat
@@ -1080,4 +1080,3 @@ MOD4      RE
   EP          0.00    0.0000             lone pair
  
 END
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/parm91.dat b/acpype/amber21-11_linux/dat/leap/parm/parm91.dat
index b076aca7..efe60da3 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/parm91.dat
+++ b/acpype/amber21-11_linux/dat/leap/parm/parm91.dat
@@ -917,5 +917,3 @@ STUB      RE
   LP       1.2        0.016
 
 END
-
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/parm91X.dat b/acpype/amber21-11_linux/dat/leap/parm/parm91X.dat
index e472abbf..14d5ff46 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/parm91X.dat
+++ b/acpype/amber21-11_linux/dat/leap/parm/parm91X.dat
@@ -928,5 +928,3 @@ STUB      RE
   LP       1.2        0.016
 
 END
-
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/parm91X.ua.dat b/acpype/amber21-11_linux/dat/leap/parm/parm91X.ua.dat
index 245baacd..95ef6584 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/parm91X.ua.dat
+++ b/acpype/amber21-11_linux/dat/leap/parm/parm91X.ua.dat
@@ -891,5 +891,3 @@ STUB      RE
   LP       1.2        0.016
 
 END
-
-
diff --git a/acpype/amber21-11_linux/dat/leap/parm/parm99.dat b/acpype/amber21-11_linux/dat/leap/parm/parm99.dat
index 25ec0f3f..4fc3342d 100644
--- a/acpype/amber21-11_linux/dat/leap/parm/parm99.dat
+++ b/acpype/amber21-11_linux/dat/leap/parm/parm99.dat
@@ -731,5 +731,3 @@ CT-CT-OS-LP   1       0.000       0.000       3.000
 CM-CM-OS-LP   1       0.000     180.000       2.000
 HA-CM-OS-LP   1       0.000     180.000       2.000
 H4-CM-OS-LP   1       0.000     180.000       2.000
-
-
diff --git a/acpype/amber21-11_linux/dat/leap/prep/oldff/all_nuc02EP.in b/acpype/amber21-11_linux/dat/leap/prep/oldff/all_nuc02EP.in
index 2bbfb2ae..f58efa10 100644
--- a/acpype/amber21-11_linux/dat/leap/prep/oldff/all_nuc02EP.in
+++ b/acpype/amber21-11_linux/dat/leap/prep/oldff/all_nuc02EP.in
@@ -2457,4 +2457,3 @@ pom
   0.0825  0.0228  0.0333  0.0280 -0.4483
   1.0720 -0.7552 -0.7552 -0.4349 -0.0212
   0.0383  0.0454  0.0926
-
diff --git a/acpype/amber21-11_linux/install_on_ubuntu_18-04 b/acpype/amber21-11_linux/install_on_ubuntu_18-04
index 00bd8aab..75c2f2ad 100644
--- a/acpype/amber21-11_linux/install_on_ubuntu_18-04
+++ b/acpype/amber21-11_linux/install_on_ubuntu_18-04
@@ -1,4 +1,3 @@
 ## To run on Ubuntu 18.04
 sudo apt update
 sudo apt-get install libgfortran5 libarpack++2-dev
-
diff --git a/acpype/amber21-11_os/bin/am1bcc b/acpype/amber21-11_os/bin/am1bcc
index 7aff7250..6ec88848 100755
--- a/acpype/amber21-11_os/bin/am1bcc
+++ b/acpype/amber21-11_os/bin/am1bcc
@@ -6,4 +6,4 @@
 this_script_dir="$(cd "$(dirname "$0")" && pwd)"
 source $this_script_dir/../amber.sh
 
-$AMBERHOME/bin/wrapped_progs/am1bcc "$@"
\ No newline at end of file
+$AMBERHOME/bin/wrapped_progs/am1bcc "$@"
diff --git a/acpype/amber21-11_os/bin/antechamber b/acpype/amber21-11_os/bin/antechamber
index 89285850..e14a11b7 100755
--- a/acpype/amber21-11_os/bin/antechamber
+++ b/acpype/amber21-11_os/bin/antechamber
@@ -6,4 +6,4 @@
 this_script_dir="$(cd "$(dirname "$0")" && pwd)"
 source $this_script_dir/../amber.sh
 
-$AMBERHOME/bin/wrapped_progs/antechamber "$@"
\ No newline at end of file
+$AMBERHOME/bin/wrapped_progs/antechamber "$@"
diff --git a/acpype/amber21-11_os/bin/atomtype b/acpype/amber21-11_os/bin/atomtype
index b3e17770..abe002e8 100755
--- a/acpype/amber21-11_os/bin/atomtype
+++ b/acpype/amber21-11_os/bin/atomtype
@@ -6,4 +6,4 @@
 this_script_dir="$(cd "$(dirname "$0")" && pwd)"
 source $this_script_dir/../amber.sh
 
-$AMBERHOME/bin/wrapped_progs/atomtype "$@"
\ No newline at end of file
+$AMBERHOME/bin/wrapped_progs/atomtype "$@"
diff --git a/acpype/amber21-11_os/bin/bondtype b/acpype/amber21-11_os/bin/bondtype
index 0efcaba2..41bfdaa2 100755
--- a/acpype/amber21-11_os/bin/bondtype
+++ b/acpype/amber21-11_os/bin/bondtype
@@ -6,4 +6,4 @@
 this_script_dir="$(cd "$(dirname "$0")" && pwd)"
 source $this_script_dir/../amber.sh
 
-$AMBERHOME/bin/wrapped_progs/bondtype "$@"
\ No newline at end of file
+$AMBERHOME/bin/wrapped_progs/bondtype "$@"
diff --git a/acpype/amber21-11_os/bin/parmchk2 b/acpype/amber21-11_os/bin/parmchk2
index 1d1a9ddb..aea6c466 100755
--- a/acpype/amber21-11_os/bin/parmchk2
+++ b/acpype/amber21-11_os/bin/parmchk2
@@ -6,4 +6,4 @@
 this_script_dir="$(cd "$(dirname "$0")" && pwd)"
 source $this_script_dir/../amber.sh
 
-$AMBERHOME/bin/wrapped_progs/parmchk2 "$@"
\ No newline at end of file
+$AMBERHOME/bin/wrapped_progs/parmchk2 "$@"
diff --git a/acpype/cli.py b/acpype/cli.py
index 03eb7759..26e7dd0b 100644
--- a/acpype/cli.py
+++ b/acpype/cli.py
@@ -1,81 +1,44 @@
 #!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-
-"""
-    Requirements: Python 3.6 or higher
-                  Antechamber (from AmberTools preferably)
-                  OpenBabel (optional, but strongly recommended)
-
-    This code is released under GNU General Public License V3.
-
-          <<<  NO WARRANTY AT ALL!!!  >>>
-
-    It was inspired by:
-
-    - amb2gmx.pl (Eric Sorin, David Mobley and John Chodera)
-      and depends on Antechamber and Openbabel
-
-    - YASARA Autosmiles:
-      http://www.yasara.org/autosmiles.htm (Elmar Krieger)
-
-    - topolbuild (Bruce Ray)
-
-    - xplo2d (G.J. Kleywegt)
-
-    For Non-uniform 1-4 scale factor conversion (e.g. if using GLYCAM06), please cite:
-
-    BERNARDI, A., FALLER, R., REITH, D., and KIRSCHNER, K. N. ACPYPE update for
-    nonuniform 1-4 scale factors: Conversion of the GLYCAM06 force field from AMBER
-    to GROMACS. SoftwareX 10 (2019), 100241. doi: 10.1016/j.softx.2019.100241
-
-    For Antechamber, please cite:
-    1. WANG, J., WANG, W., KOLLMAN, P. A., and CASE, D. A. Automatic atom type and
-       bond type perception in molecular mechanical calculations. Journal of Molecular
-       Graphics and Modelling 25, 2 (2006), 247-260. doi: 10.1016/j.jmgm.2005.12.005
-    2. WANG, J., WOLF, R. M., CALDWELL, J. W., KOLLMAN, P. A., and CASE, D. A.
-       Development and testing of a General Amber Force Field. Journal of Computational
-       Chemistry 25, 9 (2004), 1157-1174. doi: 10.1002/jcc.20035
-
-    If you use this code, I am glad if you cite:
-
-    SOUSA DA SILVA, A. W. & VRANKEN, W. F.
-    ACPYPE - AnteChamber PYthon Parser interfacE.
-    BMC Research Notes 5 (2012), 367 doi: 10.1186/1756-0500-5-367
-    http://www.biomedcentral.com/1756-0500/5/367
-
-    BATISTA, P. R.; WILTER, A.; DURHAM, E. H. A. B. & PASCUTTI, P. G. Molecular
-    Dynamics Simulations Applied to the Study of Subtypes of HIV-1 Protease.
-    Cell Biochemistry and Biophysics 44 (2006), 395-404. doi: 10.1385/CBB:44:3:395
-
-    Alan Silva, D.Sc.
-    alanwilter _at_ gmail _dot_ com
-"""
 
 import os
 import sys
 import time
-import traceback
 from shutil import rmtree
+from typing import Dict, List, Optional
 
 from acpype.logger import copy_log
 from acpype.logger import set_logging_conf as logger
+from acpype.logger import tmpLogFile
 from acpype.params import binaries
 from acpype.parser_args import get_option_parser
-from acpype.topol import ACTopol, MolTopol, header
+from acpype.topol import AbstractTopol, ACTopol, MolTopol, header
 from acpype.utils import elapsedTime, set_for_pip, while_replace
 
 
 def chk_py_ver():
     if sys.version_info < (3, 6):
         msg = "Sorry, you need python 3.6 or higher"
-        logger().exception(msg)
+        logger().error(msg)
         raise Exception(msg)
 
 
-def init_main(binaries=binaries, argv=None):
+def handle_exception(level):
+    _exceptionType, exceptionValue, _exceptionTraceback = sys.exc_info()
+    logger(level).exception(f"ACPYPE FAILED: {exceptionValue}")
+    return True
+
+
+def init_main(binaries: Dict[str, str] = binaries, argv: Optional[List[str]] = None):
 
     """
-    Main function, to satisfy Conda
+    Orchestrate the command line usage for ACPYPE with its all input arguments.
+
+    Args:
+        binaries (Dict[str, str], optional): Mostly used for debug and testing. Defaults to ``acpype.params.binaries``.
+        argv (Optional[List[str]], optional): Mostly used for debug and testing. Defaults to None.
+
+    Returns:
+        SystemExit(status): 0 or 19 (failed)
     """
     chk_py_ver()
     set_for_pip(binaries)
@@ -109,16 +72,17 @@ def init_main(binaries=binaries, argv=None):
         parser.error("either '-i' or ('-p', '-x'), but not both")
 
     logger(level).debug(f"CLI: {' '.join(argv)}")
-    texta = "Python Version %s" % sys.version
+    texta = f"Python Version {sys.version}"
     logger(level).debug(while_replace(texta))
 
     if args.direct and not amb2gmxF:
         parser.error("option -u is only meaningful in 'amb2gmx' mode (args '-p' and '-x')")
 
-    try:
-        if amb2gmxF:
-            logger(level).info("Converting Amber input files to Gromacs ...")
-            system = MolTopol(
+    acpypeFailed = False
+    if amb2gmxF:
+        logger(level).info("Converting Amber input files to Gromacs ...")
+        try:
+            molecule: AbstractTopol = MolTopol(
                 acFileXyz=args.inpcrd,
                 acFileTop=args.prmtop,
                 amb2gmx=True,
@@ -131,11 +95,17 @@ def init_main(binaries=binaries, argv=None):
                 is_sorted=args.sorted,
                 chiral=args.chiral,
             )
+        except Exception:
+            acpypeFailed = handle_exception(level)
+        if not acpypeFailed:
+            try:
+                molecule.writeGromacsTopolFiles()
+                molecule.printDebug("prmtop and inpcrd files parsed")
+            except Exception:
+                acpypeFailed = handle_exception(level)
 
-            system.printDebug("prmtop and inpcrd files parsed")
-            system.writeGromacsTopolFiles()
-            copy_log(system)
-        else:
+    else:
+        try:
             molecule = ACTopol(
                 args.input,
                 binaries=binaries,
@@ -150,7 +120,7 @@ def init_main(binaries=binaries, argv=None):
                 basename=args.basename,
                 timeTol=args.max_time,
                 qprog=args.qprog,
-                ekFlag='''"%s"''' % args.keyword,
+                ekFlag=f'''"{args.keyword}"''',
                 verbose=args.verboseless,
                 gmx4=args.gmx4,
                 merge=args.merge,
@@ -159,41 +129,55 @@ def init_main(binaries=binaries, argv=None):
                 chiral=args.chiral,
                 amb2gmx=False,
             )
-
-            molecule.createACTopol()
-            molecule.createMolTopol()
-            copy_log(molecule)
-        acpypeFailed = False
-    except Exception:
-        _exceptionType, exceptionValue, exceptionTraceback = sys.exc_info()
-        logger(level).error("ACPYPE FAILED: %s" % exceptionValue)
-        if args.debug:
-            traceback.print_tb(exceptionTraceback, file=sys.stdout)
-        acpypeFailed = True
+        except Exception:
+            acpypeFailed = handle_exception(level)
+        if not acpypeFailed:
+            try:
+                molecule.createACTopol()
+            except Exception:
+                acpypeFailed = handle_exception(level)
+        if not acpypeFailed:
+            try:
+                molecule.createMolTopol()
+            except Exception:
+                acpypeFailed = handle_exception(level)
 
     execTime = int(round(time.time() - at0))
     if execTime == 0:
         amsg = "less than a second"
     else:
         amsg = elapsedTime(execTime)
-    logger(level).info("Total time of execution: %s" % amsg)
+    logger(level).info(f"Total time of execution: {amsg}")
 
     if args.ipython:
-        import IPython  # pylint: disable=import-outside-toplevel
-
-        IPython.embed(colors="neutral")
+        try:
+            import IPython
+
+            IPython.embed(colors="neutral")
+        except ModuleNotFoundError:
+            logger(level).exception("No 'ipython' installed")
+
+    if not args.debug:
+        try:
+            rmtree(molecule.tmpDir)
+        except Exception:
+            logger(level).debug("No tmp folder left to be removed")
+    else:
+        try:
+            if molecule.tmpDir:
+                logger(level).debug(f"Keeping folder '{molecule.tmpDir}' for possible helping debugging")
+        except Exception:
+            logger(level).debug("No tmp folder left to be removed")
 
     try:
-        rmtree(molecule.tmpDir)
-    except Exception:
-        pass
+        copy_log(molecule)
+    except UnboundLocalError:
+        print(f"Log tmp location: {tmpLogFile}")
 
     if acpypeFailed:
         sys.exit(19)
-    try:
-        os.chdir(molecule.rootDir)
-    except Exception:
-        pass
+
+    os.chdir(molecule.rootDir)
 
     if not amb2gmxF and molecule.obabelExe:
         if molecule.checkSmiles():
diff --git a/acpype/logger.py b/acpype/logger.py
index 2b870947..07983684 100644
--- a/acpype/logger.py
+++ b/acpype/logger.py
@@ -44,6 +44,8 @@ def format(self, record):
 
 
 def copy_log(molecule):
+    if not os.path.exists(molecule.absHomeDir):
+        raise UnboundLocalError
     local_log = os.path.join(molecule.absHomeDir, "acpype.log")
     if os.path.exists(local_log):
         os.remove(local_log)
diff --git a/acpype/mol.py b/acpype/mol.py
index 471641e7..988a2f8e 100644
--- a/acpype/mol.py
+++ b/acpype/mol.py
@@ -1,38 +1,22 @@
-from acpype.params import Pi
+"""
+    Constructors to define and store the system's topology
 
+    It will create instances for Atoms, AtomTypes, Bonds, Angles and Dihedrals
+    where the topology (the relationships between atoms) is defined and
+    paramenters are stored.
 
-class Atom:
+    Example:
 
-    """
-    Charges in prmtop file has to be divide by 18.2223 to convert to charge
-    in units of the electron charge.
-    To convert ACOEF and BCOEF to r0 (Ang.) and epsilon (kcal/mol), as seen
-    in gaff.dat for example; same atom type (i = j):
-        r0 = 1/2 * (2 * ACOEF/BCOEF)^(1/6)
-        epsilon = 1/(4 * A) * BCOEF^2
-    To convert r0 and epsilon to ACOEF and BCOEF
-        ACOEF = sqrt(ep_i * ep_j) * (r0_i + r0_j)^12
-        BCOEF = 2 * sqrt(ep_i * ep_j) * (r0_i + r0_j)^6
-              = 2 * ACOEF/(r0_i + r0_j)^6
-    where index i and j for atom types.
-    Coord is given in Ang. and mass in Atomic Mass Unit.
-    """
+        >>> atom = acpype.mol.Atom(...) # to be improved
 
-    def __init__(self, atomName, atomType, id_, resid, mass, charge, coord):
-        self.atomName = atomName
-        self.atomType = atomType
-        self.id = id_
-        self.cgnr = id_
-        self.resid = resid
-        self.mass = mass
-        self.charge = charge  # / qConv
-        self.coords = coord
+    Attributes:
+        acpype.mol.Atom     : define Atom
+        acpype.mol.AtomType : define AtomType
+"""
 
-    def __str__(self):
-        return "<Atom id=%s, name=%s, %s>" % (self.id, self.atomName, self.atomType)
+from typing import List
 
-    def __repr__(self):
-        return "<Atom id=%s, name=%s, %s>" % (self.id, self.atomName, self.atomType)
+from acpype.params import Pi
 
 
 class AtomType:
@@ -54,6 +38,63 @@ def __repr__(self):
         return "<AtomType=%s>" % self.atomTypeName
 
 
+class Atom:
+    r"""
+    Atom Object Definition
+
+    Charges in *prmtop* file are divided by ``18.2223`` to be converted
+    in units of the electron charge.
+
+    To convert ``ACOEF`` and ``BCOEF`` to ``r0`` (Å) and ``epsilon`` (ε: kcal/mol), as seen
+    in ``gaff.dat`` for example, for a same atom type (``i = j``):
+
+    .. math::
+        r_0 &= 1/2 * (2 * A_{coef}/B_{coef})^{1/6} \\
+        \epsilon &= 1/(4 * A_{coef}) * B_{coef}^2
+
+    To convert ``r0`` and ``epsilon`` to ``ACOEF`` and ``BCOEF``:
+
+    .. math::
+        A_{coef} &= \sqrt{\epsilon_i * \epsilon_j} * (r_{0i} + r_{0j})^{12} \\
+        B_{coef} &= 2 * \sqrt{\epsilon_i * \epsilon_j} * (r_{0i} + r_{0j})^6 \\
+                          &= 2 * A_{coef}/(r_{0i} + r_{0j})^6
+
+    where index ``i`` and ``j`` for atom types.
+    Coordinates are given in Å and masses in Atomic Mass Unit.
+
+    Returns:
+        acpype.mol.Atom: atom object
+    """
+
+    def __init__(
+        self, atomName: str, atomType: AtomType, id_: int, resid: int, mass: float, charge: float, coord: List[float]
+    ):
+        """
+        Args:
+            atomName (str): atom name
+            atomType (AtomType): atomType object
+            id_ (int): atom number index
+            resid (int): residues number index
+            mass (float): atom mass
+            charge (float): atom charge
+            coord (List[float]): atom (x,y,z) coordinates
+        """
+        self.atomName = atomName
+        self.atomType = atomType
+        self.id = id_
+        self.cgnr = id_
+        self.resid = resid
+        self.mass = mass
+        self.charge = charge  # / qConv
+        self.coords = coord
+
+    def __str__(self):
+        return f"<Atom id={self.id}, name={self.atomName}, {self.atomType}>"
+
+    def __repr__(self):
+        return f"<Atom id={self.id}, name={self.atomName}, {self.atomType}>"
+
+
 class Bond:
 
     """
@@ -66,10 +107,10 @@ def __init__(self, atoms, kBond, rEq):
         self.rEq = rEq
 
     def __str__(self):
-        return "<%s, r=%s>" % (self.atoms, self.rEq)
+        return f"<{self.atoms}, r={self.rEq}>"
 
     def __repr__(self):
-        return "<%s, r=%s>" % (self.atoms, self.rEq)
+        return f"<{self.atoms}, r={self.rEq}>"
 
 
 class Angle:
@@ -84,10 +125,10 @@ def __init__(self, atoms, kTheta, thetaEq):
         self.thetaEq = thetaEq  # rad, to convert to degree: thetaEq * 180/Pi
 
     def __str__(self):
-        return "<%s, ang=%.2f>" % (self.atoms, self.thetaEq * 180 / Pi)
+        return f"<{self.atoms}, ang={self.thetaEq * 180 / Pi:.2f}>"
 
     def __repr__(self):
-        return "<%s, ang=%.2f>" % (self.atoms, self.thetaEq * 180 / Pi)
+        return f"<{self.atoms}, ang={self.thetaEq * 180 / Pi:.2f}>"
 
 
 class Dihedral:
@@ -104,7 +145,7 @@ def __init__(self, atoms, kPhi, period, phase):
         self.phase = phase  # rad, to convert to degree: kPhi * 180/Pi
 
     def __str__(self):
-        return "<%s, ang=%.2f>" % (self.atoms, self.phase * 180 / Pi)
+        return f"<{self.atoms}, ang={self.phase * 180 / Pi:.2f}>"
 
     def __repr__(self):
-        return "<%s, ang=%.2f>" % (self.atoms, self.phase * 180 / Pi)
+        return f"<{self.atoms}, ang={self.phase * 180 / Pi:.2f}>"
diff --git a/acpype/topol.py b/acpype/topol.py
index 32f2b3c1..51f87876 100644
--- a/acpype/topol.py
+++ b/acpype/topol.py
@@ -63,12 +63,12 @@
 
 date = datetime.now().ctime()
 
+pid: int
 
-class Topology_14:
 
+class Topology_14:
     """
     Amber topology abstraction for non-uniform 1-4 scale factors
-
     """
 
     def __init__(self) -> None:
@@ -122,7 +122,7 @@ def read_amber_topology(self, buff):
             try:
                 setattr(self, attributes[i], self.p7_array_read(buff, flag_strings[i]))
             except Exception:
-                logger().info("Skipping non-existent attributes", attributes[i], flag_strings[i])
+                logger().exception(f"Skipping non-existent attributes {attributes[i]} {flag_strings[i]}")
 
     @staticmethod
     def skipline(buff, index):
@@ -183,9 +183,9 @@ def print_gmx_pairs(self):
                 epsilon = lj_bcoeff / 4 / sigma6 * 4.184
                 sigma = sigma6 ** (1 / 6) / 10
                 pair_buff = (
-                    "{:>10.0f} {:>10.0f} {:>6.0f} ".format(ai + 1, al + 1, 1)
-                    + "{:>10.6f} {:>10.6f} ".format(qi, ql)
-                    + "{:>15.5e} {:>15.5e}\n".format(sigma, epsilon)
+                    f"{ai + 1:>10.0f} {al + 1:>10.0f} {1:>6.0f} "
+                    + f"{qi:>10.6f} {ql:>10.6f} "
+                    + f"{sigma:>15.5e} {epsilon:>15.5e}\n"
                 )
                 pair_list.append(pair_buff)
             j += 5
@@ -221,19 +221,14 @@ def patch_gmx_topol14(self, gmx_init_top):
         )
 
 
-class AbstractTopol:
+class AbstractTopol(abc.ABC):
 
     """
-    Super class to build topologies
+    Abstract super class to build topologies
     """
 
-    __metaclass__ = abc.ABCMeta
-
     @abc.abstractmethod
     def __init__(self):
-        if self.__class__ is AbstractTopol:
-            logger().exception("Attempt to create instance of abstract class AbstractTopol")
-            raise TypeError("Attempt to create instance of abstract class AbstractTopol")
         self.debug = None
         self.verbose = None
         self.chargeVal = None
@@ -325,12 +320,18 @@ def printMess(self, text=""):
         """Info log level"""
         logger(self.level).info(f"==> {while_replace(text)}")
 
-    def printQuoted(self, text=""):
+    def printDebugQuoted(self, text=""):
         """Print quoted messages"""
         logger(self.level).debug(10 * "+" + "start_quote" + 59 * "+")
         logger(self.level).debug(while_replace(text))
         logger(self.level).debug(10 * "+" + "end_quote" + 61 * "+")
 
+    def printErrorQuoted(self, text=""):
+        """Print quoted messages"""
+        logger(self.level).error(10 * "+" + "start_quote" + 59 * "+")
+        logger(self.level).error(while_replace(text))
+        logger(self.level).error(10 * "+" + "end_quote" + 61 * "+")
+
     def search(self, name=None, alist=False):
         """
         returns a list with all atomName matching 'name'
@@ -409,10 +410,8 @@ def guessCharge(self):
                 if in_mol == "mol":
                     in_mol = "mdl"
 
-            cmd = f"{self.acExe} -dr no -i {mol2FileForGuessCharge} -fi {in_mol} -o tmp -fo mol2 -c gas -pf y"
+            cmd = f"{self.acExe} -dr no -i {mol2FileForGuessCharge} -fi {in_mol} -o tmp -fo mol2 -c gas -pf n"
 
-            self.printDebug("Debugging...")
-            cmd = cmd.replace("-pf y", "-pf n")
             logger(self.level).debug(while_replace(cmd))
 
             log = _getoutput(cmd).strip()
@@ -429,27 +428,34 @@ def guessCharge(self):
                 except Exception:
                     error = True
 
+            if not charge:
+                error = True
+                charge = 0
             if error:
                 self.printError("guessCharge failed")
                 os.chdir(localDir)
-                self.printQuoted(log)
+                rmtree(self.tmpDir)
+                self.printErrorQuoted(log)
                 self.printMess("Trying with net charge = 0 ...")
         charge = float(charge)
         charge2 = int(round(charge))
         drift = abs(charge2 - charge)
-        self.printDebug("Net charge drift '%3.6f'" % drift)
+        self.printDebug(f"Net charge drift '{drift:3.6f}'")
         if drift > diffTol:
-            self.printError("Net charge drift '%3.5f' bigger than tolerance '%3.5f'" % (drift, diffTol))
+            self.printError(f"Net charge drift '{drift:3.5f}' bigger than tolerance '{diffTol:3.5f}'")
             if not self.force:
-                logger(self.level).exception("Error with calculated charge")
-                raise Exception("Error with calculated charge")
+                msg = "Error with calculated charge"
+                logger(self.level).error(msg)
+                rmtree(self.tmpDir)
+                raise Exception(msg)
         self.chargeVal = str(charge2)
         self.printMess(f"... charge set to {charge2}")
         os.chdir(localDir)
 
     def setResNameCheckCoords(self):
-        """Set a 3 letter residue name
-        and check coords duplication
+        """
+        Set a 3 letter residue name and check coords for issues
+        like duplication, atoms too close or too sparse
         """
         exit_ = False
         localDir = os.path.abspath(".")
@@ -461,7 +467,7 @@ def setResNameCheckCoords(self):
 
         exten = self.ext[1:]
         if self.ext == ".pdb":
-            tmpFile = open(self.inputFile, "r")
+            tmpFile = open(self.inputFile)
         else:
             if exten == "mol":
                 exten = "mdl"
@@ -471,7 +477,7 @@ def setResNameCheckCoords(self):
             if not out.isspace():
                 self.printDebug(out)
             try:
-                tmpFile = open("tmp", "r")
+                tmpFile = open("tmp")
             except Exception:
                 rmtree(self.tmpDir)
                 raise
@@ -492,8 +498,9 @@ def setResNameCheckCoords(self):
         if len(residues) > 1:
             self.printError(f"more than one residue detected '{str(residues)}'")
             self.printError(f"verify your input file '{self.inputFile}'. Aborting ...")
-            logger(self.level).exception("Only ONE Residue is allowed for ACPYPE to work")
-            raise Exception("Only ONE Residue is allowed for ACPYPE to work")
+            msg = "Only ONE Residue is allowed for ACPYPE to work"
+            logger(self.level).error(msg)
+            raise Exception(msg)
 
         dups = ""
         shortd = ""
@@ -523,17 +530,17 @@ def setResNameCheckCoords(self):
 
         if dups:
             self.printError(f"Atoms with same coordinates in '{self.inputFile}'!")
-            self.printQuoted(dups[:-1])
+            self.printErrorQuoted(dups[:-1])
             exit_ = True
 
         if shortd:
             self.printError(f"Atoms TOO close (< {minDist} Ang.)")
-            self.printQuoted(f"Dist (Ang.)    Atoms\n{shortd[:-1]}")
+            self.printErrorQuoted(f"Dist (Ang.)    Atoms\n{shortd[:-1]}")
             exit_ = True
 
         if longd:
-            self.printError(f"Atoms TOO alone (> {maxDist} Ang.)")
-            self.printQuoted(longd[:-1])
+            self.printError(f"Atoms TOO scattered (> {maxDist} Ang.)")
+            self.printErrorQuoted(longd[:-1])
             exit_ = True
 
         if exit_:
@@ -541,16 +548,19 @@ def setResNameCheckCoords(self):
                 self.printWarn("You chose to proceed anyway with '-f' option. GOOD LUCK!")
             else:
                 self.printError("Use '-f' option if you want to proceed anyway. Aborting ...")
+                if not self.debug:
+                    rmtree(self.tmpDir)
+                msg = "Coordinates issues with your system"
+                logger(self.level).error(msg)
                 rmtree(self.tmpDir)
-                logger(self.level).exception("Coordinates issues with your system")
-                raise Exception("Coordinates issues with your system")
-        try:  # scape resname list index out of range
-            resname = list(residues)[0].strip()
-            newresname = resname
-        except Exception:
-            self.printError("resname list index out of range, using default resname: 'LIG'")
+                raise Exception(msg)
+
+        # escape resname list index out of range: no RES name in pdb for example
+        resname = list(residues)[0].strip()
+        if not resname:
             resname = "LIG"
-            newresname = resname
+            self.printWarn("No residue name identified, using default resname: 'LIG'")
+        newresname = resname
 
         # To avoid resname likes: 001 (all numbers), 1e2 (sci number), ADD : reserved terms for leap
         leapWords = [
@@ -667,131 +677,140 @@ def readMol2TotalCharge(self, mol2File):
         """Reads the charges in given mol2 file and returns the total"""
         charge = 0.0
         ll = []
-        cmd = f"{self.acExe} -dr no -i {mol2File} -fi mol2 -o tmp -fo mol2 -c wc -cf tmp.crg -pf y"
-        self.printDebug("Debugging...")
-        cmd = cmd.replace("-pf y", "-pf n")
+        cmd = f"{self.acExe} -dr no -i {mol2File} -fi mol2 -o tmp -fo mol2 -c wc -cf tmp.crg -pf n"
 
         self.printDebug(cmd)
 
         log = _getoutput(cmd)
 
         if os.path.exists("tmp.crg"):
-            tmpFile = open("tmp.crg", "r")
+            tmpFile = open("tmp.crg")
             tmpData = tmpFile.readlines()
             for line in tmpData:
                 ll += line.split()
             charge = sum(map(float, ll))
         if not log.isspace():
-            self.printQuoted(log)
+            self.printDebugQuoted(log)
 
         self.printDebug("readMol2TotalCharge: " + str(charge))
 
         return charge
 
-    def execAntechamber(self, chargeType=None, atomType=None):
-        """To call Antechamber and execute it
-
-        Welcome to antechamber 21.0: molecular input file processor.
-
-        Usage: antechamber -i     input file name
-                        -fi    input file format
-                        -o     output file name
-                        -fo    output file format
-                        -c     charge method
-                        -cf    charge file name
-                        -nc    net molecular charge (int)
-                        -a     additional file name
-                        -fa    additional file format
-                        -ao    additional file operation
-                                crd   : only read in coordinate
-                                crg   : only read in charge
-                                radius: only read in radius
-                                name  : only read in atom name
-                                type  : only read in atom type
-                                bond  : only read in bond type
-                        -m     multiplicity (2S+1), default is 1
-                        -rn    residue name, overrides input file, default is MOL
-                        -rf    residue topology file name in prep input file,
-                                default is molecule.res
-                        -ch    check file name for gaussian, default is 'molecule'
-                        -ek    mopac or sqm keyword, inside quotes; overwrites previous ones
-                        -gk    gaussian job keyword, inside quotes, is ignored when both -gopt and -gsp are used
-                        -gopt  gaussian job keyword for optimization, inside quotes
-                        -gsp   gaussian job keyword for single point calculation, inside quotes
-                        -gm    gaussian memory keyword, inside quotes, such as "%mem=1000MB"
-                        -gn    gaussian number of processors keyword, inside quotes, such as "%nproc=8"
-                        -gdsk  gaussian maximum disk usage keyword, inside quotes, such as "%maxdisk=50GB"
-                        -gv    add keyword to generate gesp file (for Gaussian 09 only)
-                                1    : yes
-                                0    : no, the default
-                        -ge    gaussian esp file generated by iop(6/50=1), default is g09.gesp
-                        -tor   torsional angle list, inside a pair of quotes, such as "1-2-3-4:0,5-6-7-8"
-                                ':1' or ':0' indicates the torsional angle is frozen or not
-                        -df    am1-bcc precharge flag, 2 - use sqm(default); 0 - use mopac
-                        -at    atom type
-                                gaff : the default
-                                gaff2: for gaff2 (beta-version)
-                                amber: for PARM94/99/99SB
-                                bcc  : bcc
-                                sybyl: sybyl
-                        -du    fix duplicate atom names: yes(y)[default] or no(n)
-                        -bk    component/block Id, for ccif
-                        -an    adjust atom names: yes(y) or no(n)
-                                the default is 'y' for 'mol2' and 'ac' and 'n' for the other formats
-                        -j     atom type and bond type prediction index, default is 4
-                                0    : no assignment
-                                1    : atom type
-                                2    : full  bond types
-                                3    : part  bond types
-                                4    : atom and full bond type
-                                5    : atom and part bond type
-                        -s     status information: 0(brief), 1(default) or 2(verbose)
-                        -eq    equalizing atomic charge, default is 1 for '-c resp' and '-c bcc' and 0
-                                for the other charge methods
-                                0    : no use
-                                1    : by atomic paths
-                                2    : by atomic paths and structural information, i.e. E/Z configurations
-                        -pf    remove intermediate files: yes(y) or no(n)[default]
-                        -pl    maximum path length to determin equivalence of atomic charges for resp and bcc,
-                                the smaller the value, the faster the algorithm, default is -1 (use full length),
-                                set this parameter to 10 to 30 if your molecule is big (# atoms >= 100)
-                        -seq   atomic sequence order changable: yes(y)[default] or no(n)
-                        -dr    acdoctor mode: yes(y)[default] or no(n)
-                        -i -o -fi and -fo must appear; others are optional
-                        Use 'antechamber -L' to list the supported file formats and charge methods
-
-                             List of the File Formats
-
-                file format type  abbre. index | file format type abbre. index
-                --------------------------------------------------------------
-                Antechamber        ac       1  | Sybyl Mol2         mol2    2
-                PDB                pdb      3  | Modified PDB       mpdb    4
-                AMBER PREP (int)   prepi    5  | AMBER PREP (car)   prepc   6
-                Gaussian Z-Matrix  gzmat    7  | Gaussian Cartesian gcrt    8
-                Mopac Internal     mopint   9  | Mopac Cartesian    mopcrt 10
-                Gaussian Output    gout    11  | Mopac Output       mopout 12
-                Alchemy            alc     13  | CSD                csd    14
-                MDL                mdl     15  | Hyper              hin    16
-                AMBER Restart      rst     17  | Jaguar Cartesian   jcrt   18
-                Jaguar Z-Matrix    jzmat   19  | Jaguar Output      jout   20
-                Divcon Input       divcrt  21  | Divcon Output      divout 22
-                SQM Input          sqmcrt  23  | SQM Output         sqmout 24
-                Charmm             charmm  25  | Gaussian ESP       gesp   26
-                Component cif      ccif    27  | GAMESS dat         gamess 28
-                Orca input         orcinp  29  | Orca output        orcout 30
-                --------------------------------------------------------------
-                AMBER restart file can only be read in as additional file.
-
-                             List of the Charge Methods
-
-                charge method     abbre. index | charge method    abbre. index
-                --------------------------------------------------------------
-                RESP               resp     1  |  AM1-BCC           bcc     2
-                CM1                cm1      3  |  CM2               cm2     4
-                ESP (Kollman)      esp      5  |  Mulliken          mul     6
-                Gasteiger          gas      7  |  Read in charge    rc      8
-                Write out charge   wc       9  |  Delete Charge     dc     10
-                --------------------------------------------------------------
+    def execAntechamber(self, chargeType=None, atomType=None) -> bool:
+
+        """
+        To call Antechamber and execute it
+
+        Args:
+            chargeType ([str], optional): bcc, gas or user. Defaults to None/bcc.
+            atomType ([str], optional): gaff, amber, gaff2, amber2. Defaults to None/gaff2.
+
+        Returns:
+            bool: True if failed.
+
+        ::
+
+            Welcome to antechamber 21.0: molecular input file processor.
+
+            Usage: antechamber -i     input file name
+                               -fi    input file format
+                               -o     output file name
+                               -fo    output file format
+                               -c     charge method
+                               -cf    charge file name
+                               -nc    net molecular charge (int)
+                               -a     additional file name
+                               -fa    additional file format
+                               -ao    additional file operation
+                                       crd   : only read in coordinate
+                                       crg   : only read in charge
+                                       radius: only read in radius
+                                       name  : only read in atom name
+                                       type  : only read in atom type
+                                       bond  : only read in bond type
+                               -m     multiplicity (2S+1), default is 1
+                               -rn    residue name, overrides input file, default is MOL
+                               -rf    residue topology file name in prep input file,
+                                       default is molecule.res
+                               -ch    check file name for gaussian, default is 'molecule'
+                               -ek    mopac or sqm keyword, inside quotes; overwrites previous ones
+                               -gk    gaussian job keyword, inside quotes, is ignored when both -gopt and -gsp are used
+                               -gopt  gaussian job keyword for optimization, inside quotes
+                               -gsp   gaussian job keyword for single point calculation, inside quotes
+                               -gm    gaussian memory keyword, inside quotes, such as "%mem=1000MB"
+                               -gn    gaussian number of processors keyword, inside quotes, such as "%nproc=8"
+                               -gdsk  gaussian maximum disk usage keyword, inside quotes, such as "%maxdisk=50GB"
+                               -gv    add keyword to generate gesp file (for Gaussian 09 only)
+                                       1    : yes
+                                       0    : no, the default
+                               -ge    gaussian esp file generated by iop(6/50=1), default is g09.gesp
+                               -tor   torsional angle list, inside a pair of quotes, such as "1-2-3-4:0,5-6-7-8"
+                                       ':1' or ':0' indicates the torsional angle is frozen or not
+                               -df    am1-bcc precharge flag, 2 - use sqm(default); 0 - use mopac
+                               -at    atom type
+                                       gaff : the default
+                                       gaff2: for gaff2 (beta-version)
+                                       amber: for PARM94/99/99SB
+                                       bcc  : bcc
+                                       sybyl: sybyl
+                               -du    fix duplicate atom names: yes(y)[default] or no(n)
+                               -bk    component/block Id, for ccif
+                               -an    adjust atom names: yes(y) or no(n)
+                                       the default is 'y' for 'mol2' and 'ac' and 'n' for the other formats
+                               -j     atom type and bond type prediction index, default is 4
+                                       0    : no assignment
+                                       1    : atom type
+                                       2    : full  bond types
+                                       3    : part  bond types
+                                       4    : atom and full bond type
+                                       5    : atom and part bond type
+                               -s     status information: 0(brief), 1(default) or 2(verbose)
+                               -eq    equalizing atomic charge, default is 1 for '-c resp' and '-c bcc' and 0
+                                       for the other charge methods
+                                       0    : no use
+                                       1    : by atomic paths
+                                       2    : by atomic paths and structural information, i.e. E/Z configurations
+                               -pf    remove intermediate files: yes(y) or no(n)[default]
+                               -pl    maximum path length to determin equivalence of atomic charges for resp and bcc,
+                                       the smaller the value, the faster the algorithm, default is -1 (use full length),
+                                       set this parameter to 10 to 30 if your molecule is big (# atoms >= 100)
+                               -seq   atomic sequence order changable: yes(y)[default] or no(n)
+                               -dr    acdoctor mode: yes(y)[default] or no(n)
+                               -i -o -fi and -fo must appear; others are optional
+                               Use 'antechamber -L' to list the supported file formats and charge methods
+
+                                List of the File Formats
+
+                    file format type  abbre. index | file format type abbre. index
+                    --------------------------------------------------------------
+                    Antechamber        ac       1  | Sybyl Mol2         mol2    2
+                    PDB                pdb      3  | Modified PDB       mpdb    4
+                    AMBER PREP (int)   prepi    5  | AMBER PREP (car)   prepc   6
+                    Gaussian Z-Matrix  gzmat    7  | Gaussian Cartesian gcrt    8
+                    Mopac Internal     mopint   9  | Mopac Cartesian    mopcrt 10
+                    Gaussian Output    gout    11  | Mopac Output       mopout 12
+                    Alchemy            alc     13  | CSD                csd    14
+                    MDL                mdl     15  | Hyper              hin    16
+                    AMBER Restart      rst     17  | Jaguar Cartesian   jcrt   18
+                    Jaguar Z-Matrix    jzmat   19  | Jaguar Output      jout   20
+                    Divcon Input       divcrt  21  | Divcon Output      divout 22
+                    SQM Input          sqmcrt  23  | SQM Output         sqmout 24
+                    Charmm             charmm  25  | Gaussian ESP       gesp   26
+                    Component cif      ccif    27  | GAMESS dat         gamess 28
+                    Orca input         orcinp  29  | Orca output        orcout 30
+                    --------------------------------------------------------------
+                    AMBER restart file can only be read in as additional file.
+
+                                List of the Charge Methods
+
+                    charge method     abbre. index | charge method    abbre. index
+                    --------------------------------------------------------------
+                    RESP               resp     1  |  AM1-BCC           bcc     2
+                    CM1                cm1      3  |  CM2               cm2     4
+                    ESP (Kollman)      esp      5  |  Mulliken          mul     6
+                    Gasteiger          gas      7  |  Read in charge    rc      8
+                    Write out charge   wc       9  |  Delete Charge     dc     10
+                    --------------------------------------------------------------
         """
         global pid
 
@@ -813,7 +832,7 @@ def execAntechamber(self, chargeType=None, atomType=None):
         if exten == "mol":
             exten = "mdl"
 
-        cmd = "%s -dr no -i %s -fi %s -o %s -fo mol2 %s -nc %s -m %s -s 2 -df %s -at %s -pf y %s" % (
+        cmd = "{} -dr no -i {} -fi {} -o {} -fo mol2 {} -nc {} -m {} -s 2 -df {} -at {} -pf n {}".format(
             self.acExe,
             self.inputFile,
             exten,
@@ -826,9 +845,6 @@ def execAntechamber(self, chargeType=None, atomType=None):
             self.ekFlag,
         )
 
-        self.printDebug("Debugging...")
-        cmd = cmd.replace("-pf y", "-pf n")
-
         self.printDebug(cmd)
 
         if os.path.exists(self.acMol2FileName) and not self.force:
@@ -837,7 +853,7 @@ def execAntechamber(self, chargeType=None, atomType=None):
             try:
                 os.remove(self.acMol2FileName)
             except Exception:
-                pass
+                self.printDebug("No file left to be removed")
             signal.signal(signal.SIGALRM, self.signal_handler)
             signal.alarm(self.timeTol)
             p = sub.Popen(cmd, shell=True, stderr=sub.STDOUT, stdout=sub.PIPE)
@@ -849,7 +865,7 @@ def execAntechamber(self, chargeType=None, atomType=None):
         if os.path.exists(self.acMol2FileName):
             self.printMess("* Antechamber OK *")
         else:
-            self.printQuoted(self.acLog)
+            self.printErrorQuoted(self.acLog)
             return True
         return False
 
@@ -857,13 +873,14 @@ def signal_handler(self, _signum, _frame):  # , pid = 0):
         """Signal handler"""
         global pid
         pids = job_pids_family(pid)
-        self.printDebug("PID: %s, PIDS: %s" % (pid, pids))
-        self.printMess("Timed out! Process %s killed, max exec time (%ss) exceeded" % (pids, self.timeTol))
+        self.printDebug(f"PID: {pid}, PIDS: {pids}")
+        self.printMess(f"Timed out! Process {pids} killed, max exec time ({self.timeTol}s) exceeded")
         # os.system('kill -15 %s' % pids)
         for i in pids.split():
             os.kill(int(i), 15)
-        logger(self.level).exception("Semi-QM taking too long to finish... aborting!")
-        raise Exception("Semi-QM taking too long to finish... aborting!")
+        msg = "Semi-QM taking too long to finish... aborting!"
+        logger(self.level).error(msg)
+        raise Exception(msg)
 
     def delOutputFiles(self):
         """Delete temporary output files"""
@@ -931,7 +948,7 @@ def execTleap(self):
                 os.remove(self.acTopFileName)
                 os.remove(self.acXyzFileName)
             except Exception:
-                pass
+                self.printDebug("No crd or prm files left to be removed")
             self.printMess("Executing Tleap...")
             self.printDebug(cmd)
             self.tleapLog = _getoutput(cmd)
@@ -940,7 +957,7 @@ def execTleap(self):
         if self.checkXyzAndTopFiles():
             self.printMess("* Tleap OK *")
         else:
-            self.printQuoted(self.tleapLog)
+            self.printErrorQuoted(self.tleapLog)
             return True
         return False
 
@@ -958,7 +975,7 @@ def checkLeapLog(self, log):
                 block = False
             if block:
                 check += line
-        self.printQuoted(check[:-1])
+        self.printDebugQuoted(check[:-1])
 
     def locateDat(self, aFile):
         """locate a file pertinent to $AMBERHOME/dat/leap/parm/"""
@@ -998,18 +1015,18 @@ def execParmchk(self):
             check = self.checkFrcmod()
             if check:
                 self.printWarn("Couldn't determine all parameters:")
-                self.printMess("From file '%s'\n" % self.acFrcmodFileName + check)
+                self.printMess(f"From file '{self.acFrcmodFileName + check}'\n")
             else:
                 self.printMess("* Parmchk OK *")
         else:
-            self.printQuoted(self.parmchkLog)
+            self.printErrorQuoted(self.parmchkLog)
             return True
         return False
 
     def checkFrcmod(self):
         """Check FRCMOD file"""
         check = ""
-        frcmodContent = open(self.acFrcmodFileName, "r").readlines()
+        frcmodContent = open(self.acFrcmodFileName).readlines()
         for line in frcmodContent:
             if "ATTN, need revision" in line:
                 check += line
@@ -1026,9 +1043,11 @@ def convertPdbToMol2(self):
     def convertSmilesToMol2(self):
         """Convert Smiles to MOL2 by using obabel"""
 
-        if not self.obabelExe:
-            logger(self.level).exception("SMILES needs OpenBabel python module")
-            raise Exception("SMILES needs OpenBabel python module")
+        # if not self.obabelExe:
+        #     msg = "SMILES needs OpenBabel python module"
+        #     logger(self.level).error(msg)
+        #     raise Exception(msg)
+
         if checkOpenBabelVersion() >= 300:
             from openbabel import pybel
 
@@ -1057,7 +1076,7 @@ def execObabel(self):
         if os.path.exists(self.inputFile):
             self.printMess("* Babel OK *")
         else:
-            self.printQuoted(self.obabelLog)
+            self.printErrorQuoted(self.obabelLog)
             return True
         return False
 
@@ -1085,7 +1104,7 @@ def createMolTopol(self):
         """
         Create molTop obj
         """
-        self.topFileData = open(self.acTopFileName, "r").readlines()
+        self.topFileData = open(self.acTopFileName).readlines()
         self.molTopol = MolTopol(
             self,  # acTopolObj
             verbose=self.verbose,
@@ -1107,7 +1126,6 @@ def createMolTopol(self):
             self.pickleSave()
         except Exception:
             self.printError("pickleSave failed")
-            pass
 
         if not self.debug:
             self.delOutputFiles()  # required to use on Jupyter Notebook
@@ -1115,12 +1133,16 @@ def createMolTopol(self):
 
     def pickleSave(self):
         """
-        To restore:
-            from acpype import *
-            #import cPickle as pickle
-            import pickle
-            o = pickle.load(open('DDD.pkl','rb'))
-            NB: It fails to restore with ipython in Mac (Linux OK)
+        Example:
+
+            to restore:
+
+            .. code-block:: python
+
+                from acpype import *
+                # import cPickle as pickle
+                import pickle
+                mol = pickle.load(open('DDD.pkl','rb'))
         """
         pklFile = self.baseName + ".pkl"
         dumpFlag = False
@@ -1146,12 +1168,11 @@ def getFlagData(self, flag):
         data = ""
 
         if not self.topFileData:
-            logger(self.level).exception("PRMTOP file empty?")
-            raise Exception("PRMTOP file empty?")
+            msg = "PRMTOP file empty?"
+            logger(self.level).error(msg)
+            raise Exception(msg)
 
         for rawLine in self.topFileData:
-            if "%COMMENT" in rawLine:
-                continue
             line = rawLine.replace("\r", "").replace("\n", "")
             if tFlag in line:
                 block = True
@@ -1203,7 +1224,7 @@ def getResidueLabel(self):
         residueLabel = self.getFlagData("RESIDUE_LABEL")
         residueLabel = list(map(str, residueLabel))
         if residueLabel[0] != residueLabel[0].upper():
-            self.printWarn("residue label '%s' in '%s' is not all UPPERCASE" % (residueLabel[0], self.inputFile))
+            self.printWarn(f"residue label '{residueLabel[0]}' in '{self.inputFile}' is not all UPPERCASE")
             self.printWarn("this may raise problem with some applications like CNS")
         self.residueLabel = residueLabel
 
@@ -1213,8 +1234,9 @@ def getCoords(self):
         [[x1,y1,z1],[x2,y2,z2], etc.]
         """
         if not self.xyzFileData:
-            logger(self.level).exception("INPCRD file empty?")
-            raise Exception("INPCRD file empty?")
+            msg = "INPCRD file empty?"
+            logger(self.level).error(msg)
+            raise Exception(msg)
         data = ""
         for rawLine in self.xyzFileData[2:]:
             line = rawLine.replace("\r", "").replace("\n", "")
@@ -1403,10 +1425,8 @@ def getDihedrals(self):
                     atomPairs.add(pair)
             else:
                 improperDih.append(dihedral)
-        try:
-            atomPairs = sorted(atomPairs)
-        except Exception:
-            pass
+        if self.sorted:
+            atomPairs = sorted(atomPairs, key=lambda x: (x[0].id, x[1].id))
         self.properDihedrals = properDih
         self.improperDihedrals = improperDih
         self.condensedProperDihedrals = condProperDih  # [[],[],...]
@@ -1454,9 +1474,9 @@ def getChirals(self):
                     quad.append(bAts[0])
             if len(quad) != 4:
                 if self.chiral:
-                    self.printWarn("Atom %s has less than 4 connections to 4 different atoms. It's NOT Chiral!" % atChi)
+                    self.printWarn(f"Atom {atChi} has less than 4 connections to 4 different atoms. It's NOT Chiral!")
                 continue
-            v1, v2, v3, v4 = [x.coords for x in quad]
+            v1, v2, v3, v4 = (x.coords for x in quad)
             chiralGroups.append((atChi, quad, imprDihAngle(v1, v2, v3, v4)))
         self.chiralGroups = chiralGroups
 
@@ -1541,7 +1561,6 @@ def balanceCharges(self, chargeList, FirstNonSoluteId=None):
         else:
             lim = minVal
         nLims = chargeList.count(lim)
-        # limId = chargeList.index(lim)
         diff = totalConverted - round(totalConverted)
         fix = lim - diff * qConv / nLims
         id_ = 0
@@ -1598,8 +1617,10 @@ def setProperDihedralsCoef(self):
                 phaseRaw = dih.phase * radPi  # in degree
                 phase = int(phaseRaw)  # in degree
                 if period > 4 and self.gmx4:
-                    logger(self.level).exception("Likely trying to convert ILDN to RB, DO NOT use option '-z'")
-                    raise Exception("Likely trying to convert ILDN to RB, DO NOT use option '-z'")
+                    rmtree(self.absHomeDir)
+                    msg = "Likely trying to convert ILDN to RB, DO NOT use option '-z'"
+                    logger(self.level).error(msg)
+                    raise Exception(msg)
                 if phase in [0, 180]:
                     properDihedralsGmx45.append([item[0].atoms, phaseRaw, kPhi, period])
                     if self.gmx4:
@@ -1654,32 +1675,33 @@ def writeCharmmTopolFiles(self):
         self.getResidueLabel()
         res = self.resName
 
-        cmd = (
-            "%s -dr no -i %s -fi mol2 -o %s -fo charmm -s 2 -at %s \
-        -pf y -rn %s"
-            % (self.acExe, self.acMol2FileName, self.charmmBase, at, res)
-        )
+        cmd = f"{self.acExe} -dr no -i {self.acMol2FileName} -fi mol2 -o {self.charmmBase} \
+            -fo charmm -s 2 -at {at} -pf n -rn {res}"
 
-        cmd = cmd.replace("-pf y", "-pf n")
         self.printDebug(cmd)
 
         log = _getoutput(cmd)
-        self.printQuoted(log)
+        self.printDebugQuoted(log)
 
-    def writePdb(self, file_):
+    def writePdb(self, afile):
         """
-        Write a new PDB file_ with the atom names defined by Antechamber
-        Input: file_ path string
-        The format generated here use is slightly different from
-        old: http://www.wwpdb.org/documentation/file-format-content/format23/sect9.html
-        latest: http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html
-        respected to atom name
-        Using GAFF2 atom types
+        Write a new PDB file with the atom names defined by Antechamber
+
+        The format generated here use is slightly different from:
+
+            old: http://www.wwpdb.org/documentation/file-format-content/format23/sect9.html
+            latest: http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html
+
+        respected to atom name.
+        Using GAFF2 atom types.
         CU/Cu Copper, CL/cl Chlorine, BR/br Bromine
+
+        Args:
+            afile ([str]): file path name
         """
         # TODO: assuming only one residue ('1')
-        pdbFile = open(file_, "w")
-        fbase = os.path.basename(file_)
+        pdbFile = open(afile, "w")
+        fbase = os.path.basename(afile)
         pdbFile.write("REMARK " + head % (fbase, date))
         id_ = 1
         for atom in self.atoms:
@@ -1715,102 +1737,109 @@ def writePdb(self, file_):
 
     def writeGromacsTopolFiles(self):
         """
-        # from ~/Programmes/amber10/dat/leap/parm/gaff.dat
-        #atom type        atomic mass        atomic polarizability        comments
-        ca                12.01                 0.360                    Sp2 C in pure aromatic systems
-        ha                1.008                 0.135                    H bonded to aromatic carbon
-
-        #bonded atoms        harmonic force kcal/mol/A^2       eq. dist. Ang.  comments
-        ca-ha                  344.3*                           1.087**         SOURCE3  1496    0.0024    0.0045
-        * for gmx: 344.3 * 4.184 * 100 * 2 = 288110 kJ/mol/nm^2 (why factor 2?)
-        ** convert Ang to nm ( div by 10) for gmx: 1.087 A = 0.1087 nm
-        # CA HA      1    0.10800   307105.6 ; ged from 340. bsd on C6H6 nmodes; PHE,TRP,TYR (from ffamber99bon.itp)
-        # CA-HA  367.0    1.080       changed from 340. bsd on C6H6 nmodes; PHE,TRP,TYR (from parm99.dat)
-
-        # angle        HF kcal/mol/rad^2    eq angle degrees     comments
-        ca-ca-ha        48.5*             120.01                SOURCE3 2980   0.1509   0.2511
-        * to convert to gmx: 48.5 * 4.184 * 2 = 405.848 kJ/mol/rad^2 (why factor 2?)
-        # CA  CA  HA           1   120.000    418.400 ; new99 (from ffamber99bon.itp)
-        # CA-CA-HA    50.0      120.00 (from parm99.dat)
-
-        # dihedral    idivf        barrier hight/2 kcal/mol  phase degrees       periodicity     comments
-        X -ca-ca-X    4           14.500*                    180.000             2.000           intrpol.bsd.on C6H6
-        *convert 2 gmx: 14.5/4 * 4.184 * 2 (?) (yes in amb2gmx, not in topolbuild, why?) = 30.334 or 15.167 kJ/mol
-        # X -CA-CA-X    4   14.50        180.0     2.         intrpol.bsd.on C6H6 (from parm99.dat)
-        # X CA CA  X    3   30.334       0.000   -30.33400     0.000     0.000     0.000   ; intrpol.bsd.on C6H6
-        ;propers treated as RBs in GMX to use combine multiple AMBER torsions per quartet (from ffamber99bon.itp)
-
-        # impr. dihedral        barrier hight/2      phase degrees       periodicity     comments
-        X -X -ca-ha             1.1*                  180.                      2.       bsd.on C6H6 nmodes
-        * to convert to gmx: 1.1 * 4.184 = 4.6024 kJ/mol/rad^2
-        # X -X -CA-HA         1.1          180.          2.           bsd.on C6H6 nmodes (from parm99.dat)
-        # X   X   CA  HA       1      180.00     4.60240     2      ; bsd.on C6H6 nmodes
-        ;impropers treated as propers in GROMACS to use correct AMBER analytical function (from ffamber99bon.itp)
-
-        # 6-12 parms     sigma = 2 * r * 2^(-1/6)    epsilon
-        # atomtype        radius Ang.                    pot. well depth kcal/mol      comments
-          ha                  1.4590*                      0.0150**                         Spellmeyer
-          ca                  1.9080                    0.0860                            OPLS
-        * to convert to gmx:
-            sigma = 1.4590 * 2^(-1/6) * 2 = 2 * 1.29982 Ang. = 2 * 0.129982 nm  = 1.4590 * 2^(5/6)/10 =  0.259964 nm
-        ** to convert to gmx: 0.0150 * 4.184 = 0.06276 kJ/mol
-        # amber99_3    CA     0.0000  0.0000  A   3.39967e-01  3.59824e-01 (from ffamber99nb.itp)
-        # amber99_22   HA     0.0000  0.0000  A   2.59964e-01  6.27600e-02 (from ffamber99nb.itp)
-        # C*          1.9080  0.0860             Spellmeyer
-        # HA          1.4590  0.0150             Spellmeyer (from parm99.dat)
-        # to convert r and epsilon to ACOEF and BCOEF
-        # ACOEF = sqrt(e1*e2) * (r1 + r2)^12 ; BCOEF = 2 * sqrt(e1*e2) * (r1 + r2)^6 = 2 * ACOEF/(r1+r2)^6
-        # to convert ACOEF and BCOEF to r and epsilon
-        # r = 0.5 * (2*ACOEF/BCOEF)^(1/6); ep = BCOEF^2/(4*ACOEF)
-        # to convert ACOEF and BCOEF to sigma and epsilon (GMX)
-        # sigma = (ACOEF/BCOEF)^(1/6) * 0.1 ; epsilon = 4.184 * BCOEF^2/(4*ACOEF)
-        #   ca   ca       819971.66        531.10
-        #   ca   ha        76245.15        104.66
-        #   ha   ha         5716.30         18.52
+        Write GMX topology Files
+
+        ::
+
+            # from ~/Programmes/amber10/dat/leap/parm/gaff.dat
+            #atom type        atomic mass        atomic polarizability        comments
+            ca                12.01                 0.360                    Sp2 C in pure aromatic systems
+            ha                1.008                 0.135                    H bonded to aromatic carbon
+
+            #bonded atoms        harmonic force kcal/mol/A^2       eq. dist. Ang.  comments
+            ca-ha                  344.3*                           1.087**         SOURCE3  1496    0.0024    0.0045
+            * for gmx: 344.3 * 4.184 * 100 * 2 = 288110 kJ/mol/nm^2 (why factor 2?)
+            ** convert Ang to nm ( div by 10) for gmx: 1.087 A = 0.1087 nm
+            # CA HA      1    0.10800   307105.6 ; ged from 340. bsd on C6H6 nmodes; PHE,TRP,TYR (from ffamber99bon.itp)
+            # CA-HA  367.0    1.080       changed from 340. bsd on C6H6 nmodes; PHE,TRP,TYR (from parm99.dat)
+
+            # angle        HF kcal/mol/rad^2    eq angle degrees     comments
+            ca-ca-ha        48.5*             120.01                SOURCE3 2980   0.1509   0.2511
+            * to convert to gmx: 48.5 * 4.184 * 2 = 405.848 kJ/mol/rad^2 (why factor 2?)
+            # CA  CA  HA           1   120.000    418.400 ; new99 (from ffamber99bon.itp)
+            # CA-CA-HA    50.0      120.00 (from parm99.dat)
+
+            # dihedral    idivf        barrier hight/2 kcal/mol  phase degrees       periodicity     comments
+            X -ca-ca-X    4           14.500*                    180.000             2.000           intrpol.bsd.on C6H6
+            *convert 2 gmx: 14.5/4 * 4.184 * 2 (?) (yes in amb2gmx, not in topolbuild, why?) = 30.334 or 15.167 kJ/mol
+            # X -CA-CA-X    4   14.50        180.0     2.         intrpol.bsd.on C6H6 (from parm99.dat)
+            # X CA CA  X    3   30.334       0.000   -30.33400     0.000     0.000     0.000   ; intrpol.bsd.on C6H6
+            ;propers treated as RBs in GMX to use combine multiple AMBER torsions per quartet (from ffamber99bon.itp)
+
+            # impr. dihedral        barrier hight/2      phase degrees       periodicity     comments
+            X -X -ca-ha             1.1*                  180.                      2.       bsd.on C6H6 nmodes
+            * to convert to gmx: 1.1 * 4.184 = 4.6024 kJ/mol/rad^2
+            # X -X -CA-HA         1.1          180.          2.           bsd.on C6H6 nmodes (from parm99.dat)
+            # X   X   CA  HA       1      180.00     4.60240     2      ; bsd.on C6H6 nmodes
+            ;impropers treated as propers in GROMACS to use correct AMBER analytical function (from ffamber99bon.itp)
+
+            # 6-12 parms     sigma = 2 * r * 2^(-1/6)    epsilon
+            # atomtype        radius Ang.                    pot. well depth kcal/mol      comments
+            ha                  1.4590*                      0.0150**                         Spellmeyer
+            ca                  1.9080                    0.0860                            OPLS
+            * to convert to gmx:
+                sigma = 1.4590 * 2^(-1/6) * 2 = 2 * 1.29982 Ang. = 2 * 0.129982 nm  = 1.4590 * 2^(5/6)/10 =  0.259964 nm
+            ** to convert to gmx: 0.0150 * 4.184 = 0.06276 kJ/mol
+            # amber99_3    CA     0.0000  0.0000  A   3.39967e-01  3.59824e-01 (from ffamber99nb.itp)
+            # amber99_22   HA     0.0000  0.0000  A   2.59964e-01  6.27600e-02 (from ffamber99nb.itp)
+            # C*          1.9080  0.0860             Spellmeyer
+            # HA          1.4590  0.0150             Spellmeyer (from parm99.dat)
+            # to convert r and epsilon to ACOEF and BCOEF
+            # ACOEF = sqrt(e1*e2) * (r1 + r2)^12 ; BCOEF = 2 * sqrt(e1*e2) * (r1 + r2)^6 = 2 * ACOEF/(r1+r2)^6
+            # to convert ACOEF and BCOEF to r and epsilon
+            # r = 0.5 * (2*ACOEF/BCOEF)^(1/6); ep = BCOEF^2/(4*ACOEF)
+            # to convert ACOEF and BCOEF to sigma and epsilon (GMX)
+            # sigma = (ACOEF/BCOEF)^(1/6) * 0.1 ; epsilon = 4.184 * BCOEF^2/(4*ACOEF)
+            #   ca   ca       819971.66        531.10
+            #   ca   ha        76245.15        104.66
+            #   ha   ha         5716.30         18.52
 
         For proper dihedrals: a quartet of atoms may appear with more than
         one set of parameters and to convert to GMX they are treated as RBs;
         use the algorithm:
-          for(my $j=$i;$j<=$lines;$j++){
-            my $period = $pn{$j};
-            if($pk{$j}>0) {
-              $V[$period] = 2*$pk{$j}*$cal;
-            }
-            # assign V values to C values as predefined #
-            if($period==1){
-              $C[0]+=0.5*$V[$period];
-              if($phase{$j}==0){
-                $C[1]-=0.5*$V[$period];
-              }else{
-                $C[1]+=0.5*$V[$period];
-              }
-            }elsif($period==2){
-              if(($phase{$j}==180)||($phase{$j}==3.14)){
-                $C[0]+=$V[$period];
-                $C[2]-=$V[$period];
-              }else{
-                $C[2]+=$V[$period];
-              }
-            }elsif($period==3){
-              $C[0]+=0.5*$V[$period];
-              if($phase{$j}==0){
-                $C[1]+=1.5*$V[$period];
-                $C[3]-=2*$V[$period];
-              }else{
-                $C[1]-=1.5*$V[$period];
-                $C[3]+=2*$V[$period];
-              }
-            }elsif($period==4){
-              if(($phase{$j}==180)||($phase{$j}==3.14)){
-                $C[2]+=4*$V[$period];
-                $C[4]-=4*$V[$period];
-              }else{
-                $C[0]+=$V[$period];
-                $C[2]-=4*$V[$period];
-                $C[4]+=4*$V[$period];
-              }
+
+        .. code-block:: c++
+
+            for(my $j=$i;$j<=$lines;$j++){
+                my $period = $pn{$j};
+                if($pk{$j}>0) {
+                $V[$period] = 2*$pk{$j}*$cal;
+                }
+                # assign V values to C values as predefined #
+                if($period==1){
+                $C[0]+=0.5*$V[$period];
+                if($phase{$j}==0){
+                    $C[1]-=0.5*$V[$period];
+                }else{
+                    $C[1]+=0.5*$V[$period];
+                }
+                }elsif($period==2){
+                if(($phase{$j}==180)||($phase{$j}==3.14)){
+                    $C[0]+=$V[$period];
+                    $C[2]-=$V[$period];
+                }else{
+                    $C[2]+=$V[$period];
+                }
+                }elsif($period==3){
+                $C[0]+=0.5*$V[$period];
+                if($phase{$j}==0){
+                    $C[1]+=1.5*$V[$period];
+                    $C[3]-=2*$V[$period];
+                }else{
+                    $C[1]-=1.5*$V[$period];
+                    $C[3]+=2*$V[$period];
+                }
+                }elsif($period==4){
+                if(($phase{$j}==180)||($phase{$j}==3.14)){
+                    $C[2]+=4*$V[$period];
+                    $C[4]-=4*$V[$period];
+                }else{
+                    $C[0]+=$V[$period];
+                    $C[2]-=4*$V[$period];
+                    $C[4]+=4*$V[$period];
+                }
+                }
             }
-          }
         """
         if self.amb2gmx:
             os.chdir(self.absHomeDir)
@@ -1831,9 +1860,13 @@ def writeGromacsTopolFiles(self):
             os.chdir(self.rootDir)
 
     def setAtomType4Gromacs(self):
-        """Atom types names in Gromacs TOP file are not case sensitive;
+        """
+        Atom types names in Gromacs TOP file are not case sensitive;
         this routine will append a '_' to lower case atom type.
-        E.g.: CA and ca -> CA and ca_
+
+        Example:
+
+            >>> CA and ca -> CA and ca_
         """
 
         if self.merge:
@@ -2153,9 +2186,9 @@ def writeGromacsTop(self):
                     sigma,
                     epsilon,
                 )
-                + " ; %4.2f  %1.4f\n" % (r0, epAmber)
+                + f" ; {r0:4.2f}  {epAmber:1.4f}\n"
             )
-            oline = "; %s:%s:opls_%s: %s\n" % (aTypeName, aTypeNameOpls, oaCode[0], repr(oaCode[1:]))
+            oline = f"; {aTypeName}:{aTypeNameOpls}:opls_{oaCode[0]}: {repr(oaCode[1:])}\n"
             # tmpFile.write(line)
             temp.append(line)
             otemp.append(oline)
@@ -2177,7 +2210,7 @@ def writeGromacsTop(self):
             oitpText += otemp
         self.printDebug("GMX atomtypes done")
 
-        if len(self.atoms) > 3 * nWat + sum([x[1] for x in ionsSorted]):
+        if len(self.atoms) > 3 * nWat + sum(x[1] for x in ionsSorted):
             nSolute = 1
 
         if nWat:
@@ -2719,7 +2752,7 @@ def writeGroFile(self):
             # vZ = self.pbc[1][2]
             if vX == 90.0:
                 self.printDebug("PBC triclinic")
-                text = "%11.5f %11.5f %11.5f\n" % (boxX, boxY, boxZ)
+                text = f"{boxX:11.5f} {boxY:11.5f} {boxZ:11.5f}\n"
             elif round(vX, 2) == 109.47:
                 self.printDebug("PBC octahedron")
                 f1 = 0.471405  # 1/3 * sqrt(2)
@@ -2730,7 +2763,7 @@ def writeGroFile(self):
                 v12 = f2
                 v13 = -f2
                 v23 = f1 * boxX
-                text = "%11.5f %11.5f %11.5f %11.5f %11.5f %11.5f %11.5f %11.5f %11.5f\n" % (
+                text = "{:11.5f} {:11.5f} {:11.5f} {:11.5f} {:11.5f} {:11.5f} {:11.5f} {:11.5f} {:11.5f}\n".format(
                     boxX,
                     v22,
                     v33,
@@ -2749,7 +2782,7 @@ def writeGroFile(self):
             boxX = max(X) - min(X)  # + 2.0 # 2.0 is double of rlist
             boxY = max(Y) - min(Y)  # + 2.0
             boxZ = max(Z) - min(Z)  # + 2.0
-            text = "%11.5f %11.5f %11.5f\n" % (boxX * 20.0, boxY * 20.0, boxZ * 20.0)
+            text = f"{boxX * 20.0:11.5f} {boxY * 20.0:11.5f} {boxZ * 20.0:11.5f}\n"
         groFile.write(text)
 
     def writePosreFile(self, fc=1000):
@@ -2993,7 +3026,7 @@ def writeCnsTopolFiles(self):
         # print "Writing CNS TOP file\n"
         topFile.write("Remarks " + head % (top, date))
         topFile.write("\nset echo=false end\n")
-        topFile.write("\nautogenerate angles=%s dihedrals=%s end\n" % (autoAngleFlag, autoDihFlag))
+        topFile.write(f"\nautogenerate angles={autoAngleFlag} dihedrals={autoDihFlag} end\n")
         topFile.write("\n{ atomType  mass }\n")
 
         for at in self.atomTypes:
@@ -3202,8 +3235,9 @@ def __init__(
             )
             self.printMess(hint1)
             self.printMess(hint2)
-            logger(self.level).exception("Missing ANTECHAMBER")
-            raise Exception("Missing ANTECHAMBER")
+            msg = "Missing ANTECHAMBER"
+            logger(self.level).error(msg)
+            raise Exception(msg)
         self.inputFile = os.path.basename(inputFile)
         self.rootDir = os.path.abspath(".")
         self.absInputFile = os.path.abspath(inputFile)
@@ -3221,8 +3255,9 @@ def __init__(
                 self.is_smiles = False
                 self.smiles = None
         elif not os.path.exists(self.absInputFile):
-            logger(self.level).exception(f"Input file {inputFile} DOES NOT EXIST")
-            raise Exception(f"Input file {inputFile} DOES NOT EXIST")
+            msg = f"Input file {inputFile} DOES NOT EXIST"
+            logger(self.level).error(msg)
+            raise Exception(msg)
         baseOriginal, ext = os.path.splitext(self.inputFile)
         base = basename or baseOriginal
         self.baseOriginal = baseOriginal
@@ -3233,14 +3268,17 @@ def __init__(
             if self.ext != ".mol2" and self.ext != ".mdl":
                 self.printError(f"no '{binaries['obabel_bin']}' executable; you need it if input is PDB or SMILES")
                 self.printError("otherwise use only MOL2 or MDL file as input ... aborting!")
-                logger(self.level).exception("Missing OBABEL")
-                raise Exception("Missing OBABEL")
+                msg = "Missing OBABEL"
+                logger(self.level).error(msg)
+                raise Exception(msg)
             else:
                 self.printWarn(f"no '{binaries['obabel_bin']}' executable, no PDB file can be used as input!")
         if self.is_smiles:
             self.convertSmilesToMol2()
         self.timeTol = timeTol
         self.printDebug("Max execution time tolerance is %s" % elapsedTime(self.timeTol))
+        # ekFlag e.g. (default used by sqm):
+        # acpype -i cccc -k "qm_theory='AM1', grms_tol=0.0005, scfconv=1.d-10, ndiis_attempts=700, qmcharge=0"
         if ekFlag == '"None"' or ekFlag is None:
             self.ekFlag = ""
         else:
@@ -3268,7 +3306,7 @@ def __init__(
         self.tmpDir = os.path.join(self.rootDir, ".acpype_tmp_%s" % os.path.basename(base))
         self.setResNameCheckCoords()
         self.guessCharge()
-        acMol2FileName = "%s_%s_%s.mol2" % (base, chargeType, atomType)
+        acMol2FileName = f"{base}_{chargeType}_{atomType}.mol2"
         self.acMol2FileName = acMol2FileName
         self.charmmBase = "%s_CHARMM" % base
         self.qFlag = qDict[qprog]
@@ -3292,7 +3330,7 @@ class MolTopol(AbstractTopol):
     """ "
     Class to write topologies and parameters files for several applications
 
-    http://amber.scripps.edu/formats.html (not updated to amber 10 yet)
+    https://ambermd.org/FileFormats.php
 
     Parser, take information in AC xyz and top files and convert to objects
 
@@ -3347,11 +3385,11 @@ def __init__(
         elif not self.amb2gmx:
             self.amb2gmx = True
         if not os.path.exists(acFileXyz) or not os.path.exists(acFileTop):
-            self.printError("Files '%s' and/or '%s' don't exist" % (acFileXyz, acFileTop))
+            self.printError(f"Files '{acFileXyz}' and/or '{acFileTop}' don't exist")
             self.printError("molTopol object won't be created")
 
-        self.xyzFileData = open(acFileXyz, "r").readlines()
-        self.topFileData = [x for x in open(acFileTop, "r").readlines() if not x.startswith("%COMMENT")]
+        self.xyzFileData = open(acFileXyz).readlines()
+        self.topFileData = [x for x in open(acFileTop).readlines() if not x.startswith("%COMMENT")]
         self.topo14Data = Topology_14()
         self.topo14Data.read_amber_topology("".join(self.topFileData))
         self.printDebug("prmtop and inpcrd files loaded")
diff --git a/acpype_docker.bat b/acpype_docker.bat
index 70c896ca..e9d460c6 100755
--- a/acpype_docker.bat
+++ b/acpype_docker.bat
@@ -1,2 +1,2 @@
 @echo on
-docker run --rm -i -t -v %cd%:/wdir -w /wdir acpype/acpype acpype %*
\ No newline at end of file
+docker run --rm -i -t -v %cd%:/wdir -w /wdir acpype/acpype acpype %*
diff --git a/docs/Makefile b/docs/Makefile
new file mode 100644
index 00000000..d4bb2cbb
--- /dev/null
+++ b/docs/Makefile
@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/docs/_templates/custom-class-template.rst b/docs/_templates/custom-class-template.rst
new file mode 100644
index 00000000..b29757c5
--- /dev/null
+++ b/docs/_templates/custom-class-template.rst
@@ -0,0 +1,32 @@
+{{ fullname | escape | underline}}
+
+.. currentmodule:: {{ module }}
+
+.. autoclass:: {{ objname }}
+   :members:
+   :show-inheritance:
+   :inherited-members:
+
+   {% block methods %}
+   .. automethod:: __init__
+
+   {% if methods %}
+   .. rubric:: {{ _('Methods') }}
+
+   .. autosummary::
+   {% for item in methods %}
+      ~{{ name }}.{{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block attributes %}
+   {% if attributes %}
+   .. rubric:: {{ _('Attributes') }}
+
+   .. autosummary::
+   {% for item in attributes %}
+      ~{{ name }}.{{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
diff --git a/docs/_templates/custom-module-template.rst b/docs/_templates/custom-module-template.rst
new file mode 100644
index 00000000..f46f9f63
--- /dev/null
+++ b/docs/_templates/custom-module-template.rst
@@ -0,0 +1,66 @@
+{{ fullname | escape | underline}}
+
+.. automodule:: {{ fullname }}
+
+   {% block attributes %}
+   {% if attributes %}
+   .. rubric:: {{ _('Module Attributes') }}
+
+   .. autosummary::
+      :toctree:
+   {% for item in attributes %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block functions %}
+   {% if functions %}
+   .. rubric:: {{ _('Functions') }}
+
+   .. autosummary::
+      :toctree:
+   {% for item in functions %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block classes %}
+   {% if classes %}
+   .. rubric:: {{ _('Classes') }}
+
+   .. autosummary::
+      :toctree:
+      :template: custom-class-template.rst
+   {% for item in classes %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block exceptions %}
+   {% if exceptions %}
+   .. rubric:: {{ _('Exceptions') }}
+
+   .. autosummary::
+      :toctree:
+   {% for item in exceptions %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+{% block modules %}
+{% if modules %}
+.. rubric:: Modules
+
+.. autosummary::
+   :toctree:
+   :template: custom-module-template.rst
+   :recursive:
+{% for item in modules %}
+   {{ item }}
+{%- endfor %}
+{% endif %}
+{% endblock %}
diff --git a/docs/conf.py b/docs/conf.py
new file mode 100644
index 00000000..306779df
--- /dev/null
+++ b/docs/conf.py
@@ -0,0 +1,63 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+import os
+import sys
+from datetime import datetime
+
+sys.path.insert(0, os.path.abspath(".."))
+
+
+# -- Project information -----------------------------------------------------
+year = str(datetime.today().year)
+project = "ACPYPE"
+copyright = f"{year}, Alan Silva"
+author = "Alan Silva"
+
+release = year
+# The full version, including alpha/beta/rc tags
+try:
+    import acpype
+except ImportError:
+    print("WARNING: couldn't import acpype to read version.")
+else:
+    release = acpype.__version__
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = ["sphinx.ext.napoleon", "sphinx.ext.autodoc", "sphinx.ext.autosummary"]
+
+autosummary_generate = True
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ["_templates"]
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = "sphinx_rtd_theme"  # "classic"
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ["_static"]
diff --git a/docs/index.rst b/docs/index.rst
new file mode 100644
index 00000000..fe7c12af
--- /dev/null
+++ b/docs/index.rst
@@ -0,0 +1,28 @@
+.. ACPYPE documentation master file, created by
+   sphinx-quickstart on Tue Dec 28 23:14:53 2021.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to ACPYPE's documentation!
+==================================
+
+
+**ACPYPE - AnteChamber PYthon Parser interfacE**
+
+A tool based in **Python** to use **Antechamber** to generate topologies for chemical
+compounds and to interface with others python applications like CCPN and ARIA.
+Topologies files to be generated so far: CNS/XPLOR, GROMACS, CHARMM and AMBER.
+
+.. autosummary::
+   :toctree: _autosummary
+   :template: custom-module-template.rst
+   :recursive:
+
+   acpype
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
diff --git a/docs/make.bat b/docs/make.bat
new file mode 100644
index 00000000..153be5e2
--- /dev/null
+++ b/docs/make.bat
@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd
diff --git a/ffamber_additions/README.txt b/ffamber_additions/README.txt
index 01cb3479..9ac9605e 100644
--- a/ffamber_additions/README.txt
+++ b/ffamber_additions/README.txt
@@ -1,2 +1,2 @@
 FF.dat : updated FF.dat file to include all forcefield prefixes for ffamber
-[spc, spce, tip3p, ions].itp : modified versions to include _FF_AMBER** definitions
\ No newline at end of file
+[spc, spce, tip3p, ions].itp : modified versions to include _FF_AMBER** definitions
diff --git a/ffamber_additions/parm10gaff.dat b/ffamber_additions/parm10gaff.dat
index 6acb1f98..02d5ca1c 100644
--- a/ffamber_additions/parm10gaff.dat
+++ b/ffamber_additions/parm10gaff.dat
@@ -6682,4 +6682,3 @@ Bond angle:  437 low quality parameters were replaced and 618 new
 parameters were introduced.
 
 ---------------------------------------------------------------------------
-
diff --git a/ffamber_additions/parm99SBgaff.dat b/ffamber_additions/parm99SBgaff.dat
index 5bf072b5..533b2c9d 100644
--- a/ffamber_additions/parm99SBgaff.dat
+++ b/ffamber_additions/parm99SBgaff.dat
@@ -6574,4 +6574,3 @@ Bond angle:  437 low quality parameters were replaced and 618 new
 parameters were introduced.
 
 ---------------------------------------------------------------------------
-
diff --git a/ffamber_additions/parm99bsc0SBgaff.dat b/ffamber_additions/parm99bsc0SBgaff.dat
index 13b4219f..1bab8eff 100644
--- a/ffamber_additions/parm99bsc0SBgaff.dat
+++ b/ffamber_additions/parm99bsc0SBgaff.dat
@@ -6615,4 +6615,3 @@ Bond angle:  437 low quality parameters were replaced and 618 new
 parameters were introduced.
 
 ---------------------------------------------------------------------------
-
diff --git a/legacy/CcpnToAcpype.py b/legacy/CcpnToAcpype.py
index 742eacf0..87bfac40 100644
--- a/legacy/CcpnToAcpype.py
+++ b/legacy/CcpnToAcpype.py
@@ -1,12 +1,9 @@
-from __future__ import print_function
-
 import os
 import random
 import string
 import sys
 import time
 import traceback
-from builtins import object, range
 from shutil import rmtree
 
 from ccpnmr.format.converters import Mol2Format  # type: ignore
@@ -22,8 +19,7 @@ def dirWalk(adir):
     for f in os.listdir(adir):
         fullpath = os.path.abspath(os.path.join(adir, f))
         if os.path.isdir(fullpath) and not os.path.islink(fullpath):
-            for x in dirWalk(fullpath):  # recurse into subdir
-                yield x
+            yield from dirWalk(fullpath)
         else:
             yield fullpath
 
@@ -33,10 +29,10 @@ def addMolPep(cnsPepPath, molName):
     Add info about MOL in CNS topol*.pep file
     input: cns pep file path to be modified and MOL name
     """
-    txt = "first IONS tail + %s end\nlast IONS head - %s end\n\n" % (molName, molName)
+    txt = f"first IONS tail + {molName} end\nlast IONS head - {molName} end\n\n"
     pepFile = open(cnsPepPath).read()
     if txt in pepFile:
-        print("%s already added to %s" % (molName, cnsPepPath))
+        print(f"{molName} already added to {cnsPepPath}")
         return False
     pepFile = pepFile.splitlines(1)
     pepFile.reverse()
@@ -50,7 +46,7 @@ def addMolPep(cnsPepPath, molName):
     nPepFile = open(cnsPepPath, "w")
     nPepFile.writelines(pepFile)
     nPepFile.close()
-    print("%s added to %s" % (molName, cnsPepPath))
+    print(f"{molName} added to {cnsPepPath}")
     return True
 
 
@@ -76,7 +72,7 @@ def formatLine(line, n):
 
     parFile = open(cnsParPath).read()
     if txt in parFile:
-        print("%s already added to %s" % (molName, cnsParPath))
+        print(f"{molName} already added to {cnsParPath}")
         return False
 
     molFile = open(molParPath).readlines()
@@ -123,7 +119,7 @@ def formatLine(line, n):
     nParFile = open(cnsParPath, "w")
     nParFile.writelines(parList)
     nParFile.close()
-    print("%s added to %s" % (molName, cnsParPath))
+    print(f"{molName} added to {cnsParPath}")
     return True
 
 
@@ -151,7 +147,7 @@ def addMolTop(cnsTopPath, molTopPath):
 
     topFile = open(cnsTopPath).read()
     if txt in topFile:
-        print("%s already added to %s" % (molName, cnsTopPath))
+        print(f"{molName} already added to {cnsTopPath}")
         return False
 
     molFile = open(molTopPath).readlines()
@@ -189,11 +185,11 @@ def addMolTop(cnsTopPath, molTopPath):
     nTopFile = open(cnsTopPath, "w")
     nTopFile.writelines(topList)
     nTopFile.close()
-    print("%s added to %s" % (molName, cnsTopPath))
+    print(f"{molName} added to {cnsTopPath}")
     return True
 
 
-class AcpypeForCcpnProject(object):
+class AcpypeForCcpnProject:
     """
     Class to take a Ccpn project, check if it has an
     unusual chem comp and call ACPYPE API to generate
@@ -272,9 +268,9 @@ def run(
             res = chain.findFirstResidue()
             resName = res.ccpCode.upper()
             if chargeVal is None:
-                print("Running ACPYPE for '%s : %s' and trying to guess net charge" % (resName, chain.molecule.name))
+                print(f"Running ACPYPE for '{resName} : {chain.molecule.name}' and trying to guess net charge")
             else:
-                print("Running ACPYPE for '%s : %s' with charge '%s'" % (resName, chain.molecule.name, chargeVal))
+                print(f"Running ACPYPE for '{resName} : {chain.molecule.name}' with charge '{chargeVal}'")
             random.seed()
             d = [random.choice(letters) for x in range(10)]
             randString = "".join(d)
diff --git a/poetry.lock b/poetry.lock
index 4d2299de..98f8f9af 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,3 +1,11 @@
+[[package]]
+name = "alabaster"
+version = "0.7.12"
+description = "A configurable sidebar-enabled Sphinx theme"
+category = "dev"
+optional = false
+python-versions = "*"
+
 [[package]]
 name = "appnope"
 version = "0.1.2"
@@ -16,17 +24,28 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
 [[package]]
 name = "attrs"
-version = "21.2.0"
+version = "21.4.0"
 description = "Classes Without Boilerplate"
 category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 
 [package.extras]
-dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit"]
+dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit", "cloudpickle"]
 docs = ["furo", "sphinx", "zope.interface", "sphinx-notfound-page"]
-tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface"]
-tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins"]
+tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "cloudpickle"]
+tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "cloudpickle"]
+
+[[package]]
+name = "babel"
+version = "2.9.1"
+description = "Internationalization utilities"
+category = "dev"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+
+[package.dependencies]
+pytz = ">=2015.7"
 
 [[package]]
 name = "backcall"
@@ -66,6 +85,33 @@ jupyter = ["ipython (>=7.8.0)", "tokenize-rt (>=3.2.0)"]
 python2 = ["typed-ast (>=1.4.3)"]
 uvloop = ["uvloop (>=0.15.2)"]
 
+[[package]]
+name = "certifi"
+version = "2021.10.8"
+description = "Python package for providing Mozilla's CA Bundle."
+category = "dev"
+optional = false
+python-versions = "*"
+
+[[package]]
+name = "cfgv"
+version = "3.3.1"
+description = "Validate configuration and produce human readable error messages."
+category = "dev"
+optional = false
+python-versions = ">=3.6.1"
+
+[[package]]
+name = "charset-normalizer"
+version = "2.0.9"
+description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
+category = "dev"
+optional = false
+python-versions = ">=3.5.0"
+
+[package.extras]
+unicode_backport = ["unicodedata2"]
+
 [[package]]
 name = "click"
 version = "8.0.3"
@@ -116,6 +162,22 @@ category = "dev"
 optional = false
 python-versions = ">=3.5"
 
+[[package]]
+name = "distlib"
+version = "0.3.4"
+description = "Distribution utilities"
+category = "dev"
+optional = false
+python-versions = "*"
+
+[[package]]
+name = "docutils"
+version = "0.17.1"
+description = "Docutils -- Python Documentation Utilities"
+category = "dev"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+
 [[package]]
 name = "fancycompleter"
 version = "0.9.1"
@@ -128,6 +190,18 @@ python-versions = "*"
 pyreadline = {version = "*", markers = "platform_system == \"Windows\""}
 pyrepl = ">=0.8.2"
 
+[[package]]
+name = "filelock"
+version = "3.4.1"
+description = "A platform independent file lock."
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.extras]
+docs = ["furo (>=2021.8.17b43)", "sphinx (>=4.1)", "sphinx-autodoc-typehints (>=1.12)"]
+testing = ["covdefaults (>=1.2.0)", "coverage (>=4)", "pytest (>=4)", "pytest-cov", "pytest-timeout (>=1.4.2)"]
+
 [[package]]
 name = "flake8"
 version = "4.0.1"
@@ -142,6 +216,33 @@ mccabe = ">=0.6.0,<0.7.0"
 pycodestyle = ">=2.8.0,<2.9.0"
 pyflakes = ">=2.4.0,<2.5.0"
 
+[[package]]
+name = "identify"
+version = "2.4.1"
+description = "File identification library for Python"
+category = "dev"
+optional = false
+python-versions = ">=3.6.1"
+
+[package.extras]
+license = ["ukkonen"]
+
+[[package]]
+name = "idna"
+version = "3.3"
+description = "Internationalized Domain Names in Applications (IDNA)"
+category = "dev"
+optional = false
+python-versions = ">=3.5"
+
+[[package]]
+name = "imagesize"
+version = "1.3.0"
+description = "Getting image size from png/jpeg/jpeg2000/gif file"
+category = "dev"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+
 [[package]]
 name = "importlib-metadata"
 version = "4.2.0"
@@ -158,6 +259,21 @@ zipp = ">=0.5"
 docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"]
 testing = ["pytest (>=4.6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "packaging", "pep517", "pyfakefs", "flufl.flake8", "pytest-black (>=0.3.7)", "pytest-mypy", "importlib-resources (>=1.3)"]
 
+[[package]]
+name = "importlib-resources"
+version = "5.2.3"
+description = "Read resources from Python packages"
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""}
+
+[package.extras]
+docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"]
+testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "pytest-black (>=0.3.7)", "pytest-mypy"]
+
 [[package]]
 name = "iniconfig"
 version = "1.1.1"
@@ -179,7 +295,7 @@ ipython = {version = ">=5.1.0", markers = "python_version >= \"3.4\""}
 
 [[package]]
 name = "ipython"
-version = "7.10.0"
+version = "7.16.2"
 description = "IPython: Productive Interactive Computing"
 category = "dev"
 optional = false
@@ -190,15 +306,15 @@ appnope = {version = "*", markers = "sys_platform == \"darwin\""}
 backcall = "*"
 colorama = {version = "*", markers = "sys_platform == \"win32\""}
 decorator = "*"
-jedi = ">=0.10"
+jedi = ">=0.10,<=0.17.2"
 pexpect = {version = "*", markers = "sys_platform != \"win32\""}
 pickleshare = "*"
-prompt-toolkit = ">=2.0.0,<3.1.0"
+prompt-toolkit = ">=2.0.0,<3.0.0 || >3.0.0,<3.0.1 || >3.0.1,<3.1.0"
 pygments = "*"
 traitlets = ">=4.2"
 
 [package.extras]
-all = ["ipyparallel", "requests", "testpath", "ipywidgets", "nbformat", "notebook", "ipykernel", "qtconsole", "numpy (>=1.14)", "Sphinx (>=1.3)", "nbconvert", "nose (>=0.10.1)", "pygments"]
+all = ["Sphinx (>=1.3)", "ipykernel", "ipyparallel", "ipywidgets", "nbconvert", "nbformat", "nose (>=0.10.1)", "notebook", "numpy (>=1.14)", "pygments", "qtconsole", "requests", "testpath"]
 doc = ["Sphinx (>=1.3)"]
 kernel = ["ipykernel"]
 nbconvert = ["nbconvert"]
@@ -232,18 +348,40 @@ plugins = ["setuptools"]
 
 [[package]]
 name = "jedi"
-version = "0.18.1"
+version = "0.17.2"
 description = "An autocompletion tool for Python that can be used for text editors."
 category = "dev"
 optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+
+[package.dependencies]
+parso = ">=0.7.0,<0.8.0"
+
+[package.extras]
+qa = ["flake8 (==3.7.9)"]
+testing = ["Django (<3.1)", "colorama", "docopt", "pytest (>=3.9.0,<5.0.0)"]
+
+[[package]]
+name = "jinja2"
+version = "3.0.3"
+description = "A very fast and expressive template engine."
+category = "dev"
+optional = false
 python-versions = ">=3.6"
 
 [package.dependencies]
-parso = ">=0.8.0,<0.9.0"
+MarkupSafe = ">=2.0"
 
 [package.extras]
-qa = ["flake8 (==3.8.3)", "mypy (==0.782)"]
-testing = ["Django (<3.1)", "colorama", "docopt", "pytest (<7.0.0)"]
+i18n = ["Babel (>=2.7)"]
+
+[[package]]
+name = "markupsafe"
+version = "2.0.1"
+description = "Safely add untrusted strings to HTML/XML markup."
+category = "dev"
+optional = false
+python-versions = ">=3.6"
 
 [[package]]
 name = "mccabe"
@@ -279,6 +417,14 @@ category = "dev"
 optional = false
 python-versions = "*"
 
+[[package]]
+name = "nodeenv"
+version = "1.6.0"
+description = "Node.js virtual environment builder"
+category = "dev"
+optional = false
+python-versions = "*"
+
 [[package]]
 name = "packaging"
 version = "21.3"
@@ -292,15 +438,14 @@ pyparsing = ">=2.0.2,<3.0.5 || >3.0.5"
 
 [[package]]
 name = "parso"
-version = "0.8.3"
+version = "0.7.1"
 description = "A Python Parser"
 category = "dev"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
 [package.extras]
-qa = ["flake8 (==3.8.3)", "mypy (==0.782)"]
-testing = ["docopt", "pytest (<6.0.0)"]
+testing = ["docopt", "pytest (>=3.0.7)"]
 
 [[package]]
 name = "pathspec"
@@ -373,6 +518,24 @@ importlib-metadata = {version = ">=0.12", markers = "python_version < \"3.8\""}
 dev = ["pre-commit", "tox"]
 testing = ["pytest", "pytest-benchmark"]
 
+[[package]]
+name = "pre-commit"
+version = "2.16.0"
+description = "A framework for managing and maintaining multi-language pre-commit hooks."
+category = "dev"
+optional = false
+python-versions = ">=3.6.1"
+
+[package.dependencies]
+cfgv = ">=2.0.0"
+identify = ">=1.0.0"
+importlib-metadata = {version = "*", markers = "python_version < \"3.8\""}
+importlib-resources = {version = "<5.3", markers = "python_version < \"3.7\""}
+nodeenv = ">=0.11.1"
+pyyaml = ">=5.1"
+toml = "*"
+virtualenv = ">=20.0.8"
+
 [[package]]
 name = "prompt-toolkit"
 version = "3.0.24"
@@ -418,7 +581,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
 [[package]]
 name = "pygments"
-version = "2.10.0"
+version = "2.11.1"
 description = "Pygments is a syntax highlighting package written in Python."
 category = "dev"
 optional = false
@@ -488,6 +651,62 @@ pytest = ">=4.6"
 [package.extras]
 testing = ["fields", "hunter", "process-tests", "six", "pytest-xdist", "virtualenv"]
 
+[[package]]
+name = "pytest-random-order"
+version = "1.0.4"
+description = "Randomise the order in which pytest tests are run with some control over the randomness"
+category = "dev"
+optional = false
+python-versions = ">=3.5.0"
+
+[package.dependencies]
+pytest = ">=3.0.0"
+
+[[package]]
+name = "pytz"
+version = "2021.3"
+description = "World timezone definitions, modern and historical"
+category = "dev"
+optional = false
+python-versions = "*"
+
+[[package]]
+name = "pyupgrade"
+version = "2.31.0"
+description = "A tool to automatically upgrade syntax for newer versions."
+category = "dev"
+optional = false
+python-versions = ">=3.6.1"
+
+[package.dependencies]
+tokenize-rt = ">=3.2.0"
+
+[[package]]
+name = "pyyaml"
+version = "6.0"
+description = "YAML parser and emitter for Python"
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[[package]]
+name = "requests"
+version = "2.26.0"
+description = "Python HTTP for Humans."
+category = "dev"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
+
+[package.dependencies]
+certifi = ">=2017.4.17"
+charset-normalizer = {version = ">=2.0.0,<2.1.0", markers = "python_version >= \"3\""}
+idna = {version = ">=2.5,<4", markers = "python_version >= \"3\""}
+urllib3 = ">=1.21.1,<1.27"
+
+[package.extras]
+socks = ["PySocks (>=1.5.6,!=1.5.7)", "win-inet-pton"]
+use_chardet_on_py3 = ["chardet (>=3.0.2,<5)"]
+
 [[package]]
 name = "six"
 version = "1.16.0"
@@ -496,6 +715,116 @@ category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
 
+[[package]]
+name = "snowballstemmer"
+version = "2.2.0"
+description = "This package provides 29 stemmers for 28 languages generated from Snowball algorithms."
+category = "dev"
+optional = false
+python-versions = "*"
+
+[[package]]
+name = "sphinx"
+version = "4.3.2"
+description = "Python documentation generator"
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+alabaster = ">=0.7,<0.8"
+babel = ">=1.3"
+colorama = {version = ">=0.3.5", markers = "sys_platform == \"win32\""}
+docutils = ">=0.14,<0.18"
+imagesize = "*"
+Jinja2 = ">=2.3"
+packaging = "*"
+Pygments = ">=2.0"
+requests = ">=2.5.0"
+snowballstemmer = ">=1.1"
+sphinxcontrib-applehelp = "*"
+sphinxcontrib-devhelp = "*"
+sphinxcontrib-htmlhelp = ">=2.0.0"
+sphinxcontrib-jsmath = "*"
+sphinxcontrib-qthelp = "*"
+sphinxcontrib-serializinghtml = ">=1.1.5"
+
+[package.extras]
+docs = ["sphinxcontrib-websupport"]
+lint = ["flake8 (>=3.5.0)", "isort", "mypy (>=0.920)", "docutils-stubs", "types-typed-ast", "types-pkg-resources", "types-requests"]
+test = ["pytest", "pytest-cov", "html5lib", "cython", "typed-ast"]
+
+[[package]]
+name = "sphinxcontrib-applehelp"
+version = "1.0.2"
+description = "sphinxcontrib-applehelp is a sphinx extension which outputs Apple help books"
+category = "dev"
+optional = false
+python-versions = ">=3.5"
+
+[package.extras]
+lint = ["flake8", "mypy", "docutils-stubs"]
+test = ["pytest"]
+
+[[package]]
+name = "sphinxcontrib-devhelp"
+version = "1.0.2"
+description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp document."
+category = "dev"
+optional = false
+python-versions = ">=3.5"
+
+[package.extras]
+lint = ["flake8", "mypy", "docutils-stubs"]
+test = ["pytest"]
+
+[[package]]
+name = "sphinxcontrib-htmlhelp"
+version = "2.0.0"
+description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files"
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.extras]
+lint = ["flake8", "mypy", "docutils-stubs"]
+test = ["pytest", "html5lib"]
+
+[[package]]
+name = "sphinxcontrib-jsmath"
+version = "1.0.1"
+description = "A sphinx extension which renders display math in HTML via JavaScript"
+category = "dev"
+optional = false
+python-versions = ">=3.5"
+
+[package.extras]
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+    {file = "PyYAML-6.0-cp38-cp38-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:9fa600030013c4de8165339db93d182b9431076eb98eb40ee068700c9c813e34"},
+    {file = "PyYAML-6.0-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl", hash = "sha256:277a0ef2981ca40581a47093e9e2d13b3f1fbbeffae064c1d21bfceba2030287"},
+    {file = "PyYAML-6.0-cp38-cp38-win32.whl", hash = "sha256:d4eccecf9adf6fbcc6861a38015c2a64f38b9d94838ac1810a9023a0609e1b78"},
+    {file = "PyYAML-6.0-cp38-cp38-win_amd64.whl", hash = "sha256:1e4747bc279b4f613a09eb64bba2ba602d8a6664c6ce6396a4d0cd413a50ce07"},
+    {file = "PyYAML-6.0-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:055d937d65826939cb044fc8c9b08889e8c743fdc6a32b33e2390f66013e449b"},
+    {file = "PyYAML-6.0-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:e61ceaab6f49fb8bdfaa0f92c4b57bcfbea54c09277b1b4f7ac376bfb7a7c174"},
+    {file = "PyYAML-6.0-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:d67d839ede4ed1b28a4e8909735fc992a923cdb84e618544973d7dfc71540803"},
+    {file = "PyYAML-6.0-cp39-cp39-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:cba8c411ef271aa037d7357a2bc8f9ee8b58b9965831d9e51baf703280dc73d3"},
+    {file = "PyYAML-6.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl", hash = "sha256:40527857252b61eacd1d9af500c3337ba8deb8fc298940291486c465c8b46ec0"},
+    {file = "PyYAML-6.0-cp39-cp39-win32.whl", hash = "sha256:b5b9eccad747aabaaffbc6064800670f0c297e52c12754eb1d976c57e4f74dcb"},
+    {file = "PyYAML-6.0-cp39-cp39-win_amd64.whl", hash = "sha256:b3d267842bf12586ba6c734f89d1f5b871df0273157918b0ccefa29deb05c21c"},
+    {file = "PyYAML-6.0.tar.gz", hash = "sha256:68fb519c14306fec9720a2a5b45bc9f0c8d1b9c72adf45c37baedfcd949c35a2"},
+]
+requests = [
+    {file = "requests-2.26.0-py2.py3-none-any.whl", hash = "sha256:6c1246513ecd5ecd4528a0906f910e8f0f9c6b8ec72030dc9fd154dc1a6efd24"},
+    {file = "requests-2.26.0.tar.gz", hash = "sha256:b8aa58f8cf793ffd8782d3d8cb19e66ef36f7aba4353eec859e74678b01b07a7"},
+]
 six = [
     {file = "six-1.16.0-py2.py3-none-any.whl", hash = "sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254"},
     {file = "six-1.16.0.tar.gz", hash = "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926"},
 ]
+snowballstemmer = [
+    {file = "snowballstemmer-2.2.0-py2.py3-none-any.whl", hash = "sha256:c8e1716e83cc398ae16824e5572ae04e0d9fc2c6b985fb0f900f5f0c96ecba1a"},
+    {file = "snowballstemmer-2.2.0.tar.gz", hash = "sha256:09b16deb8547d3412ad7b590689584cd0fe25ec8db3be37788be3810cbf19cb1"},
+]
+sphinx = [
+    {file = "Sphinx-4.3.2-py3-none-any.whl", hash = "sha256:6a11ea5dd0bdb197f9c2abc2e0ce73e01340464feaece525e64036546d24c851"},
+    {file = "Sphinx-4.3.2.tar.gz", hash = "sha256:0a8836751a68306b3fe97ecbe44db786f8479c3bf4b80e3a7f5c838657b4698c"},
+]
+sphinxcontrib-applehelp = [
+    {file = "sphinxcontrib-applehelp-1.0.2.tar.gz", hash = "sha256:a072735ec80e7675e3f432fcae8610ecf509c5f1869d17e2eecff44389cdbc58"},
+    {file = "sphinxcontrib_applehelp-1.0.2-py2.py3-none-any.whl", hash = "sha256:806111e5e962be97c29ec4c1e7fe277bfd19e9652fb1a4392105b43e01af885a"},
+]
+sphinxcontrib-devhelp = [
+    {file = "sphinxcontrib-devhelp-1.0.2.tar.gz", hash = "sha256:ff7f1afa7b9642e7060379360a67e9c41e8f3121f2ce9164266f61b9f4b338e4"},
+    {file = "sphinxcontrib_devhelp-1.0.2-py2.py3-none-any.whl", hash = "sha256:8165223f9a335cc1af7ffe1ed31d2871f325254c0423bc0c4c7cd1c1e4734a2e"},
+]
+sphinxcontrib-htmlhelp = [
+    {file = "sphinxcontrib-htmlhelp-2.0.0.tar.gz", hash = "sha256:f5f8bb2d0d629f398bf47d0d69c07bc13b65f75a81ad9e2f71a63d4b7a2f6db2"},
+    {file = "sphinxcontrib_htmlhelp-2.0.0-py2.py3-none-any.whl", hash = "sha256:d412243dfb797ae3ec2b59eca0e52dac12e75a241bf0e4eb861e450d06c6ed07"},
+]
+sphinxcontrib-jsmath = [
+    {file = "sphinxcontrib-jsmath-1.0.1.tar.gz", hash = "sha256:a9925e4a4587247ed2191a22df5f6970656cb8ca2bd6284309578f2153e0c4b8"},
+    {file = "sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl", hash = "sha256:2ec2eaebfb78f3f2078e73666b1415417a116cc848b72e5172e596c871103178"},
+]
+sphinxcontrib-qthelp = [
+    {file = "sphinxcontrib-qthelp-1.0.3.tar.gz", hash = "sha256:4c33767ee058b70dba89a6fc5c1892c0d57a54be67ddd3e7875a18d14cba5a72"},
+    {file = "sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl", hash = "sha256:bd9fc24bcb748a8d51fd4ecaade681350aa63009a347a8c14e637895444dfab6"},
+]
+sphinxcontrib-serializinghtml = [
+    {file = "sphinxcontrib-serializinghtml-1.1.5.tar.gz", hash = "sha256:aa5f6de5dfdf809ef505c4895e51ef5c9eac17d0f287933eb49ec495280b6952"},
+    {file = "sphinxcontrib_serializinghtml-1.1.5-py2.py3-none-any.whl", hash = "sha256:352a9a00ae864471d3a7ead8d7d79f5fc0b57e8b3f95e9867eb9eb28999b92fd"},
+]
 tokenize-rt = [
     {file = "tokenize_rt-4.2.1-py2.py3-none-any.whl", hash = "sha256:08a27fa032a81cf45e8858d0ac706004fcd523e8463415ddf1442be38e204ea8"},
     {file = "tokenize_rt-4.2.1.tar.gz", hash = "sha256:0d4f69026fed520f8a1e0103aa36c406ef4661417f20ca643f913e33531b3b94"},
@@ -857,6 +1433,14 @@ typing-extensions = [
     {file = "typing_extensions-4.0.1-py3-none-any.whl", hash = "sha256:7f001e5ac290a0c0401508864c7ec868be4e701886d5b573a9528ed3973d9d3b"},
     {file = "typing_extensions-4.0.1.tar.gz", hash = "sha256:4ca091dea149f945ec56afb48dae714f21e8692ef22a395223bcd328961b6a0e"},
 ]
+urllib3 = [
+    {file = "urllib3-1.26.7-py2.py3-none-any.whl", hash = "sha256:c4fdf4019605b6e5423637e01bc9fe4daef873709a7973e195ceba0a62bbc844"},
+    {file = "urllib3-1.26.7.tar.gz", hash = "sha256:4987c65554f7a2dbf30c18fd48778ef124af6fab771a377103da0585e2336ece"},
+]
+virtualenv = [
+    {file = "virtualenv-20.13.0-py2.py3-none-any.whl", hash = "sha256:339f16c4a86b44240ba7223d0f93a7887c3ca04b5f9c8129da7958447d079b09"},
+    {file = "virtualenv-20.13.0.tar.gz", hash = "sha256:d8458cf8d59d0ea495ad9b34c2599487f8a7772d796f9910858376d1600dd2dd"},
+]
 wcwidth = [
     {file = "wcwidth-0.2.5-py2.py3-none-any.whl", hash = "sha256:beb4802a9cebb9144e99086eff703a642a13d6a0052920003a230f3294bbe784"},
     {file = "wcwidth-0.2.5.tar.gz", hash = "sha256:c4d647b99872929fdb7bdcaa4fbe7f01413ed3d98077df798530e5b04f116c83"},
diff --git a/pyproject.toml b/pyproject.toml
index d546c628..744bc860 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -9,6 +9,25 @@ exclude = '''
   | \.mypy_cache
   | \.tox
   | \.venv
+  | __pycache__
+  | _build
+  | buck-out
+  | build
+  | dist
+  | amber.*
+)/
+'''
+
+[tool.flake8] # it does nothing here, still need tox.ini
+max-line-length = 120
+extend-ignore = '''W503,E203,E501'''
+exclude = '''
+/(
+    \.git
+  | \.mypy_cache
+  | \.tox
+  | \.venv
+  | __pycache__
   | _build
   | buck-out
   | build
@@ -19,7 +38,7 @@ exclude = '''
 
 [tool.poetry]
 name = "acpype"
-version = "2021.12.25"
+version = "2022.1.3"
 description = "ACPYPE - AnteChamber PYthon Parser interfacE"
 authors = ["Alan Silva <alanwilter@gmail.com>"]
 license = "GPL-3.0-or-later"
@@ -37,6 +56,8 @@ classifiers = [
 [tool.poetry.urls]
 "Bug Tracker" = "https://github.com/alanwilter/acpype/issues"
 "Wiki" = "https://github.com/alanwilter/acpype/wiki"
+"Docs" = "https://acpype.readthedocs.io"
+"DOI" = "https://doi.org/10.1186/1756-0500-5-367"
 
 [tool.poetry.scripts]
 acpype = "acpype.cli:init_main"
@@ -50,9 +71,12 @@ black = { extras = ["jupyter"], version = "^21.12b0" }
 pytest-cov = "^3.0.0"
 mypy = "^0.920"
 pdbpp = "^0.10.3"
-ipython = "7.10"
 ipdb = "0.13"
 isort = "^5.10.1"
+pytest-random-order = "^1.0.4"
+pyupgrade = "^2.31.0"
+pre-commit = "^2.16.0"
+Sphinx = "^4.3.2"
 
 [build-system]
 requires = ["poetry-core>=1.0.0"]
diff --git a/release.sh b/release.sh
index 86e1cd6f..c917b90c 100755
--- a/release.sh
+++ b/release.sh
@@ -18,7 +18,7 @@ function usage() {
 
 function run_pip() {
     echo ">>> Creating pip package"
-    python3 -m build
+    poetry build
     # python3 -m twine upload --repository testpypi dist/*"$version"* # TestPyPI
     python3 -m twine upload --repository pypi dist/*"$version"* # official release
     rm -vfr dist/*"$version"*
diff --git a/run_acpype.py b/run_acpype.py
index c39e1fa7..5ba58621 100755
--- a/run_acpype.py
+++ b/run_acpype.py
@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-# -*- coding: utf-8 -*-
 
 import re
 import sys
diff --git a/scripts/analyse_test_acpype_db_ligands.py b/scripts/analyse_test_acpype_db_ligands.py
index 0a3e84bf..1d83b870 100755
--- a/scripts/analyse_test_acpype_db_ligands.py
+++ b/scripts/analyse_test_acpype_db_ligands.py
@@ -351,7 +351,7 @@ def analyseFile(mol, structure, file):
     guessChargeValue = None
     warnTypes = ""
     errorTypes = ""
-    tmpFile = open(file, "r")
+    tmpFile = open(file)
     content = tmpFile.readlines()
     for line in content:
         if "WARNING: " in line:
@@ -366,17 +366,17 @@ def analyseFile(mol, structure, file):
             elif "The unperturbed charge of the" in line:
                 warnTypes += "_3"
                 charge = round(float(line[44:54]))
-                WT3.add("%s: %s" % (mol, charge))
+                WT3.add(f"{mol}: {charge}")
             elif "Couldn't determine all parameters" in line:
                 warnTypes += "_4"
-                WT4.append("%s_%s" % (mol, structure))
+                WT4.append(f"{mol}_{structure}")
             elif "There is a bond of" in line:
                 warnTypes += "_5"
                 # _dist = round(float(line[27:37]))
-                WT5.add("%s_%s" % (mol, structure))
+                WT5.add(f"{mol}_{structure}")
             elif " atom type of " in line:
                 warnTypes += "_6"
-                WT6.add("%s_%s" % (mol, structure))
+                WT6.add(f"{mol}_{structure}")
             # elif "no 'babel' executable, no PDB" in line:
             elif "residue name will be 'MOL' instead of" in line:
                 warnTypes += "_8"
@@ -385,33 +385,33 @@ def analyseFile(mol, structure, file):
                 warnTypes += "_9"
         if "Warning: Close contact of " in line:
             warnTypes += "_7"
-            WT7.add("%s_%s" % (mol, structure))
+            WT7.add(f"{mol}_{structure}")
 
         if "ERROR: " in line:
             if "guessCharge failed" in line:
                 errorTypes += "_0"
-                ET0.append("%s_%s" % (mol, structure))
+                ET0.append(f"{mol}_{structure}")
             elif "Atoms with same coordinates in" in line:
                 errorTypes += "_1"
-                ET1.append("%s_%s" % (mol, structure))
+                ET1.append(f"{mol}_{structure}")
             elif "Atoms TOO close" in line:
                 errorTypes += "_2"
-                ET2.append("%s_%s" % (mol, structure))
+                ET2.append(f"{mol}_{structure}")
             elif "Atoms TOO alone" in line:
                 errorTypes += "_3"
-                ET3.append("%s_%s" % (mol, structure))
+                ET3.append(f"{mol}_{structure}")
             elif "Antechamber failed" in line:
                 errorTypes += "_4"
-                ET4.append("%s_%s" % (mol, structure))
+                ET4.append(f"{mol}_{structure}")
             elif "Parmchk failed" in line:
                 errorTypes += "_5"
-                ET5.append("%s_%s" % (mol, structure))
+                ET5.append(f"{mol}_{structure}")
             elif "Tleap failed" in line:
                 errorTypes += "_6"
-                ET6.append("%s_%s" % (mol, structure))
+                ET6.append(f"{mol}_{structure}")
             elif "syntax error" in line:
                 errorTypes += "_8"
-                ET8.add("%s_%s" % (mol, structure))
+                ET8.add(f"{mol}_{structure}")
             elif "Use '-f' option if you want to proceed anyway. Aborting" in line:
                 pass
             else:
@@ -419,10 +419,10 @@ def analyseFile(mol, structure, file):
                 errorTypes += "_10"
         if "No such file or directory: 'tmp'" in line:
             errorTypes += "_7"
-            ET7.add("%s_%s" % (mol, structure))
+            ET7.add(f"{mol}_{structure}")
         if "Semi-QM taking too long to finish" in line:
             errorTypes += "_9"
-            ET9.append("%s_%s" % (mol, structure))
+            ET9.append(f"{mol}_{structure}")
         if "Total time of execution:" in line:
             if mol in execTime:
                 # execTime[mol].append({structure:line[:-1].split(':')[1]})
@@ -441,7 +441,7 @@ def analyseFile(mol, structure, file):
 
     if checkChargeComparison:
         mol2FileName = file.replace(".out", ".mol2")
-        mol2File = open(mol2FileName, "r").readlines()
+        mol2File = open(mol2FileName).readlines()
         for line in mol2File:
             if "# Overall charge:" in line:
                 mol2Charge = int(line.split(":")[1])
@@ -617,7 +617,7 @@ def elapsedTime(seconds, suffixes=["y", "w", "d", "h", "m", "s"], add_s=False, s
         value = seconds / length
         if value > 0:
             seconds = seconds % length
-            time.append("%s%s" % (str(value), (suffix, (suffix, suffix + "s")[value > 1])[add_s]))
+            time.append("{}{}".format(str(value), (suffix, (suffix, suffix + "s")[value > 1])[add_s]))
         if seconds < 1:
             break
 
@@ -707,13 +707,13 @@ def locate(pattern, root=os.curdir):
                 pdbMol2 = True
                 totalPdbMol2Count += 1
         elif ".ideal.acpype/sqm.out" in file:
-            content = open(file, "r").read()
+            content = open(file).read()
             if "No convergence in SCF after" in content:
-                SCFfailedList.append("%s_%s" % (molDir, "ideal"))
+                SCFfailedList.append("{}_{}".format(molDir, "ideal"))
         elif ".pdb.acpype/sqm.out" in file:
-            content = open(file, "r").read()
+            content = open(file).read()
             if "No convergence in SCF after" in content:
-                SCFfailedList.append("%s_%s" % (molDir, "pdb"))
+                SCFfailedList.append("{}_{}".format(molDir, "pdb"))
     if countIdealMol2 > 2:
         multIdealMol2.append(molDir)
     if countPdbMol2 > 2:
@@ -778,7 +778,7 @@ def locate(pattern, root=os.curdir):
     totalTxt += "+ %i " % subTot
 totalTxt = totalTxt[2:]
 sumVal = eval(totalTxt)
-print("%s= %s" % (totalTxt, sumVal))
+print(f"{totalTxt}= {sumVal}")
 
 # print results
 
@@ -793,7 +793,7 @@ def locate(pattern, root=os.curdir):
         print("=>Mols have duplicated coordinates")
         for molLabel in ET1:
             mol, structure = molLabel.split("_")
-            cmd = "grep -e '^ATOM' %s/*%s.out" % (mol, structure)
+            cmd = f"grep -e '^ATOM' {mol}/*{structure}.out"
             out = _getoutput(cmd)
             print("# %s #" % molLabel)
             print(out, "\n")
@@ -802,7 +802,7 @@ def locate(pattern, root=os.curdir):
         print("=>Mols have atoms in close contact")
         for molLabel in WT7:
             mol, structure = molLabel.split("_")
-            cmd = "grep -e '^Warning: Close contact of' %s/*%s.out" % (mol, structure)
+            cmd = f"grep -e '^Warning: Close contact of' {mol}/*{structure}.out"
             out = _getoutput(cmd)
             print("# %s #" % molLabel)
             print(out, "\n")
@@ -811,7 +811,7 @@ def locate(pattern, root=os.curdir):
         print("=>Mols have irregular bonds")
         for molLabel in WT5:
             mol, structure = molLabel.split("_")
-            cmd = "grep -A 1 -e '^WARNING: There is a bond of' %s/*%s.out" % (mol, structure)
+            cmd = f"grep -A 1 -e '^WARNING: There is a bond of' {mol}/*{structure}.out"
             out = _getoutput(cmd)
             print("# %s #" % molLabel)
             print(out, "\n")
@@ -820,7 +820,7 @@ def locate(pattern, root=os.curdir):
         print("=>Mols have atoms too close")
         for molLabel in ET2:
             mol, structure = molLabel.split("_")
-            cmd = "grep -e '^ .*ATOM' %s/*%s.out" % (mol, structure)
+            cmd = f"grep -e '^ .*ATOM' {mol}/*{structure}.out"
             out = _getoutput(cmd)
             print("# %s #" % molLabel)
             print(out, "\n")
@@ -829,7 +829,7 @@ def locate(pattern, root=os.curdir):
         print("=>Mols have atoms too alone")
         for molLabel in ET3:
             mol, structure = molLabel.split("_")
-            cmd = r"""grep -e "^\['ATOM" %s/*%s.out""" % (mol, structure)
+            cmd = fr"""grep -e "^\['ATOM" {mol}/*{structure}.out"""
             out = _getoutput(cmd)
             print("# %s #" % molLabel)
             print(out, "\n")
@@ -893,8 +893,8 @@ def locate(pattern, root=os.curdir):
 if listMolTime:
     # print maxExecTime, minExecTime
     print("Number of clean jobs:", nJobs)
-    print("Longest job: Mol='%s', time= %s" % (maxMolTime, elapsedTime(maxExecTime)))
-    print("Fatest job: Mol='%s', time= %s" % (minMolTime, elapsedTime(minExecTime)))
+    print(f"Longest job: Mol='{maxMolTime}', time= {elapsedTime(maxExecTime)}")
+    print(f"Fatest job: Mol='{minMolTime}', time= {elapsedTime(minExecTime)}")
     print("Average time of execution per clean job: %s" % elapsedTime(totalCleanExecTime / nJobs))
 else:
     print("NO time stats available for clean jobs")
diff --git a/scripts/check_acpype.py b/scripts/check_acpype.py
index 8ba5eac0..89374195 100755
--- a/scripts/check_acpype.py
+++ b/scripts/check_acpype.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 import os
 import shutil
 from glob import glob
@@ -6,14 +6,14 @@
 from acpype.topol import ACTopol
 from acpype.utils import _getoutput
 
-usePymol = True
+usePymol = False
 ffType = "amber"  # gaff
 cType = "gas"
-debug = False
+debug = True
 
 water = " -water none"
 
-print("usePymol: %s, ffType: %s, cType: %s" % (usePymol, ffType, cType))
+print(f"usePymol: {usePymol}, ffType: {ffType}, cType: {cType}")
 
 tmpDir = "/tmp/testAcpype"
 
@@ -34,15 +34,15 @@
 exePymol = "/sw/bin/pymol"
 
 # Binaries for gromacs
-gpath = "/sw/"
+gpath = "/home/awilter/miniconda3/envs/acpype/"
 gmxTopDir = gpath + "share"
-pdb2gmx = gpath + "bin/pdb2gmx"
-grompp = gpath + "bin/grompp"
-mdrun = gpath + "bin/mdrun"
-g_energy = gpath + "bin/g_energy"
-gmxdump = gpath + "bin/gmxdump"
+pdb2gmx = gpath + "bin/gmx pdb2gmx"
+grompp = gpath + "bin/gmx grompp"
+mdrun = gpath + "bin/gmx mdrun"
+g_energy = gpath + "bin/gmx energy"
+gmxdump = gpath + "bin/gmx dump"
 
-amberff = "leaprc.ff99SB"
+amberff = "oldff/leaprc.ff99SB"
 
 genPdbTemplate = """
 source %(amberff)s
@@ -56,6 +56,7 @@
 # Create SPE.mdp file #single point energy
 cat << EOF >| SPE.mdp
 define = -DFLEXIBLE
+cutoff-scheme            = group
 integrator               = md
 nsteps                   = 0
 dt                       = 0.001
@@ -426,14 +427,14 @@ def addParam(ll, item):
             except Exception:
                 pass
         if not found:
-            print("%s %s %s not found in %s Bon" % (dict_[ll], ent, item, ffType))
+            print(f"{dict_[ll]} {ent} {item} not found in {ffType} Bon")
         # print(item, e, par)
         return par
 
     compareParameters = True
 
     agRes = parseTopFile(open("ag%s.top" % (res)).readlines())
-    acRes = parseTopFile(open("ag%s.acpype/ag%s_GMX.itp" % (res, res)).readlines())
+    acRes = parseTopFile(open(f"ag{res}.acpype/ag{res}_GMX.itp").readlines())
     ffBon = aBon
     ffgRes = agRes
 
@@ -637,13 +638,15 @@ def build_residues_tleap():
         _getoutput(cmd)
         # cmd = "%s -O; %s < restrt > %s.pdb; mv mdinfo %s.mdinfo" % (sanderExe, ambpdbExe, aai3, aai3)
         # -i mdin -o mdout -p prmtop -c inpcrd" % (sanderExe)
-        cmd = "%s -O; %s < restrt > %s.pdb" % (sanderExe, ambpdbExe, aai3)
+        cmd = f"{sanderExe} -O; {ambpdbExe} -c restrt > {aai3}.pdb"
         _getoutput(cmd)
     _getoutput("rm -f mdout mdinfo mdin restrt tleap.in prmtop inpcrd leap.log")
 
 
 def error(v1, v2):
     """percentage relative error"""
+    if v1 == v2:
+        return 0
     return abs(v1 - v2) / max(abs(v1), abs(v2)) * 100
 
 
@@ -703,8 +706,9 @@ def getEnergies(template):
     # print(dictEnerAMB)
 
     # calc Pot Ener for agXXX.acpype/agXXX.pdb (ACPYPE_GMX)
-    template = """%(grompp)s -c ag%(res)s.acpype/ag%(res)s_NEW.pdb -p ag%(res)s.acpype/ag%(res)s_GMX.top -f SPE.mdp
--o ag%(res)s.tpr -pp ag%(res)sp.top
+    template = """
+    %(grompp)s -c ag%(res)s.acpype/ag%(res)s_NEW.pdb -p ag%(res)s.acpype/ag%(res)s_GMX.top -f SPE.mdp \
+    -o ag%(res)s.tpr -pp ag%(res)sp.top
     %(mdrun)s -v -deffnm ag%(res)s
     echo %(tEner)s | %(g_energy)s -f ag%(res)s.edr
     """
@@ -776,7 +780,7 @@ def getEnergies(template):
         ff = open(tmpFile, "w")
         ff.writelines(pymolScript)
         ff.close()
-        cmd = "%s -qc %s" % (exePymol, tmpFile)
+        cmd = f"{exePymol} -qc {tmpFile}"
         os.system(cmd)
     else:
         build_residues_tleap()
@@ -787,7 +791,7 @@ def getEnergies(template):
         res, ext = os.path.splitext(resFile)  # eg. res = 'AAA'
         # if res != 'RRR': continue
         if len(resFile) == 7 and ext == ".pdb" and resFile[:3].isupper():
-            print("\nFile %s : residue %s" % (resFile, aa_dict[res[0]].upper()))
+            print(f"\nFile {resFile} : residue {aa_dict[res[0]].upper()}")
 
             _pdb = createOldPdb2(resFile)  # using my own dict
             apdb = createAmberPdb3(_pdb)  # create file aAAA.pdb with NXXX, CXXX
@@ -795,7 +799,7 @@ def getEnergies(template):
             # from ogpdb to amber pdb and top
             agpdb = "ag%s.pdb" % res  # output name
             agtop = "ag%s.top" % res
-            cmd = " %s -f %s -o %s -p %s -ff amber99sb %s" % (pdb2gmx, apdb, agpdb, agtop, water)
+            cmd = f" {pdb2gmx} -f {apdb} -o {agpdb} -p {agtop} -ff amber99sb {water}"
             pdebug(cmd)
             out = _getoutput(cmd)
             # print(out)
diff --git a/scripts/compare_itps.py b/scripts/compare_itps.py
index 23a1a080..7aee15af 100755
--- a/scripts/compare_itps.py
+++ b/scripts/compare_itps.py
@@ -44,11 +44,11 @@ def compareDicts(d1, d2):
                 try:
                     _tempD1.remove(item)
                 except Exception:
-                    print("\tDuplicate item %s in %s itp2" % (repr(item), flag))
+                    print(f"\tDuplicate item {repr(item)} in {flag} itp2")
                 try:
                     _tempD2.remove(item)
                 except Exception:
-                    print("\tDuplicate item %s in %s itp1" % (repr(item), flag))
+                    print(f"\tDuplicate item {repr(item)} in {flag} itp1")
             else:
                 t = item[:-1]
                 t.reverse()
@@ -57,11 +57,11 @@ def compareDicts(d1, d2):
                     try:
                         _tempD1.remove(item)
                     except Exception:
-                        print("\tDuplicate item %s in %s itp2" % (repr(item), flag))
+                        print(f"\tDuplicate item {repr(item)} in {flag} itp2")
                     try:
                         _tempD2.remove(itemRev)
                     except Exception:
-                        print("\tDuplicate item %s in %s itp1" % (repr(item), flag))
+                        print(f"\tDuplicate item {repr(item)} in {flag} itp1")
 
         tD1 = _tempD1[:]
         tD2 = _tempD2[:]
diff --git a/scripts/run_test_acpype_db_ligands.py b/scripts/run_test_acpype_db_ligands.py
index 08403197..82dbbc5b 100644
--- a/scripts/run_test_acpype_db_ligands.py
+++ b/scripts/run_test_acpype_db_ligands.py
@@ -37,7 +37,7 @@ def elapsedTime(seconds, suffixes=["y", "w", "d", "h", "m", "s"], add_s=False, s
         value = seconds / length
         if value > 0:
             seconds = seconds % length
-            time.append("%s%s" % (str(value), (suffix, (suffix, suffix + "s")[value > 1])[add_s]))
+            time.append("{}{}".format(str(value), (suffix, (suffix, suffix + "s")[value > 1])[add_s]))
         if seconds < 1:
             break
 
diff --git a/scripts/ver_today.sh b/scripts/ver_today.sh
index 5f3c47c2..81220f6f 100755
--- a/scripts/ver_today.sh
+++ b/scripts/ver_today.sh
@@ -5,14 +5,14 @@ last_tag=$(git describe --abbrev=0 --tags)
 
 while IFS= read -r afile; do
 	echo "Updated version to $today in file $afile"
-	perl -pi -e "s/\b[0-9]{4}\.[12]?[0-9]\.[12]?[0-9]\b/$today/g" "$afile"
+	perl -pi -e "s/\b[0-9]{4}\.[12]?[0-9]\.[123]?[0-9]\b/$today/g" "$afile"
 	git add "$afile"
-done < <(grep -lEr "\b\d{4}\.[12]?[0-9]\.[12]?[0-9]\b" -- **/*.py pyproject.toml)
+done < <(pcregrep -lwr "\d{4}\.[12]?[0-9]\.[123]?[0-9]" ./*/*.py pyproject.toml)
 
 while IFS= read -r afile; do
 	echo "Updated last_tag to $last_tag in file $afile"
-	perl -pi -e "s/\b[0-9]{4}\.[12]?[0-9]\.[12]?[0-9]\b/$last_tag/g" "$afile"
+	perl -pi -e "s/\b[0-9]{4}\.[12]?[0-9]\.[123]?[0-9]\b/$last_tag/g" "$afile"
 	git add "$afile"
-done < <(grep -lEr "\b\d{4}\.[12]?[0-9]\.[12]?[0-9]\b" -- README.md)
+done < <(pcregrep -lwr "\d{4}\.[12]?[0-9]\.[123]?[0-9]" README.md)
 
 exit 0
diff --git a/tests/AAA.mol2 b/tests/AAA.mol2
index b1d4e20e..a5fa6150 100644
--- a/tests/AAA.mol2
+++ b/tests/AAA.mol2
@@ -72,4 +72,3 @@ Energy = 0
     30    27    31    1
     31    27    32    1
     32    27    33    1
-
diff --git a/tests/Base.prmtop b/tests/Base.prmtop
index 2fedab1a..0f12b0b8 100644
--- a/tests/Base.prmtop
+++ b/tests/Base.prmtop
@@ -2,6 +2,7 @@
 %FLAG TITLE                                                                     
 %FORMAT(20a4)                                                                   
 default_name                                                                    
+%COMMENT Base test
 %FLAG POINTERS                                                                  
 %FORMAT(10I8)                                                                   
    24931      17   23327    1584    3754    2149    7229    5392       0       0
diff --git a/tests/HEM.pdb b/tests/HEM.pdb
new file mode 100644
index 00000000..768383d3
--- /dev/null
+++ b/tests/HEM.pdb
@@ -0,0 +1,121 @@
+HEADER    Ideal coordinates
+ for PDB-CCD HEM
+COMPND    HEM
+AUTHOR    pdbccdutils 0.6
+AUTHOR    RDKit 2021.03.1
+HETATM    1 CHA  HEM A   1      -2.188  -0.470   0.697  1.00 20.00           C  
+HETATM    2 CHB  HEM A   1       1.980  -3.261   0.092  1.00 20.00           C  
+HETATM    3 CHC  HEM A   1       4.525   0.841  -0.194  1.00 20.00           C  
+HETATM    4 CHD  HEM A   1       0.557   3.487   0.231  1.00 20.00           C  
+HETATM    5 C1A  HEM A   1      -1.271  -1.607   0.502  1.00 20.00           C  
+HETATM    6 C2A  HEM A   1      -1.663  -2.879   0.397  1.00 20.00           C  
+HETATM    7 C3A  HEM A   1      -0.466  -3.672   0.147  1.00 20.00           C  
+HETATM    8 C4A  HEM A   1       0.571  -2.836   0.180  1.00 20.00           C  
+HETATM    9 CMA  HEM A   1      -0.408  -5.164  -0.023  1.00 20.00           C  
+HETATM   10 CAA  HEM A   1      -3.078  -3.398   0.441  1.00 20.00           C  
+HETATM   11 CBA  HEM A   1      -3.748  -3.253  -0.927  1.00 20.00           C  
+HETATM   12 CGA  HEM A   1      -5.161  -3.740  -0.871  1.00 20.00           C  
+HETATM   13 O1A  HEM A   1      -6.093  -2.942  -0.582  1.00 20.00           O  
+HETATM   14 O2A  HEM A   1      -5.440  -5.084  -1.097  1.00 20.00           O  
+HETATM   15 C1B  HEM A   1       3.015  -2.418   0.051  1.00 20.00           C  
+HETATM   16 C2B  HEM A   1       4.419  -2.815  -0.031  1.00 20.00           C  
+HETATM   17 C3B  HEM A   1       5.107  -1.684  -0.153  1.00 20.00           C  
+HETATM   18 C4B  HEM A   1       4.141  -0.577  -0.093  1.00 20.00           C  
+HETATM   19 CMB  HEM A   1       4.966  -4.214   0.048  1.00 20.00           C  
+HETATM   20 CAB  HEM A   1       6.575  -1.530  -0.261  1.00 20.00           C  
+HETATM   21 CBB  HEM A   1       7.328  -2.316  -1.027  1.00 20.00           C  
+HETATM   22 C1C  HEM A   1       3.676   1.869  -0.094  1.00 20.00           C  
+HETATM   23 C2C  HEM A   1       4.069   3.283  -0.170  1.00 20.00           C  
+HETATM   24 C3C  HEM A   1       2.960   4.018  -0.092  1.00 20.00           C  
+HETATM   25 C4C  HEM A   1       1.829   3.099   0.095  1.00 20.00           C  
+HETATM   26 CMC  HEM A   1       5.479   3.801  -0.274  1.00 20.00           C  
+HETATM   27 CAC  HEM A   1       2.864   5.495  -0.126  1.00 20.00           C  
+HETATM   28 CBC  HEM A   1       3.524   6.236  -1.012  1.00 20.00           C  
+HETATM   29 C1D  HEM A   1      -0.584   2.572   0.410  1.00 20.00           C  
+HETATM   30 C2D  HEM A   1      -1.973   3.028   0.580  1.00 20.00           C  
+HETATM   31 C3D  HEM A   1      -2.719   1.951   0.791  1.00 20.00           C  
+HETATM   32 C4D  HEM A   1      -1.812   0.811   0.674  1.00 20.00           C  
+HETATM   33 CMD  HEM A   1      -2.446   4.454   0.585  1.00 20.00           C  
+HETATM   34 CAD  HEM A   1      -4.211   1.907   1.008  1.00 20.00           C  
+HETATM   35 CBD  HEM A   1      -4.941   1.718  -0.324  1.00 20.00           C  
+HETATM   36 CGD  HEM A   1      -6.418   1.638  -0.103  1.00 20.00           C  
+HETATM   37 O1D  HEM A   1      -6.967   0.520   0.092  1.00 20.00           O  
+HETATM   38 O2D  HEM A   1      -7.178   2.803  -0.070  1.00 20.00           O  
+HETATM   39 NA   HEM A   1       0.148  -1.487   0.385  1.00 20.00           N  
+HETATM   40 NB   HEM A   1       2.917  -0.995   0.023  1.00 20.00           N1+
+HETATM   41 NC   HEM A   1       2.265   1.739   0.085  1.00 20.00           N  
+HETATM   42 ND   HEM A   1      -0.482   1.278   0.454  1.00 20.00           N1+
+HETATM   43 FE   HEM A   1       4.176  -2.073  -0.035  1.00 20.00          FE2-
+HETATM   44 HHB  HEM A   1       2.185  -4.322   0.065  1.00 20.00           H  
+HETATM   45 HHC  HEM A   1       5.571   1.053  -0.361  1.00 20.00           H  
+HETATM   46 HHD  HEM A   1       0.340   4.545   0.217  1.00 20.00           H  
+HETATM   47 HMA  HEM A   1       0.329  -5.436  -0.808  1.00 20.00           H  
+HETATM   48 HMAA HEM A   1      -0.120  -5.637   0.938  1.00 20.00           H  
+HETATM   49 HMAB HEM A   1      -1.390  -5.563  -0.348  1.00 20.00           H  
+HETATM   50 HAA  HEM A   1      -3.077  -4.466   0.746  1.00 20.00           H  
+HETATM   51 HAAA HEM A   1      -3.660  -2.857   1.216  1.00 20.00           H  
+HETATM   52 HBA  HEM A   1      -3.739  -2.187  -1.245  1.00 20.00           H  
+HETATM   53 HBAA HEM A   1      -3.189  -3.844  -1.683  1.00 20.00           H  
+HETATM   54 HMB  HEM A   1       4.342  -4.833   0.724  1.00 20.00           H  
+HETATM   55 HMBA HEM A   1       4.971  -4.669  -0.964  1.00 20.00           H  
+HETATM   56 HMBB HEM A   1       5.994  -4.215   0.464  1.00 20.00           H  
+HETATM   57 HAB  HEM A   1       7.047  -0.697   0.243  1.00 20.00           H  
+HETATM   58 HBB  HEM A   1       8.393  -2.140  -1.097  1.00 20.00           H  
+HETATM   59 HBBA HEM A   1       6.896  -3.115  -1.615  1.00 20.00           H  
+HETATM   60 HMC  HEM A   1       6.168   3.162   0.316  1.00 20.00           H  
+HETATM   61 HMCA HEM A   1       5.798   3.800  -1.337  1.00 20.00           H  
+HETATM   62 HMCB HEM A   1       5.562   4.826   0.140  1.00 20.00           H  
+HETATM   63 HAC  HEM A   1       2.168   5.987   0.541  1.00 20.00           H  
+HETATM   64 HBC  HEM A   1       4.174   5.787  -1.752  1.00 20.00           H  
+HETATM   65 HBCA HEM A   1       3.394   7.311  -1.021  1.00 20.00           H  
+HETATM   66 HMD  HEM A   1      -1.874   5.051  -0.153  1.00 20.00           H  
+HETATM   67 HMDA HEM A   1      -3.515   4.525   0.299  1.00 20.00           H  
+HETATM   68 HMDB HEM A   1      -2.306   4.887   1.598  1.00 20.00           H  
+HETATM   69 HAD  HEM A   1      -4.458   1.072   1.697  1.00 20.00           H  
+HETATM   70 HADA HEM A   1      -4.556   2.839   1.504  1.00 20.00           H  
+HETATM   71 HBD  HEM A   1      -4.721   2.573  -0.999  1.00 20.00           H  
+HETATM   72 HBDA HEM A   1      -4.592   0.787  -0.821  1.00 20.00           H  
+HETATM   73 H2A  HEM A   1      -6.390  -5.433  -1.046  1.00 20.00           H  
+HETATM   74 H2D  HEM A   1      -8.177   2.766   0.095  1.00 20.00           H  
+HETATM   75 HHA  HEM A   1      -3.238  -0.684   0.827  1.00 20.00           H  
+CONECT    1    5   32   32   75
+CONECT    2    8   15   15   44
+CONECT    3   18   22   22   45
+CONECT    4   25   25   29   46
+CONECT    5    6    6   39
+CONECT    6    7   10
+CONECT    7    8    8    9
+CONECT    8   39
+CONECT    9   47   48   49
+CONECT   10   11   50   51
+CONECT   11   12   52   53
+CONECT   12   13   13   14
+CONECT   14   73
+CONECT   15   16   40
+CONECT   16   17   17   19
+CONECT   17   18   20
+CONECT   18   40   40
+CONECT   19   54   55   56
+CONECT   20   21   21   57
+CONECT   21   58   59
+CONECT   22   23   41
+CONECT   23   24   24   26
+CONECT   24   25   27
+CONECT   25   41
+CONECT   26   60   61   62
+CONECT   27   28   28   63
+CONECT   28   64   65
+CONECT   29   30   42   42
+CONECT   30   31   31   33
+CONECT   31   32   34
+CONECT   32   42
+CONECT   33   66   67   68
+CONECT   34   35   69   70
+CONECT   35   36   71   72
+CONECT   36   37   37   38
+CONECT   38   74
+CONECT   39   43
+CONECT   40   43
+CONECT   41   43
+CONECT   42   43
+END
diff --git a/tests/KKK.mol2 b/tests/KKK.mol2
index 9cda9362..8bc7f72a 100644
--- a/tests/KKK.mol2
+++ b/tests/KKK.mol2
@@ -144,4 +144,3 @@ Energy = 0
     66    55    67    1
     67    55    68    1
     68    55    69    1
-
diff --git a/tests/README.txt b/tests/README.txt
index 7e8ff7a6..0bc37f1d 100644
--- a/tests/README.txt
+++ b/tests/README.txt
@@ -8,4 +8,4 @@ DDD.mol2:   in mol2 format
 KKK.pdb:    a tri lysine peptide with N- and C- termini, charge +3
 KKK.mol2:   in mol2 format
 FFF.pdb:    a tri phenylalanine peptide with N- and C- termini, aromatic
-FFF.mol2:   in mol2 format
\ No newline at end of file
+FFF.mol2:   in mol2 format
diff --git a/tests/benzene.mdl b/tests/benzene.mdl
new file mode 100644
index 00000000..ded3975a
--- /dev/null
+++ b/tests/benzene.mdl
@@ -0,0 +1,29 @@
+tests/benzene.pdb
+ OpenBabel12312108183D
+
+ 12 12  0  0  0  0  0  0  0  0999 V2000
+    5.2740    1.9990   -8.5680 C   0  0  0  0  0  0  0  0  0  0  0  0
+    6.6270    2.0180   -8.2090 C   0  0  0  0  0  0  0  0  0  0  0  0
+    7.3660    0.8290   -8.2020 C   0  0  0  0  0  0  0  0  0  0  0  0
+    6.7520   -0.3790   -8.5540 C   0  0  0  0  0  0  0  0  0  0  0  0
+    5.3990   -0.3980   -8.9120 C   0  0  0  0  0  0  0  0  0  0  0  0
+    4.6600    0.7910   -8.9190 C   0  0  0  0  0  0  0  0  0  0  0  0
+    4.7040    2.9160   -8.5730 H   0  0  0  0  0  0  0  0  0  0  0  0
+    7.1010    2.9500   -7.9380 H   0  0  0  0  0  0  0  0  0  0  0  0
+    8.4100    0.8440   -7.9260 H   0  0  0  0  0  0  0  0  0  0  0  0
+    7.3220   -1.2960   -8.5480 H   0  0  0  0  0  0  0  0  0  0  0  0
+    4.9250   -1.3300   -9.1830 H   0  0  0  0  0  0  0  0  0  0  0  0
+    3.6160    0.7760   -9.1960 H   0  0  0  0  0  0  0  0  0  0  0  0
+  1  6  2  0  0  0  0
+  1  7  1  0  0  0  0
+  1  2  1  0  0  0  0
+  2  3  2  0  0  0  0
+  2  8  1  0  0  0  0
+  3  4  1  0  0  0  0
+  3  9  1  0  0  0  0
+  4  5  2  0  0  0  0
+  4 10  1  0  0  0  0
+  5 11  1  0  0  0  0
+  5  6  1  0  0  0  0
+  6 12  1  0  0  0  0
+M  END
diff --git a/tests/benzene.mol b/tests/benzene.mol
new file mode 100644
index 00000000..92a67758
--- /dev/null
+++ b/tests/benzene.mol
@@ -0,0 +1,29 @@
+tests/benzene.pdb
+ OpenBabel12312108093D
+
+ 12 12  0  0  0  0  0  0  0  0999 V2000
+    5.2740    1.9990   -8.5680 C   0  0  0  0  0  0  0  0  0  0  0  0
+    6.6270    2.0180   -8.2090 C   0  0  0  0  0  0  0  0  0  0  0  0
+    7.3660    0.8290   -8.2020 C   0  0  0  0  0  0  0  0  0  0  0  0
+    6.7520   -0.3790   -8.5540 C   0  0  0  0  0  0  0  0  0  0  0  0
+    5.3990   -0.3980   -8.9120 C   0  0  0  0  0  0  0  0  0  0  0  0
+    4.6600    0.7910   -8.9190 C   0  0  0  0  0  0  0  0  0  0  0  0
+    4.7040    2.9160   -8.5730 H   0  0  0  0  0  0  0  0  0  0  0  0
+    7.1010    2.9500   -7.9380 H   0  0  0  0  0  0  0  0  0  0  0  0
+    8.4100    0.8440   -7.9260 H   0  0  0  0  0  0  0  0  0  0  0  0
+    7.3220   -1.2960   -8.5480 H   0  0  0  0  0  0  0  0  0  0  0  0
+    4.9250   -1.3300   -9.1830 H   0  0  0  0  0  0  0  0  0  0  0  0
+    3.6160    0.7760   -9.1960 H   0  0  0  0  0  0  0  0  0  0  0  0
+  1  6  2  0  0  0  0
+  1  7  1  0  0  0  0
+  1  2  1  0  0  0  0
+  2  3  2  0  0  0  0
+  2  8  1  0  0  0  0
+  3  4  1  0  0  0  0
+  3  9  1  0  0  0  0
+  4  5  2  0  0  0  0
+  4 10  1  0  0  0  0
+  5 11  1  0  0  0  0
+  5  6  1  0  0  0  0
+  6 12  1  0  0  0  0
+M  END
diff --git a/tests/conftest.py b/tests/conftest.py
index 808e56f5..116a81ff 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -8,8 +8,23 @@
 pytest --cov=acpype --cov-report=term-missing:skip-covered
 """
 
+import os
+from shutil import rmtree
+
+import pytest
+
 from acpype import __version__ as version
 
 
 def pytest_report_header(config):
     return f">>>\tVersion: {version}\n"
+
+
+@pytest.fixture
+def janitor():
+    os.chdir(os.path.dirname(os.path.abspath(__file__)))
+    to_delete = []
+    yield to_delete
+    for item in to_delete:
+        if os.path.exists(item):
+            rmtree(item)
diff --git a/tests/dmp.mol2 b/tests/dmp.mol2
index 1f2678a3..b652ed28 100644
--- a/tests/dmp.mol2
+++ b/tests/dmp.mol2
@@ -171,4 +171,3 @@ Energy = 0
     82    35    69    1
     83    35    80    1
     84    80    73    1
-
diff --git a/tests/double_res.pdb b/tests/double_res.pdb
new file mode 100644
index 00000000..4498910b
--- /dev/null
+++ b/tests/double_res.pdb
@@ -0,0 +1,28 @@
+COMPND    benzene.pdb
+AUTHOR    GENERATED BY OPEN BABEL 2.4.1
+ATOM      1  C1  NEB     1       5.274   1.999  -8.568  1.00  0.00           C
+ATOM      2  C2  NEB     1       6.627   2.018  -8.209  1.00  0.00           C
+ATOM      3  C3  NEB     1       7.366   0.829  -8.202  1.00  0.00           C
+ATOM      4  C4  NEB     1       6.752  -0.379  -8.554  1.00  0.00           C
+ATOM      5  C5  NEB     1       5.399  -0.398  -8.912  1.00  0.00           C
+ATOM      6  C6  NEB     1       4.660   0.791  -8.919  1.00  0.00           C
+ATOM      7  H11 BEN     1       4.704   2.916  -8.573  1.00  0.00           H
+ATOM      8  H21 BEN     1       7.101   2.950  -7.938  1.00  0.00           H
+ATOM      9  H31 BEN     1       8.410   0.844  -7.926  1.00  0.00           H
+ATOM     10  H41 BEN     1       7.322  -1.296  -8.548  1.00  0.00           H
+ATOM     11  H51 BEN     1       4.925  -1.330  -9.183  1.00  0.00           H
+ATOM     12  H61 BEN     1       3.616   0.776  -9.196  1.00  0.00           H
+CONECT    1    6    7    2
+CONECT    2    1    3    8
+CONECT    3    4    2    9
+CONECT    4    5   10    3
+CONECT    5   11    6    4
+CONECT    6   12    5    1
+CONECT    7    1
+CONECT    8    2
+CONECT    9    3
+CONECT   10    4
+CONECT   11    5
+CONECT   12    6
+MASTER        0    0    0    0    0    0    0    0   12    0   12    0
+END
diff --git a/tests/drift.mol2 b/tests/drift.mol2
new file mode 100644
index 00000000..f924842e
--- /dev/null
+++ b/tests/drift.mol2
@@ -0,0 +1,88 @@
+@<TRIPOS>MOLECULE
+ADPMg.pdb
+ 39 41 0 0 0
+SMALL
+GASTEIGER
+
+@<TRIPOS>ATOM
+      1  C1'      118.4900   96.5010  146.3800 C.3     1  ADP1        0.1667
+      2  C2       116.9020   92.2900  146.4240 C.ar    1  ADP1        0.1205
+      3  C2'      119.9080   96.0790  146.0350 C.3     1  ADP1        0.1285
+      4  C3'      120.7000   97.3640  145.9120 C.3     1  ADP1        0.1135
+      5  C4       117.1480   94.5000  145.6730 C.ar    1  ADP1        0.1674
+      6  C4'      119.7060   98.4940  146.1230 C.3     1  ADP1        0.1133
+      7  C5       116.1780   94.2230  144.6030 C.ar    1  ADP1        0.1473
+      8  C5'      119.8170   99.5430  145.0210 C.3     1  ADP1        0.0836
+      9  C6       115.6020   92.8590  144.5430 C.ar    1  ADP1        0.1472
+     10  C8       116.8640   96.2860  144.4660 C.ar    1  ADP1        0.1004
+     11  N1       116.0070   91.9650  145.4730 N.ar    1  ADP1       -0.2188
+     12  N3       117.4640   93.5060  146.5380 N.ar    1  ADP1       -0.2159
+     13  N6       114.7020   92.5170  143.5900 N.pl3   1  ADP1       -0.3413
+     14  N7       116.0490   95.3610  143.8990 N.ar    1  ADP1       -0.2306
+     15  N9       117.5220   95.7730  145.5230 N.ar    1  ADP1       -0.2855
+     16  O1A      123.1970  100.7910  143.6770 O.2     1  ADP1       -0.5170
+     17  O1B      119.1040  102.6780  143.4590 O.2     1  ADP1       -0.2221
+     18  O2'      120.4500   95.2610  147.0740 O.3     1  ADP1       -0.3847
+     19  O2A      120.8840  100.7360  142.5030 O.3     1  ADP1       -0.4370
+     20  O2B      121.1050  103.6910  142.2760 O.3     1  ADP1       -0.1143
+     21  O3'      121.7130   97.4110  146.9190 O.3     1  ADP1       -0.3864
+     22  O3A      121.3880  102.4050  144.3470 O.3     1  ADP1       -0.2261
+     23  O3B      120.3410  104.6280  144.4990 O.3     1  ADP1       -0.1143
+     24  O4'      118.4030   97.9070  146.1380 O.3     1  ADP1       -0.3456
+     25  O5'      121.1850   99.9230  144.8970 O.3     1  ADP1       -0.3245
+     26  PA       121.6970  100.9390  143.7570 P.3     1  ADP1        0.2224
+     27  PB       120.4050  103.4280  143.5860 P.3     1  ADP1        0.5373
+     28  H1'      118.2860   96.2920  147.4300 H       1  ADP1        0.0866
+     29  H2       117.1850   91.5300  147.1370 H       1  ADP1        0.1048
+     30  H2'      119.9190   95.5390  145.0880 H       1  ADP1        0.0665
+     31  H3'      121.1490   97.4370  144.9220 H       1  ADP1        0.0647
+     32  H4'      119.8980   98.9650  147.0870 H       1  ADP1        0.0647
+     33  H5'      119.4640   99.1250  144.0780 H       1  ADP1        0.0591
+     34 H5''      119.2170  100.4140  145.2830 H       1  ADP1        0.0591
+     35  H8       116.9710   97.3020  144.1150 H       1  ADP1        0.1030
+     36 HN61      114.3220   91.5820  143.5670 H       1  ADP1        0.1438
+     37 HN62      114.4110   93.1980  142.9030 H       1  ADP1        0.1438
+     38 HO2'      119.9570   94.4390  147.1240 H       1  ADP1        0.2101
+     39 HO3'      122.1930   98.2400  146.8520 H       1  ADP1        0.2300
+@<TRIPOS>BOND
+     1     1     3    1
+     2     1    15    1
+     3     1    24    1
+     4     1    28    1
+     5     2    11   ar
+     6     2    12   ar
+     7     2    29    1
+     8     3     4    1
+     9     3    18    1
+    10     3    30    1
+    11     4     6    1
+    12     4    21    1
+    13     4    31    1
+    14     5     7   ar
+    15     5    12   ar
+    16     5    15   ar
+    17     6     8    1
+    18     6    24    1
+    19     6    32    1
+    20     7     9   ar
+    21     7    14   ar
+    22     8    25    1
+    23     8    33    1
+    24     8    34    1
+    25     9    11   ar
+    26     9    13    1
+    27    10    14   ar
+    28    10    15   ar
+    29    10    35    1
+    30    13    36    1
+    31    13    37    1
+    32    16    26    2
+    33    17    27    2
+    34    18    38    1
+    35    19    26    1
+    36    20    27    1
+    37    21    39    1
+    38    22    26    1
+    39    22    27    1
+    40    23    27    1
+    41    25    26    1
diff --git a/tests/glycam_corrupt.prmtop b/tests/glycam_corrupt.prmtop
new file mode 100644
index 00000000..45358a27
--- /dev/null
+++ b/tests/glycam_corrupt.prmtop
@@ -0,0 +1,320 @@
+%VERSION  VERSION_STAMP = V0001.000  DATE = 06/27/16  09:20:58
+%FLAG TITLE
+%FORMAT(20a4)
+default_name
+%FLAG POINTERS
+%FORMAT(10I8)
+      30      11      15      15      32      21      56      33       0       0
+     161       2      15      21      33      12      23      31      11       0
+       0       0       0       0       0       0       0       0      28       0
+       0
+%FLAG ATOM_NAME
+%FORMAT(20a4)
+HO1 O1  C1  H1  O5  C5  H5  C6  H62 H61 O6  H6O C4  H4  O4  H4O C3  H3  O3  H3O
+C2  H2  N2  H2N C2N O2N CME H3M H2M H1M
+%FLAG CHARGE
+%FORMAT(5E16.8)
+  8.10892350E+00 -1.16440497E+01  5.22980010E+00  0.00000000E+00 -7.89025590E+00
+  3.79023840E+00  0.00000000E+00  5.26624470E+00  0.00000000E+00  0.00000000E+00
+ -1.25551647E+01  7.72625520E+00  5.50313460E+00  0.00000000E+00 -1.30471668E+01
+  7.94492280E+00  3.28001400E+00  0.00000000E+00 -1.24093863E+01  7.70803290E+00
+  8.74670400E+00  0.00000000E+00 -1.31565006E+01  5.46669000E+00  1.18080504E+01
+ -1.04960448E+01  6.19558200E-01  0.00000000E+00  0.00000000E+00  0.00000000E+00
+%FLAG ATOMIC_NUMBER
+%FORMAT(10I8)
+       1       8       6       1       8       6       1       6       1       1
+       8       1       6       1       8       1       6       1       8       1
+       6       1       7       1       6       8       6       1       1       1
+%FLAG MASS
+%FORMAT(5E16.8)
+  1.00800000E+00  1.60000000E+01  1.20100000E+01  1.00800000E+00  1.60000000E+01
+  1.20100000E+01  1.00800000E+00  1.20100000E+01  1.00800000E+00  1.00800000E+00
+  1.60000000E+01  1.00800000E+00  1.20100000E+01  1.00800000E+00  1.60000000E+01
+  1.00800000E+00  1.20100000E+01  1.00800000E+00  1.60000000E+01  1.00800000E+00
+  1.20100000E+01  1.00800000E+00  1.40100000E+01  1.00800000E+00  1.20100000E+01
+  1.60000000E+01  1.20100000E+01  1.00800000E+00  1.00800000E+00  1.00800000E+00
+%FLAG ATOM_TYPE_INDEX
+%FORMAT(10I8)
+       1       2       3       4       5       3       6       3       6       6
+       2       1       3       6       2       1       3       6       2       1
+       3       6       7       8       9      10       3      11      11      11
+%FLAG NUMBER_EXCLUDED_ATOMS
+%FORMAT(10I8)
+       5       8      14       6      13      14       8       8       4       3
+       2       1      10       6       5       1       8       5       4       1
+       6       3       7       3       5       4       3       2       1       1
+%FLAG NONBONDED_PARM_INDEX
+%FORMAT(10I8)
+       1       2       4       7      11      16      22      29      37      46
+      56       2       3       5       8      12      17      23      30      38
+      47      57       4       5       6       9      13      18      24      31
+      39      48      58       7       8       9      10      14      19      25
+      32      40      49      59      11      12      13      14      15      20
+      26      33      41      50      60      16      17      18      19      20
+      21      27      34      42      51      61      22      23      24      25
+      26      27      28      35      43      52      62      29      30      31
+      32      33      34      35      36      44      53      63      37      38
+      39      40      41      42      43      44      45      54      64      46
+      47      48      49      50      51      52      53      54      55      65
+      56      57      58      59      60      61      62      63      64      65
+      66
+%FLAG RESIDUE_LABEL
+%FORMAT(20a4)
+ROH 0YB
+%FLAG RESIDUE_POINTER
+%FORMAT(10I8)
+       1       3
+%FLAG BOND_FORCE_CONSTANT
+%FORMAT(5E16.8)
+  3.20000000E+02  5.53000000E+02  3.40000000E+02  5.70000000E+02  2.20000000E+02
+  4.34000000E+02  4.90000000E+02  3.40000000E+02  3.37000000E+02  3.10000000E+02
+  2.85000000E+02  3.40000000E+02
+%FLAG BOND_EQUIL_VALUE
+%FORMAT(5E16.8)
+  1.43000000E+00  9.60000000E-01  1.09000000E+00  1.22900000E+00  1.53000000E+00
+  1.01000000E+00  1.33500000E+00  1.09000000E+00  1.45000000E+00  1.52000000E+00
+  1.46000000E+00  1.09000000E+00
+%FLAG ANGLE_FORCE_CONSTANT
+%FORMAT(5E16.8)
+  6.00000000E+01  1.00000000E+02  7.00000000E+01  5.50000000E+01  4.00000000E+01
+  8.00000000E+01  5.00000000E+01  5.00000000E+01  8.00000000E+01  7.00000000E+01
+  5.00000000E+01  3.00000000E+01  5.00000000E+01  6.00000000E+01  4.50000000E+01
+  8.00000000E+01  4.50000000E+01  4.50000000E+01  7.00000000E+01  6.00000000E+01
+  6.00000000E+01  4.50000000E+01  5.00000000E+01
+%FLAG ANGLE_EQUIL_VALUE
+%FORMAT(5E16.8)
+  1.91986300E+00  1.95476960E+00  1.87622975E+00  1.91113635E+00  1.91113635E+00
+  2.12406661E+00  1.91113635E+00  2.09439600E+00  2.14501057E+00  2.01760148E+00
+  1.91113635E+00  2.05948940E+00  2.09439600E+00  1.91986300E+00  1.93731630E+00
+  1.91462701E+00  1.98094955E+00  1.91113635E+00  1.89368305E+00  1.91986300E+00
+  1.91986300E+00  1.93731630E+00  1.94778828E+00
+%FLAG DIHEDRAL_FORCE_CONSTANT
+%FORMAT(5E16.8)
+  1.08000000E+00  1.38000000E+00  9.60000000E-01  1.00000000E-01  5.00000000E-02
+ -1.50000000E+00  1.80000000E-01  0.00000000E+00  2.00000000E+00  2.50000000E+00
+  0.00000000E+00  1.00000000E+00 -1.00000000E+00 -2.80000000E+00 -2.70000000E+00
+  1.70000000E-01 -1.00000000E-01  9.50000000E-01  5.50000000E-01  1.50000000E-01
+  4.00000000E-01  4.50000000E-01  1.60000000E-01 -2.70000000E-01 -1.30000000E+00
+ -1.10000000E+00  2.50000000E-01  6.00000000E-01  2.70000000E-01  1.05000000E+01
+  1.50000000E+00
+%FLAG DIHEDRAL_PERIODICITY
+%FORMAT(5E16.8)
+  1.00000000E+00  2.00000000E+00  3.00000000E+00  3.00000000E+00  3.00000000E+00
+  1.00000000E+00  3.00000000E+00  3.00000000E+00  1.00000000E+00  2.00000000E+00
+  1.00000000E+00  1.00000000E+00  1.00000000E+00  2.00000000E+00  2.00000000E+00
+  3.00000000E+00  1.00000000E+00  2.00000000E+00  3.00000000E+00  3.00000000E+00
+  1.00000000E+00  1.00000000E+00  3.00000000E+00  1.00000000E+00  1.00000000E+00
+  1.00000000E+00  2.00000000E+00  2.00000000E+00  3.00000000E+00  2.00000000E+00
+  2.00000000E+00
+%FLAG SCEE_SCALE_FACTOR
+%FORMAT(5E16.8)
+  1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00
+  1.00000000E+00  1.00000000E+00  1.00000000E+00  1.20000000E+00  1.20000000E+00
+  1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00
+  1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00
+  1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00
+  1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00  0.00000000E+00
+  0.00000000E+00
+%FLAG SCNB_SCALE_FACTOR
+%FORMAT(5E16.8)
+  1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00
+  1.00000000E+00  1.00000000E+00  1.00000000E+00  2.00000000E+00  2.00000000E+00
+  1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00
+  1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00
+  1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00
+  1.00000000E+00  1.00000000E+00  1.00000000E+00  1.00000000E+00  0.00000000E+00
+  0.00000000E+00
+%FLAG SOLTY
+%FORMAT(5E16.8)
+  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00
+%FLAG LENNARD_JONES_ACOEF
+%FORMAT(5E16.8)
+  5.03316480E-07  2.00637392E+02  5.81803229E+05  4.41079188E+02  7.91544157E+05
+  1.04308023E+06  2.53654211E+00  3.15360051E+04  4.68930885E+04  1.32801250E+03
+  1.42536451E+02  4.58874091E+05  6.28541240E+05  2.44050579E+04  3.61397723E+05
+  5.53902818E+00  4.66922514E+04  6.78771368E+04  2.09814978E+03  3.63097246E+04
+  3.25969625E+03  3.37529073E+02  7.44975864E+05  9.95480466E+05  4.24594555E+04
+  5.89818288E+05  6.20665997E+04  9.44293233E+05  1.49138681E-03  1.40467023E+03
+  2.56678134E+03  3.20009193E+01  1.03954408E+03  5.94667300E+01  2.12601181E+03
+  1.39982777E-01  3.91072368E+02  7.01803794E+05  9.24822270E+05  4.15766412E+04
+  5.57281136E+05  6.01816484E+04  8.82619071E+05  2.27577561E+03  8.19971662E+05
+  1.37147154E+02  4.71003287E+05  6.47841731E+05  2.47595516E+04  3.70622491E+05
+  3.69471530E+04  6.06829342E+05  1.02595236E+03  5.74393458E+05  3.79876399E+05
+  1.15316498E+01  6.82786631E+04  9.71708117E+04  3.25969625E+03  5.33379252E+04
+  4.98586848E+03  8.96776989E+04  1.07193646E+02  8.61541883E+04  5.44261042E+04
+  7.51607703E+03
+%FLAG LENNARD_JONES_BCOEF
+%FORMAT(5E16.8)
+  2.45760000E-04  7.98505074E+00  6.99746810E+02  1.00536306E+01  6.93079947E+02
+  6.75612247E+02  4.69252138E-01  8.51470647E+01  8.81685417E+01  9.13231543E+00
+  6.38095248E+00  5.89183300E+02  5.85549272E+02  7.10161395E+01  4.95732238E+02
+  6.93429015E-01  1.03606917E+02  1.06076943E+02  1.14788417E+01  8.66220817E+01
+  1.43076527E+01  9.81924582E+00  7.50714425E+02  7.36907417E+02  9.36708259E+01
+  6.33305958E+02  1.13252061E+02  8.01323529E+02  1.13783784E-02  1.79702257E+01
+  2.06278363E+01  1.41762397E+00  1.46567808E+01  1.93248820E+00  2.09604198E+01
+  9.37598976E-02  8.91381236E+00  6.14502845E+02  5.99015525E+02  7.81725398E+01
+  5.19163331E+02  9.40505980E+01  6.53361429E+02  1.82891803E+01  5.31102864E+02
+  6.59870227E+00  6.29300710E+02  6.26720080E+02  7.54103785E+01  5.29252520E+02
+  9.21192136E+01  6.77220874E+02  1.53505284E+01  5.55666448E+02  5.64885984E+02
+  1.00053191E+00  1.25287818E+02  1.26919150E+02  1.43076527E+01  1.04986921E+02
+  1.76949863E+01  1.36131731E+02  2.59456373E+00  1.12529845E+02  1.11805549E+02
+  2.17257828E+01
+%FLAG BONDS_INC_HYDROGEN
+%FORMAT(10I8)
+       0       3       2      78      81       3      78      84       3      78
+      87       3      66      69       6      60      63       8      54      57
+       2      48      51       8      42      45       2      36      39       8
+      30      33       2      21      24       8      21      27       8      15
+      18       8       6       9      12
+%FLAG BONDS_WITHOUT_HYDROGEN
+%FORMAT(10I8)
+       3       6       1      72      75       4      72      78       5      66
+      72       7      60      66       9      48      54       1      48      60
+      10      36      42       1      36      48      10      21      30       1
+      15      21      10      15      36      10      12      15      11       6
+      12      11       6      60      10
+%FLAG ANGLES_INC_HYDROGEN
+%FORMAT(10I8)
+       3       6       9       1       0       3       6       4      84      78
+      87       5      81      78      84       5      81      78      87       5
+      72      78      81       7      72      78      84       7      72      78
+      87       7      69      66      72       8      63      60      66      11
+      60      66      69      12      51      48      54      14      51      48
+      60      15      48      54      57       4      48      60      63      15
+      39      36      42      14      39      36      48      15      36      42
+      45       4      36      48      51      15      27      21      30      14
+      24      21      27      18      24      21      30      14      21      30
+      33       4      18      15      21      15      18      15      36      15
+      15      21      24      15      15      21      27      15      15      36
+      39      15      12      15      18      20       9       6      12      21
+       9       6      60      22       6      60      63      15
+%FLAG ANGLES_WITHOUT_HYDROGEN
+%FORMAT(10I8)
+       3       6      12       2       3       6      60       3      75      72
+      78       6      66      72      75       9      66      72      78      10
+      60      66      72      13      54      48      60       3      48      60
+      66      16      42      36      48       3      36      48      54       3
+      36      48      60      17      21      15      36      17      15      21
+      30       3      15      36      42       3      15      36      48      17
+      12       6      60      19      12      15      21      19      12      15
+      36      19       6      12      15      23       6      60      48      17
+       6      60      66      16
+%FLAG DIHEDRALS_INC_HYDROGEN
+%FORMAT(10I8)
+       3       6      60      63       5       0       3       6       9       7
+       0       3       6      12       7       0       3       6      60       7
+      75      72      78      81       8      75      72      78      84       8
+      75      72      78      87       8      69      66      72      75       9
+      69      66     -72      75      10      69      66      72      78      11
+      66      72      78      81       8      66      72      78      84       8
+      66      72      78      87       8      63      60      66      69      12
+      63      60      66      72      13      57      54      48      60       7
+      54      48      60      63       5      51      48      54      57       7
+      51      48      60      63      16      51      48      60      66       4
+      48      60      66      69       4      45      42      36      48       7
+      42      36      48      51       5      39      36      42      45       7
+      39      36      48      51      16      39      36      48      54       5
+      39      36      48      60      20      36      48      54      57       7
+      36      48      60      63      20      27      21      15      36      20
+      27      21      30      33       7      24      21      15      36      20
+      24      21      30      33       7      21      15      36      39      20
+      18      15      21      24      16      18      15      21      27      16
+      18      15      21      30       5      18      15      36      39      16
+      18      15      36      42       5      18      15      36      48      20
+      15      21      30      33       7      15      36      42      45       7
+      15      36      48      51      20      12       6      60      63       5
+      12      15      21      24       5      12      15      21      27       5
+      12      15      36      39       5       9       6      12      15      28
+       9       6     -12      15       4       9       6      60      48      20
+       9       6      60      63      16       9       6      60      66       4
+       6      12      15      18      29       6      60      48      51      20
+       6      60      66      69       4      72      69     -66     -60      31
+%FLAG DIHEDRALS_WITHOUT_HYDROGEN
+%FORMAT(10I8)
+       3       6      12      15       1       3       6     -12      15       2
+       3       6     -12      15       3       3       6      60      48       4
+       3       6      60      66       6      60      66      72      75      14
+      60      66      72      78      15      54      48      60      66       6
+      48      60      66      72       8      42      36      48      54      17
+      42      36     -48      54      18      42      36     -48      54      19
+      42      36      48      60       4      36      48      60      66      21
+      30      21      15      36       4      21      15      36      42       4
+      21      15      36      48      22      15      12       6      60      23
+      15      36      48      54       4      15      36     -48      60      22
+      12       6      60      48      24      12       6      60      66      25
+      12      15      21      30      26      12      15     -21      30      27
+      12      15      36      42      26      12      15     -36      42      27
+      12      15     -36      48      24       6      12      15      21      23
+       6      12      15      36      23       6      60     -48      36      22
+       6      60      48      54       4       6      60      66      72       8
+      78      66     -72     -75      30
+%FLAG EXCLUDED_ATOMS_LIST
+%FORMAT(10I8)
+       2       3       4       5      21       3       4       5       6      17
+      21      22      23       4       5       6       7       8      13      17
+      18      19      21      22      23      24      25       5       6      17
+      21      22      23       6       7       8       9      10      11      13
+      14      15      17      21      22      23       7       8       9      10
+      11      12      13      14      15      16      17      18      19      21
+       8       9      10      11      13      14      15      17       9      10
+      11      12      13      14      15      17      10      11      12      13
+      11      12      13      12      13       0      14      15      16      17
+      18      19      20      21      22      23      15      16      17      18
+      19      21      16      17      18      19      21      17      18      19
+      20      21      22      23      24      25      19      20      21      22
+      23      20      21      22      23      21      22      23      24      25
+      26      27      23      24      25      24      25      26      27      28
+      29      30      25      26      27      26      27      28      29      30
+      27      28      29      30      28      29      30      29      30      30
+       0
+%FLAG HBOND_ACOEF
+%FORMAT(5E16.8)
+
+%FLAG HBOND_BCOEF
+%FORMAT(5E16.8)
+
+%FLAG HBCUT
+%FORMAT(5E16.8)
+
+%FLAG AMBER_ATOM_TYPE
+%FORMAT(20a4)
+Ho  Oh  Cg  H2  Os  Cg  H1  Cg  H1  H1  Oh  Ho  Cg  H1  Oh  Ho  Cg  H1  Oh  Ho
+Cg  H1  Ng  H   C   O   Cg  Hc  Hc  Hc
+%FLAG TREE_CHAIN_CLASSIFICATION
+%FORMAT(20a4)
+M   M   M   E   S   3   E   3   E   E   S   E   3   E   S   E   3   E   S   E
+B   E   B   E   B   E   3   E   E   E
+%FLAG JOIN_ARRAY
+%FORMAT(10I8)
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+%FLAG IROTAT
+%FORMAT(10I8)
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0       0       0
+%FLAG RADIUS_SET
+%FORMAT(1a80)
+modified Bondi radii (mbondi)
+%FLAG RADII
+%FORMAT(5E16.8)
+  8.00000000E-01  1.50000000E+00  1.70000000E+00  1.30000000E+00  1.50000000E+00
+  1.70000000E+00  1.30000000E+00  1.70000000E+00  1.30000000E+00  1.30000000E+00
+  1.50000000E+00  8.00000000E-01  1.70000000E+00  1.30000000E+00  1.50000000E+00
+  8.00000000E-01  1.70000000E+00  1.30000000E+00  1.50000000E+00  8.00000000E-01
+  1.70000000E+00  1.30000000E+00  1.55000000E+00  1.30000000E+00  1.70000000E+00
+  1.50000000E+00  1.70000000E+00  1.30000000E+00  1.30000000E+00  1.30000000E+00
+%FLAG SCREEN
+%FORMAT(5E16.8)
+  8.50000000E-01  8.50000000E-01  7.20000000E-01  8.50000000E-01  8.50000000E-01
+  7.20000000E-01  8.50000000E-01  7.20000000E-01  8.50000000E-01  8.50000000E-01
+  8.50000000E-01  8.50000000E-01  7.20000000E-01  8.50000000E-01  8.50000000E-01
+  8.50000000E-01  7.20000000E-01  8.50000000E-01  8.50000000E-01  8.50000000E-01
+  7.20000000E-01  8.50000000E-01  7.90000000E-01  8.50000000E-01  7.20000000E-01
+  8.50000000E-01  7.20000000E-01  8.50000000E-01  8.50000000E-01  8.50000000E-01
+%FLAG IPOL
+%FORMAT(1I8)
+       0
diff --git a/tests/glycam_empty.inpcrd b/tests/glycam_empty.inpcrd
new file mode 100644
index 00000000..e69de29b
diff --git a/tests/glycam_empty.prmtop b/tests/glycam_empty.prmtop
new file mode 100644
index 00000000..e69de29b
diff --git a/tests/lower_res.pdb b/tests/lower_res.pdb
new file mode 100644
index 00000000..caad2a7c
--- /dev/null
+++ b/tests/lower_res.pdb
@@ -0,0 +1,28 @@
+COMPND    benzene.pdb
+AUTHOR    GENERATED BY OPEN BABEL 2.4.1
+ATOM      1  C1  ben     1       5.274   1.999  -8.568  1.00  0.00           C
+ATOM      2  C2  ben     1       6.627   2.018  -8.209  1.00  0.00           C
+ATOM      3  C3  ben     1       7.366   0.829  -8.202  1.00  0.00           C
+ATOM      4  C4  ben     1       6.752  -0.379  -8.554  1.00  0.00           C
+ATOM      5  C5  ben     1       5.399  -0.398  -8.912  1.00  0.00           C
+ATOM      6  C6  ben     1       4.660   0.791  -8.919  1.00  0.00           C
+ATOM      7  H11 ben     1       4.704   2.916  -8.573  1.00  0.00           H
+ATOM      8  H21 ben     1       7.101   2.950  -7.938  1.00  0.00           H
+ATOM      9  H31 ben     1       8.410   0.844  -7.926  1.00  0.00           H
+ATOM     10  H41 ben     1       7.322  -1.296  -8.548  1.00  0.00           H
+ATOM     11  H51 ben     1       4.925  -1.330  -9.183  1.00  0.00           H
+ATOM     12  H61 ben     1       3.616   0.776  -9.196  1.00  0.00           H
+CONECT    1    6    7    2
+CONECT    2    1    3    8
+CONECT    3    4    2    9
+CONECT    4    5   10    3
+CONECT    5   11    6    4
+CONECT    6   12    5    1
+CONECT    7    1
+CONECT    8    2
+CONECT    9    3
+CONECT   10    4
+CONECT   11    5
+CONECT   12    6
+MASTER        0    0    0    0    0    0    0    0   12    0   12    0
+END
diff --git a/tests/no_res.pdb b/tests/no_res.pdb
new file mode 100644
index 00000000..10a806cc
--- /dev/null
+++ b/tests/no_res.pdb
@@ -0,0 +1,28 @@
+COMPND    benzene.pdb
+AUTHOR    GENERATED BY OPEN BABEL 2.4.1
+ATOM      1  C1          1       5.274   1.999  -8.568  1.00  0.00           C
+ATOM      2  C2          1       6.627   2.018  -8.209  1.00  0.00           C
+ATOM      3  C3          1       7.366   0.829  -8.202  1.00  0.00           C
+ATOM      4  C4          1       6.752  -0.379  -8.554  1.00  0.00           C
+ATOM      5  C5          1       5.399  -0.398  -8.912  1.00  0.00           C
+ATOM      6  C6          1       4.660   0.791  -8.919  1.00  0.00           C
+ATOM      7  H11         1       4.704   2.916  -8.573  1.00  0.00           H
+ATOM      8  H21         1       7.101   2.950  -7.938  1.00  0.00           H
+ATOM      9  H31         1       8.410   0.844  -7.926  1.00  0.00           H
+ATOM     10  H41         1       7.322  -1.296  -8.548  1.00  0.00           H
+ATOM     11  H51         1       4.925  -1.330  -9.183  1.00  0.00           H
+ATOM     12  H61         1       3.616   0.776  -9.196  1.00  0.00           H
+CONECT    1    6    7    2
+CONECT    2    1    3    8
+CONECT    3    4    2    9
+CONECT    4    5   10    3
+CONECT    5   11    6    4
+CONECT    6   12    5    1
+CONECT    7    1
+CONECT    8    2
+CONECT    9    3
+CONECT   10    4
+CONECT   11    5
+CONECT   12    6
+MASTER        0    0    0    0    0    0    0    0   12    0   12    0
+END
diff --git a/tests/same_coord.pdb b/tests/same_coord.pdb
new file mode 100644
index 00000000..61799270
--- /dev/null
+++ b/tests/same_coord.pdb
@@ -0,0 +1,28 @@
+COMPND    benzene.pdb
+AUTHOR    GENERATED BY OPEN BABEL 2.4.1
+ATOM      1  C1  BEN     1       5.274   1.999  -8.568  1.00  0.00           C
+ATOM      2  C2  BEN     1       5.274   1.999  -8.568  1.00  0.00           C
+ATOM      3  C3  BEN     1       7.366   0.829  -8.202  1.00  0.00           C
+ATOM      4  C4  BEN     1       6.752  -0.379  -8.554  1.00  0.00           C
+ATOM      5  C5  BEN     1       5.399  -0.398  -8.912  1.00  0.00           C
+ATOM      6  C6  BEN     1       4.660   0.791  -8.919  1.00  0.00           C
+ATOM      7  H11 BEN     1       4.704   2.916  -8.573  1.00  0.00           H
+ATOM      8  H21 BEN     1       7.101   2.950  -7.938  1.00  0.00           H
+ATOM      9  H31 BEN     1       8.410   0.844  -7.926  1.00  0.00           H
+ATOM     10  H41 BEN     1       7.322  -1.296  -8.548  1.00  0.00           H
+ATOM     11  H51 BEN     1       4.925  -1.330  -9.183  1.00  0.00           H
+ATOM     12  H61 BEN     1       3.616   0.776  -9.196  1.00  0.00           H
+CONECT    1    6    7    2
+CONECT    2    1    3    8
+CONECT    3    4    2    9
+CONECT    4    5   10    3
+CONECT    5   11    6    4
+CONECT    6   12    5    1
+CONECT    7    1
+CONECT    8    2
+CONECT    9    3
+CONECT   10    4
+CONECT   11    5
+CONECT   12    6
+MASTER        0    0    0    0    0    0    0    0   12    0   12    0
+END
diff --git a/tests/test_acpype.py b/tests/test_acpype.py
index 4a76b84a..599a1f49 100644
--- a/tests/test_acpype.py
+++ b/tests/test_acpype.py
@@ -1,5 +1,4 @@
 import os
-import shutil
 
 import pytest
 from pytest import approx
@@ -17,8 +16,7 @@
         (True, 0.240324, "<Atom id=33, name=OXT, <AtomType=o>>"),
     ],
 )
-def test_mol2_sorted(issorted, charge, msg):
-    os.chdir(os.path.dirname(os.path.abspath(__file__)))
+def test_mol2_sorted(janitor, issorted, charge, msg):
     molecule = ACTopol("AAA.mol2", chargeType="gas", debug=True, is_sorted=issorted)
     molecule.createACTopol()
     molecule.createMolTopol()
@@ -30,11 +28,11 @@ def test_mol2_sorted(issorted, charge, msg):
     assert molecule.molTopol.totalCharge == 0
     assert molecule.molTopol.atoms[0].charge == approx(charge)
     assert molecule.molTopol.atoms[-1].__repr__() == msg
-    shutil.rmtree(molecule.absHomeDir)
+    janitor.append(molecule.absHomeDir)
+    janitor.append(molecule.tmpDir)
 
 
-def test_pdb(capsys):
-    os.chdir(os.path.dirname(os.path.abspath(__file__)))
+def test_pdb(janitor, capsys):
     molecule = ACTopol("FFF.pdb", chargeType="gas", debug=True)
     molecule.createACTopol()
     molecule.createMolTopol()
@@ -43,7 +41,6 @@ def test_pdb(capsys):
     assert len(molecule.molTopol.improperDihedrals) == 23
     assert molecule.molTopol.atoms[0].__repr__() == "<Atom id=1, name=N, <AtomType=nz>>"
     # check gaff2 and force
-    os.chdir(os.path.dirname(os.path.abspath(__file__)))
     molecule = ACTopol("FFF.pdb", chargeType="gas", debug=True, atomType="gaff2", force=True)
     molecule.createACTopol()
     molecule.createMolTopol()
@@ -54,22 +51,21 @@ def test_pdb(capsys):
     assert molecule.molTopol.atoms[0].__repr__() == "<Atom id=1, name=N, <AtomType=nz>>"
     assert "==> Overwriting pickle file FFF.pkl" in captured.out
     # check for already present
-    os.chdir(os.path.dirname(os.path.abspath(__file__)))
     molecule = ACTopol("FFF.mol2", chargeType="gas", debug=True)
     molecule.createACTopol()
     molecule.createMolTopol()
     captured = capsys.readouterr()
     assert molecule
     assert "==> Pickle file FFF.pkl already present... doing nothing" in captured.out
-    shutil.rmtree(molecule.absHomeDir)
+    janitor.append(molecule.absHomeDir)
+    janitor.append(molecule.tmpDir)
 
 
 @pytest.mark.parametrize(
     ("force", "at", "ndih"),
     [(False, "amber", 189), (True, "amber2", 187)],
 )
-def test_amber(force, at, ndih):
-    os.chdir(os.path.dirname(os.path.abspath(__file__)))
+def test_amber(janitor, force, at, ndih):
     molecule = ACTopol("FFF.mol2", chargeType="gas", debug=True, atomType=at, force=force)
     molecule.createACTopol()
     molecule.createMolTopol()
@@ -78,11 +74,11 @@ def test_amber(force, at, ndih):
     assert len(molecule.molTopol.properDihedrals) == ndih
     assert len(molecule.molTopol.improperDihedrals) == 23
     assert molecule.molTopol.atoms[0].__repr__() == "<Atom id=1, name=N, <AtomType=N3>>"
-    shutil.rmtree(molecule.absHomeDir)
+    janitor.append(molecule.absHomeDir)
+    janitor.append(molecule.tmpDir)
 
 
-def test_charges_chiral():
-    os.chdir(os.path.dirname(os.path.abspath(__file__)))
+def test_charges_chiral(janitor):
     molecule = ACTopol("KKK.mol2", chargeType="gas", debug=True, chiral=True)
     molecule.createACTopol()
     molecule.createMolTopol()
@@ -94,15 +90,15 @@ def test_charges_chiral():
     assert molecule.chargeVal == "3"
     assert molecule.molTopol.totalCharge == 3
     assert molecule.molTopol.chiralGroups[-1][-1] == approx(66.713290)
-    shutil.rmtree(molecule.absHomeDir)
+    janitor.append(molecule.absHomeDir)
+    janitor.append(molecule.tmpDir)
 
 
 @pytest.mark.parametrize(
     ("base", "msg"),
     [(None, "smiles_molecule.mol2"), ("thalidomide_smiles", "thalidomide_smiles.mol2")],
 )
-def test_smiles(base, msg):
-    os.chdir(os.path.dirname(os.path.abspath(__file__)))
+def test_smiles(janitor, base, msg):
     smiles = "c1ccc2c(c1)C(=O)N(C2=O)C3CCC(=NC3=O)O"
     molecule = ACTopol(smiles, basename=base, chargeType="gas", debug=True)
     molecule.createACTopol()
@@ -110,24 +106,36 @@ def test_smiles(base, msg):
     assert molecule
     assert molecule.inputFile == msg
     assert len(molecule.molTopol.atoms) == 29
-    shutil.rmtree(molecule.absHomeDir)
+    janitor.append(molecule.absHomeDir)
+    janitor.append(molecule.tmpDir)
     os.remove(molecule.absInputFile)
 
 
 @pytest.mark.parametrize(
-    ("ct", "msg"),
+    ("ct", "ft", "msg"),
     [
         (
             "bcc",
+            "pdb",
             "-dr no -i benzene.mol2 -fi mol2 -o benzene_bcc_gaff2.mol2 -fo mol2 -c bcc -nc 0 -m 1 -s 2 -df 2 -at gaff2",
         ),
-        ("user", "cannot read charges from a PDB file"),
+        (
+            "bcc",
+            "mol",
+            "-dr no -i benzene.mol -fi mdl -o benzene_bcc_gaff2.mol2 -fo mol2 -c bcc -nc 0 -m 1 -s 2 -df 2 -at gaff2",
+        ),
+        (
+            "bcc",
+            "mdl",
+            "-dr no -i benzene.mdl -fi mdl -o benzene_bcc_gaff2.mol2 -fo mol2 -c bcc -nc 0 -m 1 -s 2 -df 2 -at gaff2",
+        ),
+        ("user", "pdb", "cannot read charges from a PDB file"),
     ],
 )
-def test_sqm_tleap(capsys, ct, msg):
+def test_sqm_tleap(janitor, capsys, ct, ft, msg):
     # check chargeType user with PDB -> use bcc
-    os.chdir(os.path.dirname(os.path.abspath(__file__)))
-    molecule = ACTopol("benzene.pdb", chargeType=ct, debug=True)
+    # .mol and .mdl are the same file type
+    molecule = ACTopol(f"benzene.{ft}", chargeType=ct, debug=True)
     molecule.createACTopol()
     molecule.createMolTopol()
     captured = capsys.readouterr()
@@ -138,30 +146,34 @@ def test_sqm_tleap(capsys, ct, msg):
     assert molecule.molTopol.atoms[0].charge == approx(-0.13)
     assert molecule.molTopol.atoms[-1].charge == approx(0.13)
     assert msg in captured.out
-    shutil.rmtree(molecule.absHomeDir)
+    janitor.append(molecule.absHomeDir)
+    janitor.append(molecule.tmpDir)
+
+
+def test_ekFlag(janitor):
+    molecule = ACTopol(
+        "benzene.pdb",
+        ekFlag='''"qm_theory='AM1', grms_tol=0.0005, scfconv=1.d-10, ndiis_attempts=700, qmcharge=0"''',
+        gmx4=True,
+    )
+    molecule.createACTopol()
+    molecule.createMolTopol()
+    assert molecule
+    assert len(molecule.molTopol.atoms) == 12
+    janitor.append(molecule.absHomeDir)
+    janitor.append(molecule.tmpDir)
 
 
-def test_time_limit():
-    os.chdir(os.path.dirname(os.path.abspath(__file__)))
+def test_time_limit(janitor):
     molecule = ACTopol("KKK.pdb", chargeType="bcc", debug=True, timeTol=2)
     with pytest.raises(Exception) as e_info:
         molecule.createACTopol()
     assert e_info.value.args[0] == "Semi-QM taking too long to finish... aborting!"
-    shutil.rmtree(molecule.absHomeDir)
+    janitor.append(molecule.absHomeDir)
+    janitor.append(molecule.tmpDir)
 
 
-def test_wrong_element(capsys):
-    # Only elements are allowed: C, N, O, S, P, H, F, Cl, Br and I
-    os.chdir(os.path.dirname(os.path.abspath(__file__)))
-    with pytest.raises(Exception) as e_info:
-        ACTopol("HEM.mol2", chargeType="user", debug=True)
-    captured = capsys.readouterr()
-    assert e_info.typename == "FileNotFoundError"
-    assert "Unrecognized case-sensitive atomic symbol ( FE)." in captured.out
-
-
-def test_charge_user():
-    os.chdir(os.path.dirname(os.path.abspath(__file__)))
+def test_charge_user(janitor):
     molecule = ACTopol("ADPMg.mol2", chargeType="user", debug=True)
     molecule.createACTopol()
     molecule.createMolTopol()
@@ -171,21 +183,48 @@ def test_charge_user():
     assert len(molecule.molTopol.improperDihedrals) == 7
     assert molecule.molTopol.atoms[0].charge == 0.1667
     assert molecule.molTopol.atoms[15].charge == -0.517
-    shutil.rmtree(molecule.absHomeDir)
+    janitor.append(molecule.absHomeDir)
+    janitor.append(molecule.tmpDir)
 
 
 @pytest.mark.parametrize(
-    ("argv"),
-    [["-di", "cccc"], ["-x", "Base.inpcrd", "-p", "Base.prmtop"]],
+    ("argv", "msg"),
+    [
+        (["-i", "cccc"], "Total time of execution:"),
+        (["-x", "Base.inpcrd", "-p", "Base.prmtop", "-b", "vir_temp"], "Total time of execution:"),
+        (["-wi", "cccc", "-b", "vir_temp"], ""),
+        (
+            ["-i", "wrong_res_set.pdb", "-b", "vir_temp"],
+            "In vir_temp_AC.lib, residue name will be 'RSET' instead of 'SET' elsewhere",
+        ),
+        (
+            ["-i", "wrong_res_num.pdb", "-b", "vir_temp"],
+            "In vir_temp_AC.lib, residue name will be 'R100' instead of '100' elsewhere",
+        ),
+        (
+            ["-i", "wrong_res_sym.pdb", "-b", "vir_temp"],
+            "In vir_temp_AC.lib, residue name will be 'MOL' instead of '+++' elsewhere",
+        ),
+        (
+            ["-i", "lower_res.pdb", "-b", "vir_temp"],
+            "WARNING: this may raise problem with some applications like CNS",
+        ),
+        (
+            ["-fi", "too_close.pdb", "-b", "vir_temp"],
+            "You chose to proceed anyway with '-f' option. GOOD LUCK!",
+        ),
+        (
+            ["-i", "no_res.pdb", "-b", "vir_temp"],
+            "No residue name identified, using default resname: 'LIG'",
+        ),
+    ],
 )
-def test_inputs(capsys, argv):
-    os.chdir(os.path.dirname(os.path.abspath(__file__)))
+def test_inputs(janitor, capsys, argv, msg):
     temp_base = "vir_temp"
-    init_main(argv=argv + ["-b", temp_base])
+    init_main(argv=argv)
     captured = capsys.readouterr()
-    assert "Total time of execution:" in captured.out
-    os.chdir(os.path.dirname(os.path.abspath(__file__)))
-    _getoutput(f"rm -fr {temp_base}*")
+    assert msg in captured.out
+    _getoutput(f"rm -vfr {temp_base}* .*{temp_base}* smiles_molecule.acpype")
 
 
 @pytest.mark.parametrize(
@@ -196,15 +235,35 @@ def test_inputs(capsys, argv):
         ([], 2, "error: missing input files"),
         (["-d", "-w"], 2, "error: argument -w/--verboseless: not allowed with argument -d/--debug"),
         (["-di", "AAAx.mol2"], 19, "ACPYPE FAILED: Input file AAAx.mol2 DOES NOT EXIST"),
-        (["-di", " 123"], 19, "ACPYPE FAILED: [Errno 2] No such file or directory"),
+        (["-zx", "ILDN.inpcrd", "-p", "ILDN.prmtop"], 19, "Likely trying to convert ILDN to RB"),
+        (["-x", "glycam_exe.inpcrd", "-p", "glycam_corrupt.prmtop"], 19, "Skipping non-existent attributes dihedral_p"),
+        (["-x", "glycam_exe.inpcrd", "-p", "glycam_empty.prmtop"], 19, "ERROR: ACPYPE FAILED: PRMTOP file empty?"),
+        (["-x", "glycam_empty.inpcrd", "-p", "glycam_exe.prmtop"], 19, "ERROR: ACPYPE FAILED: INPCRD file empty?"),
+        (["-di", "cccccc", "-n", "-1", "-b", "vir_temp"], 19, "Fatal Error!"),
+        (["-di", " 123", "-b", "vir_temp"], 19, "ACPYPE FAILED: [Errno 2] No such file or directory"),
+        (["-i", "double_res.pdb", "-b", "vir_temp"], 19, "Only ONE Residue is allowed for ACPYPE to work"),
+        (["-i", "same_coord.pdb", "-b", "vir_temp"], 19, "Atoms with same coordinates in"),
+        (["-i", "too_close.pdb", "-b", "vir_temp"], 19, "Atoms TOO close (<"),
+        (["-i", "too_far.pdb", "-b", "vir_temp"], 19, "Atoms TOO scattered (>"),
         (["-di", " 123", "-x", "abc"], 2, "either '-i' or ('-p', '-x'), but not both"),
         (["-di", " 123", "-u"], 2, "option -u is only meaningful in 'amb2gmx' mode (args '-p' and '-x')"),
+        (
+            ["-i", "drift.mol2", "-c", "user", "-b", "vir_temp"],
+            19,
+            "Net charge drift '0.02020' bigger than tolerance '0.01000'",
+        ),
+        (
+            ["-di", "HEM.pdb", "-b", "vir_temp"],
+            19,
+            "Unrecognized case-sensitive atomic symbol ( FE).",  # Only Allowed: C, N, O, S, P, H, F, Cl, Br and I
+        ),
     ],
 )
-def test_args_wrong_inputs(capsys, argv, code, msg):
+def test_args_wrong_inputs(janitor, capsys, argv, code, msg):
     with pytest.raises(SystemExit) as e_info:
         init_main(argv=argv)
     captured = capsys.readouterr()
     assert msg in captured.err + captured.out
     assert e_info.typename == "SystemExit"
     assert e_info.value.code == code
+    _getoutput("rm -vfr vir_temp* .*vir_temp*")
diff --git a/tests/test_acs_api.py b/tests/test_acs_api.py
index 3acc7483..1d16d744 100644
--- a/tests/test_acs_api.py
+++ b/tests/test_acs_api.py
@@ -1,5 +1,5 @@
 import json
-import os
+from glob import glob
 
 from acpype.acs_api import acpype_api
 
@@ -27,18 +27,19 @@
 )
 
 
-def test_json_simple():
-    os.chdir(os.path.dirname(os.path.abspath(__file__)))
+def test_json_simple(janitor):
     jj = json.loads(acpype_api(inputFile="benzene.pdb", debug=True))
-    assert min([len(jj.get(x)) for x in file_types]) >= 7
+    assert min(len(jj.get(x)) for x in file_types) >= 7
     assert jj.get("file_name") == "benzene"
+    janitor.append("../.acpype_tmp_benzene")
 
 
-def test_json_failed():
-    os.chdir(os.path.dirname(os.path.abspath(__file__)))
+def test_json_failed(janitor):
     jj = json.loads(acpype_api(inputFile="_fake_", debug=True))
     assert "ERROR: [Errno 2] No such file or directory" in jj.get("file_name")
     assert "tests/_fake_" in jj.get("file_name")
+    for ii in glob(".*_fake_*"):
+        janitor.append(ii)
 
 
 def get_json():
@@ -46,8 +47,8 @@ def get_json():
     return json.loads(json_output)
 
 
-def test_json():
-    os.chdir(os.path.dirname(os.path.abspath(__file__)))
+def test_json(janitor):
     jj = get_json()
+    janitor.append("../.acpype_tmp_AAA")
     for ft in file_types:
         assert len(jj.get(ft)) > 2
diff --git a/tests/test_amb2gmx.py b/tests/test_amb2gmx.py
index 4a2fdbd6..5ba608e5 100644
--- a/tests/test_amb2gmx.py
+++ b/tests/test_amb2gmx.py
@@ -1,30 +1,26 @@
-import os
-import shutil
-
 import pytest
 
 from acpype.topol import MolTopol
 
 
-def test_glycam():
-    os.chdir(os.path.dirname(os.path.abspath(__file__)))
+def test_glycam(janitor):
     molecule = MolTopol(acFileTop="glycam_exe.prmtop", acFileXyz="glycam_exe.inpcrd", debug=True, amb2gmx=True)
     molecule.writeGromacsTopolFiles()
+    molecule.writeCnsTopolFiles()
     assert molecule
     assert molecule.topo14Data.hasNondefault14()
     assert len(molecule.topo14Data.scnb_scale_factor) == 31
-    shutil.rmtree(molecule.absHomeDir)
+    janitor.append(molecule.absHomeDir)
 
 
 @pytest.mark.parametrize(
     ("dd", "g4", "ntext"),
     [(False, False, 14193), (True, False, 31516), (False, True, 12124), (True, True, 29447)],
 )
-def test_amb2gmx(dd, g4, ntext):
+def test_amb2gmx(janitor, dd, g4, ntext):
     # oct box with water and ions
     # modified from https://ambermd.org/tutorials/basic/tutorial7/index.php
     # using addIonsRand separated for each ion and TIP3PBOX
-    os.chdir(os.path.dirname(os.path.abspath(__file__)))
     molecule = MolTopol(acFileTop="RAMP1_ion.prmtop", acFileXyz="RAMP1_ion.inpcrd", debug=True, direct=dd, gmx4=g4)
     molecule.writeGromacsTopolFiles()
     assert molecule
@@ -33,7 +29,7 @@ def test_amb2gmx(dd, g4, ntext):
     assert molecule.atoms[1300].__repr__() == "<Atom id=1301, name=NA+, <AtomType=Na+>>"
     assert molecule.atoms[1310].__repr__() == "<Atom id=1311, name=CL-, <AtomType=Cl->>"
     assert len(molecule.atoms) == 18618
-    shutil.rmtree(molecule.absHomeDir)
+    janitor.append(molecule.absHomeDir)
 
 
 @pytest.mark.parametrize(
@@ -45,8 +41,7 @@ def test_amb2gmx(dd, g4, ntext):
         (True, "2", 50, 376435.47, 469.350655, "<AtomType=o_>"),
     ],
 )
-def test_merge(merge, gaff, n_at, acoef, bcoef, msg):
-    os.chdir(os.path.dirname(os.path.abspath(__file__)))
+def test_merge(janitor, merge, gaff, n_at, acoef, bcoef, msg):
     molecule = MolTopol(acFileTop=f"ComplexG{gaff}.prmtop", acFileXyz=f"ComplexG{gaff}.inpcrd", debug=True, merge=merge)
     molecule.writeGromacsTopolFiles()
     assert molecule
@@ -54,15 +49,14 @@ def test_merge(merge, gaff, n_at, acoef, bcoef, msg):
     assert molecule.atomTypesGromacs[31].ACOEF == acoef
     assert molecule.atomTypesGromacs[31].BCOEF == bcoef
     assert molecule.atomTypesGromacs[31].__repr__() == msg
-    shutil.rmtree(molecule.absHomeDir)
+    janitor.append(molecule.absHomeDir)
 
 
 @pytest.mark.parametrize(
     ("mol", "n1", "n2", "n3", "n4", "n5", "msg"),
     [("ILDN", 24931, 12230, 577, 0, 47, "<AtomType=C6>"), ("Base", 24931, 12044, 577, 0, 43, "<AtomType=HS>")],
 )
-def test_ildn(mol, n1, n2, n3, n4, n5, msg):
-    os.chdir(os.path.dirname(os.path.abspath(__file__)))
+def test_ildn(janitor, mol, n1, n2, n3, n4, n5, msg):
     molecule = MolTopol(acFileTop=f"{mol}.prmtop", acFileXyz=f"{mol}.inpcrd", debug=True)
     molecule.writeGromacsTopolFiles()
     assert molecule
@@ -72,20 +66,18 @@ def test_ildn(mol, n1, n2, n3, n4, n5, msg):
     assert molecule.totalCharge == n4
     assert len(molecule.atomTypes) == n5
     assert molecule.atomTypes[23].__repr__() == msg
-    shutil.rmtree(molecule.absHomeDir)
+    janitor.append(molecule.absHomeDir)
 
 
-def test_ildn_gmx4_fail():
-    os.chdir(os.path.dirname(os.path.abspath(__file__)))
+def test_ildn_gmx4_fail(janitor):
     molecule = MolTopol(acFileTop="ILDN.prmtop", acFileXyz="ILDN.inpcrd", debug=True, gmx4=True)
     with pytest.raises(Exception) as e_info:
         molecule.writeGromacsTopolFiles()
     assert e_info.value.args[0] == "Likely trying to convert ILDN to RB, DO NOT use option '-z'"
-    shutil.rmtree(molecule.absHomeDir)
+    janitor.append(molecule.absHomeDir)
 
 
-def test_wrong_input():
-    os.chdir(os.path.dirname(os.path.abspath(__file__)))
+def test_wrong_input(janitor):
     with pytest.raises(Exception) as e_info:
         MolTopol(acFileTop="nope.prmtop", acFileXyz="ILDN.inpcrd", debug=True, gmx4=True)
     assert e_info.value.args == (2, "No such file or directory")
diff --git a/tests/test_scenarios.py b/tests/test_scenarios.py
index f44bd298..b96a3f05 100644
--- a/tests/test_scenarios.py
+++ b/tests/test_scenarios.py
@@ -1,16 +1,13 @@
-import os
-
 import pytest
 
 from acpype import cli
 from acpype.utils import _getoutput
 
 
-def test_no_ac(capsys):
+def test_no_ac(janitor, capsys):
     binaries = {"ac_bin": "no_ac", "obabel_bin": "obabel"}
     msg = f"ERROR: no '{binaries['ac_bin']}' executable... aborting!"
     inp = "AAA.mol2"
-    os.chdir(os.path.dirname(os.path.abspath(__file__)))
     with pytest.raises(SystemExit) as e_info:
         cli.init_main(argv=["-di", inp, "-c", "gas"], binaries=binaries)
     captured = capsys.readouterr()
@@ -19,20 +16,19 @@ def test_no_ac(capsys):
     assert e_info.value.code == 19
 
 
-def test_only_ac(capsys):
+def test_only_ac(janitor, capsys):
     binaries = {"ac_bin": "antechamber", "obabel_bin": "no_obabel"}
     msg1 = f"WARNING: no '{binaries['obabel_bin']}' executable, no PDB file can be used as input!"
     msg2 = "Total time of execution:"
     msg3 = "WARNING: No Openbabel python module, no chiral groups"
     inp = "AAA.mol2"
     temp_base = "vir_temp"
-    os.chdir(os.path.dirname(os.path.abspath(__file__)))
     cli.init_main(argv=["-di", inp, "-c", "gas", "-b", temp_base], binaries=binaries)
     captured = capsys.readouterr()
     assert msg1 in captured.out
     assert msg2 in captured.out
     assert msg3 in captured.out
-    _getoutput(f"rm -fr {temp_base}*")
+    _getoutput(f"rm -vfr {temp_base}* .*{temp_base}*")
 
 
 @pytest.mark.parametrize(
@@ -42,9 +38,8 @@ def test_only_ac(capsys):
         ("cccc", "WARNING: your input may be a SMILES but"),
     ],
 )
-def test_no_obabel(capsys, inp, msg):
+def test_no_obabel(janitor, capsys, inp, msg):
     binaries = {"ac_bin": "antechamber", "obabel_bin": "no_obabel"}
-    os.chdir(os.path.dirname(os.path.abspath(__file__)))
     with pytest.raises(SystemExit) as e_info:
         cli.init_main(argv=["-di", inp, "-c", "gas"], binaries=binaries)
     captured = capsys.readouterr()
@@ -53,13 +48,11 @@ def test_no_obabel(capsys, inp, msg):
     assert e_info.value.code == 19
 
 
-def test_amb2gmx_no_bins(capsys):
+def test_amb2gmx_no_bins(janitor, capsys):
     binaries = {"ac_bin": "no_ac", "obabel_bin": "no_obabel"}
-    os.chdir(os.path.dirname(os.path.abspath(__file__)))
     argv = ["-x", "Base.inpcrd", "-p", "Base.prmtop"]
     temp_base = "vir_temp"
     cli.init_main(argv=argv + ["-b", temp_base], binaries=binaries)
     captured = capsys.readouterr()
     assert "Total time of execution:" in captured.out
-    os.chdir(os.path.dirname(os.path.abspath(__file__)))
-    _getoutput(f"rm -fr {temp_base}*")
+    _getoutput(f"rm -vfr {temp_base}* .*{temp_base}*")
diff --git a/tests/too_close.pdb b/tests/too_close.pdb
new file mode 100644
index 00000000..74cfaa27
--- /dev/null
+++ b/tests/too_close.pdb
@@ -0,0 +1,28 @@
+COMPND    benzene.pdb
+AUTHOR    GENERATED BY OPEN BABEL 2.4.1
+ATOM      1  C1  BEN     1       5.274   1.999  -8.568  1.00  0.00           C
+ATOM      2  C2  BEN     1       6.627   2.018  -8.209  1.00  0.00           C
+ATOM      3  C3  BEN     1       7.366   0.829  -8.202  1.00  0.00           C
+ATOM      4  C4  BEN     1       6.752  -0.379  -8.554  1.00  0.00           C
+ATOM      5  C5  BEN     1       5.399  -0.398  -8.912  1.00  0.00           C
+ATOM      6  C6  BEN     1       4.660   0.791  -8.919  1.00  0.00           C
+ATOM      7  H11 BEN     1       4.704   2.916  -8.573  1.00  0.00           H
+ATOM      8  H21 BEN     1       7.101   2.950  -7.938  1.00  0.00           H
+ATOM      9  H31 BEN     1       8.410   0.844  -7.926  1.00  0.00           H
+ATOM     10  H41 BEN     1       7.322  -1.296  -8.548  1.00  0.00           H
+ATOM     11  H51 BEN     1       4.925  -1.330  -9.183  1.00  0.00           H
+ATOM     12  H61 BEN     1       4.670   0.790  -8.915  1.00  0.00           H
+CONECT    1    6    7    2
+CONECT    2    1    3    8
+CONECT    3    4    2    9
+CONECT    4    5   10    3
+CONECT    5   11    6    4
+CONECT    6   12    5    1
+CONECT    7    1
+CONECT    8    2
+CONECT    9    3
+CONECT   10    4
+CONECT   11    5
+CONECT   12    6
+MASTER        0    0    0    0    0    0    0    0   12    0   12    0
+END
diff --git a/tests/too_far.pdb b/tests/too_far.pdb
new file mode 100644
index 00000000..43ce7ead
--- /dev/null
+++ b/tests/too_far.pdb
@@ -0,0 +1,28 @@
+COMPND    benzene.pdb
+AUTHOR    GENERATED BY OPEN BABEL 2.4.1
+ATOM      1  C1  BEN     1       5.274   1.999  -8.568  1.00  0.00           C
+ATOM      2  C2  BEN     1       6.627   2.018  -8.209  1.00  0.00           C
+ATOM      3  C3  BEN     1       7.366   0.829  -8.202  1.00  0.00           C
+ATOM      4  C4  BEN     1       6.752  -0.379  -8.554  1.00  0.00           C
+ATOM      5  C5  BEN     1       5.399  -0.398  -8.912  1.00  0.00           C
+ATOM      6  C6  BEN     1       4.660   0.791  -8.919  1.00  0.00           C
+ATOM      7  H11 BEN     1       4.704   2.916  -8.573  1.00  0.00           H
+ATOM      8  H21 BEN     1       7.101   2.950  -7.938  1.00  0.00           H
+ATOM      9  H31 BEN     1       8.410   0.844  -7.926  1.00  0.00           H
+ATOM     10  H41 BEN     1       7.322  -1.296  -8.548  1.00  0.00           H
+ATOM     11  H51 BEN     1       4.925  -1.330  -9.183  1.00  0.00           H
+ATOM     12  H61 BEN     1      14.670  10.790 -18.915  1.00  0.00           H
+CONECT    1    6    7    2
+CONECT    2    1    3    8
+CONECT    3    4    2    9
+CONECT    4    5   10    3
+CONECT    5   11    6    4
+CONECT    6   12    5    1
+CONECT    7    1
+CONECT    8    2
+CONECT    9    3
+CONECT   10    4
+CONECT   11    5
+CONECT   12    6
+MASTER        0    0    0    0    0    0    0    0   12    0   12    0
+END
diff --git a/tests/wrong_res_num.pdb b/tests/wrong_res_num.pdb
new file mode 100644
index 00000000..cae209b8
--- /dev/null
+++ b/tests/wrong_res_num.pdb
@@ -0,0 +1,28 @@
+COMPND    benzene.pdb
+AUTHOR    GENERATED BY OPEN BABEL 2.4.1
+ATOM      1  C1  100     1       5.274   1.999  -8.568  1.00  0.00           C
+ATOM      2  C2  100     1       6.627   2.018  -8.209  1.00  0.00           C
+ATOM      3  C3  100     1       7.366   0.829  -8.202  1.00  0.00           C
+ATOM      4  C4  100     1       6.752  -0.379  -8.554  1.00  0.00           C
+ATOM      5  C5  100     1       5.399  -0.398  -8.912  1.00  0.00           C
+ATOM      6  C6  100     1       4.660   0.791  -8.919  1.00  0.00           C
+ATOM      7  H11 100     1       4.704   2.916  -8.573  1.00  0.00           H
+ATOM      8  H21 100     1       7.101   2.950  -7.938  1.00  0.00           H
+ATOM      9  H31 100     1       8.410   0.844  -7.926  1.00  0.00           H
+ATOM     10  H41 100     1       7.322  -1.296  -8.548  1.00  0.00           H
+ATOM     11  H51 100     1       4.925  -1.330  -9.183  1.00  0.00           H
+ATOM     12  H61 100     1       3.616   0.776  -9.196  1.00  0.00           H
+CONECT    1    6    7    2
+CONECT    2    1    3    8
+CONECT    3    4    2    9
+CONECT    4    5   10    3
+CONECT    5   11    6    4
+CONECT    6   12    5    1
+CONECT    7    1
+CONECT    8    2
+CONECT    9    3
+CONECT   10    4
+CONECT   11    5
+CONECT   12    6
+MASTER        0    0    0    0    0    0    0    0   12    0   12    0
+END
diff --git a/tests/wrong_res_set.pdb b/tests/wrong_res_set.pdb
new file mode 100644
index 00000000..ef1c2142
--- /dev/null
+++ b/tests/wrong_res_set.pdb
@@ -0,0 +1,28 @@
+COMPND    benzene.pdb
+AUTHOR    GENERATED BY OPEN BABEL 2.4.1
+ATOM      1  C1  SET     1       5.274   1.999  -8.568  1.00  0.00           C
+ATOM      2  C2  SET     1       6.627   2.018  -8.209  1.00  0.00           C
+ATOM      3  C3  SET     1       7.366   0.829  -8.202  1.00  0.00           C
+ATOM      4  C4  SET     1       6.752  -0.379  -8.554  1.00  0.00           C
+ATOM      5  C5  SET     1       5.399  -0.398  -8.912  1.00  0.00           C
+ATOM      6  C6  SET     1       4.660   0.791  -8.919  1.00  0.00           C
+ATOM      7  H11 SET     1       4.704   2.916  -8.573  1.00  0.00           H
+ATOM      8  H21 SET     1       7.101   2.950  -7.938  1.00  0.00           H
+ATOM      9  H31 SET     1       8.410   0.844  -7.926  1.00  0.00           H
+ATOM     10  H41 SET     1       7.322  -1.296  -8.548  1.00  0.00           H
+ATOM     11  H51 SET     1       4.925  -1.330  -9.183  1.00  0.00           H
+ATOM     12  H61 SET     1       3.616   0.776  -9.196  1.00  0.00           H
+CONECT    1    6    7    2
+CONECT    2    1    3    8
+CONECT    3    4    2    9
+CONECT    4    5   10    3
+CONECT    5   11    6    4
+CONECT    6   12    5    1
+CONECT    7    1
+CONECT    8    2
+CONECT    9    3
+CONECT   10    4
+CONECT   11    5
+CONECT   12    6
+MASTER        0    0    0    0    0    0    0    0   12    0   12    0
+END
diff --git a/tests/wrong_res_sym.pdb b/tests/wrong_res_sym.pdb
new file mode 100644
index 00000000..3454f8ef
--- /dev/null
+++ b/tests/wrong_res_sym.pdb
@@ -0,0 +1,28 @@
+COMPND    benzene.pdb
+AUTHOR    GENERATED BY OPEN BABEL 2.4.1
+ATOM      1  C1  +++     1       5.274   1.999  -8.568  1.00  0.00           C
+ATOM      2  C2  +++     1       6.627   2.018  -8.209  1.00  0.00           C
+ATOM      3  C3  +++     1       7.366   0.829  -8.202  1.00  0.00           C
+ATOM      4  C4  +++     1       6.752  -0.379  -8.554  1.00  0.00           C
+ATOM      5  C5  +++     1       5.399  -0.398  -8.912  1.00  0.00           C
+ATOM      6  C6  +++     1       4.660   0.791  -8.919  1.00  0.00           C
+ATOM      7  H11 +++     1       4.704   2.916  -8.573  1.00  0.00           H
+ATOM      8  H21 +++     1       7.101   2.950  -7.938  1.00  0.00           H
+ATOM      9  H31 +++     1       8.410   0.844  -7.926  1.00  0.00           H
+ATOM     10  H41 +++     1       7.322  -1.296  -8.548  1.00  0.00           H
+ATOM     11  H51 +++     1       4.925  -1.330  -9.183  1.00  0.00           H
+ATOM     12  H61 +++     1       3.616   0.776  -9.196  1.00  0.00           H
+CONECT    1    6    7    2
+CONECT    2    1    3    8
+CONECT    3    4    2    9
+CONECT    4    5   10    3
+CONECT    5   11    6    4
+CONECT    6   12    5    1
+CONECT    7    1
+CONECT    8    2
+CONECT    9    3
+CONECT   10    4
+CONECT   11    5
+CONECT   12    6
+MASTER        0    0    0    0    0    0    0    0   12    0   12    0
+END
diff --git a/tox.ini b/tox.ini
index b743a92e..356824d4 100644
--- a/tox.ini
+++ b/tox.ini
@@ -6,4 +6,4 @@ exclude =
     __pycache__,
     venv,
     build,
-    amber*
\ No newline at end of file
+    amber*