Restructured pdb reader and added alpha carbon argument

.github/workflows/test.yml

@@ -30,6 +30,8 @@ jobs:
           pwd
           which python
           conda info
+      - run: pip install .
+      - run: which calculate_rmsd
       - run: |
           make test python=python
       - run: |

.pre-commit-config.yaml

@@ -38,14 +38,7 @@ repos:
     hooks:
       - id: isort
         name: sorts imports
-        args: [
-          # Align isort with black formatting
-          "--multi-line=3",
-          "--trailing-comma",
-          "--force-grid-wrap=0",
-          "--use-parentheses",
-          "--line-width=99",
-        ]
+        args: ["--profile", "black", "--filter-files", "--line-width=99"]
 
 
   - repo: https://github.com/psf/black

Makefile

@@ -18,7 +18,7 @@ format:
 	${python} -m pre_commit run --all-files
 
 test:
-	${python} -m pytest -rs ./tests
+	${python} -m pytest ./tests
 
 test-dist:
 	${python} -m twine check dist/*

README.rst

@@ -111,7 +111,8 @@ Hungarian_ (default), distance (very approximate) and brute force (slow).
     calculate_rmsd --reorder tests/water_16.xyz tests/water_16_idx.xyz
 
 
-It is also possible to use RMSD as a library in other scripts, see `example.py` for example usage.
+It is also possible to use RMSD as a library in other scripts, see
+``example.py`` and ``tests/*`` for example usage.
 
 
 Problems?
@@ -120,21 +121,11 @@ Problems?
 Submit issues or pull requests on GitHub.
 
 
-Contributions
+A note on PDB
 -------------
 
-Please note that we are using ``black`` with line length of 99. Easiest way to
-abide to the code standard is to install the following package.
+Protein Data Bank format (PDB) is column-based; however, countless examples of non-standard ``.pdb`` files exist.
+We try to read them, but if you have trouble reading the file, check if the file format is compliant with PDB.
+For example, some hydrogens are noted as ``HG11``, which we assume is not mercury.
 
-.. code-block:: bash
-
-    pip install pre-commit
-
-and run the following command in your repository
-
-.. code-block:: bash
-
-    pre-commit install
-
-This will install a hook in your git and re-format your code to adhere to the standard.
-As well as check for code quality.
+- https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM

pyproject.toml

@@ -26,8 +26,11 @@ Homepage = "https://github.com/charnley/rmsd"
 [options.packages.find]
 where="."
 
+[project.scripts]
+calculate_rmsd = "rmsd.calculate_rmsd:main"
+
 [tool.setuptools]
 include-package-data = true
 
 [tool.setuptools.dynamic]
-version = {attr = "rmsd.__version__"}
+version = {attr = "rmsd.version.__version__"}