pyjess 0.7.0a4__tar.gz → 0.7.0a6__tar.gz

{pyjess-0.7.0a4 → pyjess-0.7.0a6}/.github/workflows/test.yml

@@ -14,40 +14,18 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        include:
-        - python-version: 3.7
-          python-release: v3.7
-          python-impl: CPython
-        - python-version: 3.8
-          python-release: v3.8
-          python-impl: CPython
-        - python-version: 3.9
-          python-release: v3.9
-          python-impl: CPython
-        - python-version: '3.10'
-          python-release: v3.10
-          python-impl: CPython
-        - python-version: 3.11
-          python-release: v3.11
-          python-impl: CPython
-        - python-version: 3.12
-          python-release: v3.12
-          python-impl: CPython
-        - python-version: 3.13
-          python-release: v3.13
-          python-impl: CPython
-        - python-version: pypy-3.7
-          python-release: v3.7
-          python-impl: PyPy
-        - python-version: pypy-3.8
-          python-release: v3.8
-          python-impl: PyPy
-        - python-version: pypy-3.9
-          python-release: v3.9
-          python-impl: PyPy
-        - python-version: pypy-3.10
-          python-release: v3.10
-          python-impl: PyPy
+        python-version:
+          - "3.7"
+          - "3.8"
+          - "3.9"
+          - "3.10"
+          - "3.11"
+          - "3.12"
+          - "3.13"
+          - "pypy-3.7"
+          - "pypy-3.8"
+          - "pypy-3.9"
+          - "pypy-3.10"
     steps:
     - name: Checkout code
       uses: actions/checkout@v4
@@ -63,7 +41,13 @@ jobs:
       run: python -m pip install -r .github/workflows/requirements.txt
     - name: Build C extension in debug mode
       run: python -m pip install -e . -vv --no-build-isolation 
-    - name: Test package
+    - name: Test package without optional dependencies
+      run: python -m unittest pyjess.tests -vv
+    - name: Install Python requirements
+      if: ${{ !startsWith(matrix.python-version, 'pypy') }}
+      run: python -m pip install gemmi biopython biotite
+    - name: Test package with optional dependencies
+      if: ${{ !startsWith(matrix.python-version, 'pypy') }}
       run: python -m unittest pyjess.tests -vv
     # - name: Upload to Codecov
     #   if: matrix.python-impl == 'CPython'
@@ -82,34 +66,18 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        include:
-        - python-version: 3.8
-          python-release: v3.8
-          python-impl: CPython
-        - python-version: 3.9
-          python-release: v3.9
-          python-impl: CPython
-        - python-version: '3.10'
-          python-release: v3.10
-          python-impl: CPython
-        - python-version: '3.11'
-          python-release: v3.11
-          python-impl: CPython
-        - python-version: '3.12'
-          python-release: v3.12
-          python-impl: CPython
-        - python-version: 3.13
-          python-release: v3.13
-          python-impl: CPython
-        - python-version: pypy-3.8
-          python-release: v3.8
-          python-impl: PyPy
-        - python-version: pypy-3.9
-          python-release: v3.9
-          python-impl: PyPy
-        - python-version: pypy-3.10
-          python-release: v3.10
-          python-impl: PyPy
+        python-version:
+          - "3.7"
+          - "3.8"
+          - "3.9"
+          - "3.10"
+          - "3.11"
+          - "3.12"
+          - "3.13"
+          - "pypy-3.7"
+          - "pypy-3.8"
+          - "pypy-3.9"
+          - "pypy-3.10"
     steps:
     - name: Checkout code
       uses: actions/checkout@v4
@@ -129,7 +97,13 @@ jobs:
       run: python -m pip install -r .github/workflows/requirements.txt
     - name: Build C extension in debug mode
       run: python -m pip install -e . -vv --no-build-isolation 
-    - name: Test package
+    - name: Test package without optional dependencies
+      run: python -m unittest pyjess.tests -vv
+    - name: Install Python requirements
+      if: ${{ !startsWith(matrix.python-version, 'pypy') }}
+      run: python -m pip install gemmi biopython biotite
+    - name: Test package with optional dependencies
+      if: ${{ !startsWith(matrix.python-version, 'pypy') }}
       run: python -m unittest pyjess.tests -vv
     # - name: Upload to Codecov
     #   if: matrix.python-impl == 'CPython'
@@ -148,40 +122,18 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        include:
-        - python-version: 3.7
-          python-release: v3.7
-          python-impl: CPython
-        - python-version: 3.8
-          python-release: v3.8
-          python-impl: CPython
-        - python-version: 3.9
-          python-release: v3.9
-          python-impl: CPython
-        - python-version: '3.10'
-          python-release: v3.10
-          python-impl: CPython
-        - python-version: '3.11'
-          python-release: v3.11
-          python-impl: CPython
-        - python-version: '3.12'
-          python-release: v3.12
-          python-impl: CPython
-        - python-version: 3.13
-          python-release: v3.13
-          python-impl: CPython
-        - python-version: pypy-3.7
-          python-release: v3.7
-          python-impl: PyPy
-        - python-version: pypy-3.8
-          python-release: v3.8
-          python-impl: PyPy
-        - python-version: pypy-3.9
-          python-release: v3.9
-          python-impl: PyPy
-        - python-version: pypy-3.10
-          python-release: v3.10
-          python-impl: PyPy
+        python-version:
+          - "3.7"
+          - "3.8"
+          - "3.9"
+          - "3.10"
+          - "3.11"
+          - "3.12"
+          - "3.13"
+          - "pypy-3.7"
+          - "pypy-3.8"
+          - "pypy-3.9"
+          - "pypy-3.10"
     steps:
     - name: Checkout code
       uses: actions/checkout@v4
@@ -198,5 +150,11 @@ jobs:
       run: python -m pip install -r .github/workflows/requirements.txt
     - name: Build C extension
       run: python -m pip install . -vv --no-build-isolation 
-    - name: Test without coverage
+    - name: Test package without optional dependencies
+      run: python -m unittest pyjess.tests -vv
+    - name: Install Python requirements
+      if: ${{ !startsWith(matrix.python-version, 'pypy') }}
+      run: python -m pip install gemmi biopython biotite
+    - name: Test package with optional dependencies
+      if: ${{ !startsWith(matrix.python-version, 'pypy') }}
       run: python -m unittest pyjess.tests -vv

{pyjess-0.7.0a4 → pyjess-0.7.0a6}/CHANGELOG.md

@@ -6,7 +6,35 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 
 ## [Unreleased]
-[Unreleased]: https://github.com/althonos/pyjess/compare/v0.7.0-alpha.4...HEAD
+[Unreleased]: https://github.com/althonos/pyjess/compare/v0.7.0-alpha.6...HEAD
+
+
+## [v0.7.0-alpha.6] - 2025-09-12
+[v0.7.0-alpha.6]: https://github.com/althonos/pyjess/compare/v0.7.0-alpha.5...v0.7.0-alpha.6
+
+### Added
+- Command Line Interface with the same features as the Jess CLI.
+- `Molecule.from_biopython`, `Molecule.from_biotite` and `Molecule.from_gemmi` to create a `Molecule` with objects from other libraries.
+- `Hit.dump` and `Hit.dumps` methods to write a hit to PDB format.
+- `Molecule.load` option to skip parsing of `HETATM` from PDB files.
+
+### Fixed
+- Issue with alignment of atom names in `TemplateAtom`.
+- Validate data in PDB parser to ensure it is not parsing a mmCIF file.
+- Parsing of mmCIF files with atoms missing occupancy values.
+- Incorrect alignment of `TemplateAtom` names for names of less than 4 characters.
+
+### Changed
+- Setup deployment of Limited API wheels for CPython 3.8 onwards.
+- Implement format detection between PDB and mmCIF in `Molecule.load`.
+- Implement `Template.copy` and `TemplateAtom.copy` using C-level API rather than Python copy.
+
+
+## [v0.7.0-alpha.5] - 2025-09-03
+[v0.7.0-alpha.5]: https://github.com/althonos/pyjess/compare/v0.7.0-alpha.4...v0.7.0-alpha.5
+
+### Fixed
+- Issue with new residue support introduced in `v0.7.0-alpha.4`.
 
 
 ## [v0.7.0-alpha.4] - 2025-09-03

{pyjess-0.7.0a4 → pyjess-0.7.0a6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: pyjess
-Version: 0.7.0a4
+Version: 0.7.0a6
 Summary: Cython bindings and Python interface to JESS, a 3D template matching software.
 Keywords: bioinformatics,structure,template,matching
 Author-Email: Martin Larralde <martin.larralde@embl.de>
@@ -131,7 +131,9 @@ Jess if you are using it in an academic work, for instance as:
 
 ## 💡 Example
 
-Load [`Template`](https://pyjess.readthedocs.io/en/latest/api/template.html#pyjess.Template) 
+#### Prepare templates
+
+Load [`Template`](https://pyjess.readthedocs.io/en/latest/api/template.html#pyjess.Template)
 objects to be used as references from different template files:
 
 ```python
@@ -143,15 +145,46 @@ for path in sorted(pathlib.Path("vendor/jess/examples").glob("template_*.qry")):
     templates.append(pyjess.Template.load(path, id=path.stem))
 ```
 
-Create a [`Jess`](https://pyjess.readthedocs.io/en/latest/api/jess.html#pyjess.Jess) instance and use it to query a [`Molecule`](https://pyjess.readthedocs.io/en/latest/api/molecule.html#pyjess.Molecule) (a PDB structure)
-against the stored templates:
+#### Prepare query structures
+
+Load a [`Molecule`](https://pyjess.readthedocs.io/en/latest/api/molecule.html#pyjess.Molecule)
+(a PDB structure) from a PDB file, create one with the Python API, or
+convert it from a [`Bio.Model`](https://biopython.org/docs/1.76/api/Bio.PDB.Model.html),
+[`gemmi.Model`](https://gemmi.readthedocs.io/en/latest/mol.html#model),
+or [`biotite.structure.AtomArray`](https://www.biotite-python.org/latest/apidoc/biotite.structure.AtomArray.html)
+object:
 
 ```python
-jess = pyjess.Jess(templates)
+# load from PDB file or mmCIF file
 mol = pyjess.Molecule.load("vendor/jess/examples/test_pdbs/pdb1a0p.ent")
+
+# load with BioPython
+parser = Bio.PDB.PDBParser()
+structure = parser.get_structure('pdb1a0p', "vendor/jess/examples/test_pdbs/pdb1a0p.ent")
+mol = Molecule.from_biopython(structure, id="1a0p")
+
+# load with Gemmi
+structure = gemmi.read_pdb_string("vendor/jess/examples/test_pdbs/pdb1a0p.ent")
+mol = Molecule.from_gemmi(structure[0], id="1a0p")
+
+# load with Biotite
+pdb_file = biotite.structure.io.pdb.PDBFile.read(f)
+structure = pdb_file.get_structure(altloc="all", extra_fields=["atom_id", "b_factor", "occupancy", "charge"])
+mol = Molecule.from_biotite(structure[0])
+```
+
+### Match templates
+
+Create a [`Jess`](https://pyjess.readthedocs.io/en/latest/api/jess.html#pyjess.Jess)
+instance and use it to query a against the stored templates:
+
+```python
+jess = pyjess.Jess(templates)
 query = jess.query(mol, rmsd_threshold=2.0, distance_cutoff=3.0, max_dynamic_distance=3.0)
 ```
 
+### Process hits
+
 The hits are computed iteratively, and the different output statistics are
 computed on-the-fly when requested:
 
@@ -162,13 +195,19 @@ for hit in query:
         print(atom.name, atom.x, atom.y, atom.z)
 ```
 
+Hits can also be rendered in PDB format like in the original Jess output,
+either by writing to a file directly, or to a Python string:
+```python
+for hit in query:
+    hit.dump(sys.stdout, format="pdb")
+```
 
 ## 🧶 Thread-safety
 
-Once a [`Jess`](https://pyjess.readthedocs.io/en/latest/api/jess.html#pyjess.Jess) 
+Once a [`Jess`](https://pyjess.readthedocs.io/en/latest/api/jess.html#pyjess.Jess)
 instance has been created, the templates cannot be edited anymore,
-making the [`Jess.query`](https://pyjess.readthedocs.io/en/latest/api/jess.html#pyjess.Jess.query) method re-entrant and thread-safe. This allows querying 
-several molecules against the same templates in parallel using e.g a 
+making the [`Jess.query`](https://pyjess.readthedocs.io/en/latest/api/jess.html#pyjess.Jess.query) method re-entrant and thread-safe. This allows querying
+several molecules against the same templates in parallel using e.g a
 [`ThreadPool`](https://docs.python.org/3/library/multiprocessing.html#multiprocessing.pool.ThreadPool):
 
 ```python
@@ -185,8 +224,8 @@ If running Jess in parallel, make sure to use `v0.2.1` or later to use the code
 
 ## ⏱️ Benchmarks
 
-The following table reports the runtime of PyJess to match N=132 protein 
-structures to the M=7607 templates of 
+The following table reports the runtime of PyJess to match N=132 protein
+structures to the M=7607 templates of
 [EnzyMM](https://github.com/RayHackett/enzymm), using J=12 threads to parallelize.
 
 | Version     | Runtime (s) | Match Speed (N * M / s * J) | Speedup     |
@@ -198,7 +237,7 @@ structures to the M=7607 templates of
 | ``v0.6.0``  | 54.5        | 1535.4                      | x11.34      |
 | ``v0.7.0``  | 52.4        | 1597.5                      | **x11.80**  |
 
-*Benchmarks were run on a quiet [i7-1255U](https://www.intel.com/content/www/us/en/products/sku/226259/intel-core-i71255u-processor-12m-cache-up-to-4-70-ghz/specifications.html) 
+*Benchmarks were run on a quiet [i7-1255U](https://www.intel.com/content/www/us/en/products/sku/226259/intel-core-i71255u-processor-12m-cache-up-to-4-70-ghz/specifications.html)
 CPU running @4.70GHz with 10 physical cores / 12 logical cores.*
 
 ## 💭 Feedback
@@ -227,7 +266,8 @@ in the [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) format.
 
 ## ⚖️ License
 
-This library is provided under the [MIT License](https://choosealicense.com/licenses/mit/). The JESS code is distributed under the [MIT License](https://choosealicense.com/licenses/mit/) as well.
+This library is provided under the [MIT License](https://choosealicense.com/licenses/mit/).
+The JESS code is distributed under the [MIT License](https://choosealicense.com/licenses/mit/) as well.
 
 *This project is in no way not affiliated, sponsored, or otherwise endorsed
 by the JESS authors. It was developed

{pyjess-0.7.0a4 → pyjess-0.7.0a6}/README.md

@@ -69,7 +69,9 @@ Jess if you are using it in an academic work, for instance as:
 
 ## 💡 Example
 
-Load [`Template`](https://pyjess.readthedocs.io/en/latest/api/template.html#pyjess.Template) 
+#### Prepare templates
+
+Load [`Template`](https://pyjess.readthedocs.io/en/latest/api/template.html#pyjess.Template)
 objects to be used as references from different template files:
 
 ```python
@@ -81,15 +83,46 @@ for path in sorted(pathlib.Path("vendor/jess/examples").glob("template_*.qry")):
     templates.append(pyjess.Template.load(path, id=path.stem))
 ```
 
-Create a [`Jess`](https://pyjess.readthedocs.io/en/latest/api/jess.html#pyjess.Jess) instance and use it to query a [`Molecule`](https://pyjess.readthedocs.io/en/latest/api/molecule.html#pyjess.Molecule) (a PDB structure)
-against the stored templates:
+#### Prepare query structures
+
+Load a [`Molecule`](https://pyjess.readthedocs.io/en/latest/api/molecule.html#pyjess.Molecule)
+(a PDB structure) from a PDB file, create one with the Python API, or
+convert it from a [`Bio.Model`](https://biopython.org/docs/1.76/api/Bio.PDB.Model.html),
+[`gemmi.Model`](https://gemmi.readthedocs.io/en/latest/mol.html#model),
+or [`biotite.structure.AtomArray`](https://www.biotite-python.org/latest/apidoc/biotite.structure.AtomArray.html)
+object:
 
 ```python
-jess = pyjess.Jess(templates)
+# load from PDB file or mmCIF file
 mol = pyjess.Molecule.load("vendor/jess/examples/test_pdbs/pdb1a0p.ent")
+
+# load with BioPython
+parser = Bio.PDB.PDBParser()
+structure = parser.get_structure('pdb1a0p', "vendor/jess/examples/test_pdbs/pdb1a0p.ent")
+mol = Molecule.from_biopython(structure, id="1a0p")
+
+# load with Gemmi
+structure = gemmi.read_pdb_string("vendor/jess/examples/test_pdbs/pdb1a0p.ent")
+mol = Molecule.from_gemmi(structure[0], id="1a0p")
+
+# load with Biotite
+pdb_file = biotite.structure.io.pdb.PDBFile.read(f)
+structure = pdb_file.get_structure(altloc="all", extra_fields=["atom_id", "b_factor", "occupancy", "charge"])
+mol = Molecule.from_biotite(structure[0])
+```
+
+### Match templates
+
+Create a [`Jess`](https://pyjess.readthedocs.io/en/latest/api/jess.html#pyjess.Jess)
+instance and use it to query a against the stored templates:
+
+```python
+jess = pyjess.Jess(templates)
 query = jess.query(mol, rmsd_threshold=2.0, distance_cutoff=3.0, max_dynamic_distance=3.0)
 ```
 
+### Process hits
+
 The hits are computed iteratively, and the different output statistics are
 computed on-the-fly when requested:
 
@@ -100,13 +133,19 @@ for hit in query:
         print(atom.name, atom.x, atom.y, atom.z)
 ```
 
+Hits can also be rendered in PDB format like in the original Jess output,
+either by writing to a file directly, or to a Python string:
+```python
+for hit in query:
+    hit.dump(sys.stdout, format="pdb")
+```
 
 ## 🧶 Thread-safety
 
-Once a [`Jess`](https://pyjess.readthedocs.io/en/latest/api/jess.html#pyjess.Jess) 
+Once a [`Jess`](https://pyjess.readthedocs.io/en/latest/api/jess.html#pyjess.Jess)
 instance has been created, the templates cannot be edited anymore,
-making the [`Jess.query`](https://pyjess.readthedocs.io/en/latest/api/jess.html#pyjess.Jess.query) method re-entrant and thread-safe. This allows querying 
-several molecules against the same templates in parallel using e.g a 
+making the [`Jess.query`](https://pyjess.readthedocs.io/en/latest/api/jess.html#pyjess.Jess.query) method re-entrant and thread-safe. This allows querying
+several molecules against the same templates in parallel using e.g a
 [`ThreadPool`](https://docs.python.org/3/library/multiprocessing.html#multiprocessing.pool.ThreadPool):
 
 ```python
@@ -123,8 +162,8 @@ If running Jess in parallel, make sure to use `v0.2.1` or later to use the code
 
 ## ⏱️ Benchmarks
 
-The following table reports the runtime of PyJess to match N=132 protein 
-structures to the M=7607 templates of 
+The following table reports the runtime of PyJess to match N=132 protein
+structures to the M=7607 templates of
 [EnzyMM](https://github.com/RayHackett/enzymm), using J=12 threads to parallelize.
 
 | Version     | Runtime (s) | Match Speed (N * M / s * J) | Speedup     |
@@ -136,7 +175,7 @@ structures to the M=7607 templates of
 | ``v0.6.0``  | 54.5        | 1535.4                      | x11.34      |
 | ``v0.7.0``  | 52.4        | 1597.5                      | **x11.80**  |
 
-*Benchmarks were run on a quiet [i7-1255U](https://www.intel.com/content/www/us/en/products/sku/226259/intel-core-i71255u-processor-12m-cache-up-to-4-70-ghz/specifications.html) 
+*Benchmarks were run on a quiet [i7-1255U](https://www.intel.com/content/www/us/en/products/sku/226259/intel-core-i71255u-processor-12m-cache-up-to-4-70-ghz/specifications.html)
 CPU running @4.70GHz with 10 physical cores / 12 logical cores.*
 
 ## 💭 Feedback
@@ -165,7 +204,8 @@ in the [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) format.
 
 ## ⚖️ License
 
-This library is provided under the [MIT License](https://choosealicense.com/licenses/mit/). The JESS code is distributed under the [MIT License](https://choosealicense.com/licenses/mit/) as well.
+This library is provided under the [MIT License](https://choosealicense.com/licenses/mit/).
+The JESS code is distributed under the [MIT License](https://choosealicense.com/licenses/mit/) as well.
 
 *This project is in no way not affiliated, sponsored, or otherwise endorsed
 by the JESS authors. It was developed

{pyjess-0.7.0a4 → pyjess-0.7.0a6}/docs/conf.py

@@ -74,6 +74,7 @@ extensions = [
     "sphinx.ext.extlinks",
     "sphinx_design",
     "sphinxcontrib.jquery",
+    "sphinxarg.ext",
     "nbsphinx",
     "recommonmark",
     "IPython.sphinxext.ipython_console_highlighting",
@@ -190,6 +191,9 @@ autosummary_generate = []
 # Example configuration for intersphinx: refer to the Python standard library.
 intersphinx_mapping = {
     "python": ("https://docs.python.org/3/", None),
+    "biopython": ("https://biopython.org/docs/latest/", None),
+    "biotite": ("https://www.biotite-python.org/latest/", None),
+    "gemmi": ("https://gemmi.readthedocs.io/en/latest/", None),
 }
 
 # -- Options for recommonmark extension --------------------------------------

pyjess-0.7.0a6/docs/guide/cli.rst

@@ -0,0 +1,15 @@
+Command Line Interface
+======================
+
+Starting from ``v0.7.0``, PyJess features a command-line interface that is 
+automatically installed with the package. It features the same options as
+the Jess command-line, as well as some options specific to PyJess.
+
+.. rubric:: Usage
+
+.. argparse::
+    :module: pyjess.cli
+    :func: argument_parser
+    :prog: pyjess
+    :nodescription:
+    :noepilog:

{pyjess-0.7.0a4 → pyjess-0.7.0a6}/docs/guide/index.rst

@@ -8,6 +8,7 @@ This section contains guides and documents about PyJess usage.
    :caption: Getting Started
 
     Installation <install>
+    Command Line Interface <cli>
 
 .. toctree::
    :maxdepth: 1

{pyjess-0.7.0a4 → pyjess-0.7.0a6}/docs/guide/install.rst

@@ -15,12 +15,19 @@ PyPi
 PyJess is hosted on GitHub, but the easiest way to install it is to download
 the latest release from its `PyPi repository <https://pypi.python.org/pypi/pyjess>`_.
 It will install all dependencies then install ``pyjess`` either from a wheel if
-one is available, or from source after compiling the Rust code :
+one is available, or from source after compiling the C source code from Jess :
 
 .. code:: console
 
 	$ pip install --user pyjess
 
+To install additional dependencies required for parsing mmCIF files in 
+addition to PDB files, run instead:
+
+.. code:: console
+
+	$ pip install --user pyjess[cif]
+
 
 Conda
 ^^^^^

{pyjess-0.7.0a4 → pyjess-0.7.0a6}/docs/guide/optimizations.rst

@@ -4,7 +4,7 @@ Optimizations
 .. currentmodule:: pyjess
 
 While PyJess started as a Cython wrapper of Jess, it also 
-contains several optimizations to make the code write better
+contains several optimizations to make the software perform better
 while maintaining consistency with the original Jess code.
 Some of these optimizations are described below, as well as
 the version where they were introduced.
@@ -256,3 +256,20 @@ as it creates a new `Scanner` which allocates memory for each `Template` / `Mole
 pair to match. Effectively, most of these buffers can actually be reused 
 across `Templates` for a given `Molecule`, provided sufficient bookkeeping. Our
 implementation keeps allocation to a minimum across an entire `Query`.
+
+
+Manual case-insensitive string comparison
+-----------------------------------------
+
+.. versionadded:: 0.7.0
+
+The original Jess code uses the ``strcasecmp`` function to compare atom names,
+an operation that is perfomed on most match modes. This function is optimized
+for long strings: for instance, the GNU libc contains an AVX2 implementation 
+of the equality code. In Jess, however, this function is usually called with 
+very short strings (3 or 4 characters). 
+
+To reduce overhead due to calling an external function, and encourage the 
+compiler to unroll the equality comparison loop, we implement name 
+comparison in an inline function defined in the ``TessAtom.h`` header. On 
+a single template, this saved around 5% of the CPU cycles.

{pyjess-0.7.0a4 → pyjess-0.7.0a6}/docs/requirements.txt

@@ -12,4 +12,5 @@ pygments ~=2.4
 nbsphinx ~=0.8
 sphinxcontrib-jquery ~=4.1
 sphinx-design
-pydata-sphinx-theme
+pydata-sphinx-theme
+sphinx-argparse

{pyjess-0.7.0a4 → pyjess-0.7.0a6}/patches/TessAtom.c.patch

@@ -1,5 +1,5 @@
 diff --git a/src/TessAtom.c b/src/TessAtom.c
-index e1cce1a..eecf682 100644
+index e1cce1a..3f06daa 100644
 --- a/src/TessAtom.c
 +++ b/src/TessAtom.c
 @@ -7,40 +7,13 @@
@@ -54,7 +54,7 @@ index e1cce1a..eecf682 100644
  	{
  		{ 'A',"ALA" },
  		{ 'C',"CYS" },
-@@ -66,10 +39,12 @@ static const char *TessAtom_convertResidue(char p)
+@@ -66,18 +39,20 @@ static const char *TessAtom_convertResidue(char p)
  		{ 'M',"MET" },
  		{ 'N',"ASN" },
  		{ 'P',"PRO" },
@@ -67,6 +67,16 @@ index e1cce1a..eecf682 100644
  		{ 'V',"VAL" },
  		{ 'W',"TRP" },
  		{ 'Y',"TYR" },
+ 		{ 'X',"XXX" }
+ 	};
+ 
+-	for(k=0; k<21 && p!=table[k].one; k++);
+-	return k<21 ? table[k].three:NULL;
++	for(k=0; k<23 && p!=table[k].one; k++);
++	return k<23 ? table[k].three:NULL;
+ }
+ 
+ TessAtom *TessAtom_create(const char *s)
 @@ -91,7 +66,7 @@ TessAtom *TessAtom_create(const char *s)
  	int rq;
  	const char *q;

{pyjess-0.7.0a4 → pyjess-0.7.0a6}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "scikit_build_core.build"
 
 [project]
 name = "pyjess"
-version = "0.7.0-alpha.4"
+version = "0.7.0-alpha.6"
 description = "Cython bindings and Python interface to JESS, a 3D template matching software."
 readme = "README.md"
 requires-python = ">=3.7"
@@ -49,8 +49,15 @@ classifiers = [
 test = ["importlib-resources ; python_version < '3.9'"]
 cif = ["gemmi ~=0.7.0"]
 
+[project.scripts]
+pyjess = "pyjess.cli:main"
+
+[project.entry-points.console_scripts]
+pyjess = "pyjess.cli:main"
+
 [tool.scikit-build]
 build-dir = "build/{build_type}"
+wheel.py-api = "cp38"
 editable.rebuild = true
 editable.verbose = false
 sdist.exclude = ["vendor/jess/examples"]
@@ -74,8 +81,7 @@ if.env.MOLD = true
 cmake.define.CMAKE_LINKER_TYPE = "mold"
 
 [tool.cibuildwheel]
-before-build = "pip install scikit-build-core cython"
-build-frontend = { name = "pip", args = ["--no-build-isolation"] }
+build-frontend = { name = "pip" }
 build-verbosity = 1
 free-threaded-support = false
 test-command = "python -m unittest pyjess.tests -v"

pyjess-0.7.0a6/src/pyjess/__main__.py

@@ -0,0 +1,4 @@
+import sys
+from .cli import main
+
+sys.exit(main())