pyjess 0.5.2__tar.gz → 0.7.0__tar.gz

{pyjess-0.5.2 → pyjess-0.7.0}/.github/workflows/package.yml

@@ -15,6 +15,7 @@ jobs:
       with:
         submodules: true
     - name: Build manylinux wheels
+      if: "!contains(github.ref, 'rc') && !contains(github.ref, 'alpha')"
       uses: pypa/cibuildwheel@v2.21.3
       env:
         CIBW_ARCHS: aarch64
@@ -35,6 +36,7 @@ jobs:
       with:
         submodules: true
     - name: Build manylinux wheels
+      if: "!contains(github.ref, 'rc') && !contains(github.ref, 'alpha')"
       uses: pypa/cibuildwheel@v2.21.3
       env:
         CIBW_ARCHS: x86_64
@@ -55,6 +57,7 @@ jobs:
       with:
         submodules: true
     - name: Build manylinux wheels
+      if: "!contains(github.ref, 'rc') && !contains(github.ref, 'alpha')"
       uses: pypa/cibuildwheel@v2.21.3
       env:
         CIBW_ARCHS: x86_64
@@ -75,6 +78,7 @@ jobs:
       with:
         submodules: true
     - name: Build manylinux wheels
+      if: "!contains(github.ref, 'rc') && !contains(github.ref, 'alpha')"
       uses: pypa/cibuildwheel@v2.21.3
       env:
         CIBW_ARCHS: arm64
@@ -99,6 +103,7 @@ jobs:
       with:
         arch: amd64
     - name: Build manylinux wheels
+      if: "!contains(github.ref, 'rc') && !contains(github.ref, 'alpha')"
       uses: pypa/cibuildwheel@v2.21.3
       env:
         CIBW_ARCHS: AMD64
@@ -187,7 +192,7 @@ jobs:
     environment: GitHub Releases
     runs-on: ubuntu-latest
     permissions: write-all
-    if: "!contains(github.ref, 'rc')"
+    if: "!contains(github.ref, 'rc') && !contains(github.ref, 'alpha')"
     name: Release
     needs: upload
     steps:
@@ -201,7 +206,7 @@ jobs:
   aur:
     environment: Arch User Repository
     runs-on: ubuntu-latest
-    if: "!contains(github.ref, 'rc')"
+    if: "!contains(github.ref, 'rc') && !contains(github.ref, 'alpha')"
     name: Update AUR package
     needs:
     - sdist

{pyjess-0.5.2 → pyjess-0.7.0}/.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-0.5.2 → pyjess-0.7.0}/CHANGELOG.md

@@ -6,7 +6,53 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 
 ## [Unreleased]
-[Unreleased]: https://github.com/althonos/pyjess/compare/v0.5.2...HEAD
+[Unreleased]: https://github.com/althonos/pyjess/compare/v0.7.0...HEAD
+
+
+## [v0.7.0] - 2025-09-13
+[v0.7.0]: https://github.com/althonos/pyjess/compare/v0.6.0...v0.7.0
+
+### 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.
+- Support for [Selenocysteine](https://en.wikipedia.org/wiki/Selenocysteine) and [Pyrrolysine](https://en.wikipedia.org/wiki/Pyrrolysine) residues in `TemplateAtom`.
+- Support for parsing `Molecule` objects from CIF files using [`gemmi`](https://gemmi.readthedocs.io/).
+
+### Fixed
+- **breaking**: Incorrect handling of `max_candidates` in `Jess.query`, causing PyJess to erroneously ignore some templates.
+- `Template.dimension` reporting incorrect numbers for identical residues across different residues.
+- 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.
+- `max_candidates` causing `Query` to stop before reaching the actual number of maximum candidates.
+
+### Changed
+- **breaking**: Set the `max_candidates` default value to `None` in `Jess.query`, disabling max candidates filtering by default.
+- **breaking**: Use string variants instead of `bool` to control the behaviour of `ignore_chain` argument.
+- **breaking**: Make `id` and `ignore_endmdl` arguments of `Molecule.load` and `Molecule.loads` keyword-only.
+- Use unrolled string comparison to compare atom names instead of `strcasecmp` in Jess code.
+- Make `altloc` and `insertion_code` arguments of `Atom` optional.
+- 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.
+
+
+## [v0.6.0] - 2025-09-01
+[v0.6.0]: https://github.com/althonos/pyjess/compare/v0.5.2...v0.6.0
+
+### Added
+- Several [algorithmic optimizations](https://pyjess.readthedocs.io/en/v0.6.0/guide/optimizations.html) to Jess, greatly improving runtime:
+  - Use QuickSelect ($O(n)$) instead of QuickSort ($O(nlog(n))$) to select the medians used for space partitioning on k-d tree initialization.
+  - Use approximate intersection on bounding boxes rather than exact code involving multiple annuli when querying the k-d tree for atoms.
+  - **breaking**: Reorder the matching order of template atoms to reduce the amount of backtracking and k-d tree querying performed in the average and worst case.
+- `reorder` argument to `Jess.query` to support disabling template atom reordering if needed for Jess 1-to-1 consistency.
+
+### Changed
+- Hardcode space dimensions to 3 to encourage compilers to unroll loops over dimensions.
+- Recycle memory between templates within a query to reduce total amount of allocation/deallocation in hot paths.
 
 
 ## [v0.5.2] - 2025-08-26

{pyjess-0.5.2 → pyjess-0.7.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: pyjess
-Version: 0.5.2
+Version: 0.7.0
 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>
@@ -56,6 +56,8 @@ Project-URL: PiWheels, https://piwheels.org/project/pyjess/
 Requires-Python: >=3.7
 Provides-Extra: test
 Requires-Dist: importlib-resources; python_version < "3.9" and extra == "test"
+Provides-Extra: cif
+Requires-Dist: gemmi~=0.7.0; extra == "cif"
 Description-Content-Type: text/markdown
 
 # 🐍🔍 PyJess [![Stars](https://img.shields.io/github/stars/althonos/pyjess.svg?style=social&maxAge=3600&label=Star)](https://github.com/althonos/pyjess/stargazers)
@@ -93,7 +95,9 @@ during his PhD in the [Thornton group](https://www.ebi.ac.uk/research/thornton/)
 PyJess is a Python module that provides bindings to Jess using
 [Cython](https://cython.org/). It allows creating templates, querying them
 with protein structures, and retrieving the hits using a Python API without
-performing any external I/O.
+performing any external I/O. It's also more than 10x faster than Jess thanks to
+[algorithmic optimizations](https://pyjess.readthedocs.io/en/latest/guide/optimizations.html)
+added to improve the original Jess code while producing consistent results.
 
 
 ## 🔧 Installing
@@ -113,7 +117,7 @@ package:
 $ conda install -c bioconda pyjess
 ```
 
-Check the [*install* page](https://pyjess.readthedocs.io/en/stable/install.html)
+Check the [*install* page](https://pyjess.readthedocs.io/en/stable/guide/install.html)
 of the documentation for other ways to install PyJess on your machine.
 
 
@@ -127,7 +131,10 @@ Jess if you are using it in an academic work, for instance as:
 
 ## 💡 Example
 
-Load templates to be used as references from different template files:
+#### 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
 import pathlib
@@ -135,19 +142,49 @@ import pyjess
 
 templates = []
 for path in sorted(pathlib.Path("vendor/jess/examples").glob("template_*.qry")):
-    with path.open() as file:
-        templates.append(pyjess.Template.load(file, id=path.stem))
+    templates.append(pyjess.Template.load(path, id=path.stem))
 ```
 
-Create a `Jess` instance and use it to query a 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:
 
@@ -158,12 +195,20 @@ 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` instance has been created, the templates cannot be edited anymore,
-making the `Jess.query` method re-entrant. This allows querying several
-molecules against the same templates in parallel using a thread pool:
+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
+[`ThreadPool`](https://docs.python.org/3/library/multiprocessing.html#multiprocessing.pool.ThreadPool):
 
 ```python
 molecules = []
@@ -177,8 +222,23 @@ with multiprocessing.ThreadPool() as pool:
 *⚠️ Prior to PyJess `v0.2.1`, the Jess code was running some thread-unsafe operations which have now been patched.
 If running Jess in parallel, make sure to use `v0.2.1` or later to use the code patched with re-entrant functions*.
 
-<!-- ## ⏱️ Benchmarks -->
+## ⏱️ Benchmarks
+
+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     |
+| ----------- | ----------- | --------------------------- | ----------- |
+| ``v0.4.2``  | 618.1       | 135.4                       | N/A         |
+| ``v0.5.0``  | 586.3       | 142.7                       | x1.05       |
+| ``v0.5.1``  | 365.6       | 228.9                       | x1.69       |
+| ``v0.5.2``  | 327.2       | 255.7                       | x1.88       |
+| ``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)
+CPU running @4.70GHz with 10 physical cores / 12 logical cores.*
 
 ## 💭 Feedback
 
@@ -206,12 +266,13 @@ 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
 by [Martin Larralde](https://github.com/althonos/) during his PhD project
-at the [European Molecular Biology Laboratory](https://www.embl.de/) in
+at the [Leiden University Medical Center](https://www.lumc.nl/en/) in
 the [Zeller team](https://github.com/zellerlab).*
 
 

{pyjess-0.5.2 → pyjess-0.7.0}/README.md

@@ -33,7 +33,9 @@ during his PhD in the [Thornton group](https://www.ebi.ac.uk/research/thornton/)
 PyJess is a Python module that provides bindings to Jess using
 [Cython](https://cython.org/). It allows creating templates, querying them
 with protein structures, and retrieving the hits using a Python API without
-performing any external I/O.
+performing any external I/O. It's also more than 10x faster than Jess thanks to
+[algorithmic optimizations](https://pyjess.readthedocs.io/en/latest/guide/optimizations.html)
+added to improve the original Jess code while producing consistent results.
 
 
 ## 🔧 Installing
@@ -53,7 +55,7 @@ package:
 $ conda install -c bioconda pyjess
 ```
 
-Check the [*install* page](https://pyjess.readthedocs.io/en/stable/install.html)
+Check the [*install* page](https://pyjess.readthedocs.io/en/stable/guide/install.html)
 of the documentation for other ways to install PyJess on your machine.
 
 
@@ -67,7 +69,10 @@ Jess if you are using it in an academic work, for instance as:
 
 ## 💡 Example
 
-Load templates to be used as references from different template files:
+#### 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
 import pathlib
@@ -75,19 +80,49 @@ import pyjess
 
 templates = []
 for path in sorted(pathlib.Path("vendor/jess/examples").glob("template_*.qry")):
-    with path.open() as file:
-        templates.append(pyjess.Template.load(file, id=path.stem))
+    templates.append(pyjess.Template.load(path, id=path.stem))
 ```
 
-Create a `Jess` instance and use it to query a 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:
 
@@ -98,12 +133,20 @@ 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` instance has been created, the templates cannot be edited anymore,
-making the `Jess.query` method re-entrant. This allows querying several
-molecules against the same templates in parallel using a thread pool:
+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
+[`ThreadPool`](https://docs.python.org/3/library/multiprocessing.html#multiprocessing.pool.ThreadPool):
 
 ```python
 molecules = []
@@ -117,8 +160,23 @@ with multiprocessing.ThreadPool() as pool:
 *⚠️ Prior to PyJess `v0.2.1`, the Jess code was running some thread-unsafe operations which have now been patched.
 If running Jess in parallel, make sure to use `v0.2.1` or later to use the code patched with re-entrant functions*.
 
-<!-- ## ⏱️ Benchmarks -->
+## ⏱️ Benchmarks
+
+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     |
+| ----------- | ----------- | --------------------------- | ----------- |
+| ``v0.4.2``  | 618.1       | 135.4                       | N/A         |
+| ``v0.5.0``  | 586.3       | 142.7                       | x1.05       |
+| ``v0.5.1``  | 365.6       | 228.9                       | x1.69       |
+| ``v0.5.2``  | 327.2       | 255.7                       | x1.88       |
+| ``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)
+CPU running @4.70GHz with 10 physical cores / 12 logical cores.*
 
 ## 💭 Feedback
 
@@ -146,12 +204,13 @@ 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
 by [Martin Larralde](https://github.com/althonos/) during his PhD project
-at the [European Molecular Biology Laboratory](https://www.embl.de/) in
+at the [Leiden University Medical Center](https://www.lumc.nl/en/) in
 the [Zeller team](https://github.com/zellerlab).*
 
 

{pyjess-0.5.2 → pyjess-0.7.0}/docs/_static/json/switcher.json

@@ -1,6 +1,16 @@
 [
     {
-        "name": "v0.5 (latest)",
+        "name": "v0.7 (latest)",
+        "version": "0.7.0",
+        "url": "https://pyjess.readthedocs.io/en/v0.7.0/"
+    },
+    {
+        "name": "v0.6",
+        "version": "0.6.0",
+        "url": "https://pyjess.readthedocs.io/en/v0.6.0/"
+    },
+    {
+        "name": "v0.5",
         "version": "0.5.2",
         "url": "https://pyjess.readthedocs.io/en/v0.5.2/"
     },

{pyjess-0.5.2 → pyjess-0.7.0}/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 --------------------------------------