pyjess 0.7.0__cp38-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl

pyjess-0.7.0.dist-info/METADATA

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+Metadata-Version: 2.2
+Name: pyjess
+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>
+License: MIT License
+         
+         Copyright (c) 2024-2025 Martin Larralde <martin.larralde@embl.de>
+         
+         Permission is hereby granted, free of charge, to any person obtaining a copy
+         of this software and associated documentation files (the "Software"), to deal
+         in the Software without restriction, including without limitation the rights
+         to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+         copies of the Software, and to permit persons to whom the Software is
+         furnished to do so, subject to the following conditions:
+         
+         The above copyright notice and this permission notice shall be included in all
+         copies or substantial portions of the Software.
+         
+         THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+         IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+         FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+         AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+         LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+         OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+         SOFTWARE.
+         
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: C
+Classifier: Programming Language :: Cython
+Classifier: Programming Language :: Python :: 3.7
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: Implementation :: CPython
+Classifier: Programming Language :: Python :: Implementation :: PyPy
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Classifier: Typing :: Typed
+Project-URL: Homepage, https://github.com/althonos/pyjess/
+Project-URL: Documentation, https://pyjess.readthedocs.io/en/stable/
+Project-URL: Bug Tracker, https://github.com/althonos/pyjess/issues
+Project-URL: Changelog, https://github.com/althonos/pyjess/blob/master/CHANGELOG.md
+Project-URL: Coverage, https://codecov.io/gh/althonos/pyjess/
+Project-URL: Builds, https://github.com/althonos/pyjess/actions
+Project-URL: PyPI, https://pypi.org/project/pyjess
+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)
+
+*[Cython](https://cython.org/) bindings and Python interface to [Jess](https://github.com/iriziotis/jess), a 3D template matching software.*
+
+[![Actions](https://img.shields.io/github/actions/workflow/status/althonos/pyjess/test.yml?branch=main&logo=github&style=flat-square&maxAge=300)](https://github.com/althonos/pyjess/actions)
+[![Coverage](https://img.shields.io/codecov/c/gh/althonos/pyjess?style=flat-square&maxAge=3600&logo=codecov)](https://codecov.io/gh/althonos/pyjess/)
+[![License](https://img.shields.io/badge/license-MIT-blue.svg?style=flat-square&maxAge=2678400)](https://choosealicense.com/licenses/mit/)
+[![PyPI](https://img.shields.io/pypi/v/pyjess.svg?style=flat-square&maxAge=3600&logo=PyPI)](https://pypi.org/project/pyjess)
+[![Bioconda](https://img.shields.io/conda/vn/bioconda/pyjess?style=flat-square&maxAge=3600&logo=anaconda)](https://anaconda.org/bioconda/pyjess)
+[![AUR](https://img.shields.io/aur/version/python-pyjess?logo=archlinux&style=flat-square&maxAge=3600)](https://aur.archlinux.org/packages/python-pyjess)
+[![Wheel](https://img.shields.io/pypi/wheel/pyjess.svg?style=flat-square&maxAge=3600)](https://pypi.org/project/pyjess/#files)
+[![Python Versions](https://img.shields.io/pypi/pyversions/pyjess.svg?style=flat-square&maxAge=600&logo=python)](https://pypi.org/project/pyjess/#files)
+[![Python Implementations](https://img.shields.io/pypi/implementation/pyjess.svg?style=flat-square&maxAge=600&label=impl)](https://pypi.org/project/pyjess/#files)
+[![Source](https://img.shields.io/badge/source-GitHub-303030.svg?maxAge=2678400&style=flat-square)](https://github.com/althonos/pyjess/)
+[![Mirror](https://img.shields.io/badge/mirror-LUMC-003EAA.svg?maxAge=2678400&style=flat-square)](https://git.lumc.nl/mflarralde/pyjess/)
+[![Issues](https://img.shields.io/github/issues/althonos/pyjess.svg?style=flat-square&maxAge=600)](https://github.com/althonos/pyjess/issues)
+[![Docs](https://img.shields.io/readthedocs/pyjess/latest?style=flat-square&maxAge=600)](https://pyjess.readthedocs.io)
+[![Changelog](https://img.shields.io/badge/keep%20a-changelog-8A0707.svg?maxAge=2678400&style=flat-square)](https://github.com/althonos/pyjess/blob/main/CHANGELOG.md)
+[![Downloads](https://img.shields.io/badge/dynamic/regex?url=https%3A%2F%2Fpepy.tech%2Fprojects%2Fpyjess&search=%5B0-9%5D%2B.%5B0-9%5D%2B(k%7CM)&style=flat-square&label=downloads&color=303f9f&cacheSeconds=86400)](https://pepy.tech/project/pyjess)
+
+
+## 🗺️ Overview
+
+Jess is an algorithm for constraint-based structural template matching
+proposed by Jonathan Barker *et al.*[\[1\]](#ref1). It can be used to identify
+catalytic residues from a known template inside a protein structure. Jess
+is an evolution of TESS, a geometric hashing algorithm developed by
+Andrew Wallace *et al.*[\[2\]](#ref2), removing some pre-computation and
+structural requirements from the original algorithm. Jess was further
+updated and maintained by [Ioannis Riziotis](https://github.com/iriziotis)
+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. 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
+
+PyJess is available for all modern Python versions (3.7+).
+
+It can be installed directly from [PyPI](https://pypi.org/project/pyjess/),
+which hosts some pre-built x86-64 wheels for Linux, MacOS, and Windows,
+as well as the code required to compile from source with Cython:
+```console
+$ pip install pyjess
+```
+
+Otherwise, PyJess is also available as a [Bioconda](https://bioconda.github.io/)
+package:
+```console
+$ conda install -c bioconda pyjess
+```
+
+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.
+
+
+## 🔖 Citation
+
+PyJess is scientific software, and builds on top of Jess. Please cite
+Jess if you are using it in an academic work, for instance as:
+
+> PyJess, a Python library binding to Jess (Barker *et al.*, 2003).
+
+
+## 💡 Example
+
+#### 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
+import pyjess
+
+templates = []
+for path in sorted(pathlib.Path("vendor/jess/examples").glob("template_*.qry")):
+    templates.append(pyjess.Template.load(path, id=path.stem))
+```
+
+#### 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
+# 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:
+
+```python
+for hit in query:
+    print(hit.molecule.id, hit.template.id, hit.rmsd, hit.log_evalue)
+    for atom in hit.atoms():
+        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)
+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 = []
+for path in glob.glob("vendor/jess/examples/test_pdbs/*.ent"):
+    molecules.append(Molecule.load(path))
+
+with multiprocessing.ThreadPool() as pool:
+    hits = pool.map(jess.query, molecules)
+```
+
+*⚠️ 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
+
+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
+
+### ⚠️ Issue Tracker
+
+Found a bug ? Have an enhancement request ? Head over to the [GitHub issue tracker](https://github.com/althonos/pyjess/issues)
+if you need to report or ask something. If you are filing in on a bug,
+please include as much information as you can about the issue, and try to
+recreate the same bug in a simple, easily reproducible situation.
+
+
+### 🏗️ Contributing
+
+Contributions are more than welcome! See
+[`CONTRIBUTING.md`](https://github.com/althonos/pyjess/blob/main/CONTRIBUTING.md)
+for more details.
+
+
+## 📋 Changelog
+
+This project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html)
+and provides a [changelog](https://github.com/althonos/pyjess/blob/main/CHANGELOG.md)
+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 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 [Leiden University Medical Center](https://www.lumc.nl/en/) in
+the [Zeller team](https://github.com/zellerlab).*
+
+
+## 📚 References
+
+- <a id="ref1">\[1\]</a> Barker, J. A., & Thornton, J. M. (2003). An algorithm for constraint-based structural template matching: application to 3D templates with statistical analysis. Bioinformatics (Oxford, England), 19(13), 1644–1649. [doi:10.1093/bioinformatics/btg226](https://doi.org/10.1093/bioinformatics/btg226).
+- <a id="ref2">\[2\]</a> Wallace, A. C., Borkakoti, N., & Thornton, J. M. (1997). TESS: a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites. Protein science : a publication of the Protein Society, 6(11), 2308–2323. [doi:10.1002/pro.5560061104](https://doi.org/10.1002/pro.5560061104).

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pyjess-0.7.0.dist-info/entry_points.txt

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pyjess-0.7.0.dist-info/licenses/COPYING

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024-2025 Martin Larralde <martin.larralde@embl.de>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.