# 🐍🔍 PyJess [](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.*
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[](https://codecov.io/gh/althonos/pyjess/)
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[](https://pypi.org/project/pyjess)
[](https://anaconda.org/bioconda/pyjess)
[](https://aur.archlinux.org/packages/python-pyjess)
[](https://pypi.org/project/pyjess/#files)
[](https://pypi.org/project/pyjess/#files)
[](https://pypi.org/project/pyjess/#files)
[](https://github.com/althonos/pyjess/)
[](https://github.com/althonos/pyjess/issues)
[](https://pyjess.readthedocs.io)
[](https://github.com/althonos/pyjess/blob/main/CHANGELOG.md)
[](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.
## 🔧 Installing
PyJess is available for all modern Python versions (3.6+).
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/install.html)
of the documentation for other ways to install PyJess on your machine.
## 💡 Example
Load templates to be used as references from different template files:
```python
import glob
import pyjess
templates = []
for path in sorted(glob.iglob("vendor/jess/examples/template_*.qry")):
templates.append(Template.load(path, id=os.path.basename(path)))
```
Create a `Jess` instance and use it to query a molecule (a PDB structure)
against the stored templates:
```python
jess = Jess(templates)
mol = Molecule("vendor/jess/examples/test_pdbs/pdb1a0p.ent")
query = jess.query(mol, rmsd_threshold=2.0, distance_cutoff=3.0, max_dynamic_distance=3.0)
```
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)
```
## 🧶 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:
```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)
```
<!-- ## ⏱️ Benchmarks -->
## 💭 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 [European Molecular Biology Laboratory](https://www.embl.de/) 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).
Raw data
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"description": "# \ud83d\udc0d\ud83d\udd0d PyJess [](https://github.com/althonos/pyjess/stargazers)\n\n*[Cython](https://cython.org/) bindings and Python interface to [Jess](https://github.com/iriziotis/jess), a 3D template matching software.*\n\n[](https://github.com/althonos/pyjess/actions)\n[](https://codecov.io/gh/althonos/pyjess/)\n[](https://choosealicense.com/licenses/mit/)\n[](https://pypi.org/project/pyjess)\n[](https://anaconda.org/bioconda/pyjess)\n[](https://aur.archlinux.org/packages/python-pyjess)\n[](https://pypi.org/project/pyjess/#files)\n[](https://pypi.org/project/pyjess/#files)\n[](https://pypi.org/project/pyjess/#files)\n[](https://github.com/althonos/pyjess/)\n[](https://github.com/althonos/pyjess/issues)\n[](https://pyjess.readthedocs.io)\n[](https://github.com/althonos/pyjess/blob/main/CHANGELOG.md)\n[](https://pepy.tech/project/pyjess)\n\n\n## \ud83d\uddfa\ufe0f Overview\n\nJess is an algorithm for constraint-based structural template matching\nproposed by Jonathan Barker *et al.*[\\[1\\]](#ref1). It can be used to identify\ncatalytic residues from a known template inside a protein structure. Jess\nis an evolution of TESS, a geometric hashing algorithm developed by\nAndrew Wallace *et al.*[\\[2\\]](#ref2), removing some pre-computation and \nstructural requirements from the original algorithm. Jess was further \nupdated and maintained by [Ioannis Riziotis](https://github.com/iriziotis)\nduring his PhD in the [Thornton group](https://www.ebi.ac.uk/research/thornton/).\n\nPyJess is a Python module that provides bindings to Jess using\n[Cython](https://cython.org/). It allows creating templates, querying them\nwith protein structures, and retrieving the hits using a Python API without\nperforming any external I/O.\n\n\n## \ud83d\udd27 Installing\n\nPyJess is available for all modern Python versions (3.6+).\n\nIt can be installed directly from [PyPI](https://pypi.org/project/pyjess/),\nwhich hosts some pre-built x86-64 wheels for Linux, MacOS, and Windows,\nas well as the code required to compile from source with Cython:\n```console\n$ pip install pyjess\n```\n\n<!-- Otherwise, PyJess is also available as a [Bioconda](https://bioconda.github.io/)\npackage:\n```console\n$ conda install -c bioconda pyjess\n``` -->\n\nCheck the [*install* page](https://pyjess.readthedocs.io/en/stable/install.html)\nof the documentation for other ways to install PyJess on your machine.\n\n## \ud83d\udca1 Example\n\nLoad templates to be used as references from different template files:\n\n```python\nimport glob\nimport pyjess\n\ntemplates = []\nfor path in sorted(glob.iglob(\"vendor/jess/examples/template_*.qry\")):\n templates.append(Template.load(path, id=os.path.basename(path)))\n```\n\nCreate a `Jess` instance and use it to query a molecule (a PDB structure)\nagainst the stored templates:\n\n```python\njess = Jess(templates)\nmol = Molecule(\"vendor/jess/examples/test_pdbs/pdb1a0p.ent\")\nquery = jess.query(mol, rmsd_threshold=2.0, distance_cutoff=3.0, max_dynamic_distance=3.0)\n```\n\nThe hits are computed iteratively, and the different output statistics are\ncomputed on-the-fly when requested:\n\n```python\nfor hit in query:\n print(hit.molecule.id, hit.template.id, hit.rmsd, hit.log_evalue)\n for atom in hit.atoms():\n print(atom.name, atom.x, atom.y, atom.z)\n```\n\n\n## \ud83e\uddf6 Thread-safety\n\nOnce a `Jess` instance has been created, the templates cannot be edited anymore,\nmaking the `Jess.query` method re-entrant. This allows querying several\nmolecules against the same templates in parallel using a thread pool:\n\n```python\nmolecules = []\nfor path in glob.glob(\"vendor/jess/examples/test_pdbs/*.ent\"):\n molecules.append(Molecule.load(path))\n\nwith multiprocessing.ThreadPool() as pool:\n hits = pool.map(jess.query, molecules)\n```\n\n<!-- ## \u23f1\ufe0f Benchmarks -->\n\n\n## \ud83d\udcad Feedback\n\n### \u26a0\ufe0f Issue Tracker\n\nFound a bug ? Have an enhancement request ? Head over to the [GitHub issue tracker](https://github.com/althonos/[pyjess]/issues)\nif you need to report or ask something. If you are filing in on a bug,\nplease include as much information as you can about the issue, and try to\nrecreate the same bug in a simple, easily reproducible situation.\n\n\n### \ud83c\udfd7\ufe0f Contributing\n\nContributions are more than welcome! See\n[`CONTRIBUTING.md`](https://github.com/althonos/pyjess/blob/main/CONTRIBUTING.md)\nfor more details.\n\n\n## \ud83d\udccb Changelog\n\nThis project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html)\nand provides a [changelog](https://github.com/althonos/pyjess/blob/main/CHANGELOG.md)\nin the [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) format.\n\n\n## \u2696\ufe0f License\n\nThis 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.\n\n*This project is in no way not affiliated, sponsored, or otherwise endorsed\nby the JESS authors. It was developed\nby [Martin Larralde](https://github.com/althonos/) during his PhD project\nat the [European Molecular Biology Laboratory](https://www.embl.de/) in\nthe [Zeller team](https://github.com/zellerlab).*\n\n\n## \ud83d\udcda References\n\n- <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\u20131649. [doi:10.1093/bioinformatics/btg226](https://doi.org/10.1093/bioinformatics/btg226).\n- <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\u20132323. [doi:10.1002/pro.5560061104](https://doi.org/10.1002/pro.5560061104).\n",
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