pyjess 0.5.2__cp37-cp37m-win_amd64.whl → 0.7.0__cp37-cp37m-win_amd64.whl

{pyjess-0.5.2.dist-info → pyjess-0.7.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 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>
@@ -54,7 +54,9 @@ Project-URL: Pypi, https://pypi.org/project/pyjess
 Project-URL: Piwheels, https://piwheels.org/project/pyjess/
 Requires-Python: >=3.7
 Provides-Extra: test
+Provides-Extra: cif
 Requires-Dist: importlib-resources; python_version < "3.9" and extra == "test"
+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)
@@ -92,7 +94,9 @@ 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
@@ -112,7 +116,7 @@ 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.
 
 
@@ -126,7 +130,10 @@ 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
@@ -134,19 +141,49 @@ 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:
 
@@ -157,12 +194,20 @@ 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 = []
@@ -176,8 +221,23 @@ 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
 
@@ -205,12 +265,13 @@ 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-0.7.0.dist-info/RECORD

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pyjess-0.7.0.dist-info/entry_points.txt

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+[console_scripts]
+pyjess = pyjess.cli:main
+

pyjess-0.5.2.dist-info/RECORD

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