pyjess 0.1.0__tar.gz

pyjess-0.1.0/CHANGELOG.md

@@ -0,0 +1,15 @@
+# Changelog
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
+and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
+
+
+## [Unreleased]
+[Unreleased]: https://github.com/althonos/pyjess/compare/v0.1.0...HEAD
+
+
+## [v0.1.0] - 2024-04-18
+[v0.1.0]: https://github.com/althonos/pyjess/compare/3f2a7e9...v0.1.0
+
+Initial release.

pyjess-0.1.0/CONTRIBUTING.md

@@ -0,0 +1,44 @@
+# Contributing to PyJess
+
+For bug fixes or new features, please file an issue before submitting a
+pull request. If the change isn't trivial, it may be best to wait for
+feedback.
+
+## Coding guidelines
+
+### Versions
+
+This project targets Python 3.5 or later.
+
+Python objects should be typed; since it is not supported by Cython,
+you must manually declare types in type stubs (`.pyi` files). In Python
+files, you can add type annotations to function signatures (supported in
+Python 3.5) but not in variable assignments (supported only from Python
+3.6 onward). However, Cython allows you to use [f-strings](https://www.python.org/dev/peps/pep-0498/)
+even when compiling the code for Python 3.5.
+
+### Interfacing with C
+
+When interfacing with C, and in particular with pointers, use assertions
+everywhere you assume the pointer to be non-NULL. Also consider using
+assertions when accessing raw C arrays, if applicable.
+
+## Setting up a local repository
+
+Make sure you clone the repository in recursive mode, so you also get the
+wrapped code of Jess which is exposed as a ``git`` submodule:
+
+```console
+$ git clone --recursive https://github.com/althonos/pyjess
+```
+
+## Running tests
+
+Tests are written as usual Python unit tests with the `unittest` module of
+the standard library. Running them requires the extension to be built
+locally:
+
+```console
+$ python setup.py build_ext --debug --inplace
+$ python -m unittest discover -vv
+```

pyjess-0.1.0/COPYING

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 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.

pyjess-0.1.0/MANIFEST.in

@@ -0,0 +1,17 @@
+include COPYING
+include CHANGELOG.md
+include CONTRIBUTING.md
+include README.md
+
+recursive-include include           *.pxd
+recursive-include patches           *.patch
+recursive-include pyjess            *.py *.pyi *.pxi *.pyx *.pxd *.h py.typed
+recursive-include pyjess/tests/data *
+
+recursive-include vendor/jess       README.md LICENSE AUTHORS CHANGELOG
+recursive-include vendor/jess       *.c *.h
+prune                               vendor/sword/vendor
+
+recursive-include pyjess            *.py *.pyi *.pxi *.pyx *.pxd *.h py.typed
+recursive-exclude pyjess            *.cpp *.html
+

pyjess-0.1.0/PKG-INFO

@@ -0,0 +1,189 @@
+Metadata-Version: 2.1
+Name: pyjess
+Version: 0.1.0
+Summary: Cython bindings and Python interface to JESS, a 3D template matching software.
+Home-page: https://github.com/althonos/pyjess
+Author: Martin Larralde
+Author-email: martin.larralde@embl.de
+License: MIT
+Project-URL: Bug Tracker, https://github.com/althonos/pyjess/issues
+Project-URL: Changelog, https://github.com/althonos/pyjess/blob/main/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
+Keywords: bioinformatics,structure,template,matching
+Platform: any
+Classifier: Development Status :: 3 - Alpha
+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 :: 3.6
+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 :: Implementation :: CPython
+Classifier: Programming Language :: Python :: Implementation :: PyPy
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Classifier: Typing :: Typed
+Requires-Python: >=3.5
+Description-Content-Type: text/markdown
+License-File: COPYING
+
+# 🔍🐍 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-EMBL-009f4d?style=flat-square&maxAge=2678400)](https://git.embl.de/larralde/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/pypi/dm/pyjess?style=flat-square&color=303f9f&maxAge=86400&label=downloads)](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")):
+    with open(path) as f:
+        templates.append(Template.load(f, 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)
+with open("vendor/jess/examples/test_pdbs/pdb1a0p.ent") as f:
+    mol = Molecule(f)
+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"):
+    with open(path) as f:
+        molecules.append(Molecule.load(f))
+
+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).

pyjess-0.1.0/README.md

@@ -0,0 +1,151 @@
+# 🔍🐍 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-EMBL-009f4d?style=flat-square&maxAge=2678400)](https://git.embl.de/larralde/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/pypi/dm/pyjess?style=flat-square&color=303f9f&maxAge=86400&label=downloads)](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")):
+    with open(path) as f:
+        templates.append(Template.load(f, 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)
+with open("vendor/jess/examples/test_pdbs/pdb1a0p.ent") as f:
+    mol = Molecule(f)
+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"):
+    with open(path) as f:
+        molecules.append(Molecule.load(f))
+
+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).

pyjess-0.1.0/include/jess/annulus.pxd

@@ -0,0 +1,6 @@
+from .region cimport Region
+
+
+cdef extern from "Annulus.h" nogil:
+    Region* Annulus_create(double*, double, double, int)
+    void Annulus_free(Region*)

pyjess-0.1.0/include/jess/atom.pxd

@@ -0,0 +1,21 @@
+cdef extern from "Atom.h" nogil:
+
+    struct _Atom:
+        int serial
+        char[5] name
+        char altLoc
+        char[4] resName
+        char chainID1
+        char chainID2
+        int resSeq
+        char iCode
+        double[3] x
+        double occupancy
+        double tempFactor
+        char[4] segID
+        char[3] element
+        int charge
+
+    ctypedef _Atom Atom
+
+    int Atom_parse(Atom*, const char*)

pyjess-0.1.0/include/jess/jess.pxd

@@ -0,0 +1,30 @@
+from .atom cimport Atom
+from .molecule cimport Molecule
+from .super cimport Superposition
+from .template cimport Template
+
+
+cdef extern from "Jess.h" nogil:
+
+    ctypedef struct _Jess:
+        pass
+
+    ctypedef struct _JessQuery:
+        pass
+
+    ctypedef _Jess Jess
+    ctypedef _JessQuery JessQuery
+
+    Jess* Jess_create()
+    void Jess_free(Jess*)
+    void Jess_addTemplate(Jess*, Template*)
+    JessQuery* Jess_query(Jess*, Molecule*, double, double)
+
+    void JessQuery_free(JessQuery*)
+    int JessQuery_next(JessQuery*, int)
+    Template* JessQuery_template(JessQuery*)
+    const Molecule* JessQuery_molecule(JessQuery*)
+    Atom** JessQuery_atoms(JessQuery*)
+    Superposition* JessQuery_superposition(JessQuery*)
+
+

pyjess-0.1.0/include/jess/join.pxd

@@ -0,0 +1,12 @@
+from .region cimport Region
+
+
+cdef extern from "Join.h" nogil:
+
+    ctypedef enum JoinType:
+        innerJoin
+        outerJoin
+
+    Region* Join_create(Region**, int, JoinType)
+    void Join_free(Region*)
+

pyjess-0.1.0/include/jess/kdtree.pxd

@@ -0,0 +1,19 @@
+from .region cimport Region
+
+
+cdef extern from "KdTree.h" nogil:
+
+    cdef struct _KdTree:
+        pass
+    cdef struct _KdTreeQuery:
+        pass
+
+    ctypedef _KdTree KdTree
+    ctypedef _KdTreeQuery KdTreeQuery
+
+    KdTree* KdTree_create(double**, int, int)
+    void KdTree_free(KdTree**)
+    KdTreeQuery* KdTree_query(KdTree*, Region*)
+
+    void KdTreeQuery_free(KdTreeQuery*)
+    int KdTreeQuery_next(KdTreeQuery*)

pyjess-0.1.0/include/jess/molecule.pxd

@@ -0,0 +1,19 @@
+from libc.stdio cimport FILE
+
+from .atom cimport Atom
+
+
+cdef extern from "Molecule.h" nogil:
+
+    cdef struct _Molecule:
+        int count
+        char[5] id
+        Atom** atom
+
+    ctypedef _Molecule Molecule
+
+    Molecule* Molecule_create(FILE*, int, double)
+    void Molecule_free(Molecule*) 
+    int Molecule_count(const Molecule*)
+    Atom* Molecule_atom(const Molecule*, int)
+    const char* Molecule_id(const Molecule*)

pyjess-0.1.0/include/jess/region.pxd

@@ -0,0 +1,9 @@
+cdef extern from "Region.h" nogil:
+
+    struct _Region:
+        int (*intersectionQ)(Region*, double*, double*, int)
+        int (*inclusionQ)(Region*, double*, int)
+        void (*free)(Region*)
+    ctypedef _Region Region
+
+    double Region_volume(Region*, double, double*, double*, int)

pyjess-0.1.0/include/jess/scanner.pxd

@@ -0,0 +1,15 @@
+from .molecule import Molecule
+from .template import Template
+
+
+cdef extern from "Scanner.h" nogil:
+
+    cdef struct _Scanner:
+        pass
+    ctypedef _Scanner Scanner
+
+    Scanner* Scanner_create(Molecule*, Template*, double, double)
+    void Scanner_free(Scanner*)
+    Atom** Scanner_next(Scanner*, int)
+    double Scanner_rmsd(Scanner*)
+

pyjess-0.1.0/include/jess/super.pxd

@@ -0,0 +1,14 @@
+cdef extern from "Super.h" nogil:
+
+    cdef struct _Superposition:
+        pass
+    ctypedef _Superposition Superposition
+
+    Superposition* Superposition_create()
+    void Superposition_free(Superposition*)
+    void Superposition_align(Superposition*, const double*, const double*)
+    int Superposition_count(const Superposition*)
+    double Superposition_rmsd(Superposition*)
+    double Superposition_rmsd100(Superposition*)
+    const double* Superposition_centroid(Superposition*, int)
+    const double* Superposition_rotation(Superposition*)

pyjess-0.1.0/include/jess/template.pxd

@@ -0,0 +1,17 @@
+from .atom cimport Atom
+
+
+cdef extern from "Template.h" nogil:
+
+    ctypedef _Template Template
+    cdef struct _Template:
+        void (*free)(Template*) nogil
+        int (*count)(const Template*) nogil
+        int (*match)(const Template*, int, const Atom*) nogil
+        int (*range)(const Template*, int, int, double*, double*) nogil
+        int (*check)(const Template*, Atom**, int, int) nogil
+        const double* (*position)(const Template*, int) nogil
+        const char* (*name)(const Template*) nogil
+        double (*logE)(const Template*, double, int) nogil
+        double (*distWeight)(const Template*, int) nogil
+        Template* (*copy)(const Template*) nogil

pyjess-0.1.0/include/jess/tess_atom.pxd

@@ -0,0 +1,29 @@
+from .atom cimport Atom
+
+cdef extern from "TessAtom.h" nogil:
+
+    struct _TessAtom:
+        int code
+        int resSeq
+        int nameCount
+        int resNameCount
+        char chainID1
+        char chainID2
+        char **name
+        char **resName
+        double pos[3]
+        double distWeight
+
+    ctypedef _TessAtom TessAtom
+
+    TessAtom* TessAtom_create(const char*)
+    void TessAtom_free(TessAtom*)
+    const double* TessAtom_position(const TessAtom*)
+    int TessAtom_match(const TessAtom*, const Atom*)
+    int TessAtom_resSeq(const TessAtom*)
+    char TessAtom_chainID1(const TessAtom*)
+    char TessAtom_chainID2(const TessAtom*)
+    double TessAtom_distWeight(const TessAtom*)
+    
+    TessAtom* TessAtom_copy(const TessAtom*)
+    double TessAtom_distance(const TessAtom*, const TessAtom*)