pyjess 0.4.1__tar.gz → 0.5.1__tar.gz

{pyjess-0.4.1 → pyjess-0.5.1}/.github/workflows/package.yml

@@ -9,16 +9,11 @@ jobs:
 
   wheel-linux-aarch64:
     name: Build Linux wheels (Aarch64)
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-22.04-arm
     steps:
     - uses: actions/checkout@v3
       with:
         submodules: true
-    - name: Set up QEMU
-      id: qemu
-      uses: docker/setup-qemu-action@v3
-      with:
-        platforms: arm64
     - name: Build manylinux wheels
       uses: pypa/cibuildwheel@v2.21.3
       env:
@@ -94,7 +89,7 @@ jobs:
 
   wheel-win32-x86_64:
     name: Build Windows wheels (x86-64)
-    runs-on: windows-2019
+    runs-on: windows-latest
     steps:
     - uses: actions/checkout@v4
       with:

{pyjess-0.4.1 → pyjess-0.5.1}/.github/workflows/test.yml

@@ -76,7 +76,7 @@ jobs:
 
   test_osx:
     name: Test (OSX)
-    runs-on: macos-latest
+    runs-on: macos-13
     env:
       OS: OSX
     strategy:

{pyjess-0.4.1 → pyjess-0.5.1}/CHANGELOG.md

@@ -6,7 +6,27 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 
 ## [Unreleased]
-[Unreleased]: https://github.com/althonos/pyjess/compare/v0.4.1...HEAD
+[Unreleased]: https://github.com/althonos/pyjess/compare/v0.5.1...HEAD
+
+
+## [v0.5.1] - 2025-08-20
+[v0.5.1]: https://github.com/althonos/pyjess/compare/v0.5.0...v0.5.1
+
+### Fixed
+- Typo in `Hit.molecule` returning incorrect coordinates when transformation is required.
+
+### Changed
+- Implement an index to quickly access atoms by residue names in a `Molecule`, and accelerate initial candidate set creation for compatible match modes.
+
+
+## [v0.5.0] - 2025-04-09
+[v0.5.0]: https://github.com/althonos/pyjess/compare/v0.4.1...v0.5.0
+
+### Fixed
+- Remove invalid `platform` key from `pyproject.toml`.
+
+### Changed
+- `Hit.molecule` is now a method and can optionally rotate the hit molecule.
 
 
 ## [v0.4.1] - 2024-11-29

{pyjess-0.4.1 → pyjess-0.5.1}/COPYING

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2024 Martin Larralde <martin.larralde@embl.de>
+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

{pyjess-0.4.1 → pyjess-0.5.1}/PKG-INFO

@@ -1,30 +1,31 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: pyjess
-Version: 0.4.1
+Version: 0.5.1
 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 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.
+         
+         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
@@ -46,11 +47,12 @@ 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: 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: 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"
@@ -74,7 +76,7 @@ Description-Content-Type: text/markdown
 [![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)
+[![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
@@ -83,8 +85,8 @@ 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 
+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/).
 
@@ -105,34 +107,44 @@ as well as the code required to compile from source with Cython:
 $ pip install pyjess
 ```
 
-<!-- Otherwise, PyJess is also available as a [Bioconda](https://bioconda.github.io/)
+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.
 
+
+## 🔖 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
 
 Load templates to be used as references from different template files:
 
 ```python
-import glob
+import pathlib
 import pyjess
 
 templates = []
-for path in sorted(glob.iglob("vendor/jess/examples/template_*.qry")):
-    templates.append(Template.load(path, id=os.path.basename(path)))
+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))
 ```
 
 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")
+jess = pyjess.Jess(templates)
+mol = pyjess.Molecule.load("vendor/jess/examples/test_pdbs/pdb1a0p.ent")
 query = jess.query(mol, rmsd_threshold=2.0, distance_cutoff=3.0, max_dynamic_distance=3.0)
 ```
 
@@ -162,7 +174,7 @@ 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. 
+*⚠️ 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 -->
@@ -172,7 +184,7 @@ If running Jess in parallel, make sure to use `v0.2.1` or later to use the code
 
 ### ⚠️ Issue Tracker
 
-Found a bug ? Have an enhancement request ? Head over to the [GitHub issue tracker](https://github.com/althonos/[pyjess]/issues)
+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.

{pyjess-0.4.1 → pyjess-0.5.1}/README.md

@@ -16,7 +16,7 @@
 [![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)
+[![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
@@ -25,8 +25,8 @@ 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 
+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/).
 
@@ -47,34 +47,44 @@ as well as the code required to compile from source with Cython:
 $ pip install pyjess
 ```
 
-<!-- Otherwise, PyJess is also available as a [Bioconda](https://bioconda.github.io/)
+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.
 
+
+## 🔖 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
 
 Load templates to be used as references from different template files:
 
 ```python
-import glob
+import pathlib
 import pyjess
 
 templates = []
-for path in sorted(glob.iglob("vendor/jess/examples/template_*.qry")):
-    templates.append(Template.load(path, id=os.path.basename(path)))
+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))
 ```
 
 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")
+jess = pyjess.Jess(templates)
+mol = pyjess.Molecule.load("vendor/jess/examples/test_pdbs/pdb1a0p.ent")
 query = jess.query(mol, rmsd_threshold=2.0, distance_cutoff=3.0, max_dynamic_distance=3.0)
 ```
 
@@ -104,7 +114,7 @@ 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. 
+*⚠️ 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 -->
@@ -114,7 +124,7 @@ If running Jess in parallel, make sure to use `v0.2.1` or later to use the code
 
 ### ⚠️ Issue Tracker
 
-Found a bug ? Have an enhancement request ? Head over to the [GitHub issue tracker](https://github.com/althonos/[pyjess]/issues)
+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.

{pyjess-0.4.1 → pyjess-0.5.1}/docs/_static/json/switcher.json

@@ -1,6 +1,11 @@
 [
     {
-        "name": "v0.4 (latest)",
+        "name": "v0.5.1",
+        "version": "0.5.1",
+        "url": "https://pyjess.readthedocs.io/en/v0.5.1/"
+    },
+    {
+        "name": "v0.4",
         "version": "0.4.1",
         "url": "https://pyjess.readthedocs.io/en/v0.4.1/"
     },

{pyjess-0.4.1 → pyjess-0.5.1}/docs/index.rst

@@ -65,7 +65,7 @@ PyJess |Stars|
    :target: https://github.com/althonos/pyjess/blob/main/CHANGELOG.md
    :class: dark-light
 
-.. |Downloads| image:: https://img.shields.io/pypi/dm/pyjess?style=flat-square&color=303f9f&maxAge=3600&label=downloads
+.. |Downloads| image:: 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
    :target: https://pepy.tech/project/pyjess
    :class: dark-light
 

pyjess-0.5.1/include/jess/candidate_set.pxd

@@ -0,0 +1,15 @@
+from .atom cimport Atom
+from .molecule cimport Molecule
+
+
+cdef extern from "CandidateSet.h" nogil:
+
+    struct _CandidateSet:
+        int count
+        Atom **atom
+        double **coord
+
+    ctypedef _CandidateSet CandidateSet
+
+    CandidateSet *CandidateSet_create(const Molecule *M)
+    void CandidateSet_free(CandidateSet*)

{pyjess-0.4.1 → pyjess-0.5.1}/include/jess/molecule.pxd

@@ -1,6 +1,7 @@
 from libc.stdio cimport FILE
 
 from .atom cimport Atom
+from .res_index cimport ResIndex
 
 
 cdef extern from "Molecule.h" nogil:
@@ -8,6 +9,7 @@ cdef extern from "Molecule.h" nogil:
     cdef struct _Molecule:
         int count
         char[5] id
+        ResIndex* index
         Atom** atom
 
     ctypedef _Molecule Molecule
@@ -15,5 +17,5 @@ cdef extern from "Molecule.h" nogil:
     Molecule* Molecule_create(FILE*, int, double)
     void Molecule_free(Molecule*) 
     int Molecule_count(const Molecule*)
-    Atom* Molecule_atom(const Molecule*, int)
+    const Atom* Molecule_atom(const Molecule*, int)
     const char* Molecule_id(const Molecule*)

pyjess-0.5.1/include/jess/res_index.pxd

@@ -0,0 +1,15 @@
+from .atom cimport Atom
+
+
+cdef extern from "ResIndex.h" nogil:
+
+    struct _ResIndex:
+        int count
+        Atom **atom
+        double **coord
+
+    ctypedef _ResIndex ResIndex
+
+    extern ResIndex* ResIndex_create(Atom**, int)
+    extern Atom** ResIndex_get(ResIndex*, const char[4])
+    extern void ResIndex_free(ResIndex*)

{pyjess-0.4.1 → pyjess-0.5.1}/include/jess/template.pxd

@@ -1,5 +1,6 @@
 from .atom cimport Atom
-
+from .molecule cimport Molecule
+from .candidate_set cimport CandidateSet
 
 cdef extern from "Template.h" nogil:
 
@@ -10,6 +11,7 @@ cdef extern from "Template.h" 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
+        CandidateSet* (*candidates)(const Template*, const Molecule*, int);
         const double* (*position)(const Template*, int) nogil
         const char* (*name)(const Template*) nogil
         double (*logE)(const Template*, double, int) nogil

{pyjess-0.4.1 → pyjess-0.5.1}/include/jess/tess_template.pxd

@@ -3,6 +3,8 @@ from libc.stdio cimport FILE
 from .atom cimport Atom
 from .tess_atom cimport TessAtom
 from .template cimport Template
+from .molecule cimport Molecule
+from .candidate_set cimport CandidateSet
 
 
 cdef extern from "TessTemplate.h" nogil:
@@ -22,6 +24,7 @@ cdef extern from "TessTemplate.h" nogil:
     const double *TessTemplate_position(const Template *T, int k)
     double TessTemplate_distWeight(const Template *T, int k)
     int TessTemplate_check(const Template *T, Atom **A, int k, int ignore_chain)
+    CandidateSet* TessTemplate_candidates(const Template *T, const Molecule *M, int k)
     const char *TessTemplate_name(const Template *T)
     double TessTemplate_logE(const Template *T,double rmsd, int n)
     void TessTemplate_free(Template *T)

pyjess-0.5.1/patches/CMakeLists.txt.patch

@@ -0,0 +1,35 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+new file mode 100644
+index 0000000..b34b6e7
+--- /dev/null
++++ b/CMakeLists.txt
+@@ -0,0 +1,29 @@
++cmake_minimum_required(VERSION 3.10)
++project(Jess)
++
++include(CheckSymbolExists)
++check_symbol_exists(alloca "alloca.h" HAVE_ALLOCA)
++
++add_library(jess)
++target_sources(jess PRIVATE
++	src/Annulus.c
++	src/Join.c
++	src/Molecule.c
++	src/Super.c
++	src/Atom.c
++	src/KdTree.c
++	src/Region.c
++	src/TessAtom.c
++	src/Jess.c
++	src/Scanner.c
++	src/TessTemplate.c
++	src/CandidateSet.c
++	src/ResIndex.c)
++if(HAVE_ALLOCA)
++	target_compile_definitions(jess PUBLIC -DHAVE_ALLOCA)
++endif()
++
++add_executable(jess_bin)
++target_sources(jess_bin PRIVATE src/Main.c)
++target_link_libraries(jess_bin jess m)
++set_property(TARGET jess_bin PROPERTY OUTPUT_NAME jess)

pyjess-0.5.1/patches/CandidateSet.c.patch

@@ -0,0 +1,71 @@
+diff --git a/src/CandidateSet.c b/src/CandidateSet.c
+new file mode 100644
+index 0000000..a67e878
+--- /dev/null
++++ b/src/CandidateSet.c
+@@ -0,0 +1,65 @@
++// ==================================================================
++// CandidateSet.h
++// Copyright (c) Jonathan Barker, 2002
++// Copyright (c) Martin Larralde, 2025
++// ==================================================================
++// Implementation of type CandidateSet.
++// ==================================================================
++
++#include <stdlib.h>
++
++#include "CandidateSet.h"
++#include "Atom.h"
++#include "Molecule.h"
++#include "Template.h"
++
++// ==================================================================
++// Methods of local type CandidateSet
++// ==================================================================
++
++CandidateSet *CandidateSet_create(const Molecule *M)
++{
++	CandidateSet *S;
++	Atom *A;
++	int n = Molecule_count(M);
++	int m;
++
++	S = (CandidateSet*)calloc(1,sizeof(CandidateSet));
++    if(!S) return NULL;
++
++	S->atom=(Atom**)calloc(n,sizeof(Atom*));
++	S->coord = NULL;
++	S->count = 0;
++    
++    return S;
++}
++
++void CandidateSet_addAtom(CandidateSet *S, Atom *A)
++{
++	S->atom[S->count]=A;
++	S->count++;
++}
++
++void CandidateSet_recordCoordinates(CandidateSet *S)
++{
++	int m;
++	
++	S->atom=(Atom**)realloc(S->atom,sizeof(Atom*)*S->count);
++	S->coord=(double**)calloc(S->count,sizeof(double*));
++
++	for(m=0; m<S->count; m++)
++		S->coord[m]=S->atom[m]->x;
++}
++
++
++void CandidateSet_free(CandidateSet *S)
++{
++	if(S)
++	{
++		if(S->atom) free(S->atom);
++		if(S->coord) free(S->coord);
++		free(S);
++	}
++}
++
++// ==================================================================

pyjess-0.5.1/patches/CandidateSet.h.patch

@@ -0,0 +1,51 @@
+diff --git a/src/CandidateSet.h b/src/CandidateSet.h
+new file mode 100644
+index 0000000..9b12e6e
+--- /dev/null
++++ b/src/CandidateSet.h
+@@ -0,0 +1,44 @@
++// ==================================================================
++// CandidateSet.h
++// Copyright (c) Jonathan Barker, 2002
++// Copyright (c) Martin Larralde, 2025
++// ==================================================================
++// Declaration of type CandidateSet.
++// ==================================================================
++
++#ifndef CANDIDATESET_H
++#define CANDIDATESET_H
++
++#include "Atom.h"
++#include "Molecule.h"
++
++// ==================================================================
++// Local type CandidateSet
++// ==================================================================
++// count				Number of atoms in the set
++// atom[k]				Points to ATOM record for kth candidate
++// coord[k]				Points to coordinates for kth candidate
++// ==================================================================
++
++struct _CandidateSet
++{
++	int count;
++	Atom **atom;
++	double **coord;
++};
++
++typedef struct _CandidateSet CandidateSet;
++
++// ==================================================================
++// Declaration of methods of local type CandidateSet
++// ==================================================================
++// create(M,T,k)		Create from molecule M, atom k of T
++// free(S)				Free candidate set
++// ==================================================================
++
++CandidateSet *CandidateSet_create(const Molecule*);
++void CandidateSet_addAtom(CandidateSet*, Atom*);
++void CandidateSet_recordCoordinates(CandidateSet*);
++void CandidateSet_free(CandidateSet*);
++
++#endif
+

{pyjess-0.4.1 → pyjess-0.5.1}/patches/Jess.c.patch

@@ -1,8 +1,30 @@
 diff --git a/src/Jess.c b/src/Jess.c
-index e81bda0..6d44558 100644
+index e81bda0..c4e581b 100644
 --- a/src/Jess.c
 +++ b/src/Jess.c
-@@ -91,8 +91,10 @@ void Jess_free(Jess *J)
+@@ -4,15 +4,17 @@
+ // Implementation of types Jess and JessQuery.
+ // ==================================================================
+ 
++#include <stdio.h>
++#include <stdlib.h>
++#include <math.h>
++#include <string.h>
++
+ #include "Jess.h"
+ #include "Molecule.h"
+ #include "Scanner.h"
+ #include "TessTemplate.h"
+ #include "Super.h"
+-#include <stdio.h>
+-#include <stdlib.h>
+-#include <math.h>
+-#include <string.h>
++
+ 
+ // ==================================================================
+ // Forward declarations of local types
+@@ -91,8 +93,10 @@ void Jess_free(Jess *J)
  			n=J->head->next;
  			T=J->head->template;
  			if(T) T->free(T);
@@ -13,13 +35,13 @@ index e81bda0..6d44558 100644
  	}
  }
  
-@@ -157,26 +159,26 @@ Superposition *JessQuery_superposition(JessQuery *Q)
+@@ -156,27 +160,25 @@ Superposition *JessQuery_superposition(JessQuery *Q)
+ 	int count;
  	Template *T;
  	Atom **A;
- 
+-
 -	if(Q->super) return Q->super;
 +	Superposition* super;
-+	// if(Q->super) return Q->super;
  
  	A = Q->atoms;
  	T = Q->node->template;