pyjess 0.4.1__cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl → 0.5.1__cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl

pyjess/_jess.pyi

@@ -39,7 +39,7 @@ class Molecule(Sequence[Atom]):
 
 class Atom:
     @classmethod
-    def load(cls, file: Union[str, bytes, os.PathLike[Any], TextIO]) -> Atom: ...
+    def load(cls, file: Union[TextIO, str, os.PathLike[str]]) -> Atom: ...
     @classmethod
     def loads(cls, text: str) -> Atom: ...
     def __init__(
@@ -100,7 +100,7 @@ class Atom:
 
 class TemplateAtom:
     @classmethod
-    def load(cls, file: Union[str, bytes, os.PathLike[Any], TextIO]) -> Atom: ...
+    def load(cls, file: Union[TextIO, str, os.PathLike[str]]) -> Atom: ...
     @classmethod
     def loads(cls, text: str) -> TemplateAtom: ...
     def __init__(
@@ -188,14 +188,13 @@ class Hit(Generic[_T]):
     @property
     def template(self) -> _T: ...
     @property
-    def molecule(self) -> Molecule: ...
-    @property
     def determinant(self) -> float: ...
     @property
     def log_evalue(self) -> float: ...
     @property
     def evalue(self) -> float: ...
     def atoms(self, transform: bool = True) -> List[Atom]: ...
+    def molecule(self, transform: bool = False) -> Molecule: ...
 
 class Jess(Generic[_T], Sequence[_T]):
     def __init__(self, templates: Iterable[_T] = ()): ...

pyjess/_jess.pyx

@@ -31,6 +31,7 @@ cimport jess.molecule
 cimport jess.super
 cimport jess.tess_template
 cimport jess.tess_atom
+cimport jess.res_index
 from jess.atom cimport Atom as _Atom
 from jess.jess cimport Jess as _Jess
 from jess.jess cimport JessQuery as _JessQuery
@@ -172,6 +173,7 @@ cdef class Molecule:
         if self._mol is NULL:
             raise MemoryError("Failed to allocate molecule")
 
+        self._mol.index = NULL
         self._mol.count = count
         for i in range(count):
             self._mol.atom[i] = NULL
@@ -184,6 +186,10 @@ cdef class Molecule:
                 raise MemoryError("Failed to allocate atom")
             memcpy(self._mol.atom[i], atom._atom, sizeof(_Atom))
 
+        self._mol.index = jess.res_index.ResIndex_create(self._mol.atom, count)
+        if self._mol.index is NULL:
+            raise MemoryError("Failed to allocate residue index")
+
     def __len__(self):
         assert self._mol is not NULL
         return self._mol.count
@@ -274,6 +280,7 @@ cdef class Molecule:
             if copy._mol is NULL:
                 raise MemoryError("Failed to allocate molecule")
             # copy molecule attributes
+            copy._mol.index = NULL
             copy._mol.count = self._mol.count
             memset(copy._mol.id, b' ', 5)
             # copy molecule atoms
@@ -282,6 +289,10 @@ cdef class Molecule:
                 if copy._mol.atom[i] is NULL:
                     raise MemoryError("Failed to allocate atom")
                 memcpy(copy._mol.atom[i], self._mol.atom[i], sizeof(_Atom))
+            # regenerate index
+            copy._mol.index = jess.res_index.ResIndex_create(copy._mol.atom, copy._mol.count)
+            if copy._mol.index is NULL:
+                raise MemoryError("Failed to allocate residue index")
 
         copy._id = self._id
         return copy
@@ -461,7 +472,7 @@ cdef class Atom:
             return NotImplemented
         other_ = other
         # FIXME: it should be possible to do a memcmp here.
-        return self._state() == other_._state()  
+        return self._state() == other_._state()
 
     def __hash__(self):
         return hash(tuple(self._state().values()))
@@ -598,11 +609,16 @@ cdef class TemplateAtom:
         """Load a template atom from the given file.
 
         Arguments:
-            file (file-like object): A file-like object opened in
-                text mode to read the template atom from.
+            file (str, os.PathLike or file-like object): A file-like object
+                opened in text or binary mode to read the template atom from.
 
         """
-        return cls.loads(file.read())
+        try:
+            handle = open(file)
+        except TypeError:
+            handle = nullcontext(file)
+        with handle as f:
+            return cls.loads(f.read())
 
     @classmethod
     def loads(cls, text):
@@ -849,7 +865,7 @@ cdef class TemplateAtom:
 
         .. versionchanged:: 0.4.1
            Property now returns a `tuple` rather than a `list`.
-           
+
         """
         assert self._atom is not NULL
 
@@ -871,11 +887,11 @@ cdef class TemplateAtom:
         """Create a copy of this template atom.
 
         Returns:
-            `~pyjess.TemplateAtom`: A new template atom object with 
+            `~pyjess.TemplateAtom`: A new template atom object with
             identical attributes.
-            
+
         .. versionadded:: 0.4.0
-        
+
         """
         return type(self)(**self._state())
 
@@ -894,10 +910,42 @@ cdef class Template:
 
     @classmethod
     def loads(cls, text, str id = None):
+        """Load a template from a string.
+
+        Arguments:
+            file (`str`, `os.PathLike`, or file-like object): Either the path
+                to a file, or a file-like object opened in **text mode**
+                containing the template.
+            id (`str`, optional): The identifier of the template. By default,
+                the parser will take the one from the ``PDB_ID`` remark if
+                found in the header.
+
+        Returns:
+            `~pyjess.Template`: The template parsed from the given string.
+
+        See Also:
+            `Template.load` to load a template from a file-like object or
+            from a path.
+
+        """
         return cls.load(io.StringIO(text), id=id)
 
     @classmethod
     def load(cls, file, str id = None):
+        """Load a template from the given file.
+
+        Arguments:
+            file (`str`, `os.PathLike` or file-like object): Either the
+                path to a file, or a file-like object opened in **text mode**
+                to read the template from.
+            id (`str`, optional): The identifier of the template. By default,
+                the parser will take the one from the ``PDB_ID`` remark if
+                found in the header.
+
+        Returns:
+            `~pyjess.Template`: The template parsed from the given file.
+
+        """
         try:
             handle = open(file)
         except TypeError:
@@ -974,6 +1022,7 @@ cdef class Template:
         self._tpl.count = jess.tess_template.TessTemplate_count
         self._tpl.range = jess.tess_template.TessTemplate_range
         self._tpl.check = jess.tess_template.TessTemplate_check
+        self._tpl.candidates = jess.tess_template.TessTemplate_candidates
         self._tpl.name = jess.tess_template.TessTemplate_name
         self._tpl.logE = jess.tess_template.TessTemplate_logE
         self._tpl.distWeight = jess.tess_template.TessTemplate_distWeight
@@ -1181,7 +1230,7 @@ cdef class Query:
         hit._sup = NULL
         hit._atoms = NULL
         hit.rmsd = INFINITY
-        hit.molecule = self.molecule
+        hit._molecule = self.molecule
         hit_tpl = NULL
 
         # search the next hit without the GIL to allow parallel queries.
@@ -1261,7 +1310,7 @@ cdef class Hit:
 
     cdef readonly double   rmsd
     cdef readonly Template template
-    cdef readonly Molecule molecule
+    cdef          Molecule _molecule
 
     def __dealloc__(self):
         jess.super.Superposition_free(self._sup)
@@ -1292,7 +1341,7 @@ cdef class Hit:
         cdef double e
 
         with nogil:
-            n = jess.molecule.Molecule_count(self.molecule._mol)
+            n = jess.molecule.Molecule_count(self._molecule._mol)
             e = self.template._tpl.logE(self.template._tpl, self.rmsd, n)
         return e
 
@@ -1304,7 +1353,7 @@ cdef class Hit:
         cdef double e
 
         with nogil:
-            n = jess.molecule.Molecule_count(self.molecule._mol)
+            n = jess.molecule.Molecule_count(self._molecule._mol)
             e = exp(self.template._tpl.logE(self.template._tpl, self.rmsd, n))
         return e
 
@@ -1349,6 +1398,45 @@ cdef class Hit:
 
         return atoms
 
+    cpdef Molecule molecule(self, bint transform=False):
+        """Get the molecule matching the template.
+
+        Arguments:
+            transform (`bool`): Whether or not to transform coordinates
+                of the molecule atoms into template frame.
+
+        Returns:
+            `~pyjess.Molecule`: The matching molecule, optionally
+            rotated to match the template coordinate.
+
+        .. versionadded:: 0.5.0
+
+        """
+        assert self.template._tpl is not NULL
+        assert self._sup is not NULL
+
+        cdef _Atom*        atom
+        cdef Molecule      mol
+        cdef size_t        i
+        cdef size_t        j
+        cdef size_t        k
+        cdef const double* M    = jess.super.Superposition_rotation(self._sup)
+        cdef const double* c    = jess.super.Superposition_centroid(self._sup, 0)
+        cdef const double* v    = jess.super.Superposition_centroid(self._sup, 1)
+
+        if not transform:
+            return self._molecule
+
+        mol = self._molecule.copy()
+        for k in range(mol._mol.count):
+            atom = mol._mol.atom[k]
+            for i in range(3):
+                atom.x[i] = v[i]
+                for j in range(3):
+                    atom.x[i] += M[3*i + j] * (self._molecule._mol.atom[k].x[j] - c[j])
+
+        return mol
+
 
 cdef class Jess:
     """A handle to run Jess over a list of templates.

pyjess/tests/test_jess.py

@@ -92,6 +92,29 @@ class TestJess(unittest.TestCase):
         self.assertEqual(len(jess[:1]), 1)
         self.assertEqual(len(jess[1:]), 0)
 
+
+    @unittest.skipUnless(files, "importlib.resources not available")
+    def test_multiple_query_split(self):
+        with files(data).joinpath("template_01.qry").open() as f:
+            template1 = Template.load(f)
+        with files(data).joinpath("template_02.qry").open() as f:
+            template2 = Template.load(f)
+        j0 = Jess([template1, template2])
+        j1 = Jess([template1])
+        j2 = Jess([template2])
+
+        with files(data).joinpath("1AMY.pdb").open() as f:
+            molecule = Molecule.load(f)
+
+        h0 = list(j0.query(molecule, 2, 5, 5))
+        h1 = list(j1.query(molecule, 2, 5, 5))
+        h2 = list(j2.query(molecule, 2, 5, 5))
+
+        self.assertEqual(len(h0), len(h1) + len(h2))
+        for hit0, hit1 in zip(h0, (*h1, *h2)):
+            self.assertEqual(hit0.atoms(), hit1.atoms())
+            self.assertEqual(hit0.evalue, hit1.evalue)
+
     @unittest.skipUnless(files, "importlib.resources not available")
     def test_query_template_subclass(self):
 

{pyjess-0.4.1.dist-info → pyjess-0.5.1.dist-info}/METADATA

@@ -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.dist-info → pyjess-0.5.1.dist-info}/RECORD

@@ -1,25 +1,25 @@
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 pyjess/CMakeLists.txt,sha256=Oa0pniEQx9jXyFCJGyrswn9ahWSSVuW1madyeP6StoI,35
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 pyjess/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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 pyjess/tests/test_atom.py,sha256=omNznNbRXMDt2j1plAUlfWPGCfmtkYpj2jysEX1zQuY,4631
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 pyjess/tests/test_molecule.py,sha256=RHBE0yL_j71nQOwXJ6t_PzkZi4BaFPY5Q0VwKWM6elk,5311
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 pyjess/tests/data/template_02.qry,sha256=IAI6eiDA-Qji7cFYW9S8e0XYNTlHb8XtJibP3PVGuHw,607
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 pyjess/tests/data/pdb1lnb.pdb,sha256=E9Jjy4qQ75O1UKIXcVyVJHE1XDNx1Rb7ENPVrehW6N8,270054
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-pyjess-0.4.1.dist-info/WHEEL,sha256=xVfALr-PjH4P3cUBvdv4kqYHNbGwV0Tghj5iW6pjP2M,154
-pyjess-0.4.1.dist-info/licenses/COPYING,sha256=W3hXwpT6UtiSFrO8yeDddZLU5tKIAX238e0N5slPQGA,1098
+pyjess/tests/data/1AMY.pdb,sha256=t2CaGLdOyPrhyeMpe1TbwZ8u7QmfxCIG1Pit8-vzvgo,319221
+pyjess/tests/data/1AMY+1.3.3.txt,sha256=41R3aa6jozzSSfzboxhyK5xfX8e47aiq2U4W7aCzRm8,103584
+pyjess/tests/data/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+pyjess/tests/data/1.3.3.tpl,sha256=mg3STlRiNESM0chuOQ8CodW3Ohnxbt1_nx4PId63iOI,988
+pyjess-0.5.1.dist-info/RECORD,,
+pyjess-0.5.1.dist-info/WHEEL,sha256=ss7GlFc9AR0tdo9xZyyrp3UiAYrcDGPUzPps17BmN40,154
+pyjess-0.5.1.dist-info/METADATA,sha256=OMnKlTvBTrR8tfxUFdUJXnJPezgo10GrHWTxap3eG7A,11248
+pyjess-0.5.1.dist-info/licenses/COPYING,sha256=gLCfHtBLTrghVX7GkpmZqoozWMNN46502m_OUiYy01Y,1103

{pyjess-0.4.1.dist-info → pyjess-0.5.1.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: scikit-build-core 0.10.7
+Generator: scikit-build-core 0.11.5
 Root-Is-Purelib: false
 Tag: cp39-cp39-manylinux_2_17_aarch64
 Tag: cp39-cp39-manylinux2014_aarch64

{pyjess-0.4.1.dist-info → pyjess-0.5.1.dist-info}/licenses/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