pyjess 0.4.1__cp37-cp37m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl → 0.5.0__cp37-cp37m-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

@@ -461,7 +461,7 @@ 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 +598,16 @@ 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 +854,7 @@ cdef class TemplateAtom:
 
         .. versionchanged:: 0.4.1
            Property now returns a `tuple` rather than a `list`.
-           
+
         """
         assert self._atom is not NULL
 
@@ -871,11 +876,11 @@ 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 +899,42 @@ 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:
@@ -1181,7 +1218,7 @@ 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 +1298,7 @@ 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 +1329,7 @@ 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 +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 = exp(self.template._tpl.logE(self.template._tpl, self.rmsd, n))
         return e
 
@@ -1349,6 +1386,45 @@ 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[i]
+            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-0.4.1.dist-info → pyjess-0.5.0.dist-info}/METADATA

@@ -1,12 +1,12 @@
 Metadata-Version: 2.1
 Name: pyjess
-Version: 0.4.1
+Version: 0.5.0
 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>
 License: 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
@@ -51,6 +51,7 @@ Project-URL: Changelog, https://github.com/althonos/pyjess/blob/master/CHANGELOG
 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: Piwheels, https://piwheels.org/project/pyjess/
 Requires-Python: >=3.7
 Provides-Extra: test
 Requires-Dist: importlib-resources; python_version < "3.9" and extra == "test"
@@ -83,8 +84,8 @@ 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 +106,44 @@ 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 +173,7 @@ 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 -->

{pyjess-0.4.1.dist-info → pyjess-0.5.0.dist-info}/RECORD

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 pyjess/.gitignore,sha256=uQBOufp4v50qn0aZKv6zbSo00cjfB-v9KySog7rlmIU,19
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 pyjess/__init__.py,sha256=h4XXLdS4FnyVa-MBs_k3eZMG1jWxeiOJnwfBaJA9gyQ,745
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 pyjess/CMakeLists.txt,sha256=Oa0pniEQx9jXyFCJGyrswn9ahWSSVuW1madyeP6StoI,35
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 pyjess/tests/utils.py,sha256=dsaphex7qomJCvSHWnVy79iYDPGiL59xqGAtRoVAeWc,196
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 pyjess/tests/__init__.py,sha256=MdHWtr6A8S4TBWlkoj4olFK2FXAGc5uJdbWtgFrDLpk,528
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 pyjess/tests/test_jess.py,sha256=mgHx6kDW5yzdvZiiybAVrd1J4k3Li3r-t4le6RFEE5o,9757
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 pyjess/tests/test_template_atom.py,sha256=s9tJ_SAgvKeGwbVjaTWY-EtsUeQp3eu4NF5ja3oO_84,3405
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 pyjess/tests/data/1AMY.pdb,sha256=t2CaGLdOyPrhyeMpe1TbwZ8u7QmfxCIG1Pit8-vzvgo,319221
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{pyjess-0.4.1.dist-info → pyjess-0.5.0.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