pyjess 0.5.1__cp312-cp312-win_amd64.whl → 0.5.2__cp312-cp312-win_amd64.whl

pyjess/_jess.pyi

@@ -183,6 +183,8 @@ class Query(Generic[_T], Iterator[Hit[_T]]):
     def __next__(self) -> Hit[_T]: ...
 
 class Hit(Generic[_T]):
+    def __getstate__(self) -> Dict[str, object]: ...
+    def __setstate__(self, state: Dict[str, object]) -> None: ...
     @property
     def rmsd(self) -> float: ...
     @property

pyjess/_jess.pyx

@@ -1205,7 +1205,7 @@ cdef class Query:
     cdef bint _rewind(self) noexcept nogil:
         self._partial = True
 
-    cdef int _copy_atoms(self, _Template* tpl, Hit hit) except -1 nogil:
+    cdef int _copy_atoms(self, const _Template* tpl, Hit hit) except -1 nogil:
         cdef _Atom** atoms = jess.jess.JessQuery_atoms(self._jq)
         cdef int     count = tpl.count(tpl)
 
@@ -1216,6 +1216,15 @@ cdef class Query:
             memcpy(&hit._atoms[i], atoms[i], sizeof(_Atom))
         return count
 
+    cdef int _copy_superposition(self, _Superposition* sup, Hit hit) noexcept nogil:
+        cdef const double* M = jess.super.Superposition_rotation(sup)
+        cdef const double* c = jess.super.Superposition_centroid(sup, 0)
+        cdef const double* v = jess.super.Superposition_centroid(sup, 1)
+        memcpy(hit._rotation, M, 9*sizeof(double))
+        memcpy(hit._centre[0], c, 3*sizeof(double))
+        memcpy(hit._centre[1], v, 3*sizeof(double))
+        return 0
+
     def __next__(self):
         assert self._jq is not NULL
 
@@ -1227,11 +1236,11 @@ cdef class Query:
         cdef Hit             hit     = Hit.__new__(Hit)
 
         # prepare the hit to be returned
-        hit._sup = NULL
-        hit._atoms = NULL
         hit.rmsd = INFINITY
+        hit._atoms = NULL
         hit._molecule = self.molecule
         hit_tpl = NULL
+        hit_found = False
 
         # search the next hit without the GIL to allow parallel queries.
         with nogil:
@@ -1240,14 +1249,13 @@ cdef class Query:
                 # was obtained with the current template and not with the
                 # previous one
                 tpl = jess.jess.JessQuery_template(self._jq)
-                if hit._sup != NULL and hit_tpl != tpl:
+                if hit_found and hit_tpl != tpl:
                     self._rewind()
                     break
 
                 # load superposition and compute RMSD for the current iteration
                 sup = jess.jess.JessQuery_superposition(self._jq)
                 rmsd = jess.super.Superposition_rmsd(sup)
-                keep_sup = False
 
                 # NB(@althonos): we don't need to compute the E-value to get the
                 #                best match by molecule/template pair since the
@@ -1272,22 +1280,20 @@ cdef class Query:
                                 stacklevel=2,
                             )
                     else:
-                        if hit._sup != NULL:
-                            jess.super.Superposition_free(hit._sup)
                         self._copy_atoms(tpl, hit)
-                        hit._sup = sup
+                        self._copy_superposition(sup, hit)
                         hit.rmsd = rmsd
                         hit_tpl = tpl
+                        hit_found = True
 
                 # free superposition items that are not used in a hit, and
                 # return hits immediately if we are not in best match mode
                 self._candidates += 1
-                if hit._sup != sup:
-                    jess.super.Superposition_free(sup)
-                if hit._sup != NULL and not self.best_match:
+                jess.super.Superposition_free(sup)
+                if hit_found and not self.best_match:
                     break
 
-        if hit._sup == NULL:
+        if not hit_found:
             raise StopIteration
 
         # get the template object for the hit
@@ -1305,7 +1311,8 @@ cdef class Hit:
         molecule (`~pyjess.Molecule`): The query molecule.
 
     """
-    cdef _Superposition* _sup
+    cdef double[9]       _rotation
+    cdef double[2][3]    _centre
     cdef _Atom*          _atoms
 
     cdef readonly double   rmsd
@@ -1313,19 +1320,49 @@ cdef class Hit:
     cdef          Molecule _molecule
 
     def __dealloc__(self):
-        jess.super.Superposition_free(self._sup)
         free(self._atoms)
 
+    def __getstate__(self):
+        return {
+            "rotation": list(self._rotation),
+            "centre": list(self._centre),
+            "atoms": self.atoms(transform=False),
+            "rmsd": self.rmsd,
+            "template": self.template,
+            "molecule": self.molecule(transform=False),
+        }
+
+    def __setstate__(self, state):
+        cdef size_t i
+        cdef size_t count
+        cdef Atom   atom
+
+        self.rmsd = state["rmsd"]
+        self.template = state["template"]
+        self._molecule = state["molecule"]
+        self._rotation = state["rotation"]
+        self._centre = state["centre"]
+
+        # check number of atoms is consistent
+        count = len(self.template)
+        if len(state["atoms"]) != count:
+            raise ValueError(f"unexpected number of atoms: {len(state['atoms'])!r} (expected {count!r})")
+        # allocate or reallocate memory for atoms
+        self._atoms = <_Atom*> realloc(self._atoms, count * sizeof(_Atom))
+        if self._atoms is NULL:
+            raise MemoryError("Failed to allocate hit atoms")
+        # copy atom data
+        for i, atom in enumerate(state["atoms"]):
+            memcpy(&self._atoms[i], atom._atom, sizeof(_Atom))
+
     @property
     def determinant(self):
         """`float`: The determinant of the rotation matrix.
         """
-        assert self._sup is not NULL
-        cdef const double* p
+        cdef const double* p   = self._rotation
         cdef double        det = 0.0
 
         with nogil:
-            p = jess.super.Superposition_rotation(self._sup)
             det += p[0] * (p[4] * p[8] - p[5] * p[7])
             det -= p[1] * (p[3] * p[8] - p[5] * p[6])
             det += p[2] * (p[3] * p[7] - p[4] * p[6])
@@ -1369,7 +1406,6 @@ cdef class Hit:
 
         """
         assert self.template._tpl is not NULL
-        assert self._sup is not NULL
 
         cdef Atom atom
         cdef int  i
@@ -1378,21 +1414,23 @@ cdef class Hit:
         cdef int  count = self.template._tpl.count(self.template._tpl)
         cdef list atoms = []
 
-        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)
+        cdef const double* M = self._rotation
+        cdef const double* c = self._centre[0]
+        cdef const double* v = self._centre[1]
 
         for k in range(count):
-
             atom = Atom.__new__(Atom)
-            atom._atom = <_Atom*> malloc(sizeof(_Atom))
-            memcpy(atom._atom, &self._atoms[k], sizeof(_Atom))
-
             if transform:
+                atom._atom = <_Atom*> malloc(sizeof(_Atom))
+                memcpy(atom._atom, &self._atoms[k], sizeof(_Atom))
                 for i in range(3):
                     atom._atom.x[i] = v[i]
                     for j in range(3):
                         atom._atom.x[i] += M[3*i + j] * (self._atoms[k].x[j] - c[j])
+            else:
+                atom.owned = True
+                atom.owner = self
+                atom._atom = &self._atoms[k]
 
             atoms.append(atom)
 
@@ -1413,16 +1451,15 @@ cdef class Hit:
 
         """
         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)
+        cdef const double* M = self._rotation
+        cdef const double* c = self._centre[0]
+        cdef const double* v = self._centre[1]
 
         if not transform:
             return self._molecule

pyjess/tests/__init__.py

@@ -1,5 +1,6 @@
 from . import (
     test_atom,
+    test_hit,
     test_jess,
     test_molecule,
     test_template_atom,
@@ -8,6 +9,7 @@ from . import (
 
 def load_tests(loader, suite, pattern):
     suite.addTests(loader.loadTestsFromModule(test_atom))
+    suite.addTests(loader.loadTestsFromModule(test_hit))
     suite.addTests(loader.loadTestsFromModule(test_jess))
     suite.addTests(loader.loadTestsFromModule(test_molecule))
     suite.addTests(loader.loadTestsFromModule(test_template_atom))

pyjess/tests/test_hit.py

@@ -0,0 +1,33 @@
+import math
+import unittest
+import sys
+import pickle
+
+from .._jess import Template, Molecule, Jess
+from .utils import files
+from . import data
+
+
+class TestHit(unittest.TestCase):
+
+    @unittest.skipUnless(files, "importlib.resources not available")
+    @classmethod
+    def setUpClass(cls):
+        with files(data).joinpath("template_01.qry").open() as f:
+            template = Template.load(f)
+            jess = Jess([template])
+        with files(data).joinpath("pdb1lnb.pdb").open() as f:
+            molecule = Molecule.load(f)
+
+        cls.hit = next(jess.query(molecule, 1, 2, 2))
+        
+    def test_pickle(self):
+        hit = pickle.loads(pickle.dumps(self.hit))
+        self.assertIsNot(self.hit, hit)
+        self.assertEqual(self.hit.rmsd, hit.rmsd)
+        self.assertEqual(self.hit.determinant, hit.determinant)
+        self.assertEqual(self.hit.evalue, hit.evalue)
+        self.assertEqual(self.hit.template, hit.template)
+        self.assertListEqual(self.hit.atoms(transform=True), hit.atoms(transform=True))
+        self.assertListEqual(self.hit.atoms(transform=False), hit.atoms(transform=False))
+        self.assertEqual(self.hit.molecule(transform=False), hit.molecule(transform=False))

pyjess/tests/test_jess.py

@@ -240,3 +240,14 @@ class TestJess(unittest.TestCase):
                 self.assertAlmostEqual(atom.occupancy, float(atom_line[55:61]), places=3)
                 self.assertAlmostEqual(atom.temperature_factor, float(atom_line[61:67]), places=3)
 
+            atoms = hit.atoms(transform=False)
+            self.assertEqual(len(atoms), len(atom_lines))
+            for atom, atom_line in zip(atoms, atom_lines):
+                self.assertEqual(atom.serial, int(atom_line[7:12]))
+                self.assertEqual(atom.name, atom_line[13:17].strip())
+                self.assertEqual(atom.residue_name, atom_line[17:21].strip())
+                self.assertEqual(atom.chain_id, atom_line[21:23].strip())
+                self.assertEqual(atom.residue_number, int(atom_line[23:27]))
+                self.assertAlmostEqual(atom.occupancy, float(atom_line[55:61]), places=3)
+                self.assertAlmostEqual(atom.temperature_factor, float(atom_line[61:67]), places=3)
+

{pyjess-0.5.1.dist-info → pyjess-0.5.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: pyjess
-Version: 0.5.1
+Version: 0.5.2
 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>

{pyjess-0.5.1.dist-info → pyjess-0.5.2.dist-info}/RECORD

@@ -1,11 +1,11 @@
 pyjess/.gitignore,sha256=u14v4OOy8U50Kp9SUKU8DupCG-mQIuel47gdbNDmAwg,21
 pyjess/__init__.py,sha256=Xe9GBQUBm9ik-ty5tcE3UQ9Ip1p-C_IGvTPuGULolng,766
-pyjess/_jess.cp312-win_amd64.pyd,sha256=OA7iRmEwNCLhTfaQoli5hmBBSJw6X6y0nb-X9mgXTPo,302080
-pyjess/_jess.pyi,sha256=oWlqpqnhOKFcq2UCpGJrUJaZZF1ZlLodKxINwoR3vrw,7118
-pyjess/_jess.pyx,sha256=hHDaW9FgJXln5uFQWadGZH5aQ1iAtzWvscIj-8MawEo,52130
+pyjess/_jess.cp312-win_amd64.pyd,sha256=Ho-TAV-b8x4Pw5doINzpgGicogT8Qec1XbkHTMuKc_0,317440
+pyjess/_jess.pyi,sha256=1U7KeCDydiOT0vGts0sidGz_gI2PycD1sBiUmcafd7c,7239
+pyjess/_jess.pyx,sha256=tyAyYZaYYm8-dAMDMrH6WrpV5hM8hnn9DYHh4idoAOA,53500
 pyjess/CMakeLists.txt,sha256=H9eXbrFcGF2OLP8muQctb4cOb27Qp2uZj5KRjoDAROg,36
 pyjess/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-pyjess/tests/__init__.py,sha256=h83kBzYKH_i1InkM8mOA23zE3PBaB9lrNDCuhC8LOl4,544
+pyjess/tests/__init__.py,sha256=J7rYASCuQsCu5gktf5XqjNxJoBkBqxbREAiaSOta5xE,617
 pyjess/tests/data/1.3.3.tpl,sha256=gleyiSSHAVJbRJaK8Nlh9setsj6EI38Sr1XU5OEduQE,1011
 pyjess/tests/data/1AMY+1.3.3.txt,sha256=Wyq9Eh9QVaOPH_jsZ6iF9WYhFdTGESqOzjfX14-0gAo,105456
 pyjess/tests/data/1AMY.pdb,sha256=fIbowuYS46hQh82xBtVaIPC50o7U08CnHNcnq4nM944,323162
@@ -14,12 +14,13 @@ pyjess/tests/data/pdb1lnb.pdb,sha256=F8A6OdRly5c-pxsDw1LjTFINI75r1HaKaYB_eXv1QuM
 pyjess/tests/data/template_01.qry,sha256=izCIhUUTEk-IvQowhSVLiJaCAhpPbyvrfyoR4Q6-Pm0,616
 pyjess/tests/data/template_02.qry,sha256=5IYRTqsvO_roB2INLwfFDEaWJW9VRcXdbK4oe8VKMxE,618
 pyjess/tests/test_atom.py,sha256=clLN9IVuivadztGtagDhdPBDGoMkUgs41lEWuTCCmFA,4741
-pyjess/tests/test_jess.py,sha256=EEiPW-CtdFa3RLoI1TTSloBhtmj3kvhy987GUAexMJM,10884
+pyjess/tests/test_hit.py,sha256=3p7MkvZL84e-tSbVlMSXHbO1yCZkaLIMD2e09occw1A,1244
+pyjess/tests/test_jess.py,sha256=Hp12b3xkRX0U8RFcejwDPFTEX8JzpOQTF6_zMXYAWDM,11616
 pyjess/tests/test_molecule.py,sha256=9k6uiTeOWc5NiO7epyxY9lm_GgksPb7-o-ZcNFNxutw,5452
 pyjess/tests/test_template.py,sha256=AIN-ba5-YTnGdT9SGPU4q45AZ03QnPE769WyItSpoPs,4657
 pyjess/tests/test_template_atom.py,sha256=oK8cfKe4_k3Pm1PqoTTxTzAoeUVLiCFsg6QmiTQ-RCQ,3496
 pyjess/tests/utils.py,sha256=Z7rUPC-D8dZlRfHAnLaXHUg6M10D3zFvNiwDvvHA3xc,202
-pyjess-0.5.1.dist-info/METADATA,sha256=OMnKlTvBTrR8tfxUFdUJXnJPezgo10GrHWTxap3eG7A,11248
-pyjess-0.5.1.dist-info/WHEEL,sha256=TcMXEVBP2SQds4YZwJ6flDTTNRzCE5owNAganfIqM0g,106
-pyjess-0.5.1.dist-info/licenses/COPYING,sha256=Iyx2bRDPnLgoEzW2KVanb61cjhW8lnhJNU-mjS-KhIY,1124
-pyjess-0.5.1.dist-info/RECORD,,
+pyjess-0.5.2.dist-info/METADATA,sha256=tsCMCW4Qh7vkECoA8aybf9sb0I8QTcdifZ7P7SDm1oI,11248
+pyjess-0.5.2.dist-info/WHEEL,sha256=chqeLhPBtPdrOoreR34YMcofSk3yWDQhkrsDJ2n48LU,106
+pyjess-0.5.2.dist-info/licenses/COPYING,sha256=Iyx2bRDPnLgoEzW2KVanb61cjhW8lnhJNU-mjS-KhIY,1124
+pyjess-0.5.2.dist-info/RECORD,,

{pyjess-0.5.1.dist-info → pyjess-0.5.2.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: scikit-build-core 0.11.5
+Generator: scikit-build-core 0.11.6
 Root-Is-Purelib: false
 Tag: cp312-cp312-win_amd64