pyjess 0.5.0__cp38-cp38-macosx_11_0_arm64.whl → 0.5.2__cp38-cp38-macosx_11_0_arm64.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

@@ -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
@@ -1011,6 +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
@@ -1193,7 +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)
 
@@ -1204,6 +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
 
@@ -1215,11 +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:
@@ -1228,14 +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
@@ -1260,22 +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
@@ -1293,7 +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
@@ -1301,19 +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])
@@ -1357,7 +1406,6 @@ cdef class Hit:
 
         """
         assert self.template._tpl is not NULL
-        assert self._sup is not NULL
 
         cdef Atom atom
         cdef int  i
@@ -1366,21 +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)
 
@@ -1401,23 +1451,22 @@ 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
 
         mol = self._molecule.copy()
         for k in range(mol._mol.count):
-            atom = mol._mol.atom[i]
+            atom = mol._mol.atom[k]
             for i in range(3):
                 atom.x[i] = v[i]
                 for j in range(3):

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

@@ -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):
 
@@ -217,3 +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-0.5.0.dist-info → pyjess-0.5.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: pyjess
-Version: 0.5.0
+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>
@@ -76,7 +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
@@ -184,7 +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-0.5.0.dist-info → pyjess-0.5.2.dist-info}/RECORD

@@ -1,19 +1,20 @@
-pyjess-0.5.0.dist-info/RECORD,,
-pyjess-0.5.0.dist-info/WHEEL,sha256=e866hv7yNJ_T12xjD8b55JO_Epn_ySKlJm4M2IOihtU,112
-pyjess-0.5.0.dist-info/METADATA,sha256=sz5NWDSx0uyq_myc5StGdXX-lD3tNYVXz1K4efR5wZg,11151
-pyjess-0.5.0.dist-info/licenses/COPYING,sha256=gLCfHtBLTrghVX7GkpmZqoozWMNN46502m_OUiYy01Y,1103
-pyjess/_jess.cpython-38-darwin.so,sha256=mB47c-3-o9D9xzk6TlJztE-aoJxVQqbST63iostzTZM,315848
-pyjess/_jess.pyi,sha256=OjbEcgr16eFEnAFbT_zp-jqjd4XME2V_gxuKZJBXVoc,6896
+pyjess-0.5.2.dist-info/RECORD,,
+pyjess-0.5.2.dist-info/WHEEL,sha256=SvMeeWsTcOo2F3V-vhJiezSDbD8qncDjW76bNJE9h4A,112
+pyjess-0.5.2.dist-info/METADATA,sha256=tsCMCW4Qh7vkECoA8aybf9sb0I8QTcdifZ7P7SDm1oI,11248
+pyjess-0.5.2.dist-info/licenses/COPYING,sha256=gLCfHtBLTrghVX7GkpmZqoozWMNN46502m_OUiYy01Y,1103
+pyjess/_jess.cpython-38-darwin.so,sha256=5ZSM_SScDpVp9DP6tZLcCCtGMW91KNxKSr9acNyBN6M,350312
+pyjess/_jess.pyi,sha256=PhDo0l5LoYyLQPC2l-ZwyXKmyrC7y8T0i-yQYwcx--4,7015
 pyjess/CMakeLists.txt,sha256=Oa0pniEQx9jXyFCJGyrswn9ahWSSVuW1madyeP6StoI,35
 pyjess/__init__.py,sha256=h4XXLdS4FnyVa-MBs_k3eZMG1jWxeiOJnwfBaJA9gyQ,745
 pyjess/.gitignore,sha256=uQBOufp4v50qn0aZKv6zbSo00cjfB-v9KySog7rlmIU,19
-pyjess/_jess.pyx,sha256=tRPxQyvCBxvVbIjAb8iuCLtIpPAP0w_P_42Uy1wv8oc,49965
+pyjess/_jess.pyx,sha256=7fZoPrLnUBXmE9eCq1wiBBrbGIcuOxyn9Szbct-nBKw,51879
 pyjess/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-pyjess/tests/__init__.py,sha256=MdHWtr6A8S4TBWlkoj4olFK2FXAGc5uJdbWtgFrDLpk,528
+pyjess/tests/__init__.py,sha256=ka1wkfXesesZ3f6p5Dg55P4YYyS3R4gKRmhpQRtWVec,599
 pyjess/tests/test_molecule.py,sha256=RHBE0yL_j71nQOwXJ6t_PzkZi4BaFPY5Q0VwKWM6elk,5311
 pyjess/tests/utils.py,sha256=dsaphex7qomJCvSHWnVy79iYDPGiL59xqGAtRoVAeWc,196
+pyjess/tests/test_hit.py,sha256=qN0qcGWHdvM9PZzBLWwuORhAXaZLp9c-CuZgO3GAbr8,1212
 pyjess/tests/test_atom.py,sha256=omNznNbRXMDt2j1plAUlfWPGCfmtkYpj2jysEX1zQuY,4631
-pyjess/tests/test_jess.py,sha256=mgHx6kDW5yzdvZiiybAVrd1J4k3Li3r-t4le6RFEE5o,9757
+pyjess/tests/test_jess.py,sha256=tEu0K2B2-zLEMPFgQ1wk7lXhsZuRDyMzm58crT6G_ZY,11363
 pyjess/tests/test_template.py,sha256=XMLELYRB4j7xavziZ-ntq15PjhNHNfJJkctUq9BkvEI,4541
 pyjess/tests/test_template_atom.py,sha256=s9tJ_SAgvKeGwbVjaTWY-EtsUeQp3eu4NF5ja3oO_84,3405
 pyjess/tests/data/pdb1lnb.pdb,sha256=E9Jjy4qQ75O1UKIXcVyVJHE1XDNx1Rb7ENPVrehW6N8,270054

{pyjess-0.5.0.dist-info → pyjess-0.5.2.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: scikit-build-core 0.11.1
+Generator: scikit-build-core 0.11.6
 Root-Is-Purelib: false
 Tag: cp38-cp38-macosx_11_0_arm64