pyjess 0.4.0__cp39-cp39-macosx_11_0_arm64.whl → 0.4.1__cp39-cp39-macosx_11_0_arm64.whl

pyjess/_jess.pyi

@@ -134,9 +134,9 @@ class TemplateAtom:
     @property
     def z(self) -> float: ...
     @property
-    def atom_names(self) -> List[str]: ...
+    def atom_names(self) -> Tuple[str, ...]: ...
     @property
-    def residue_names(self) -> List[str]: ...
+    def residue_names(self) -> Tuple[str, ...]: ...
     @property
     def distance_weight(self) -> float: ...
     def copy(self: _SELF) -> _SELF: ...

pyjess/_jess.pyx

@@ -828,7 +828,11 @@ cdef class TemplateAtom:
 
     @property
     def atom_names(self):
-        """`list` of `str`: The different atom names for this atom.
+        """`tuple` of `str`: The different atom names for this atom.
+
+        .. versionchanged:: 0.4.1
+           Property now returns a `tuple` rather than a `list`.
+
         """
         assert self._atom is not NULL
 
@@ -837,11 +841,15 @@ cdef class TemplateAtom:
 
         for i in range(self._atom.nameCount):
             l.append(self._atom.name[i].replace(b'_', b'').decode())
-        return l
+        return tuple(l)
 
     @property
     def residue_names(self):
-        """`list` of `str`: The different residue names for this atom.
+        """`tuple` of `str`: The different residue names for this atom.
+
+        .. versionchanged:: 0.4.1
+           Property now returns a `tuple` rather than a `list`.
+           
         """
         assert self._atom is not NULL
 
@@ -850,7 +858,7 @@ cdef class TemplateAtom:
 
         for i in range(self._atom.resNameCount):
             l.append(self._atom.resName[i].replace(b'_', b'').decode())
-        return l
+        return tuple(l)
 
     @property
     def distance_weight(self):
@@ -1037,10 +1045,10 @@ cdef class Template:
         return all(x == y for x,y in zip(self, other_))
 
     def __hash__(self):
-        return hash(
+        return hash((
             self.id,
             *(hash(x) for x in self)
-        )
+        ))
 
     def __reduce__(self):
         return type(self), (list(self), self.id)
@@ -1351,7 +1359,7 @@ cdef class Jess:
     """
     cdef _Jess* _jess
     cdef dict   _indices
-    cdef list   _templates
+    cdef tuple  _templates
     cdef size_t length
 
     def __cinit__(self):
@@ -1379,10 +1387,10 @@ cdef class Jess:
         """
         cdef Template   template
         cdef _Template* tpl
+        cdef list       _templates = []
 
         self._jess = jess.jess.Jess_create()
         self._indices = {}
-        self._templates = []
 
         for template in templates:
             # NOTE: the Jess storage owns the data, so we make a copy of the
@@ -1390,9 +1398,11 @@ cdef class Jess:
             tpl = template._tpl.copy(template._tpl)
             jess.jess.Jess_addTemplate(self._jess, tpl)
             self._indices[<size_t> tpl] = self.length
-            self._templates.append(template)
+            _templates.append(template)
             self.length += 1
 
+        self._templates = tuple(_templates)
+
     def __copy__(self):
         return self.copy()
 
@@ -1407,7 +1417,7 @@ cdef class Jess:
         return self._templates == other_._templates
 
     def __hash__(self):
-        return hash(tuple(hash(t) for t in self._templates))
+        return hash((Jess, self._templates))
 
     def __len__(self):
         return self.length

pyjess/tests/test_atom.py

@@ -59,9 +59,18 @@ class TestAtom(unittest.TestCase):
     def test_hash(self):
         a1 = self._create_atom()
         a2 = self._create_atom()
-        self.assertEqual(a1, a2)
         self.assertEqual(hash(a1), hash(a2))
         self.assertIsNot(a1, a2)
+        a3 = self._create_atom(x=1.0)
+        self.assertNotEqual(hash(a1), hash(a3))
+
+    def test_eq(self):
+        a1 = self._create_atom()
+        a2 = self._create_atom()
+        self.assertEqual(a1, a2)
+        self.assertIsNot(a1, a2)
+        a3 = self._create_atom(x=1.0)
+        self.assertNotEqual(a1, a3)
 
     def test_repr_roundtrip(self):
         atom = self._create_atom()

pyjess/tests/test_jess.py

@@ -21,6 +21,13 @@ class TestJess(unittest.TestCase):
         hits = jess.query(mol, 2, 2, 4)
         self.assertRaises(StopIteration, next, hits)
 
+    def test_hash_empty(self):
+        j1 = Jess()
+        j2 = Jess()
+        self.assertEqual(j1, j2)
+        self.assertEqual(hash(j1), hash(j2))
+        self.assertIsNot(j1, j2)
+
     @unittest.skipUnless(files, "importlib.resources not available")
     def test_copy(self):
         with files(data).joinpath("template_01.qry").open() as f:
@@ -31,6 +38,32 @@ class TestJess(unittest.TestCase):
         copy = jess.copy()
         self.assertEqual(jess, copy)
 
+    @unittest.skipUnless(files, "importlib.resources not available")
+    def test_hash(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)
+        j1 = Jess([template1, template2])
+        j2 = Jess([template1, template2])
+        self.assertEqual(hash(j1), hash(j2))
+        self.assertIsNot(j1, j2)
+        j3 = Jess([template1])
+        self.assertNotEqual(hash(j1), hash(j3))
+
+    @unittest.skipUnless(files, "importlib.resources not available")
+    def test_eq(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)
+        j1 = Jess([template1, template2])
+        j2 = Jess([template1, template2])
+        self.assertEqual(j1, j2)
+        self.assertIsNot(j1, j2)
+        j3 = Jess([template1])
+        self.assertNotEqual(j1, j3)
+
     @unittest.skipUnless(files, "importlib.resources not available")
     def test_pickle_roundtrip(self):
         with files(data).joinpath("template_01.qry").open() as f:

pyjess/tests/test_molecule.py

@@ -96,7 +96,23 @@ class TestMolecule(unittest.TestCase):
         mol1 = Molecule(atoms)
         mol2 = Molecule(atoms)
         self.assertEqual(hash(mol1), hash(mol2))
+        self.assertIsNot(mol1, mol2)
+        mol3 = Molecule(atoms[:-1])
+        self.assertNotEqual(hash(mol1), hash(mol3))
+
+    def test_eq(self):
+        atoms = [
+            self._create_atom(serial=1, name='N'),
+            self._create_atom(serial=2, name='CA'),
+            self._create_atom(serial=3, name='C'),
+            self._create_atom(serial=4, name='O'),
+        ]
+        mol1 = Molecule(atoms)
+        mol2 = Molecule(atoms)
         self.assertEqual(mol1, mol2)
+        self.assertIsNot(mol1, mol2)
+        mol3 = Molecule(atoms[:-1])
+        self.assertNotEqual(mol1, mol3)
 
     def test_copy(self):
         atoms = [

pyjess/tests/test_template.py

@@ -30,9 +30,9 @@ class TestTemplate(unittest.TestCase):
         template = Template.loads(TEMPLATE)
         self.assertEqual(len(template), 11)
         self.assertEqual(template.dimension, 5)
-        self.assertEqual(template[0].residue_names, ["LYS"])
-        self.assertEqual(template[0].atom_names, ["NZ"])
-        self.assertEqual(template[1].atom_names, ["CG"])
+        self.assertEqual(template[0].residue_names, ("LYS",))
+        self.assertEqual(template[0].atom_names, ("NZ",))
+        self.assertEqual(template[1].atom_names, ("CG",))
         self.assertEqual(template[2].residue_number, 1132)
         self.assertEqual(template[-1].residue_number, 1150)
 
@@ -42,9 +42,9 @@ class TestTemplate(unittest.TestCase):
             f.write(TEMPLATE)
             f.flush()
             template = Template.load(f.name)
-        self.assertEqual(template[0].residue_names, ["LYS"])
-        self.assertEqual(template[0].atom_names, ["NZ"])
-        self.assertEqual(template[1].atom_names, ["CG"])
+        self.assertEqual(template[0].residue_names, ("LYS",))
+        self.assertEqual(template[0].atom_names, ("NZ",))
+        self.assertEqual(template[1].atom_names, ("CG",))
         self.assertEqual(template[2].residue_number, 1132)
         self.assertEqual(template[-1].residue_number, 1150)
 
@@ -55,9 +55,9 @@ class TestTemplate(unittest.TestCase):
             f.flush()
             f.seek(0)
             template = Template.load(f)
-        self.assertEqual(template[0].residue_names, ["LYS"])
-        self.assertEqual(template[0].atom_names, ["NZ"])
-        self.assertEqual(template[1].atom_names, ["CG"])
+        self.assertEqual(template[0].residue_names, ("LYS",))
+        self.assertEqual(template[0].atom_names, ("NZ",))
+        self.assertEqual(template[1].atom_names, ("CG",))
         self.assertEqual(template[2].residue_number, 1132)
         self.assertEqual(template[-1].residue_number, 1150)
 
@@ -87,6 +87,23 @@ class TestTemplate(unittest.TestCase):
         tpl2 = tpl1[1:4]
         self.assertEqual(len(tpl2), 3)
 
+    def test_hash(self):
+        tpl1 = Template.loads(TEMPLATE, id="tpl1")
+        tpl2 = Template.loads(TEMPLATE, id="tpl1")
+        self.assertEqual(tpl1, tpl2)
+        self.assertEqual(hash(tpl1), hash(tpl2))
+        self.assertIsNot(tpl1, tpl2)
+        tpl3 = Template.loads(TEMPLATE, id="tpl3")
+        self.assertNotEqual(hash(tpl1), hash(tpl3))
+
+    def test_eq(self):
+        tpl1 = Template.loads(TEMPLATE, id="tpl1")
+        tpl2 = Template.loads(TEMPLATE, id="tpl1")
+        self.assertEqual(tpl1, tpl2)
+        self.assertIsNot(tpl1, tpl2)
+        tpl3 = Template.loads(TEMPLATE, id="tpl3")
+        self.assertNotEqual(tpl1, tpl3)
+
     def test_copy(self):
         tpl1 = Template.loads(TEMPLATE, id="tpl1")
         tpl2 = tpl1.copy()

pyjess/tests/test_template_atom.py

@@ -10,8 +10,8 @@ class TestTemplateAtom(unittest.TestCase):
     def test_load(self):
         atom = TemplateAtom.loads("ATOM      1  NE  ARG A1136       3.953   0.597  -1.721 K")
         self.assertEqual(atom.match_mode, 1)
-        self.assertEqual(atom.atom_names, ["NE"])
-        self.assertEqual(atom.residue_names, ["ARG", "LYS"])
+        self.assertEqual(atom.atom_names, ("NE",))
+        self.assertEqual(atom.residue_names, ("ARG", "LYS",))
         self.assertEqual(atom.chain_id, "A")
         self.assertEqual(atom.residue_number, 1136)
         self.assertEqual(atom.x, 3.953)
@@ -32,6 +32,22 @@ class TestTemplateAtom(unittest.TestCase):
         default.update(kwargs)
         return TemplateAtom(**default)
 
+    def test_hash(self):
+        a1 = self._create_atom()
+        a2 = self._create_atom()
+        self.assertEqual(hash(a1), hash(a2))
+        self.assertIsNot(a1, a2)
+        a3 = self._create_atom(x=1.0)
+        self.assertNotEqual(hash(a1), hash(a3))
+
+    def test_eq(self):
+        a1 = self._create_atom()
+        a2 = self._create_atom()
+        self.assertEqual(a1, a2)
+        self.assertIsNot(a1, a2)
+        a3 = self._create_atom(x=1.0)
+        self.assertNotEqual(a1, a3)
+
     @unittest.skipUnless(sys.implementation.name == "cpython", "only available on CPython")
     def test_sizeof(self):
         atom = self._create_atom()

{pyjess-0.4.0.dist-info → pyjess-0.4.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyjess
-Version: 0.4.0
+Version: 0.4.1
 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>

{pyjess-0.4.0.dist-info → pyjess-0.4.1.dist-info}/RECORD

@@ -1,21 +1,21 @@
-pyjess-0.4.0.dist-info/RECORD,,
-pyjess-0.4.0.dist-info/WHEEL,sha256=Qmm8uWPQTspuPJ9tUBLJdmqmcf0_LWu4zzBSlc_SSWo,112
-pyjess-0.4.0.dist-info/METADATA,sha256=vaDoU5JzpxXjRTl-M43Stw7evHX75QHWTexO_TF7_DE,10785
-pyjess-0.4.0.dist-info/licenses/COPYING,sha256=W3hXwpT6UtiSFrO8yeDddZLU5tKIAX238e0N5slPQGA,1098
-pyjess/_jess.pyi,sha256=MlI0vWppDF11o9iZs635jn7gUpebG9DF_KNvhZrymuI,6887
+pyjess-0.4.1.dist-info/RECORD,,
+pyjess-0.4.1.dist-info/WHEEL,sha256=Qmm8uWPQTspuPJ9tUBLJdmqmcf0_LWu4zzBSlc_SSWo,112
+pyjess-0.4.1.dist-info/METADATA,sha256=iHTTiJz29i7uRreAEeB_ow4-DArxSGb5Nz2Y9N4RblQ,10785
+pyjess-0.4.1.dist-info/licenses/COPYING,sha256=W3hXwpT6UtiSFrO8yeDddZLU5tKIAX238e0N5slPQGA,1098
+pyjess/_jess.pyi,sha256=QIQSeQgNG-w0QZTuvacHjnv3IlEfV-3AOll9To3ZdM4,6899
 pyjess/CMakeLists.txt,sha256=Oa0pniEQx9jXyFCJGyrswn9ahWSSVuW1madyeP6StoI,35
-pyjess/_jess.cpython-39-darwin.so,sha256=OF443Eu3wnHjuxNGkqrEgw3T3CErmMvXnSssETEj7c8,315992
+pyjess/_jess.cpython-39-darwin.so,sha256=0wpZ92UkgfR5qvgndf8VpBI1DlpNBoLXYocxB6vzeME,315912
 pyjess/__init__.py,sha256=h4XXLdS4FnyVa-MBs_k3eZMG1jWxeiOJnwfBaJA9gyQ,745
 pyjess/.gitignore,sha256=uQBOufp4v50qn0aZKv6zbSo00cjfB-v9KySog7rlmIU,19
-pyjess/_jess.pyx,sha256=JFFC_PrVMAjaoLeLsyfkC9kFKdDCCNSwt7yvgQ6mnVo,47039
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 pyjess/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 pyjess/tests/__init__.py,sha256=MdHWtr6A8S4TBWlkoj4olFK2FXAGc5uJdbWtgFrDLpk,528
-pyjess/tests/test_molecule.py,sha256=qltjlOKvc2mvrW1DhA20AdKpu2DCEELx-cfbNmldvdo,4754
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 pyjess/tests/utils.py,sha256=dsaphex7qomJCvSHWnVy79iYDPGiL59xqGAtRoVAeWc,196
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-pyjess/tests/test_template.py,sha256=kUDJ-A9eNsL8aE51Jr1HLKmvKflTUuMGT2D3vKUxp-o,3887
-pyjess/tests/test_template_atom.py,sha256=fO6ChincKARc86J2zpDc0xrybSb4CQnyzoo2kJCAkoU,2917
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 pyjess/tests/data/pdb1lnb.pdb,sha256=E9Jjy4qQ75O1UKIXcVyVJHE1XDNx1Rb7ENPVrehW6N8,270054
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 pyjess/tests/data/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0