pyjess 0.5.0__cp37-cp37m-macosx_10_12_x86_64.whl → 0.5.1__cp37-cp37m-macosx_10_12_x86_64.whl

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
@@ -1417,7 +1429,7 @@ cdef class Hit:
 
         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/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-0.5.0.dist-info → pyjess-0.5.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyjess
-Version: 0.5.0
+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>
@@ -75,7 +75,7 @@ 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
@@ -183,7 +183,7 @@ 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-0.5.1.dist-info}/RECORD

@@ -1,19 +1,19 @@
-pyjess-0.5.0.dist-info/RECORD,,
-pyjess-0.5.0.dist-info/WHEEL,sha256=Wsi_lXX_sKLMtJHeb1WxDLuMVTM1ph0TYt9swrajcwI,115
-pyjess-0.5.0.dist-info/METADATA,sha256=qsP6LSYDn0V3i8bpx2KZw3w8pmH5zad6gIAnjfL053o,11121
-pyjess-0.5.0.dist-info/licenses/COPYING,sha256=gLCfHtBLTrghVX7GkpmZqoozWMNN46502m_OUiYy01Y,1103
-pyjess/_jess.cpython-37m-darwin.so,sha256=di9jgKmYK4BSrMVTL6K5l_syGgIS9_67q1VF_O19mOU,305112
+pyjess-0.5.1.dist-info/RECORD,,
+pyjess-0.5.1.dist-info/WHEEL,sha256=Wsi_lXX_sKLMtJHeb1WxDLuMVTM1ph0TYt9swrajcwI,115
+pyjess-0.5.1.dist-info/METADATA,sha256=PhFPRpjXmBV5buGbsOCI_POYVUNYzVksJ4LSYcBkZn0,11218
+pyjess-0.5.1.dist-info/licenses/COPYING,sha256=gLCfHtBLTrghVX7GkpmZqoozWMNN46502m_OUiYy01Y,1103
+pyjess/_jess.cpython-37m-darwin.so,sha256=b9-ZHzZLwKk1z4AbBIrT7C9SjYP4-VIOxoIO4veSq88,310080
 pyjess/_jess.pyi,sha256=OjbEcgr16eFEnAFbT_zp-jqjd4XME2V_gxuKZJBXVoc,6896
 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=kbAp0zWfxliPvzJ9c5G3oeRUKFcxtedo4oav-1uQotQ,50546
 pyjess/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 pyjess/tests/__init__.py,sha256=MdHWtr6A8S4TBWlkoj4olFK2FXAGc5uJdbWtgFrDLpk,528
 pyjess/tests/test_molecule.py,sha256=RHBE0yL_j71nQOwXJ6t_PzkZi4BaFPY5Q0VwKWM6elk,5311
 pyjess/tests/utils.py,sha256=dsaphex7qomJCvSHWnVy79iYDPGiL59xqGAtRoVAeWc,196
 pyjess/tests/test_atom.py,sha256=omNznNbRXMDt2j1plAUlfWPGCfmtkYpj2jysEX1zQuY,4631
-pyjess/tests/test_jess.py,sha256=mgHx6kDW5yzdvZiiybAVrd1J4k3Li3r-t4le6RFEE5o,9757
+pyjess/tests/test_jess.py,sha256=lTp_KzkbPF5J0nWewO4LJrKeKuXtSlzj114kPG-54zM,10642
 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