pyjess 0.6.0__tar.gz → 0.7.0a1__tar.gz

{pyjess-0.6.0 → pyjess-0.7.0a1}/.github/workflows/package.yml

@@ -15,6 +15,7 @@ jobs:
       with:
         submodules: true
     - name: Build manylinux wheels
+      if: "!contains(github.ref, 'rc') && !contains(github.ref, 'alpha')"
       uses: pypa/cibuildwheel@v2.21.3
       env:
         CIBW_ARCHS: aarch64
@@ -35,6 +36,7 @@ jobs:
       with:
         submodules: true
     - name: Build manylinux wheels
+      if: "!contains(github.ref, 'rc') && !contains(github.ref, 'alpha')"
       uses: pypa/cibuildwheel@v2.21.3
       env:
         CIBW_ARCHS: x86_64
@@ -55,6 +57,7 @@ jobs:
       with:
         submodules: true
     - name: Build manylinux wheels
+      if: "!contains(github.ref, 'rc') && !contains(github.ref, 'alpha')"
       uses: pypa/cibuildwheel@v2.21.3
       env:
         CIBW_ARCHS: x86_64
@@ -75,6 +78,7 @@ jobs:
       with:
         submodules: true
     - name: Build manylinux wheels
+      if: "!contains(github.ref, 'rc') && !contains(github.ref, 'alpha')"
       uses: pypa/cibuildwheel@v2.21.3
       env:
         CIBW_ARCHS: arm64
@@ -99,6 +103,7 @@ jobs:
       with:
         arch: amd64
     - name: Build manylinux wheels
+      if: "!contains(github.ref, 'rc') && !contains(github.ref, 'alpha')"
       uses: pypa/cibuildwheel@v2.21.3
       env:
         CIBW_ARCHS: AMD64
@@ -187,7 +192,7 @@ jobs:
     environment: GitHub Releases
     runs-on: ubuntu-latest
     permissions: write-all
-    if: "!contains(github.ref, 'rc')"
+    if: "!contains(github.ref, 'rc') && !contains(github.ref, 'alpha')"
     name: Release
     needs: upload
     steps:
@@ -201,7 +206,7 @@ jobs:
   aur:
     environment: Arch User Repository
     runs-on: ubuntu-latest
-    if: "!contains(github.ref, 'rc')"
+    if: "!contains(github.ref, 'rc') && !contains(github.ref, 'alpha')"
     name: Update AUR package
     needs:
     - sdist

{pyjess-0.6.0 → pyjess-0.7.0a1}/CHANGELOG.md

@@ -6,7 +6,17 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 
 ## [Unreleased]
-[Unreleased]: https://github.com/althonos/pyjess/compare/v0.6.0...HEAD
+[Unreleased]: https://github.com/althonos/pyjess/compare/v0.7.0-alpha.1...HEAD
+
+
+## [v0.7.0-alpha.1] - 2025-09-02
+[v0.7.0-alpha.1]: https://github.com/althonos/pyjess/compare/v0.6.0...v0.7.0-alpha.1
+
+### Fixed
+- **breaking**: Incorrect handling of `max_candidates` in `Jess.query`, causing PyJess to erroneously ignore some templates.
+
+### Changed
+- **breaking**: Set the `max_candidates` default value to `None` in `Jess.query`, disabling max candidates filtering by default.
 
 
 ## [v0.6.0] - 2025-09-01

{pyjess-0.6.0 → pyjess-0.7.0a1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: pyjess
-Version: 0.6.0
+Version: 0.7.0a1
 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-0.6.0 → pyjess-0.7.0a1}/include/jess/jess.pxd

@@ -22,6 +22,7 @@ cdef extern from "Jess.h" nogil:
 
     void JessQuery_free(JessQuery*)
     int JessQuery_next(JessQuery*, int)
+    int JessQuery_nextTemplate(JessQuery*)
     Template* JessQuery_template(JessQuery*)
     const Molecule* JessQuery_molecule(JessQuery*)
     Atom** JessQuery_atoms(JessQuery*)

{pyjess-0.6.0 → pyjess-0.7.0a1}/patches/Jess.c.patch

@@ -1,5 +1,5 @@
 diff --git a/src/Jess.c b/src/Jess.c
-index e81bda0..5601c07 100644
+index e81bda0..44fa672 100644
 --- a/src/Jess.c
 +++ b/src/Jess.c
 @@ -4,15 +4,18 @@
@@ -96,7 +96,7 @@ index e81bda0..5601c07 100644
  
  	return Q;
  }
-@@ -129,74 +151,80 @@ void JessQuery_free(JessQuery *Q)
+@@ -129,74 +151,90 @@ void JessQuery_free(JessQuery *Q)
  	{
  		Scanner_free(Q->scanner);
  		Superposition_free(Q->super);
@@ -150,6 +150,16 @@ index e81bda0..5601c07 100644
  
 -	return Q->super;
 +	return super;
++}
++
++int JessQuery_nextTemplate(JessQuery *Q)
++{
++	Q->scan=false;
++	Superposition_free(Q->super);
++	Q->super=NULL;
++	Q->atoms=NULL;
++	Q->node=Q->node->next;
++	return (Q->node) ? 1 : 0;
  }
  
  int JessQuery_next(JessQuery *Q, int ignore_chain)
@@ -191,7 +201,7 @@ index e81bda0..5601c07 100644
  		}
  
  		if((A=Scanner_next(Q->scanner, ignore_chain)))
-@@ -207,8 +235,9 @@ int JessQuery_next(JessQuery *Q, int ignore_chain)
+@@ -207,8 +245,9 @@ int JessQuery_next(JessQuery *Q, int ignore_chain)
  			return 1;
  		}
  

{pyjess-0.6.0 → pyjess-0.7.0a1}/patches/Jess.h.patch

@@ -1,5 +1,5 @@
 diff --git a/src/Jess.h b/src/Jess.h
-index c90abe6..f5e3dd4 100644
+index c90abe6..704b5e8 100644
 --- a/src/Jess.h
 +++ b/src/Jess.h
 @@ -8,6 +8,8 @@
@@ -27,7 +27,7 @@ index c90abe6..f5e3dd4 100644
  
  // ==================================================================
  // Methods of type JessQuery
-@@ -50,10 +52,10 @@ extern JessQuery *Jess_query(Jess*,Molecule*,double,double);
+@@ -50,10 +52,11 @@ extern JessQuery *Jess_query(Jess*,Molecule*,double,double);
  
  extern void JessQuery_free(JessQuery*);
  extern int JessQuery_next(JessQuery*, int);
@@ -35,6 +35,7 @@ index c90abe6..f5e3dd4 100644
 -extern const Molecule *JessQuery_molecule(JessQuery*);
 -extern Atom **JessQuery_atoms(JessQuery*);
 -extern Superposition *JessQuery_superposition(JessQuery*);
++extern int JessQuery_nextTemplate(JessQuery*);
 +extern Template *JessQuery_template(const JessQuery*);
 +extern const Molecule *JessQuery_molecule(const JessQuery*);
 +extern Atom **JessQuery_atoms(const JessQuery*);

{pyjess-0.6.0 → pyjess-0.7.0a1}/patches/Main.c.patch

@@ -1,8 +1,16 @@
 diff --git a/src/Main.c b/src/Main.c
-index dff22b9..9b09cc5 100644
+index dff22b9..476cb01 100644
 --- a/src/Main.c
 +++ b/src/Main.c
-@@ -116,7 +116,7 @@ static void output(
+@@ -14,6 +14,7 @@
+ #include <ctype.h>
+ #include <errno.h>
+ #include <stdarg.h>
++#include <stdint.h>
+ 
+ // ==================================================================
+ // Global constants
+@@ -116,11 +117,11 @@ static void output(
  		A->charge
  		);
  }
@@ -11,25 +19,46 @@ index dff22b9..9b09cc5 100644
  {
  	Molecule *M;
  	Superposition *sup;
-@@ -145,7 +145,7 @@ static void search(const char *filename,Jess *J,double tRmsd,double tDistance,do
+-	Template *T;
++	Template *T, *Tprev;
+ 	Atom **A;
+ 	FILE *file;
+ 	JessQuery *Q;
+@@ -145,11 +146,21 @@ static void search(const char *filename,Jess *J,double tRmsd,double tDistance,do
  		return;
  	}
  
 -	Q=Jess_query(J,M,tDistance,max_total_threshold);
 +	Q=Jess_query(J,M,tDistance,max_total_threshold,fastScan);
++	T=JessQuery_template(Q);
  
- 	while(JessQuery_next(Q, ignore_chain) && killswitch<1000)
+-	while(JessQuery_next(Q, ignore_chain) && killswitch<1000)
++	while(JessQuery_next(Q, ignore_chain))
  	{
-@@ -193,6 +193,8 @@ static void search(const char *filename,Jess *J,double tRmsd,double tDistance,do
++		Tprev=T;
+ 		T=JessQuery_template(Q);
++		// printf("current template: %s\n", T->name(T));
++
++		killswitch = (T!=Tprev) ? 0 : killswitch + 1;
++		if(killswitch == 1000)
++		{
++			JessQuery_nextTemplate(Q);
++			continue;
++		}
+ 
+ 		count=T->count(T);
+ 		sup = JessQuery_superposition(Q);
+@@ -193,7 +204,8 @@ static void search(const char *filename,Jess *J,double tRmsd,double tDistance,do
  
  			printf("ENDMDL\n\n");
  		}
+-		killswitch+=1;
 +
 +		Superposition_free(sup);
- 		killswitch+=1;
  	}
  
-@@ -339,6 +341,7 @@ int main(int argc, char **argv)
+ 	JessQuery_free(Q);
+@@ -339,6 +351,7 @@ int main(int argc, char **argv)
  	int ignore_chain=0;
  	int write_filename=0;
  	int ignore_endmdl=0;
@@ -37,7 +66,7 @@ index dff22b9..9b09cc5 100644
  
  	if(argc<7 || argc>8) help();
  
-@@ -354,6 +357,7 @@ int main(int argc, char **argv)
+@@ -354,6 +367,7 @@ int main(int argc, char **argv)
  			else if(*s=='i') ignore_chain=1;
  			else if(*s=='q') write_filename=1;
  			else if(*s=='e') ignore_endmdl=1;
@@ -45,7 +74,7 @@ index dff22b9..9b09cc5 100644
  			else help();
  		}
  	}
-@@ -388,10 +392,11 @@ int main(int argc, char **argv)
+@@ -388,10 +402,11 @@ int main(int argc, char **argv)
  		if(strlen(s)==0) continue;
  
  		if(feedbackQ) fprintf(stderr,"%s\n",s);

{pyjess-0.6.0 → pyjess-0.7.0a1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "scikit_build_core.build"
 
 [project]
 name = "pyjess"
-version = "0.6.0"
+version = "0.7.0-alpha.1"
 description = "Cython bindings and Python interface to JESS, a 3D template matching software."
 readme = "README.md"
 requires-python = ">=3.7"

{pyjess-0.6.0 → pyjess-0.7.0a1}/src/pyjess/_jess.pyi

@@ -176,7 +176,7 @@ class Query(Generic[_T], Iterator[Hit[_T]]):
     @property
     def rmsd_threshold(self) -> float: ...
     @property
-    def max_candidates(self) -> int: ...
+    def max_candidates(self) -> Optional[int]: ...
     @property
     def best_match(self) -> bool: ...
     def __iter__(self) -> Query[_T]: ...
@@ -218,7 +218,7 @@ class Jess(Generic[_T], Sequence[_T]):
         distance_cutoff: float,
         max_dynamic_distance: float,
         *,
-        max_candidates: int = 1000,
+        max_candidates: Optional[int] = None,
         ignore_chain: bool = False,
         best_match: bool = False,
         reorder: bool = True,

{pyjess-0.6.0 → pyjess-0.7.0a1}/src/pyjess/_jess.pyx

@@ -22,6 +22,7 @@ from cpython.unicode cimport PyUnicode_FromStringAndSize
 
 from libc.math cimport isnan, exp, INFINITY, NAN
 from libc.stdio cimport FILE, fclose, fdopen, printf
+from libc.stdint cimport uintptr_t
 from libc.stdlib cimport calloc, realloc, free, malloc
 from libc.string cimport memcpy, memset, strncpy, strdup
 
@@ -1050,7 +1051,14 @@ cdef class Template:
                 self._tess.distance[j][i] = dist
 
         # compute dimension
-        residues = { self._tess.atom[i].resSeq for i in range(count) }
+        residues = { 
+            (
+                self._tess.atom[i].resSeq , 
+                self._tess.atom[i].chainID1,
+                self._tess.atom[i].chainID2,
+            )
+            for i in range(count) 
+        }
         self._tess.dim = len(residues)
 
     def __copy__(self):
@@ -1168,8 +1176,6 @@ cdef class Query:
             the templates.
         rmsd_threshold (`float`): The RMSD threshold for reporting
             results.
-        max_candidates (`int`): The maximum number of candidate hits
-            to report.
         ignore_chain (`bool`): Whether to check or ignore the chain of
             the atoms to match.
         best_match (`bool`): Whether the query will return only the
@@ -1179,18 +1185,20 @@ cdef class Query:
     cdef _JessQuery* _jq
     cdef bint        _partial
     cdef int         _candidates
+    cdef uintptr_t   _prev_tpl
+    cdef int         _max_candidates
 
     cdef readonly Jess     jess
     cdef readonly Molecule molecule
     cdef readonly bint     ignore_chain
     cdef readonly bint     best_match
     cdef readonly double   rmsd_threshold
-    cdef readonly int      max_candidates
 
     def __cinit__(self):
         self._jq = NULL
         self._candidates = 0
         self._partial = False
+        self._prev_tpl = 0
 
     def __dealloc__(self):
         jess.jess.JessQuery_free(self._jq)
@@ -1198,6 +1206,21 @@ cdef class Query:
     def __iter__(self):
         return self
 
+    @property
+    def max_candidates(self):
+        """`int`: The maximum number of candidate hits to report *by template*.
+        """
+        return None if self._max_candidates == -1 else self._max_candidates
+
+    @max_candidates.setter
+    def max_candidates(self, max_candidates):
+        if max_candidates is None:
+            self._max_candidates = -1
+        elif max_candidates >= 0:
+            self._max_candidates = max_candidates
+        else:
+            raise ValueError(f"invalid value for `max_candidates` argument: {max_candidates!r}")
+
     cdef bint _advance(self) noexcept nogil:
         if self._partial:
             self._partial = False
@@ -1246,15 +1269,28 @@ cdef class Query:
 
         # search the next hit without the GIL to allow parallel queries.
         with nogil:
-            while self._advance() and self._candidates < self.max_candidates:
+            while self._advance():
                 # load current iteration template, and check that the hit
                 # was obtained with the current template and not with the
                 # previous one
+                self._prev_tpl = <uintptr_t> tpl
                 tpl = jess.jess.JessQuery_template(self._jq)
                 if hit_found and hit_tpl != tpl:
                     self._rewind()
                     break
 
+                # check if we already made it to the next template,
+                # or if we need to short-circuit the iteration and
+                # force the query to move to the next template as
+                # we found too many candidates already.
+                if <uintptr_t> tpl != self._prev_tpl:
+                    self._candidates = 0 
+                else:
+                    self._candidates += 1
+                if self._candidates == self._max_candidates:
+                    jess.jess.JessQuery_nextTemplate(self._jq)
+                    continue
+
                 # load superposition and compute RMSD for the current iteration
                 sup = jess.jess.JessQuery_superposition(self._jq)
                 rmsd = jess.super.Superposition_rmsd(sup)
@@ -1288,9 +1324,9 @@ cdef class Query:
                         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
+                # free superposition items (as relevant data was copied in
+                # the Hit if needed) and return hits immediately if we are
+                # not in best match mode
                 jess.super.Superposition_free(sup)
                 if hit_found and not self.best_match:
                     break
@@ -1581,7 +1617,7 @@ cdef class Jess:
         double distance_cutoff,
         double max_dynamic_distance,
         *,
-        int max_candidates = 1000,
+        object max_candidates = None,
         bint ignore_chain = False,
         bint best_match = False,
         bint reorder = True,
@@ -1599,6 +1635,8 @@ cdef class Jess:
                 dynamic distance after adding the global distance cutoff
                 and the individual atom distance cutoff defined for each
                 atom of the template.
+            max_candidates (`int` or `None`): The maximum number of candidate 
+                hits to report *by template*.
             ignore_chain (`bool`): Whether to check or ignore the chain of
                 the atoms to match.
             best_match (`bool`): Pass `True` to return only the best match
@@ -1607,7 +1645,7 @@ cdef class Jess:
                 to accelerate matching in the scanner algorithm. Pass 
                 `False` to reverse to the original, slower algorithm
                 which matches atoms in the same order as they appear in
-                the template, at the cost
+                the template, at the cost of longer run times.
 
         Returns:
             `~pyjess.Query`: An iterator over the query hits.
@@ -1624,10 +1662,13 @@ cdef class Jess:
         .. versionadded:: 0.6.0
             The ``reorder`` argument, defaulting to `True`.
 
+        .. versionchanged:: 0.7.0
+            Default value of ``max_candidates`` argument to `None`.
+
         """
         cdef Query query = Query.__new__(Query)
-        query.ignore_chain = ignore_chain
         query.max_candidates = max_candidates
+        query.ignore_chain = ignore_chain
         query.rmsd_threshold = rmsd_threshold
         query.best_match = best_match
         query.molecule = molecule

pyjess-0.7.0a1/src/pyjess/tests/data/1sur.qry

@@ -0,0 +1,26 @@
+REMARK TEMPLATE
+REMARK CLUSTER 1_1_1
+REMARK REPRESENTING 1 CATALYTIC SITES
+REMARK ID 1sur_AA204-AA208-A204-A208
+REMARK MCSA_ID 279
+REMARK PDB_ID 1sur
+REMARK UNIPROT_ID P17854
+REMARK EC 1.8.4.8
+REMARK ENZYME PAPS REDUCTASE
+REMARK EXPERIMENTAL_METHOD X-ray diffraction
+REMARK RESOLUTION 2.0
+REMARK ORGANISM_NAME Escherichia coli
+REMARK ORGANISM_ID 562
+ATOM      0  NE1ZTRPAA 204      38.872   1.684 110.358 W     0.00 
+ATOM      0  CZ2ZTRPAA 204      41.345   1.476 110.794 W     0.00 
+ATOM      0  CH2ZTRPAA 204      42.567   1.626 110.193 W     0.00 
+ATOM      3  CE1ZTYRAA 208      40.509  -1.903  99.734 Y     0.00 
+ATOM      3  CZ ZTYRAA 208      41.503  -1.926  98.771 Y     0.00 
+ATOM      1  OH ZTYRAA 208      41.320  -2.643  97.607 Y     0.00 
+ATOM      0  NE1ZTRP A 204      43.868   1.684  54.342 W     0.00 
+ATOM      0  CZ2ZTRP A 204      41.395   1.476  53.906 W     0.00 
+ATOM      0  CH2ZTRP A 204      40.173   1.626  54.507 W     0.00 
+ATOM      3  CE1ZTYR A 208      42.231  -1.903  64.966 Y     0.00 
+ATOM      3  CZ ZTYR A 208      41.237  -1.926  65.929 Y     0.00 
+ATOM      1  OH ZTYR A 208      41.420  -2.643  67.093 Y     0.00 
+END

{pyjess-0.6.0 → pyjess-0.7.0a1}/src/pyjess/tests/test_template.py

@@ -6,6 +6,8 @@ import textwrap
 import sys
 
 from .._jess import Template
+from .utils import files
+from . import data
 
 TEMPLATE = textwrap.dedent(
     """
@@ -114,4 +116,10 @@ class TestTemplate(unittest.TestCase):
         tpl1 = Template.loads(TEMPLATE, id="tpl1")
         tpl2 = pickle.loads(pickle.dumps(tpl1))
         self.assertEqual(len(tpl1), len(tpl2))
-        self.assertEqual(tpl1, tpl2)
+        self.assertEqual(tpl1, tpl2)
+
+    @unittest.skipUnless(files, "importlib.resources not available")
+    def test_dimension_multiple_chains(self):
+        with files(data).joinpath("1sur.qry").open() as f:
+            template1 = Template.load(f)
+        self.assertEqual(template1.dimension, 4)