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glotzerlab · Jan 14, 2025 · 1ea8ab3 · 1ea8ab3
1 parent b6a6e56
commit 1ea8ab3
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Showing 3 changed files with 14 additions and 13 deletions.
diff --git a/freud/environment/MatchEnv.cc b/freud/environment/MatchEnv.cc
@@ -711,8 +711,8 @@ void EnvironmentMotifMatch::compute(const freud::locality::NeighborQuery* nq,
 /****************************
  * EnvironmentRMSDMinimizer *
  ****************************/
-void EnvironmentRMSDMinimizer::compute(const freud::locality::NeighborQuery* nq,
-                                       const freud::locality::NeighborList* nlist_arg,
+void EnvironmentRMSDMinimizer::compute(const std::shared_ptr<freud::locality::NeighborQuery>& nq,
+                                       const std::shared_ptr<freud::locality::NeighborList>& nlist_arg,
                                        locality::QueryArgs qargs, const vec3<float>* motif,
                                        unsigned int motif_size, bool registration)
 {

diff --git a/freud/environment/MatchEnv.h b/freud/environment/MatchEnv.h
@@ -263,7 +263,7 @@ class EnvironmentCluster : public MatchEnv
      *                     orient the second set of vectors such that it
      *                     minimizes the RMSD between the two sets
      */
-    void compute(const freud::locality::NeighborQuery* nq, const freud::locality::NeighborList* nlist_arg,
+    void compute(const std::shared_ptr<freud::locality::NeighborQuery>& nq, const std::shared_ptr<freud::locality::NeighborList>& nlist_arg,
                  locality::QueryArgs qargs, const freud::locality::NeighborList* env_nlist_arg,
                  locality::QueryArgs env_qargs, float threshold, bool registration = false);
 
@@ -350,7 +350,7 @@ class EnvironmentMotifMatch : public MatchEnv
      *                     orient the second set of vectors such that it
      *                     minimizes the RMSD between the two sets
      */
-    void compute(const freud::locality::NeighborQuery* nq, const freud::locality::NeighborList* nlist_arg,
+    void compute(const std::shared_ptr<freud::locality::NeighborQuery> nq, const std::shared_ptr<freud::locality::NeighborList> nlist_arg,
                  locality::QueryArgs qargs, const vec3<float>* motif, unsigned int motif_size,
                  float threshold, bool registration = false);
 
@@ -412,7 +412,7 @@ class EnvironmentRMSDMinimizer : public MatchEnv
      *                     orient the second set of vectors such that it
      *                     minimizes the RMSD between the two sets
      */
-    void compute(const freud::locality::NeighborQuery* nq, const freud::locality::NeighborList* nlist_arg,
+    void compute(const std::shared_ptr<freud::locality::NeighborQuery>& nq, const std::shared_ptr<freud::locality::NeighborList>& nlist_arg,
                  locality::QueryArgs qargs, const vec3<float>* motif, unsigned int motif_size,
                  bool registration = false);
 

diff --git a/freud/environment/export-MatchEnv.cc b/freud/environment/export-MatchEnv.cc
@@ -5,6 +5,7 @@
 #include <nanobind/nanobind.h>
 #include <nanobind/ndarray.h>
 #include <nanobind/stl/shared_ptr.h> // NOLINT(misc-include-cleaner): used implicitly
+#include <nanobind/stl/function.h> // NOLINT(misc-include-cleaner): used implicitly
 #include <nanobind/stl/vector.h>     // NOLINT(misc-include-cleaner): used implicitly
 
 #include "MatchEnv.h"
@@ -54,30 +55,30 @@ namespace detail {
 void export_MatchEnv(nb::module_& module)
 {
     // export minimizeRMSD function, move convenience to wrap? TODO
-    nb::function("minimizeRMSD", &minimizeRMSD);//carefull ths fn is overloaded for easier python interactivity. You should use the one that takes box etc in.
+    // module.def("minimizeRMSD", &minimizeRMSD); //carefull ths fn is overloaded for easier python interactivity. You should use the one that takes box etc in.
     // export isSimilar function, move convenience to wrap? TODO
-    nb::function("isSimilar", &isSimilar); //carefull ths fn is overloaded for easier python interactivity. You should use the one that takes box etc in.
+    // module.def("isSimilar", &isSimilar); //carefull ths fn is overloaded for easier python interactivity. You should use the one that takes box etc in.
 
     nb::class_<MatchEnv>(module, "MatchEnv")
-        .def(nb::init<>)
-        .def("getPointEnvironments", &MatchEnv::getPointEnvironments)
+        .def(nb::init<>())
+        .def("getPointEnvironments", &MatchEnv::getPointEnvironments);
 
     nb::class_<EnvironmentCluster>(module, "EnvironmentCluster")
         .def(nb::init<>())
         .def("compute", &EnvironmentCluster::compute)
-        .def("getClusters", &EnvironmentCluster::getClusterIdx)
+        // .def("getClusters", &EnvironmentCluster::getClusterIdx) // TODO: should be there
         .def("getClusterEnvironments", &EnvironmentCluster::getClusterEnvironments)
-        .def("getNumClusters", &EnvironmentCluster::getNumClusters)
+        .def("getNumClusters", &EnvironmentCluster::getNumClusters);
 
     nb::class_<EnvironmentMotifMatch>(module, "EnvironmentMotifMatch")
         .def(nb::init<>())
         .def("compute", &wrap::compute_env_motif_match, nb::arg("nq"), nb::arg("nlist"), nb::arg("qargs"), nb::arg("motif"), nb::arg("motif_size"), nb::arg("threshold"), nb::arg("registration"))
-        .def("getMatches", &EnvironmentMotifMatch::getMatches)
+        .def("getMatches", &EnvironmentMotifMatch::getMatches);
 
     nb::class_<EnvironmentRMSDMinimizer>(module, "EnvironmentRMSDMinimizer")
         .def(nb::init<>())
         .def("compute", &wrap::compute_env_rmsd_min, nb::arg("nq"), nb::arg("nlist"), nb::arg("qargs"), nb::arg("motif"), nb::arg("motif_size"), nb::arg("threshold"), nb::arg("registration"))
-        .def("getRMSDs", &EnvironmentRMSDMinimizer::getRMSDs)
+        .def("getRMSDs", &EnvironmentRMSDMinimizer::getRMSDs);
 
 }