diff --git a/modules/mol/alg/src/accessibility.cc b/modules/mol/alg/src/accessibility.cc index 276b53ba2256802e9c9afc52c2f4b49e308e796f..be95bfeb03421916779f12af120dab8af8841faa 100644 --- a/modules/mol/alg/src/accessibility.cc +++ b/modules/mol/alg/src/accessibility.cc @@ -24,14 +24,15 @@ struct Cube { }; struct CubeGrid { - CubeGrid(Real cel, int x_cubes, int y_cubes, int z_cubes, + CubeGrid(Real cel, int x_c, int y_c, int z_c, Real x_min, Real y_min, Real z_min): cube_edge_length(cel), - x_cubes(x_cubes), - y_cubes(y_cubes), - z_cubes(z_cubes), - x_min(x_min), - y_min(y_min), - z_min(z_min) { + x_min(x_min), + y_min(y_min), + z_min(z_min) { + + x_cubes = std::max(1, x_c); + y_cubes = std::max(1, y_c); + z_cubes = std::max(1, z_c); int num_cubes = x_cubes * y_cubes * z_cubes; cubes = new Cube*[num_cubes]; // assign NULL to each cube @@ -49,11 +50,18 @@ struct CubeGrid { delete [] cubes; } + int GetCubeIdx(Real x, Real y, Real z) { + int x_cube = std::min(static_cast<int>((x - x_min) / cube_edge_length), + x_cubes - 1); + int y_cube = std::min(static_cast<int>((y - y_min) / cube_edge_length), + y_cubes - 1); + int z_cube = std::min(static_cast<int>((z - z_min) / cube_edge_length), + z_cubes - 1); + return x_cube * y_cubes * z_cubes + y_cube * z_cubes + z_cube; + } + void AddIndex(Real x, Real y, Real z, int idx) { - int x_cube = (x - x_min) / cube_edge_length; - int y_cube = (y - y_min) / cube_edge_length; - int z_cube = (z - z_min) / cube_edge_length; - int cube_idx = x_cube * y_cubes * z_cubes + y_cube * z_cubes + z_cube; + int cube_idx = this->GetCubeIdx(x, y, z); if(cubes[cube_idx] == NULL) cubes[cube_idx] = new Cube; cubes[cube_idx]->AddIndex(idx); } diff --git a/modules/mol/base/doc/entity.rst b/modules/mol/base/doc/entity.rst index 3b0aa5c9fdcd51cdb563922b9fb384f8ec046736..424bda032f10bcc6dba3278dae229ef14dd5ed42 100644 --- a/modules/mol/base/doc/entity.rst +++ b/modules/mol/base/doc/entity.rst @@ -1865,7 +1865,7 @@ Other Entity-Related Functions Residue Numbering -------------------------------------------------------------------------------- -.. class:: ResNum(num, ins_code='\0') +.. class:: ResNum(num, ins_code='\\0') Number for a residue. The residue number has a numeric part and an (optional) insertion-code. You can work with this object as if it was an integer and diff --git a/modules/mol/base/pymod/export_entity_view.cc b/modules/mol/base/pymod/export_entity_view.cc index 2422c154ad6a9f6e764a824264066b550807d9b3..19781a94f2ae3e6019d7e57b0eb55e6119b3d1e2 100644 --- a/modules/mol/base/pymod/export_entity_view.cc +++ b/modules/mol/base/pymod/export_entity_view.cc @@ -197,10 +197,10 @@ void export_EntityView() make_function(&EntityView::GetBondList, return_value_policy<reference_existing_object>())) .def("GetChainList", &EntityView::GetChainList, - return_value_policy<reference_existing_object>()) + return_value_policy<copy_const_reference>()) .add_property("chains", make_function(&EntityView::GetChainList, - return_value_policy<reference_existing_object>())) + return_value_policy<copy_const_reference>())) .def(self==self) .def(self!=self) .def("Dump", &EntityView::Dump)