diff --git a/CMakeLists.txt b/CMakeLists.txt
index 82b1b67d718e2b0e6f3b8ff1a7e1485772f9995a..fb1b1fa0c1e59ee4621e56166fc76b28b8114763 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -22,6 +22,8 @@ option(ENABLE_GFX "whether graphics support should be enabled"
ON)
option(ENABLE_IMG "whether the image processing module should be compiled"
ON)
+option(USE_NUMPY "whether numpy support is added"
+ OFF)
option(USE_DOUBLE_PRECISION "whether to compile in double precision"
OFF)
option(ENABLE_SPNAV "whether 3DConnexion devices should be supported"
@@ -87,6 +89,11 @@ if (USE_SHADER)
else()
set(_SHADER OFF)
endif()
+if (USE_NUMPY)
+ set(_NUMPY ON)
+else()
+ set(_NUMPY OFF)
+endif()
if (COMPILE_TMTOOLS)
set(_TM_TOOLS ON)
else()
@@ -219,6 +226,10 @@ find_package(PNG REQUIRED)
find_package(Eigen 2.0.0 REQUIRED)
find_package(Python 2.4 REQUIRED)
+if(USE_NUMPY)
+ find_package(Numpy REQUIRED)
+endif()
+
if (ENABLE_IMG)
find_package(FFTW REQUIRED)
find_package(TIFF REQUIRED)
@@ -252,6 +263,10 @@ include_directories(${Boost_INCLUDE_DIRS}
${TIFF_INCLUDE_DIR}
${SPNAV_INCLUDE_DIR}
)
+if(USE_NUMPY)
+include_directories(${PYTHON_NUMPY_INCLUDE_DIR})
+endif()
+
if (UNIX)
SET(CMAKE_SKIP_BUILD_RPATH FALSE)
SET(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE)
@@ -284,6 +299,7 @@ message(STATUS
" OpenGL support (-DENABLE_GFX) : ${_OPENGL}\n"
" Image Processing support (-DENABLE_IMG) : ${_IMG}\n"
" Shader support (-DUSE_SHADER) : ${_SHADER}\n"
+ " Numpy support (-DUSE_NUMPY) : ${_NUMPY}\n"
" Optimize (-DOPTIMIZE) : ${_OPT}\n"
" Profiling support (-DPROFILE) : ${_PROFILE}\n"
" Double Precision (-DUSE_DOUBLE_PRECISION) : ${_DOUBLE_PREC}\n"
diff --git a/cmake_support/FindNumpy.cmake b/cmake_support/FindNumpy.cmake
new file mode 100644
index 0000000000000000000000000000000000000000..6348b9c91a934e4c01edac011cc861adc9fd059a
--- /dev/null
+++ b/cmake_support/FindNumpy.cmake
@@ -0,0 +1,32 @@
+if (PYTHON_NUMPY_INCLUDE_DIR)
+ # in cache already
+ set (PYTHON_NUMPY_FIND_QUIETLY TRUE)
+endif (PYTHON_NUMPY_INCLUDE_DIR)
+
+#INCLUDE(FindPython)
+
+IF(PYTHON_BINARY)
+ EXEC_PROGRAM ("${PYTHON_BINARY}"
+ ARGS "-c 'import numpy; print numpy.get_include()'"
+ OUTPUT_VARIABLE PYTHON_NUMPY_INCLUDE_DIR
+ RETURN_VALUE PYTHON_NUMPY_NOT_FOUND)
+
+ if (PYTHON_NUMPY_INCLUDE_DIR)
+ set (PYTHON_NUMPY_FOUND TRUE)
+ set (PYTHON_NUMPY_INCLUDE_DIR ${PYTHON_NUMPY_INCLUDE_DIR} CACHE STRING "Numpy include path")
+ else (PYTHON_NUMPY_INCLUDE_DIR)
+ set(PYTHON_NUMPY_FOUND FALSE)
+ endif (PYTHON_NUMPY_INCLUDE_DIR)
+ENDIF(PYTHON_BINARY)
+
+if (PYTHON_NUMPY_FOUND)
+ if (NOT PYTHON_NUMPY_FIND_QUIETLY)
+ message (STATUS "Numpy headers found")
+ endif (NOT PYTHON_NUMPY_FIND_QUIETLY)
+else (PYTHON_NUMPY_FOUND)
+ if (PYTHON_NUMPY_FIND_REQUIRED)
+ message (FATAL_ERROR "Numpy headers missing")
+ endif (PYTHON_NUMPY_FIND_REQUIRED)
+endif (PYTHON_NUMPY_FOUND)
+
+MARK_AS_ADVANCED (PYTHON_NUMPY_INCLUDE_DIR)
\ No newline at end of file
diff --git a/modules/config/CMakeLists.txt b/modules/config/CMakeLists.txt
index ddf07651188d815e51ae669972981c4aeab469c1..65c9ca6bebf69a4def544c5c58dfc50be04ee98d 100644
--- a/modules/config/CMakeLists.txt
+++ b/modules/config/CMakeLists.txt
@@ -5,14 +5,20 @@ dllexport.hh
version.hh
)
-
set(animations_enabled 0)
+
if (USE_SHADER)
set(shader_support 1)
else()
set(shader_support 0)
endif()
+if (USE_NUMPY)
+ set(numpy_support 1)
+else()
+ set(numpy_support 0)
+endif()
+
if (PROFILE)
set(profiling_enabled 1)
else()
diff --git a/modules/config/config.hh.in b/modules/config/config.hh.in
index 0095327dd737efa71141f72144cf9d8b5bfed213..88653c1e8df5bc5f75bf99dd6554c5a25c5ffaa6 100644
--- a/modules/config/config.hh.in
+++ b/modules/config/config.hh.in
@@ -31,4 +31,5 @@
#define OST_STATIC_PROPERTY_WORKAROUND @static_props@
#define OST_SPNAV_ENABLED @spnav_enabled@
#define OST_FFT_USE_THREADS @fftw_use_threads@
+#define OST_NUMPY_SUPPORT_ENABLED @numpy_support@
#endif
diff --git a/modules/mol/base/pymod/export_entity.cc b/modules/mol/base/pymod/export_entity.cc
index 34a8adcf80163945bd1ab6cd4e29145c3fbb1b3b..36ab544f1e7cea0335a0f84a02c922b0bbaf9309 100644
--- a/modules/mol/base/pymod/export_entity.cc
+++ b/modules/mol/base/pymod/export_entity.cc
@@ -30,6 +30,10 @@ using namespace ost::mol;
#include <ost/export_helper/generic_property_def.hh>
+#if OST_NUMPY_SUPPORT_ENABLED
+#include <numpy/arrayobject.h>
+#endif
+
namespace {
EntityHandle create1() { return CreateEntity(); }
@@ -65,10 +69,96 @@ ICSEditor depr_request_ics_editor(EntityHandle e, EditMode m)
}
+PyObject* get_pos(EntityHandle& entity)
+{
+#if OST_NUMPY_SUPPORT_ENABLED
+ npy_intp dims[]={entity.GetAtomCount(),3};
+ PyObject* na = PyArray_SimpleNew(2,dims,NPY_DOUBLE);
+ npy_double* nad = reinterpret_cast<npy_double*>(PyArray_DATA(na));
+ for(AtomHandleIter it=entity.AtomsBegin();it!=entity.AtomsEnd();++it,nad+=3) {
+ geom::Vec3 pos=(*it).GetPos();
+ nad[0]=static_cast<npy_double>(pos[0]);
+ nad[1]=static_cast<npy_double>(pos[1]);
+ nad[2]=static_cast<npy_double>(pos[2]);
+ }
+ return na;
+#else
+ throw std::runtime_error("GetPositions disabled, since numpy support is not compiled in");
+ return 0;
+#endif
+}
+
+
+#if OST_NUMPY_SUPPORT_ENABLED
+template <typename T>
+void set_pos_t(PyArrayObject* na, EntityHandle& entity)
+{
+ XCSEditor ed=entity.EditXCS(BUFFERED_EDIT);
+
+ if(PyArray_ISCONTIGUOUS(na)) {
+ T* data = reinterpret_cast<T*>(PyArray_DATA(na));
+ size_t count=0;
+ for(AtomHandleIter it=entity.AtomsBegin();it!=entity.AtomsEnd();++it,++count) {
+ ed.SetAtomPos(*it,geom::Vec3(static_cast<Real>(data[count*3+0]),
+ static_cast<Real>(data[count*3+1]),
+ static_cast<Real>(data[count*3+2])));
+ }
+ } else {
+ size_t count=0;
+ for(AtomHandleIter it=entity.AtomsBegin();it!=entity.AtomsEnd();++it,++count) {
+ ed.SetAtomPos(*it,geom::Vec3(static_cast<Real>(*reinterpret_cast<T*>(PyArray_GETPTR2(na,count,0))),
+ static_cast<Real>(*reinterpret_cast<T*>(PyArray_GETPTR2(na,count,1))),
+ static_cast<Real>(*reinterpret_cast<T*>(PyArray_GETPTR2(na,count,2)))));
+ }
+ }
+}
+#endif
+
+void set_pos(EntityHandle& entity, object& pyobj)
+{
+#if OST_NUMPY_SUPPORT_ENABLED
+ size_t acount = entity.GetAtomCount();
+
+ if(!PyArray_Check(pyobj.ptr())) {
+ throw std::runtime_error(std::string("expected a numpy array"));
+ return;
+ }
+ PyArrayObject* na=reinterpret_cast<PyArrayObject*>(pyobj.ptr());
+
+ if(PyArray_NDIM(na)!=2 || PyArray_DIM(na,0)!=acount || PyArray_DIM(na,1)!=3) {
+ throw std::runtime_error("excpected a numpy array of shape (NAtoms, 3)");
+ return;
+ }
+
+ switch(PyArray_TYPE(na)) {
+ case NPY_FLOAT:
+ set_pos_t<float>(na,entity); break;
+ case NPY_DOUBLE:
+ set_pos_t<double>(na,entity); break;
+ case NPY_INT:
+ set_pos_t<int>(na,entity); break;
+ case NPY_LONG:
+ set_pos_t<long>(na,entity); break;
+ case NPY_SHORT:
+ set_pos_t<short>(na,entity); break;
+ default:
+ throw std::runtime_error("excpected a numpy array of type float, double, int, long or short");
+ return;
+ };
+
+#else
+ throw std::runtime_error("SetPositions disabled, since numpy support is not compiled in");
+#endif
}
+} // ns
+
void export_Entity()
{
+#if OST_NUMPY_SUPPORT_ENABLED
+ import_array();
+#endif
+
class_<EntityBase> ent_base("EntityBase", no_init);
ent_base
.def(self_ns::str(self))
@@ -139,6 +229,11 @@ void export_Entity()
.def("IsTransformationIdentity",&EntityHandle::IsTransformationIdentity)
.def(self==self)
.def(self!=self)
+#if OST_NUMPY_SUPPORT_ENABLED
+ .def("SetPositions",set_pos)
+ .def("GetPositions",get_pos)
+ .add_property("positions",get_pos,set_pos)
+#endif
;
def("CreateEntity",create1);
diff --git a/modules/mol/base/tests/test_numpy.py b/modules/mol/base/tests/test_numpy.py
new file mode 100644
index 0000000000000000000000000000000000000000..e496bf585758812ba1253ad646af6ccf17437046
--- /dev/null
+++ b/modules/mol/base/tests/test_numpy.py
@@ -0,0 +1,41 @@
+import sys,unittest
+sys.path.append("../../../../stage/lib64/openstructure")
+from ost import *
+import numpy
+
+class TestNumpy(unittest.TestCase):
+ def setUp(self):
+ pass
+
+ def test_(self):
+ entity=mol.CreateEntity()
+ ed=entity.EditXCS()
+ ch=ed.InsertChain("X")
+ re=ed.AppendResidue(ch,"ALA")
+ a0=ed.InsertAtom(re,"A",geom.Vec3(0,0,0))
+ a1=ed.InsertAtom(re,"B",geom.Vec3(1,0,0))
+ a2=ed.InsertAtom(re,"C",geom.Vec3(2,0,0))
+ a3=ed.InsertAtom(re,"D",geom.Vec3(3,0,0))
+
+ self.assertTrue(geom.Distance(a0.pos,geom.Vec3(0,0,0))<1e-10)
+ self.assertTrue(geom.Distance(a1.pos,geom.Vec3(1,0,0))<1e-10)
+ self.assertTrue(geom.Distance(a2.pos,geom.Vec3(2,0,0))<1e-10)
+ self.assertTrue(geom.Distance(a3.pos,geom.Vec3(3,0,0))<1e-10)
+
+ entity.positions=numpy.array([[0,1,0],[0,2,0],[0,3,0],[0,4,0]])
+
+ self.assertTrue(geom.Distance(a0.pos,geom.Vec3(0,1,0))<1e-10)
+ self.assertTrue(geom.Distance(a1.pos,geom.Vec3(0,2,0))<1e-10)
+ self.assertTrue(geom.Distance(a2.pos,geom.Vec3(0,3,0))<1e-10)
+ self.assertTrue(geom.Distance(a3.pos,geom.Vec3(0,4,0))<1e-10)
+
+ na=entity.positions
+
+ self.assertTrue(geom.Distance(geom.Vec3(na[0][0],na[0][1],na[0][2]),geom.Vec3(0,1,0))<1e-10)
+ self.assertTrue(geom.Distance(geom.Vec3(na[1][0],na[1][1],na[1][2]),geom.Vec3(0,2,0))<1e-10)
+ self.assertTrue(geom.Distance(geom.Vec3(na[2][0],na[2][1],na[2][2]),geom.Vec3(0,3,0))<1e-10)
+ self.assertTrue(geom.Distance(geom.Vec3(na[3][0],na[3][1],na[3][2]),geom.Vec3(0,4,0))<1e-10)
+
+if __name__== '__main__':
+ unittest.main()
+