Merge pull request #2305 from peastman/setpos

Optimized setPositions() from Python

wrappers/python/src/swig_doxygen/swig_lib/python/typemaps.i

@@ -194,13 +194,59 @@ int Py_SequenceToVecDouble(PyObject* obj, std::vector<double>& out) {
 }
 
 %fragment("Py_SequenceToVecVec3", "header", fragment="Py_SequenceToVec3") {
+int isNumpyAvailable() {
+    static bool initialized = false;
+    static bool available = false;
+    if (!initialized) {
+        initialized = true;
+        available = (_import_array() >= 0);
+    }
+    return available;
+}
+
 int Py_SequenceToVecVec3(PyObject* obj, std::vector<Vec3>& out) {
+    PyObject* stripped = Py_StripOpenMMUnits(obj);      // new reference
+    if (isNumpyAvailable()) {
+        if (PyArray_Check(stripped) && PyArray_ISCARRAY_RO(stripped) && PyArray_NDIM(stripped) == 2 && PyArray_DIM(stripped, 1) == 3) {
+            int type = PyArray_TYPE(stripped);
+            int length = PyArray_DIM(stripped, 0);
+            void* data = PyArray_DATA((PyArrayObject*) stripped);
+            if (type == NPY_DOUBLE) {
+                out.resize(length);
+                memcpy(&out[0][0], data, 3*sizeof(double)*length);
+                Py_DECREF(stripped);
+                return SWIG_OK;
+            }
+            if (type == NPY_FLOAT) {
+                out.resize(length);
+                float* floatData = (float*) data;
+                for (int i = 0; i < length; i++)
+                    out[i] = Vec3(floatData[3*i], floatData[3*i+1], floatData[3*i+2]);
+                Py_DECREF(stripped);
+                return SWIG_OK;
+            }
+            if (type == NPY_INT32) {
+                out.resize(length);
+                int* intData = (int*) data;
+                for (int i = 0; i < length; i++)
+                    out[i] = Vec3(intData[3*i], intData[3*i+1], intData[3*i+2]);
+                Py_DECREF(stripped);
+                return SWIG_OK;
+            }
+            if (type == NPY_INT64) {
+                out.resize(length);
+                long long* longData = (long long*) data;
+                for (int i = 0; i < length; i++)
+                    out[i] = Vec3(longData[3*i], longData[3*i+1], longData[3*i+2]);
+                Py_DECREF(stripped);
+                return SWIG_OK;
+            }
+        }
+    }
     int ret = 0;
-    PyObject* stripped = NULL;
     PyObject* item = NULL;
     PyObject* item1 = NULL;
     PyObject* iterator = NULL;
-    stripped = Py_StripOpenMMUnits(obj);      // new reference
     iterator = PyObject_GetIter(stripped);    // new reference
 
     if (iterator == NULL) {