Generated by Cython 0.29.28
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Click on a line that starts with a "+
" to see the C code that Cython generated for it.
Raw output: GE_routine.c
+01: '''Cython implementation of the G' computation'''
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02: cimport cython
03:
04: @cython.boundscheck(False) # Deactivate bounds checking
05: @cython.wraparound(False) # Deactivate negative indexing.
+06: cdef void cross(
static void __pyx_f_5utils_10GE_routine_cross(__Pyx_memviewslice __pyx_v_x, __Pyx_memviewslice __pyx_v_a, __Pyx_memviewslice __pyx_v_b) { __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("cross", 0); /* … */ /* function exit code */ __Pyx_RefNannyFinishContext(); }
07: double[:] x,
08: double[:] a,
09: double[:] b):
10: '''Computes the cross product'''
+11: x[0] = a[1]*b[2] - a[2]*b[1]
__pyx_t_1 = 1; __pyx_t_2 = 2; __pyx_t_3 = 2; __pyx_t_4 = 1; __pyx_t_5 = 0; *((double *) ( /* dim=0 */ (__pyx_v_x.data + __pyx_t_5 * __pyx_v_x.strides[0]) )) = (((*((double *) ( /* dim=0 */ (__pyx_v_a.data + __pyx_t_1 * __pyx_v_a.strides[0]) ))) * (*((double *) ( /* dim=0 */ (__pyx_v_b.data + __pyx_t_2 * __pyx_v_b.strides[0]) )))) - ((*((double *) ( /* dim=0 */ (__pyx_v_a.data + __pyx_t_3 * __pyx_v_a.strides[0]) ))) * (*((double *) ( /* dim=0 */ (__pyx_v_b.data + __pyx_t_4 * __pyx_v_b.strides[0]) )))));
+12: x[1] = a[2]*b[0] - a[0]*b[2]
__pyx_t_4 = 2; __pyx_t_3 = 0; __pyx_t_2 = 0; __pyx_t_1 = 2; __pyx_t_5 = 1; *((double *) ( /* dim=0 */ (__pyx_v_x.data + __pyx_t_5 * __pyx_v_x.strides[0]) )) = (((*((double *) ( /* dim=0 */ (__pyx_v_a.data + __pyx_t_4 * __pyx_v_a.strides[0]) ))) * (*((double *) ( /* dim=0 */ (__pyx_v_b.data + __pyx_t_3 * __pyx_v_b.strides[0]) )))) - ((*((double *) ( /* dim=0 */ (__pyx_v_a.data + __pyx_t_2 * __pyx_v_a.strides[0]) ))) * (*((double *) ( /* dim=0 */ (__pyx_v_b.data + __pyx_t_1 * __pyx_v_b.strides[0]) )))));
+13: x[2] = a[0]*b[1] - a[1]*b[0]
__pyx_t_1 = 0; __pyx_t_2 = 1; __pyx_t_3 = 1; __pyx_t_4 = 0; __pyx_t_5 = 2; *((double *) ( /* dim=0 */ (__pyx_v_x.data + __pyx_t_5 * __pyx_v_x.strides[0]) )) = (((*((double *) ( /* dim=0 */ (__pyx_v_a.data + __pyx_t_1 * __pyx_v_a.strides[0]) ))) * (*((double *) ( /* dim=0 */ (__pyx_v_b.data + __pyx_t_2 * __pyx_v_b.strides[0]) )))) - ((*((double *) ( /* dim=0 */ (__pyx_v_a.data + __pyx_t_3 * __pyx_v_a.strides[0]) ))) * (*((double *) ( /* dim=0 */ (__pyx_v_b.data + __pyx_t_4 * __pyx_v_b.strides[0]) )))));
14:
15: @cython.boundscheck(False) # Deactivate bounds checking
16: @cython.wraparound(False) # Deactivate negative indexing.
+17: cdef double dot(
static double __pyx_f_5utils_10GE_routine_dot(__Pyx_memviewslice __pyx_v_a, __Pyx_memviewslice __pyx_v_b) { double __pyx_r; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("dot", 0); /* … */ /* function exit code */ __pyx_L0:; __Pyx_RefNannyFinishContext(); return __pyx_r; }
18: double[:] a,
19: double[:] b):
20: '''Compute dot product'''
+21: return a[0]*b[0] + a[1]*b[1] + a[2]*b[2]
__pyx_t_1 = 0; __pyx_t_2 = 0; __pyx_t_3 = 1; __pyx_t_4 = 1; __pyx_t_5 = 2; __pyx_t_6 = 2; __pyx_r = ((((*((double *) ( /* dim=0 */ (__pyx_v_a.data + __pyx_t_1 * __pyx_v_a.strides[0]) ))) * (*((double *) ( /* dim=0 */ (__pyx_v_b.data + __pyx_t_2 * __pyx_v_b.strides[0]) )))) + ((*((double *) ( /* dim=0 */ (__pyx_v_a.data + __pyx_t_3 * __pyx_v_a.strides[0]) ))) * (*((double *) ( /* dim=0 */ (__pyx_v_b.data + __pyx_t_4 * __pyx_v_b.strides[0]) ))))) + ((*((double *) ( /* dim=0 */ (__pyx_v_a.data + __pyx_t_5 * __pyx_v_a.strides[0]) ))) * (*((double *) ( /* dim=0 */ (__pyx_v_b.data + __pyx_t_6 * __pyx_v_b.strides[0]) ))))); goto __pyx_L0;
22:
23: @cython.boundscheck(False) # Deactivate bounds checking
24: @cython.wraparound(False) # Deactivate negative indexing.
+25: def computeGE(
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Py_ssize_t __pyx_v_j; Py_ssize_t __pyx_v_k; double __pyx_v_ge; double __pyx_v_PI; double __pyx_v_dR_C[3]; __Pyx_memviewslice __pyx_v_dR = { 0, 0, { 0 }, { 0 }, { 0 } }; double __pyx_v_ddR_C[3]; __Pyx_memviewslice __pyx_v_ddR = { 0, 0, { 0 }, { 0 }, { 0 } }; PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("computeGE", 0); /* … */ /* function exit code */ __pyx_L1_error:; __Pyx_XDECREF(((PyObject *)__pyx_t_1)); __Pyx_XDECREF(__pyx_t_2); __Pyx_XDECREF(__pyx_t_3); __PYX_XDEC_MEMVIEW(&__pyx_t_4, 1); __PYX_XDEC_MEMVIEW(&__pyx_t_17, 1); __Pyx_AddTraceback("utils.GE_routine.computeGE", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __PYX_XDEC_MEMVIEW(&__pyx_v_dR, 1); __PYX_XDEC_MEMVIEW(&__pyx_v_ddR, 1); __PYX_XDEC_MEMVIEW(&__pyx_v_R, 1); __PYX_XDEC_MEMVIEW(&__pyx_v_deltaR, 1); __Pyx_XGIVEREF(__pyx_r); __Pyx_RefNannyFinishContext(); return __pyx_r; } /* … */ __pyx_tuple__24 = PyTuple_Pack(15, __pyx_n_s_i1, __pyx_n_s_i2, __pyx_n_s_j1, __pyx_n_s_j2, __pyx_n_s_R, __pyx_n_s_deltaR, __pyx_n_s_i, __pyx_n_s_j, __pyx_n_s_k, __pyx_n_s_ge, __pyx_n_s_PI, __pyx_n_s_dR_C, __pyx_n_s_dR, __pyx_n_s_ddR_C, __pyx_n_s_ddR); if (unlikely(!__pyx_tuple__24)) __PYX_ERR(0, 25, __pyx_L1_error) __Pyx_GOTREF(__pyx_tuple__24); __Pyx_GIVEREF(__pyx_tuple__24); /* … */ __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_5utils_10GE_routine_1computeGE, NULL, __pyx_n_s_utils_GE_routine); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 25, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); if (PyDict_SetItem(__pyx_d, __pyx_n_s_computeGE, __pyx_t_1) < 0) __PYX_ERR(0, 25, __pyx_L1_error) __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __pyx_codeobj__25 = (PyObject*)__Pyx_PyCode_New(6, 0, 15, 0, CO_OPTIMIZED|CO_NEWLOCALS, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__24, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_analysis_utils_GE_routine_pyx, __pyx_n_s_computeGE, 25, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__25)) __PYX_ERR(0, 25, __pyx_L1_error)
26: Py_ssize_t i1,
27: Py_ssize_t i2,
28: Py_ssize_t j1,
29: Py_ssize_t j2,
30: double[:, :] R,
31: double[:, :] deltaR):
32: '''Returns G' for loop starting from residue i1 to i2 and
33: thread starting from residue j1 to j2'''
34:
35: cdef Py_ssize_t i, j, k
+36: cdef double ge = 0
__pyx_v_ge = 0.0;
+37: cdef double PI = 3.141592653589793
__pyx_v_PI = 3.141592653589793;
38:
39: cdef double dR_C[3] # C array implementation
+40: cdef double[:] dR = dR_C # memoryview for efficient memory access
__pyx_t_3 = __pyx_format_from_typeinfo(&__Pyx_TypeInfo_double); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 40, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_3); __pyx_t_2 = Py_BuildValue((char*) "(" __PYX_BUILD_PY_SSIZE_T ")", ((Py_ssize_t)3)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 40, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_2); __pyx_t_1 = __pyx_array_new(__pyx_t_2, sizeof(double), PyBytes_AS_STRING(__pyx_t_3), (char *) "fortran", (char *) __pyx_v_dR_C); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 40, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __pyx_t_4 = __Pyx_PyObject_to_MemoryviewSlice_ds_double(((PyObject *)__pyx_t_1), PyBUF_WRITABLE); if (unlikely(!__pyx_t_4.memview)) __PYX_ERR(0, 40, __pyx_L1_error) __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; __pyx_v_dR = __pyx_t_4; __pyx_t_4.memview = NULL; __pyx_t_4.data = NULL;
41: cdef double ddR_C[3]
+42: cdef double[:] ddR = ddR_C
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43:
+44: for i in range(i1, i2):
__pyx_t_5 = __pyx_v_i2; __pyx_t_6 = __pyx_t_5; for (__pyx_t_7 = __pyx_v_i1; __pyx_t_7 < __pyx_t_6; __pyx_t_7+=1) { __pyx_v_i = __pyx_t_7;
+45: for j in range(j1, j2):
__pyx_t_8 = __pyx_v_j2; __pyx_t_9 = __pyx_t_8; for (__pyx_t_10 = __pyx_v_j1; __pyx_t_10 < __pyx_t_9; __pyx_t_10+=1) { __pyx_v_j = __pyx_t_10;
46:
+47: for k in range(3):
for (__pyx_t_11 = 0; __pyx_t_11 < 3; __pyx_t_11+=1) { __pyx_v_k = __pyx_t_11;
+48: dR[k] = R[i][k] - R[j][k]
__pyx_t_12 = __pyx_v_i; __pyx_t_13 = __pyx_v_k; __pyx_t_14 = __pyx_v_j; __pyx_t_15 = __pyx_v_k; __pyx_t_16 = __pyx_v_k; *((double *) ( /* dim=0 */ (__pyx_v_dR.data + __pyx_t_16 * __pyx_v_dR.strides[0]) )) = ((*((double *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_R.data + __pyx_t_12 * __pyx_v_R.strides[0]) ) + __pyx_t_13 * __pyx_v_R.strides[1]) ))) - (*((double *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_R.data + __pyx_t_14 * __pyx_v_R.strides[0]) ) + __pyx_t_15 * __pyx_v_R.strides[1]) )))); }
49:
+50: cross(ddR, deltaR[i], deltaR[j])
__pyx_t_4.data = __pyx_v_deltaR.data; __pyx_t_4.memview = __pyx_v_deltaR.memview; __PYX_INC_MEMVIEW(&__pyx_t_4, 0); { Py_ssize_t __pyx_tmp_idx = __pyx_v_i; Py_ssize_t __pyx_tmp_stride = __pyx_v_deltaR.strides[0]; __pyx_t_4.data += __pyx_tmp_idx * __pyx_tmp_stride; } __pyx_t_4.shape[0] = __pyx_v_deltaR.shape[1]; __pyx_t_4.strides[0] = __pyx_v_deltaR.strides[1]; __pyx_t_4.suboffsets[0] = -1; __pyx_t_17.data = __pyx_v_deltaR.data; __pyx_t_17.memview = __pyx_v_deltaR.memview; __PYX_INC_MEMVIEW(&__pyx_t_17, 0); { Py_ssize_t __pyx_tmp_idx = __pyx_v_j; Py_ssize_t __pyx_tmp_stride = __pyx_v_deltaR.strides[0]; __pyx_t_17.data += __pyx_tmp_idx * __pyx_tmp_stride; } __pyx_t_17.shape[0] = __pyx_v_deltaR.shape[1]; __pyx_t_17.strides[0] = __pyx_v_deltaR.strides[1]; __pyx_t_17.suboffsets[0] = -1; __pyx_f_5utils_10GE_routine_cross(__pyx_v_ddR, __pyx_t_4, __pyx_t_17); __PYX_XDEC_MEMVIEW(&__pyx_t_4, 1); __pyx_t_4.memview = NULL; __pyx_t_4.data = NULL; __PYX_XDEC_MEMVIEW(&__pyx_t_17, 1); __pyx_t_17.memview = NULL; __pyx_t_17.data = NULL;
+51: ge += dot(dR, ddR)/(dot(dR, dR)**(3/2))
__pyx_t_18 = __pyx_f_5utils_10GE_routine_dot(__pyx_v_dR, __pyx_v_ddR); __pyx_t_19 = pow(__pyx_f_5utils_10GE_routine_dot(__pyx_v_dR, __pyx_v_dR), (3.0 / 2.0)); if (unlikely(__pyx_t_19 == 0)) { PyErr_SetString(PyExc_ZeroDivisionError, "float division"); __PYX_ERR(0, 51, __pyx_L1_error) } __pyx_v_ge = (__pyx_v_ge + (__pyx_t_18 / __pyx_t_19)); } }
52:
+53: return ge/(4*PI)
__Pyx_XDECREF(__pyx_r); __pyx_t_19 = (4.0 * __pyx_v_PI); if (unlikely(__pyx_t_19 == 0)) { PyErr_SetString(PyExc_ZeroDivisionError, "float division"); __PYX_ERR(0, 53, __pyx_L1_error) } __pyx_t_2 = PyFloat_FromDouble((__pyx_v_ge / __pyx_t_19)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 53, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_2); __pyx_r = __pyx_t_2; __pyx_t_2 = 0; goto __pyx_L0;