From ef90f9b3d2bf89cb270459608065a54dc339f7e0 Mon Sep 17 00:00:00 2001 From: Richard Gowers Date: Sat, 3 Jun 2017 21:36:24 +0100 Subject: [PATCH] Updated c sources for 0.16.1 --- package/MDAnalysis/lib/c_distances.c | 2 +- package/MDAnalysis/lib/c_distances_openmp.c | 2 +- package/MDAnalysis/lib/formats/libmdaxdr.c | 4 +- package/MDAnalysis/lib/qcprot.c | 648 ++++++++++---------- 4 files changed, 328 insertions(+), 328 deletions(-) diff --git a/package/MDAnalysis/lib/c_distances.c b/package/MDAnalysis/lib/c_distances.c index 2c0a5ea0966..36688db999d 100644 --- a/package/MDAnalysis/lib/c_distances.c +++ b/package/MDAnalysis/lib/c_distances.c @@ -1988,7 +1988,7 @@ static const char __pyx_k_calc_distance_array_triclinic[] = "calc_distance_array static const char __pyx_k_unable_to_allocate_array_data[] = "unable to allocate array data."; static const char __pyx_k_calc_self_distance_array_ortho[] = "calc_self_distance_array_ortho"; static const char __pyx_k_strided_and_direct_or_indirect[] = ""; -static const char __pyx_k_Distance_calculation_library_mo[] = "\nDistance calculation library --- :mod:`MDAnalysis.lib.c_distances`\n=================================================================\n\nSerial versions of all distance calculations\n"; +static const char __pyx_k_Distance_calculation_library_mo[] = "\nDistance calculation library --- :mod:`MDAnalysis.lib.c_distances`\n==================================================================\n\nSerial versions of all distance calculations\n"; static const char __pyx_k_home_richard_code_mdanalysis_pa[] = "/home/richard/code/mdanalysis/package/MDAnalysis/lib/c_distances.pyx"; static const char __pyx_k_numpy_core_multiarray_failed_to[] = "numpy.core.multiarray failed to import"; static const char __pyx_k_unknown_dtype_code_in_numpy_pxd[] = "unknown dtype code in numpy.pxd (%d)"; diff --git a/package/MDAnalysis/lib/c_distances_openmp.c b/package/MDAnalysis/lib/c_distances_openmp.c index 92ecc207acd..66dc7fff721 100644 --- a/package/MDAnalysis/lib/c_distances_openmp.c +++ b/package/MDAnalysis/lib/c_distances_openmp.c @@ -1375,7 +1375,7 @@ static const char __pyx_k_ndarray_is_not_C_contiguous[] = "ndarray is not C cont static const char __pyx_k_calc_bond_distance_triclinic[] = "calc_bond_distance_triclinic"; static const char __pyx_k_calc_distance_array_triclinic[] = "calc_distance_array_triclinic"; static const char __pyx_k_calc_self_distance_array_ortho[] = "calc_self_distance_array_ortho"; -static const char __pyx_k_Parallel_distance_calculation_l[] = "\nParallel distance calculation library --- :mod:`MDAnalysis.lib.c_distances_openmp`\n=================================================================================\n\n\nContains OpenMP versions of the contents of \"calc_distances.h\"\n"; +static const char __pyx_k_Parallel_distance_calculation_l[] = "\nParallel distance calculation library --- :mod:`MDAnalysis.lib.c_distances_openmp`\n==================================================================================\n\n\nContains OpenMP versions of the contents of \"calc_distances.h\"\n"; static const char __pyx_k_home_richard_code_mdanalysis_pa[] = "/home/richard/code/mdanalysis/package/MDAnalysis/lib/c_distances_openmp.pyx"; static const char __pyx_k_numpy_core_multiarray_failed_to[] = "numpy.core.multiarray failed to import"; static const char __pyx_k_unknown_dtype_code_in_numpy_pxd[] = "unknown dtype code in numpy.pxd (%d)"; diff --git a/package/MDAnalysis/lib/formats/libmdaxdr.c b/package/MDAnalysis/lib/formats/libmdaxdr.c index 16b6f3173da..cb5eaa8ecea 100644 --- a/package/MDAnalysis/lib/formats/libmdaxdr.c +++ b/package/MDAnalysis/lib/formats/libmdaxdr.c @@ -6786,7 +6786,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_9libmdaxdr_7TRRFile_4read(s /* Python wrapper */ static PyObject *__pyx_pw_10MDAnalysis_3lib_7formats_9libmdaxdr_7TRRFile_7write(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static char __pyx_doc_10MDAnalysis_3lib_7formats_9libmdaxdr_7TRRFile_6write[] = "write one frame into TRR file.\n\n Parameters\n ----------\n xyz : ndarray, shape=(n_atoms, 3)\n cartesion coordinates\n box : ndarray, shape=(3, 3)\n Box vectors for this frame\n step : int\n current step number, 1 indexed\n time : float\n current time\n _lambda : float\n current lambda value\n natoms : int\n number of atoms in frame\n\n Raises\n ------\n IOError\n "; +static char __pyx_doc_10MDAnalysis_3lib_7formats_9libmdaxdr_7TRRFile_6write[] = "write one frame into TRR file.\n\n Parameters\n ----------\n xyz : ndarray, shape=(`n_atoms`, 3)\n cartesion coordinates\n box : ndarray, shape=(3, 3)\n Box vectors for this frame\n step : int\n current step number, 1 indexed\n time : float\n current time\n _lambda : float\n current lambda value\n natoms : int\n number of atoms in frame\n\n Raises\n ------\n IOError\n "; static PyObject *__pyx_pw_10MDAnalysis_3lib_7formats_9libmdaxdr_7TRRFile_7write(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_xyz = 0; PyObject *__pyx_v_velocity = 0; @@ -8942,7 +8942,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_7formats_9libmdaxdr_7XTCFile_4read(s /* Python wrapper */ static PyObject *__pyx_pw_10MDAnalysis_3lib_7formats_9libmdaxdr_7XTCFile_7write(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static char __pyx_doc_10MDAnalysis_3lib_7formats_9libmdaxdr_7XTCFile_6write[] = "write one frame to the XTC file\n\n Parameters\n ----------\n xyz : ndarray, shape=(n_atoms, 3)\n cartesion coordinates\n box : ndarray, shape=(3, 3)\n Box vectors for this frame\n step : int\n current step number, 1 indexed\n time : float\n current time\n precision : float (optional)\n precision of saved trajectory, see Notes\n\n\n Notes\n -----\n Gromacs specifies the precision a little bit strange. The coordinates\n will be multiplied by precision and then converted to an integer. This\n means a precision of 1000 yields an accuracy of 3 decimal places.\n\n Raises\n ------\n IOError\n\n "; +static char __pyx_doc_10MDAnalysis_3lib_7formats_9libmdaxdr_7XTCFile_6write[] = "write one frame to the XTC file\n\n Parameters\n ----------\n xyz : ndarray, shape=(`n_atoms`, 3)\n cartesion coordinates\n box : ndarray, shape=(3, 3)\n Box vectors for this frame\n step : int\n current step number, 1 indexed\n time : float\n current time\n precision : float (optional)\n precision of saved trajectory, see Notes\n\n\n Notes\n -----\n Gromacs specifies the precision a little bit strange. The coordinates\n will be multiplied by precision and then converted to an integer. This\n means a precision of 1000 yields an accuracy of 3 decimal places.\n\n Raises\n ------\n IOError\n\n "; static PyObject *__pyx_pw_10MDAnalysis_3lib_7formats_9libmdaxdr_7XTCFile_7write(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_xyz = 0; PyObject *__pyx_v_box = 0; diff --git a/package/MDAnalysis/lib/qcprot.c b/package/MDAnalysis/lib/qcprot.c index 04ef165ab08..ccc8aa24890 100644 --- a/package/MDAnalysis/lib/qcprot.c +++ b/package/MDAnalysis/lib/qcprot.c @@ -1535,7 +1535,7 @@ static const char __pyx_k_MDAnalysis_lib_qcprot[] = "MDAnalysis.lib.qcprot"; static const char __pyx_k_FastCalcRMSDAndRotation[] = "FastCalcRMSDAndRotation"; static const char __pyx_k_CalcRMSDRotationalMatrix[] = "CalcRMSDRotationalMatrix"; static const char __pyx_k_ndarray_is_not_C_contiguous[] = "ndarray is not C contiguous"; -static const char __pyx_k_Fast_QCP_RMSD_structure_alignme[] = "\nFast QCP RMSD structure alignment --- :mod:`MDAnalysis.lib.qcprot`\n==================================================================\n\n:Author: Joshua L. Adelman, University of Pittsburgh\n:Author: Robert R. Delgado, Cornell University and Arizona State University\n:Contact: jla65@pitt.edu\n:Year: 2011, 2016\n:Licence: BSD\n\nPyQCPROT_ is a python/cython implementation of Douglas Theobald's QCP\nmethod for calculating the minimum RMSD between two structures\n[Theobald2005]_ and determining the optimal least-squares rotation\nmatrix [Liu2010]_.\n\nA full description of the method, along with the original C implementation can\nbe found at http://theobald.brandeis.edu/qcp/\n\n.. SeeAlso:: The :func:`CalcRMSDRotationalMatrix` function is used in\n :mod:`MDAnalysis.analysis.align` and\n :mod:`MDAnalysis.analysis.rmsd`.\n\n.. versionchanged:: 0.16.0\n Call signatures were changed to directly interface with MDAnalysis\n coordinate arrays: shape (N, 3)\n\nReferences\n----------\n\nIf you use this QCP rotation calculation method in a publication, please\nreference:\n\n.. [Theobald2005] Douglas L. Theobald (2005)\n \"Rapid calculation of RMSD using a quaternion-based characteristic\n polynomial.\" Acta Crystallographica A 61(4):478-480.\n\n.. [Liu2010] Pu Liu, Dmitris K. Agrafiotis, and Douglas L. Theobald (2010)\n \"Fast determination of the optimal rotational matrix for macromolecular\n superpositions.\" J. Comput. Chem. 31, 1561-1563.\n\n.. _PyQCPROT: https://github.com/synapticarbors/pyqcprot\n\n\nFunctions\n---------\n\nUsers will typically use the :func:`CalcRMSDRotationalMatrix` function.\n\n.. autofunction:: CalcRMSDRotationalMatrix\n\n.. autofunction:: InnerProduct\n\n.. autofunction:: FastCalcRMSDAndRotation\n\n"; +static const char __pyx_k_Fast_QCP_RMSD_structure_alignme[] = "\nFast QCP RMSD structure alignment --- :mod:`MDAnalysis.lib.qcprot`\n==================================================================\n\n:Author: Joshua L. Adelman, University of Pittsburgh\n:Author: Robert R. Delgado, Cornell University and Arizona State University\n:Contact: jla65@pitt.edu\n:Year: 2011, 2016\n:Licence: BSD\n\nPyQCPROT_ is a python/cython implementation of Douglas Theobald's QCP\nmethod for calculating the minimum RMSD between two structures\n[Theobald2005]_ and determining the optimal least-squares rotation\nmatrix [Liu2010]_.\n\nA full description of the method, along with the original C implementation can\nbe found at http://theobald.brandeis.edu/qcp/\n\nSee Also\n--------\nMDAnalysis.analysis.align:\n Align structures using :func:`CalcRMSDRotationalMatrix`\nMDAnalysis.analysis.rms.rmsd:\n Calculate the RMSD between two structures using\n :func:`CalcRMSDRotationalMatrix`\n\n\n.. versionchanged:: 0.16.0\n Call signatures were changed to directly interface with MDAnalysis\n coordinate arrays: shape (N, 3)\n\nReferences\n----------\n\nIf you use this QCP rotation calculation method in a publication, please\nreference:\n\n.. [Theobald2005] Douglas L. Theobald (2005)\n \"Rapid calculation of RMSD using a quaternion-based characteristic\n polynomial.\" Acta Crystallographica A 61(4):478-480.\n\n.. [Liu2010] Pu Liu, Dmitris K. Agrafiotis, and Douglas L. Theobald (2010)\n \"Fast determination of the optimal rotational matrix for macromolecular\n superpositions.\" J. Comput. Chem. 31, 1561-1563.\n\n.. _PyQCPROT: https://github.com/synapticarbors/pyqcprot\n\n\nFunctions\n---------\n\nUsers will typically use the :func:`CalcRMSDRotationalMatrix` function.\n\n.. autofunction:: CalcRMSDRotationalMatrix\n\n.. autofunction:: InnerProduct\n\n.. autofunction:: FastCalcRMSDAndRotation\n\n"; static const char __pyx_k_home_richard_code_mdanalysis_pa[] = "/home/richard/code/mdanalysis/package/MDAnalysis/lib/qcprot.pyx"; static const char __pyx_k_numpy_core_multiarray_failed_to[] = "numpy.core.multiarray failed to import"; static const char __pyx_k_unknown_dtype_code_in_numpy_pxd[] = "unknown dtype code in numpy.pxd (%d)"; @@ -1693,7 +1693,7 @@ static PyObject *__pyx_codeobj__13; static PyObject *__pyx_codeobj__15; static PyObject *__pyx_codeobj__17; -/* "MDAnalysis/lib/qcprot.pyx":145 +/* "MDAnalysis/lib/qcprot.pyx":150 * @cython.boundscheck(False) * @cython.wraparound(False) * def InnerProduct(np.ndarray[np.float64_t, ndim=1] A, # <<<<<<<<<<<<<< @@ -1737,26 +1737,26 @@ static PyObject *__pyx_pw_10MDAnalysis_3lib_6qcprot_1InnerProduct(PyObject *__py case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_coords1)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("InnerProduct", 1, 5, 5, 1); __PYX_ERR(0, 145, __pyx_L3_error) + __Pyx_RaiseArgtupleInvalid("InnerProduct", 1, 5, 5, 1); __PYX_ERR(0, 150, __pyx_L3_error) } case 2: if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_coords2)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("InnerProduct", 1, 5, 5, 2); __PYX_ERR(0, 145, __pyx_L3_error) + __Pyx_RaiseArgtupleInvalid("InnerProduct", 1, 5, 5, 2); __PYX_ERR(0, 150, __pyx_L3_error) } case 3: if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_N)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("InnerProduct", 1, 5, 5, 3); __PYX_ERR(0, 145, __pyx_L3_error) + __Pyx_RaiseArgtupleInvalid("InnerProduct", 1, 5, 5, 3); __PYX_ERR(0, 150, __pyx_L3_error) } case 4: if (likely((values[4] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_weight)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("InnerProduct", 1, 5, 5, 4); __PYX_ERR(0, 145, __pyx_L3_error) + __Pyx_RaiseArgtupleInvalid("InnerProduct", 1, 5, 5, 4); __PYX_ERR(0, 150, __pyx_L3_error) } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "InnerProduct") < 0)) __PYX_ERR(0, 145, __pyx_L3_error) + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "InnerProduct") < 0)) __PYX_ERR(0, 150, __pyx_L3_error) } } else if (PyTuple_GET_SIZE(__pyx_args) != 5) { goto __pyx_L5_argtuple_error; @@ -1770,21 +1770,21 @@ static PyObject *__pyx_pw_10MDAnalysis_3lib_6qcprot_1InnerProduct(PyObject *__py __pyx_v_A = ((PyArrayObject *)values[0]); __pyx_v_coords1 = ((PyArrayObject *)values[1]); __pyx_v_coords2 = ((PyArrayObject *)values[2]); - __pyx_v_N = __Pyx_PyInt_As_int(values[3]); if (unlikely((__pyx_v_N == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 148, __pyx_L3_error) + __pyx_v_N = __Pyx_PyInt_As_int(values[3]); if (unlikely((__pyx_v_N == (int)-1) && PyErr_Occurred())) __PYX_ERR(0, 153, __pyx_L3_error) __pyx_v_weight = ((PyArrayObject *)values[4]); } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; - __Pyx_RaiseArgtupleInvalid("InnerProduct", 1, 5, 5, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(0, 145, __pyx_L3_error) + __Pyx_RaiseArgtupleInvalid("InnerProduct", 1, 5, 5, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(0, 150, __pyx_L3_error) __pyx_L3_error:; __Pyx_AddTraceback("MDAnalysis.lib.qcprot.InnerProduct", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_A), __pyx_ptype_5numpy_ndarray, 1, "A", 0))) __PYX_ERR(0, 145, __pyx_L1_error) - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords1), __pyx_ptype_5numpy_ndarray, 1, "coords1", 0))) __PYX_ERR(0, 146, __pyx_L1_error) - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords2), __pyx_ptype_5numpy_ndarray, 1, "coords2", 0))) __PYX_ERR(0, 147, __pyx_L1_error) - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_weight), __pyx_ptype_5numpy_ndarray, 1, "weight", 0))) __PYX_ERR(0, 149, __pyx_L1_error) + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_A), __pyx_ptype_5numpy_ndarray, 1, "A", 0))) __PYX_ERR(0, 150, __pyx_L1_error) + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords1), __pyx_ptype_5numpy_ndarray, 1, "coords1", 0))) __PYX_ERR(0, 151, __pyx_L1_error) + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_coords2), __pyx_ptype_5numpy_ndarray, 1, "coords2", 0))) __PYX_ERR(0, 152, __pyx_L1_error) + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_weight), __pyx_ptype_5numpy_ndarray, 1, "weight", 0))) __PYX_ERR(0, 154, __pyx_L1_error) __pyx_r = __pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(__pyx_self, __pyx_v_A, __pyx_v_coords1, __pyx_v_coords2, __pyx_v_N, __pyx_v_weight); /* function exit code */ @@ -1901,26 +1901,26 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_pybuffernd_weight.rcbuffer = &__pyx_pybuffer_weight; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_A.rcbuffer->pybuffer, (PyObject*)__pyx_v_A, &__Pyx_TypeInfo_nn___pyx_t_5numpy_float64_t, PyBUF_FORMAT| PyBUF_STRIDES| PyBUF_WRITABLE, 1, 0, __pyx_stack) == -1)) __PYX_ERR(0, 145, __pyx_L1_error) + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_A.rcbuffer->pybuffer, (PyObject*)__pyx_v_A, &__Pyx_TypeInfo_nn___pyx_t_5numpy_float64_t, PyBUF_FORMAT| PyBUF_STRIDES| PyBUF_WRITABLE, 1, 0, __pyx_stack) == -1)) __PYX_ERR(0, 150, __pyx_L1_error) } __pyx_pybuffernd_A.diminfo[0].strides = __pyx_pybuffernd_A.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_A.diminfo[0].shape = __pyx_pybuffernd_A.rcbuffer->pybuffer.shape[0]; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_coords1.rcbuffer->pybuffer, (PyObject*)__pyx_v_coords1, &__Pyx_TypeInfo_nn___pyx_t_5numpy_float64_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) __PYX_ERR(0, 145, __pyx_L1_error) + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_coords1.rcbuffer->pybuffer, (PyObject*)__pyx_v_coords1, &__Pyx_TypeInfo_nn___pyx_t_5numpy_float64_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) __PYX_ERR(0, 150, __pyx_L1_error) } __pyx_pybuffernd_coords1.diminfo[0].strides = __pyx_pybuffernd_coords1.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_coords1.diminfo[0].shape = __pyx_pybuffernd_coords1.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_coords1.diminfo[1].strides = __pyx_pybuffernd_coords1.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_coords1.diminfo[1].shape = __pyx_pybuffernd_coords1.rcbuffer->pybuffer.shape[1]; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_coords2.rcbuffer->pybuffer, (PyObject*)__pyx_v_coords2, &__Pyx_TypeInfo_nn___pyx_t_5numpy_float64_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) __PYX_ERR(0, 145, __pyx_L1_error) + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_coords2.rcbuffer->pybuffer, (PyObject*)__pyx_v_coords2, &__Pyx_TypeInfo_nn___pyx_t_5numpy_float64_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) __PYX_ERR(0, 150, __pyx_L1_error) } __pyx_pybuffernd_coords2.diminfo[0].strides = __pyx_pybuffernd_coords2.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_coords2.diminfo[0].shape = __pyx_pybuffernd_coords2.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_coords2.diminfo[1].strides = __pyx_pybuffernd_coords2.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_coords2.diminfo[1].shape = __pyx_pybuffernd_coords2.rcbuffer->pybuffer.shape[1]; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_weight.rcbuffer->pybuffer, (PyObject*)__pyx_v_weight, &__Pyx_TypeInfo_nn___pyx_t_5numpy_float64_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) __PYX_ERR(0, 145, __pyx_L1_error) + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_weight.rcbuffer->pybuffer, (PyObject*)__pyx_v_weight, &__Pyx_TypeInfo_nn___pyx_t_5numpy_float64_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) __PYX_ERR(0, 150, __pyx_L1_error) } __pyx_pybuffernd_weight.diminfo[0].strides = __pyx_pybuffernd_weight.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_weight.diminfo[0].shape = __pyx_pybuffernd_weight.rcbuffer->pybuffer.shape[0]; - /* "MDAnalysis/lib/qcprot.pyx":187 + /* "MDAnalysis/lib/qcprot.pyx":192 * cdef double G1, G2 * * G1 = 0.0 # <<<<<<<<<<<<<< @@ -1929,7 +1929,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P */ __pyx_v_G1 = 0.0; - /* "MDAnalysis/lib/qcprot.pyx":188 + /* "MDAnalysis/lib/qcprot.pyx":193 * * G1 = 0.0 * G2 = 0.0 # <<<<<<<<<<<<<< @@ -1938,7 +1938,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P */ __pyx_v_G2 = 0.0; - /* "MDAnalysis/lib/qcprot.pyx":190 + /* "MDAnalysis/lib/qcprot.pyx":195 * G2 = 0.0 * * A[0] = A[1] = A[2] = A[3] = A[4] = A[5] = A[6] = A[7] = A[8] = 0.0 # <<<<<<<<<<<<<< @@ -1964,7 +1964,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_t_9 = 8; *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_A.rcbuffer->pybuffer.buf, __pyx_t_9, __pyx_pybuffernd_A.diminfo[0].strides) = 0.0; - /* "MDAnalysis/lib/qcprot.pyx":192 + /* "MDAnalysis/lib/qcprot.pyx":197 * A[0] = A[1] = A[2] = A[3] = A[4] = A[5] = A[6] = A[7] = A[8] = 0.0 * * if (weight is not None): # <<<<<<<<<<<<<< @@ -1975,7 +1975,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_t_11 = (__pyx_t_10 != 0); if (__pyx_t_11) { - /* "MDAnalysis/lib/qcprot.pyx":193 + /* "MDAnalysis/lib/qcprot.pyx":198 * * if (weight is not None): * for i in range(N): # <<<<<<<<<<<<<< @@ -1986,7 +1986,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P for (__pyx_t_13 = 0; __pyx_t_13 < __pyx_t_12; __pyx_t_13+=1) { __pyx_v_i = __pyx_t_13; - /* "MDAnalysis/lib/qcprot.pyx":194 + /* "MDAnalysis/lib/qcprot.pyx":199 * if (weight is not None): * for i in range(N): * x1 = weight[i] * coords1[i, 0] # <<<<<<<<<<<<<< @@ -1998,7 +1998,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_t_16 = 0; __pyx_v_x1 = ((*__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_weight.rcbuffer->pybuffer.buf, __pyx_t_14, __pyx_pybuffernd_weight.diminfo[0].strides)) * (*__Pyx_BufPtrStrided2d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_coords1.rcbuffer->pybuffer.buf, __pyx_t_15, __pyx_pybuffernd_coords1.diminfo[0].strides, __pyx_t_16, __pyx_pybuffernd_coords1.diminfo[1].strides))); - /* "MDAnalysis/lib/qcprot.pyx":195 + /* "MDAnalysis/lib/qcprot.pyx":200 * for i in range(N): * x1 = weight[i] * coords1[i, 0] * y1 = weight[i] * coords1[i, 1] # <<<<<<<<<<<<<< @@ -2010,7 +2010,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_t_19 = 1; __pyx_v_y1 = ((*__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_weight.rcbuffer->pybuffer.buf, __pyx_t_17, __pyx_pybuffernd_weight.diminfo[0].strides)) * (*__Pyx_BufPtrStrided2d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_coords1.rcbuffer->pybuffer.buf, __pyx_t_18, __pyx_pybuffernd_coords1.diminfo[0].strides, __pyx_t_19, __pyx_pybuffernd_coords1.diminfo[1].strides))); - /* "MDAnalysis/lib/qcprot.pyx":196 + /* "MDAnalysis/lib/qcprot.pyx":201 * x1 = weight[i] * coords1[i, 0] * y1 = weight[i] * coords1[i, 1] * z1 = weight[i] * coords1[i, 2] # <<<<<<<<<<<<<< @@ -2022,7 +2022,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_t_22 = 2; __pyx_v_z1 = ((*__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_weight.rcbuffer->pybuffer.buf, __pyx_t_20, __pyx_pybuffernd_weight.diminfo[0].strides)) * (*__Pyx_BufPtrStrided2d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_coords1.rcbuffer->pybuffer.buf, __pyx_t_21, __pyx_pybuffernd_coords1.diminfo[0].strides, __pyx_t_22, __pyx_pybuffernd_coords1.diminfo[1].strides))); - /* "MDAnalysis/lib/qcprot.pyx":198 + /* "MDAnalysis/lib/qcprot.pyx":203 * z1 = weight[i] * coords1[i, 2] * * G1 += x1 * coords1[i, 0] + y1 * coords1[i, 1] + z1 * coords1[i, 2] # <<<<<<<<<<<<<< @@ -2037,7 +2037,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_t_28 = 2; __pyx_v_G1 = (__pyx_v_G1 + (((__pyx_v_x1 * (*__Pyx_BufPtrStrided2d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_coords1.rcbuffer->pybuffer.buf, __pyx_t_23, __pyx_pybuffernd_coords1.diminfo[0].strides, __pyx_t_24, __pyx_pybuffernd_coords1.diminfo[1].strides))) + (__pyx_v_y1 * (*__Pyx_BufPtrStrided2d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_coords1.rcbuffer->pybuffer.buf, __pyx_t_25, __pyx_pybuffernd_coords1.diminfo[0].strides, __pyx_t_26, __pyx_pybuffernd_coords1.diminfo[1].strides)))) + (__pyx_v_z1 * (*__Pyx_BufPtrStrided2d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_coords1.rcbuffer->pybuffer.buf, __pyx_t_27, __pyx_pybuffernd_coords1.diminfo[0].strides, __pyx_t_28, __pyx_pybuffernd_coords1.diminfo[1].strides))))); - /* "MDAnalysis/lib/qcprot.pyx":200 + /* "MDAnalysis/lib/qcprot.pyx":205 * G1 += x1 * coords1[i, 0] + y1 * coords1[i, 1] + z1 * coords1[i, 2] * * x2 = coords2[i, 0] # <<<<<<<<<<<<<< @@ -2048,7 +2048,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_t_30 = 0; __pyx_v_x2 = (*__Pyx_BufPtrStrided2d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_coords2.rcbuffer->pybuffer.buf, __pyx_t_29, __pyx_pybuffernd_coords2.diminfo[0].strides, __pyx_t_30, __pyx_pybuffernd_coords2.diminfo[1].strides)); - /* "MDAnalysis/lib/qcprot.pyx":201 + /* "MDAnalysis/lib/qcprot.pyx":206 * * x2 = coords2[i, 0] * y2 = coords2[i, 1] # <<<<<<<<<<<<<< @@ -2059,7 +2059,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_t_32 = 1; __pyx_v_y2 = (*__Pyx_BufPtrStrided2d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_coords2.rcbuffer->pybuffer.buf, __pyx_t_31, __pyx_pybuffernd_coords2.diminfo[0].strides, __pyx_t_32, __pyx_pybuffernd_coords2.diminfo[1].strides)); - /* "MDAnalysis/lib/qcprot.pyx":202 + /* "MDAnalysis/lib/qcprot.pyx":207 * x2 = coords2[i, 0] * y2 = coords2[i, 1] * z2 = coords2[i, 2] # <<<<<<<<<<<<<< @@ -2070,7 +2070,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_t_34 = 2; __pyx_v_z2 = (*__Pyx_BufPtrStrided2d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_coords2.rcbuffer->pybuffer.buf, __pyx_t_33, __pyx_pybuffernd_coords2.diminfo[0].strides, __pyx_t_34, __pyx_pybuffernd_coords2.diminfo[1].strides)); - /* "MDAnalysis/lib/qcprot.pyx":204 + /* "MDAnalysis/lib/qcprot.pyx":209 * z2 = coords2[i, 2] * * G2 += weight[i] * (x2 * x2 + y2 * y2 + z2 * z2) # <<<<<<<<<<<<<< @@ -2080,7 +2080,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_t_35 = __pyx_v_i; __pyx_v_G2 = (__pyx_v_G2 + ((*__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_weight.rcbuffer->pybuffer.buf, __pyx_t_35, __pyx_pybuffernd_weight.diminfo[0].strides)) * (((__pyx_v_x2 * __pyx_v_x2) + (__pyx_v_y2 * __pyx_v_y2)) + (__pyx_v_z2 * __pyx_v_z2)))); - /* "MDAnalysis/lib/qcprot.pyx":206 + /* "MDAnalysis/lib/qcprot.pyx":211 * G2 += weight[i] * (x2 * x2 + y2 * y2 + z2 * z2) * * A[0] += (x1 * x2) # <<<<<<<<<<<<<< @@ -2090,7 +2090,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_t_36 = 0; *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_A.rcbuffer->pybuffer.buf, __pyx_t_36, __pyx_pybuffernd_A.diminfo[0].strides) += (__pyx_v_x1 * __pyx_v_x2); - /* "MDAnalysis/lib/qcprot.pyx":207 + /* "MDAnalysis/lib/qcprot.pyx":212 * * A[0] += (x1 * x2) * A[1] += (x1 * y2) # <<<<<<<<<<<<<< @@ -2100,7 +2100,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_t_37 = 1; *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_A.rcbuffer->pybuffer.buf, __pyx_t_37, __pyx_pybuffernd_A.diminfo[0].strides) += (__pyx_v_x1 * __pyx_v_y2); - /* "MDAnalysis/lib/qcprot.pyx":208 + /* "MDAnalysis/lib/qcprot.pyx":213 * A[0] += (x1 * x2) * A[1] += (x1 * y2) * A[2] += (x1 * z2) # <<<<<<<<<<<<<< @@ -2110,7 +2110,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_t_38 = 2; *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_A.rcbuffer->pybuffer.buf, __pyx_t_38, __pyx_pybuffernd_A.diminfo[0].strides) += (__pyx_v_x1 * __pyx_v_z2); - /* "MDAnalysis/lib/qcprot.pyx":210 + /* "MDAnalysis/lib/qcprot.pyx":215 * A[2] += (x1 * z2) * * A[3] += (y1 * x2) # <<<<<<<<<<<<<< @@ -2120,7 +2120,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_t_39 = 3; *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_A.rcbuffer->pybuffer.buf, __pyx_t_39, __pyx_pybuffernd_A.diminfo[0].strides) += (__pyx_v_y1 * __pyx_v_x2); - /* "MDAnalysis/lib/qcprot.pyx":211 + /* "MDAnalysis/lib/qcprot.pyx":216 * * A[3] += (y1 * x2) * A[4] += (y1 * y2) # <<<<<<<<<<<<<< @@ -2130,7 +2130,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_t_40 = 4; *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_A.rcbuffer->pybuffer.buf, __pyx_t_40, __pyx_pybuffernd_A.diminfo[0].strides) += (__pyx_v_y1 * __pyx_v_y2); - /* "MDAnalysis/lib/qcprot.pyx":212 + /* "MDAnalysis/lib/qcprot.pyx":217 * A[3] += (y1 * x2) * A[4] += (y1 * y2) * A[5] += (y1 * z2) # <<<<<<<<<<<<<< @@ -2140,7 +2140,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_t_41 = 5; *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_A.rcbuffer->pybuffer.buf, __pyx_t_41, __pyx_pybuffernd_A.diminfo[0].strides) += (__pyx_v_y1 * __pyx_v_z2); - /* "MDAnalysis/lib/qcprot.pyx":214 + /* "MDAnalysis/lib/qcprot.pyx":219 * A[5] += (y1 * z2) * * A[6] += (z1 * x2) # <<<<<<<<<<<<<< @@ -2150,7 +2150,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_t_42 = 6; *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_A.rcbuffer->pybuffer.buf, __pyx_t_42, __pyx_pybuffernd_A.diminfo[0].strides) += (__pyx_v_z1 * __pyx_v_x2); - /* "MDAnalysis/lib/qcprot.pyx":215 + /* "MDAnalysis/lib/qcprot.pyx":220 * * A[6] += (z1 * x2) * A[7] += (z1 * y2) # <<<<<<<<<<<<<< @@ -2160,7 +2160,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_t_43 = 7; *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_A.rcbuffer->pybuffer.buf, __pyx_t_43, __pyx_pybuffernd_A.diminfo[0].strides) += (__pyx_v_z1 * __pyx_v_y2); - /* "MDAnalysis/lib/qcprot.pyx":216 + /* "MDAnalysis/lib/qcprot.pyx":221 * A[6] += (z1 * x2) * A[7] += (z1 * y2) * A[8] += (z1 * z2) # <<<<<<<<<<<<<< @@ -2171,7 +2171,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_A.rcbuffer->pybuffer.buf, __pyx_t_44, __pyx_pybuffernd_A.diminfo[0].strides) += (__pyx_v_z1 * __pyx_v_z2); } - /* "MDAnalysis/lib/qcprot.pyx":192 + /* "MDAnalysis/lib/qcprot.pyx":197 * A[0] = A[1] = A[2] = A[3] = A[4] = A[5] = A[6] = A[7] = A[8] = 0.0 * * if (weight is not None): # <<<<<<<<<<<<<< @@ -2181,7 +2181,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P goto __pyx_L3; } - /* "MDAnalysis/lib/qcprot.pyx":219 + /* "MDAnalysis/lib/qcprot.pyx":224 * * else: * for i in range(N): # <<<<<<<<<<<<<< @@ -2193,7 +2193,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P for (__pyx_t_13 = 0; __pyx_t_13 < __pyx_t_12; __pyx_t_13+=1) { __pyx_v_i = __pyx_t_13; - /* "MDAnalysis/lib/qcprot.pyx":220 + /* "MDAnalysis/lib/qcprot.pyx":225 * else: * for i in range(N): * x1 = coords1[i, 0] # <<<<<<<<<<<<<< @@ -2204,7 +2204,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_t_46 = 0; __pyx_v_x1 = (*__Pyx_BufPtrStrided2d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_coords1.rcbuffer->pybuffer.buf, __pyx_t_45, __pyx_pybuffernd_coords1.diminfo[0].strides, __pyx_t_46, __pyx_pybuffernd_coords1.diminfo[1].strides)); - /* "MDAnalysis/lib/qcprot.pyx":221 + /* "MDAnalysis/lib/qcprot.pyx":226 * for i in range(N): * x1 = coords1[i, 0] * y1 = coords1[i, 1] # <<<<<<<<<<<<<< @@ -2215,7 +2215,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_t_48 = 1; __pyx_v_y1 = (*__Pyx_BufPtrStrided2d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_coords1.rcbuffer->pybuffer.buf, __pyx_t_47, __pyx_pybuffernd_coords1.diminfo[0].strides, __pyx_t_48, __pyx_pybuffernd_coords1.diminfo[1].strides)); - /* "MDAnalysis/lib/qcprot.pyx":222 + /* "MDAnalysis/lib/qcprot.pyx":227 * x1 = coords1[i, 0] * y1 = coords1[i, 1] * z1 = coords1[i, 2] # <<<<<<<<<<<<<< @@ -2226,7 +2226,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_t_50 = 2; __pyx_v_z1 = (*__Pyx_BufPtrStrided2d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_coords1.rcbuffer->pybuffer.buf, __pyx_t_49, __pyx_pybuffernd_coords1.diminfo[0].strides, __pyx_t_50, __pyx_pybuffernd_coords1.diminfo[1].strides)); - /* "MDAnalysis/lib/qcprot.pyx":224 + /* "MDAnalysis/lib/qcprot.pyx":229 * z1 = coords1[i, 2] * * G1 += (x1 * x1 + y1 * y1 + z1 * z1) # <<<<<<<<<<<<<< @@ -2235,7 +2235,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P */ __pyx_v_G1 = (__pyx_v_G1 + (((__pyx_v_x1 * __pyx_v_x1) + (__pyx_v_y1 * __pyx_v_y1)) + (__pyx_v_z1 * __pyx_v_z1))); - /* "MDAnalysis/lib/qcprot.pyx":226 + /* "MDAnalysis/lib/qcprot.pyx":231 * G1 += (x1 * x1 + y1 * y1 + z1 * z1) * * x2 = coords2[i, 0] # <<<<<<<<<<<<<< @@ -2246,7 +2246,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_t_52 = 0; __pyx_v_x2 = (*__Pyx_BufPtrStrided2d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_coords2.rcbuffer->pybuffer.buf, __pyx_t_51, __pyx_pybuffernd_coords2.diminfo[0].strides, __pyx_t_52, __pyx_pybuffernd_coords2.diminfo[1].strides)); - /* "MDAnalysis/lib/qcprot.pyx":227 + /* "MDAnalysis/lib/qcprot.pyx":232 * * x2 = coords2[i, 0] * y2 = coords2[i, 1] # <<<<<<<<<<<<<< @@ -2257,7 +2257,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_t_54 = 1; __pyx_v_y2 = (*__Pyx_BufPtrStrided2d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_coords2.rcbuffer->pybuffer.buf, __pyx_t_53, __pyx_pybuffernd_coords2.diminfo[0].strides, __pyx_t_54, __pyx_pybuffernd_coords2.diminfo[1].strides)); - /* "MDAnalysis/lib/qcprot.pyx":228 + /* "MDAnalysis/lib/qcprot.pyx":233 * x2 = coords2[i, 0] * y2 = coords2[i, 1] * z2 = coords2[i, 2] # <<<<<<<<<<<<<< @@ -2268,7 +2268,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_t_56 = 2; __pyx_v_z2 = (*__Pyx_BufPtrStrided2d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_coords2.rcbuffer->pybuffer.buf, __pyx_t_55, __pyx_pybuffernd_coords2.diminfo[0].strides, __pyx_t_56, __pyx_pybuffernd_coords2.diminfo[1].strides)); - /* "MDAnalysis/lib/qcprot.pyx":230 + /* "MDAnalysis/lib/qcprot.pyx":235 * z2 = coords2[i, 2] * * G2 += (x2 * x2 + y2 * y2 + z2 * z2) # <<<<<<<<<<<<<< @@ -2277,7 +2277,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P */ __pyx_v_G2 = (__pyx_v_G2 + (((__pyx_v_x2 * __pyx_v_x2) + (__pyx_v_y2 * __pyx_v_y2)) + (__pyx_v_z2 * __pyx_v_z2))); - /* "MDAnalysis/lib/qcprot.pyx":232 + /* "MDAnalysis/lib/qcprot.pyx":237 * G2 += (x2 * x2 + y2 * y2 + z2 * z2) * * A[0] += (x1 * x2) # <<<<<<<<<<<<<< @@ -2287,7 +2287,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_t_57 = 0; *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_A.rcbuffer->pybuffer.buf, __pyx_t_57, __pyx_pybuffernd_A.diminfo[0].strides) += (__pyx_v_x1 * __pyx_v_x2); - /* "MDAnalysis/lib/qcprot.pyx":233 + /* "MDAnalysis/lib/qcprot.pyx":238 * * A[0] += (x1 * x2) * A[1] += (x1 * y2) # <<<<<<<<<<<<<< @@ -2297,7 +2297,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct(CYTHON_UNUSED P __pyx_t_58 = 1; 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- /* "MDAnalysis/lib/qcprot.pyx":347 + /* "MDAnalysis/lib/qcprot.pyx":352 * Sxy2 = Sxy * Sxy * Syz2 = Syz * Syz * Sxz2 = Sxz * Sxz # <<<<<<<<<<<<<< @@ -3343,7 +3343,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_Sxz2 = (__pyx_v_Sxz * __pyx_v_Sxz); - /* "MDAnalysis/lib/qcprot.pyx":349 + /* "MDAnalysis/lib/qcprot.pyx":354 * Sxz2 = Sxz * Sxz * * Syx2 = Syx * Syx # <<<<<<<<<<<<<< @@ -3352,7 +3352,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_Syx2 = (__pyx_v_Syx * __pyx_v_Syx); - /* "MDAnalysis/lib/qcprot.pyx":350 + /* "MDAnalysis/lib/qcprot.pyx":355 * * Syx2 = Syx * Syx * Szy2 = Szy * Szy # <<<<<<<<<<<<<< @@ -3361,7 +3361,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_Szy2 = (__pyx_v_Szy * __pyx_v_Szy); - /* "MDAnalysis/lib/qcprot.pyx":351 + /* "MDAnalysis/lib/qcprot.pyx":356 * Syx2 = Syx * Syx * Szy2 = Szy * Szy * Szx2 = Szx * Szx # <<<<<<<<<<<<<< @@ -3370,7 +3370,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_Szx2 = (__pyx_v_Szx * __pyx_v_Szx); - /* "MDAnalysis/lib/qcprot.pyx":353 + /* "MDAnalysis/lib/qcprot.pyx":358 * Szx2 = Szx * Szx * * SyzSzymSyySzz2 = 2.0 * (Syz*Szy - Syy*Szz) # <<<<<<<<<<<<<< @@ -3379,7 +3379,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_SyzSzymSyySzz2 = (2.0 * ((__pyx_v_Syz * __pyx_v_Szy) - (__pyx_v_Syy * __pyx_v_Szz))); - /* "MDAnalysis/lib/qcprot.pyx":354 + /* "MDAnalysis/lib/qcprot.pyx":359 * * SyzSzymSyySzz2 = 2.0 * (Syz*Szy - Syy*Szz) * Sxx2Syy2Szz2Syz2Szy2 = Syy2 + Szz2 - Sxx2 + Syz2 + Szy2 # <<<<<<<<<<<<<< @@ -3388,7 +3388,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_Sxx2Syy2Szz2Syz2Szy2 = ((((__pyx_v_Syy2 + __pyx_v_Szz2) - __pyx_v_Sxx2) + __pyx_v_Syz2) + __pyx_v_Szy2); - /* "MDAnalysis/lib/qcprot.pyx":356 + /* "MDAnalysis/lib/qcprot.pyx":361 * Sxx2Syy2Szz2Syz2Szy2 = Syy2 + Szz2 - Sxx2 + Syz2 + Szy2 * * C[2] = -2.0 * (Sxx2 + Syy2 + Szz2 + Sxy2 + Syx2 + Sxz2 + Szx2 + Syz2 + Szy2) # <<<<<<<<<<<<<< @@ -3403,11 +3403,11 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT } else if (unlikely(__pyx_t_14 >= __pyx_pybuffernd_C.diminfo[0].shape)) __pyx_t_5 = 0; if (unlikely(__pyx_t_5 != -1)) { __Pyx_RaiseBufferIndexError(__pyx_t_5); - __PYX_ERR(0, 356, __pyx_L1_error) + __PYX_ERR(0, 361, __pyx_L1_error) } *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_C.rcbuffer->pybuffer.buf, __pyx_t_14, __pyx_pybuffernd_C.diminfo[0].strides) = (-2.0 * ((((((((__pyx_v_Sxx2 + __pyx_v_Syy2) + __pyx_v_Szz2) + __pyx_v_Sxy2) + __pyx_v_Syx2) + __pyx_v_Sxz2) + __pyx_v_Szx2) + __pyx_v_Syz2) + __pyx_v_Szy2)); - /* "MDAnalysis/lib/qcprot.pyx":357 + /* "MDAnalysis/lib/qcprot.pyx":362 * * C[2] = -2.0 * (Sxx2 + Syy2 + Szz2 + Sxy2 + Syx2 + Sxz2 + Szx2 + Syz2 + Szy2) * C[1] = 8.0 * (Sxx*Syz*Szy + Syy*Szx*Sxz + Szz*Sxy*Syx - Sxx*Syy*Szz - Syz*Szx*Sxy - Szy*Syx*Sxz) # <<<<<<<<<<<<<< @@ -3422,11 +3422,11 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT } else if (unlikely(__pyx_t_15 >= __pyx_pybuffernd_C.diminfo[0].shape)) __pyx_t_5 = 0; if (unlikely(__pyx_t_5 != -1)) { __Pyx_RaiseBufferIndexError(__pyx_t_5); - __PYX_ERR(0, 357, __pyx_L1_error) + __PYX_ERR(0, 362, __pyx_L1_error) } *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_C.rcbuffer->pybuffer.buf, __pyx_t_15, __pyx_pybuffernd_C.diminfo[0].strides) = (8.0 * (((((((__pyx_v_Sxx * __pyx_v_Syz) * __pyx_v_Szy) + ((__pyx_v_Syy * __pyx_v_Szx) * __pyx_v_Sxz)) + ((__pyx_v_Szz * __pyx_v_Sxy) * __pyx_v_Syx)) - ((__pyx_v_Sxx * __pyx_v_Syy) * __pyx_v_Szz)) - ((__pyx_v_Syz * __pyx_v_Szx) * __pyx_v_Sxy)) - ((__pyx_v_Szy * __pyx_v_Syx) * __pyx_v_Sxz))); - /* "MDAnalysis/lib/qcprot.pyx":359 + /* "MDAnalysis/lib/qcprot.pyx":364 * C[1] = 8.0 * (Sxx*Syz*Szy + Syy*Szx*Sxz + Szz*Sxy*Syx - Sxx*Syy*Szz - Syz*Szx*Sxy - Szy*Syx*Sxz) * * SxzpSzx = Sxz + Szx # <<<<<<<<<<<<<< @@ -3435,7 +3435,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_SxzpSzx = (__pyx_v_Sxz + __pyx_v_Szx); - /* "MDAnalysis/lib/qcprot.pyx":360 + /* "MDAnalysis/lib/qcprot.pyx":365 * * SxzpSzx = Sxz + Szx * SyzpSzy = Syz + Szy # <<<<<<<<<<<<<< @@ -3444,7 +3444,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_SyzpSzy = (__pyx_v_Syz + __pyx_v_Szy); - /* "MDAnalysis/lib/qcprot.pyx":361 + /* "MDAnalysis/lib/qcprot.pyx":366 * SxzpSzx = Sxz + Szx * SyzpSzy = Syz + Szy * SxypSyx = Sxy + Syx # <<<<<<<<<<<<<< @@ -3453,7 +3453,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_SxypSyx = (__pyx_v_Sxy + __pyx_v_Syx); - /* "MDAnalysis/lib/qcprot.pyx":362 + /* "MDAnalysis/lib/qcprot.pyx":367 * SyzpSzy = Syz + Szy * SxypSyx = Sxy + Syx * SyzmSzy = Syz - Szy # <<<<<<<<<<<<<< @@ -3462,7 +3462,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_SyzmSzy = (__pyx_v_Syz - __pyx_v_Szy); - /* "MDAnalysis/lib/qcprot.pyx":363 + /* "MDAnalysis/lib/qcprot.pyx":368 * SxypSyx = Sxy + Syx * SyzmSzy = Syz - Szy * SxzmSzx = Sxz - Szx # <<<<<<<<<<<<<< @@ -3471,7 +3471,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_SxzmSzx = (__pyx_v_Sxz - __pyx_v_Szx); - /* "MDAnalysis/lib/qcprot.pyx":364 + /* "MDAnalysis/lib/qcprot.pyx":369 * SyzmSzy = Syz - Szy * SxzmSzx = Sxz - Szx * SxymSyx = Sxy - Syx # <<<<<<<<<<<<<< @@ -3480,7 +3480,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_SxymSyx = (__pyx_v_Sxy - __pyx_v_Syx); - /* "MDAnalysis/lib/qcprot.pyx":365 + /* "MDAnalysis/lib/qcprot.pyx":370 * SxzmSzx = Sxz - Szx * SxymSyx = Sxy - Syx * SxxpSyy = Sxx + Syy # <<<<<<<<<<<<<< @@ -3489,7 +3489,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_SxxpSyy = (__pyx_v_Sxx + __pyx_v_Syy); - /* "MDAnalysis/lib/qcprot.pyx":366 + /* "MDAnalysis/lib/qcprot.pyx":371 * SxymSyx = Sxy - Syx * SxxpSyy = Sxx + Syy * SxxmSyy = Sxx - Syy # <<<<<<<<<<<<<< @@ -3498,7 +3498,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_SxxmSyy = (__pyx_v_Sxx - __pyx_v_Syy); - /* "MDAnalysis/lib/qcprot.pyx":367 + /* "MDAnalysis/lib/qcprot.pyx":372 * SxxpSyy = Sxx + Syy * SxxmSyy = Sxx - Syy * Sxy2Sxz2Syx2Szx2 = Sxy2 + Sxz2 - Syx2 - Szx2 # <<<<<<<<<<<<<< @@ -3507,7 +3507,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_Sxy2Sxz2Syx2Szx2 = (((__pyx_v_Sxy2 + __pyx_v_Sxz2) - __pyx_v_Syx2) - __pyx_v_Szx2); - /* "MDAnalysis/lib/qcprot.pyx":369 + /* "MDAnalysis/lib/qcprot.pyx":374 * Sxy2Sxz2Syx2Szx2 = Sxy2 + Sxz2 - Syx2 - Szx2 * * C[0] = (Sxy2Sxz2Syx2Szx2 * Sxy2Sxz2Syx2Szx2 # <<<<<<<<<<<<<< @@ -3522,11 +3522,11 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT } else if (unlikely(__pyx_t_16 >= __pyx_pybuffernd_C.diminfo[0].shape)) __pyx_t_5 = 0; if (unlikely(__pyx_t_5 != -1)) { __Pyx_RaiseBufferIndexError(__pyx_t_5); - __PYX_ERR(0, 369, __pyx_L1_error) + __PYX_ERR(0, 374, __pyx_L1_error) } *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_C.rcbuffer->pybuffer.buf, __pyx_t_16, __pyx_pybuffernd_C.diminfo[0].strides) = ((((((__pyx_v_Sxy2Sxz2Syx2Szx2 * __pyx_v_Sxy2Sxz2Syx2Szx2) + ((__pyx_v_Sxx2Syy2Szz2Syz2Szy2 + __pyx_v_SyzSzymSyySzz2) * (__pyx_v_Sxx2Syy2Szz2Syz2Szy2 - __pyx_v_SyzSzymSyySzz2))) + ((((-__pyx_v_SxzpSzx) * __pyx_v_SyzmSzy) + (__pyx_v_SxymSyx * (__pyx_v_SxxmSyy - __pyx_v_Szz))) * (((-__pyx_v_SxzmSzx) * __pyx_v_SyzpSzy) + (__pyx_v_SxymSyx * (__pyx_v_SxxmSyy + __pyx_v_Szz))))) + ((((-__pyx_v_SxzpSzx) * __pyx_v_SyzpSzy) - (__pyx_v_SxypSyx * (__pyx_v_SxxpSyy - __pyx_v_Szz))) * (((-__pyx_v_SxzmSzx) * __pyx_v_SyzmSzy) - (__pyx_v_SxypSyx * (__pyx_v_SxxpSyy + __pyx_v_Szz))))) + (((__pyx_v_SxypSyx * __pyx_v_SyzpSzy) + (__pyx_v_SxzpSzx * (__pyx_v_SxxmSyy + __pyx_v_Szz))) * (((-__pyx_v_SxymSyx) * __pyx_v_SyzmSzy) + (__pyx_v_SxzpSzx * (__pyx_v_SxxpSyy + __pyx_v_Szz))))) + (((__pyx_v_SxypSyx * __pyx_v_SyzmSzy) + (__pyx_v_SxzmSzx * (__pyx_v_SxxmSyy - __pyx_v_Szz))) * (((-__pyx_v_SxymSyx) * __pyx_v_SyzpSzy) + (__pyx_v_SxzmSzx * (__pyx_v_SxxpSyy - __pyx_v_Szz))))); - /* "MDAnalysis/lib/qcprot.pyx":376 + /* "MDAnalysis/lib/qcprot.pyx":381 * + (+(SxypSyx)*(SyzmSzy)+(SxzmSzx)*(SxxmSyy-Szz)) * (-(SxymSyx)*(SyzpSzy)+(SxzmSzx)*(SxxpSyy-Szz))) * * mxEigenV = E0 # <<<<<<<<<<<<<< @@ -3535,7 +3535,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_mxEigenV = __pyx_v_E0; - /* "MDAnalysis/lib/qcprot.pyx":377 + /* "MDAnalysis/lib/qcprot.pyx":382 * * mxEigenV = E0 * for i in range(50): # <<<<<<<<<<<<<< @@ -3545,7 +3545,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT for (__pyx_t_17 = 0; __pyx_t_17 < 50; __pyx_t_17+=1) { __pyx_v_i = __pyx_t_17; - /* "MDAnalysis/lib/qcprot.pyx":378 + /* "MDAnalysis/lib/qcprot.pyx":383 * mxEigenV = E0 * for i in range(50): * oldg = mxEigenV # <<<<<<<<<<<<<< @@ -3554,7 +3554,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_oldg = __pyx_v_mxEigenV; - /* "MDAnalysis/lib/qcprot.pyx":379 + /* "MDAnalysis/lib/qcprot.pyx":384 * for i in range(50): * oldg = mxEigenV * x2 = mxEigenV*mxEigenV # <<<<<<<<<<<<<< @@ -3563,7 +3563,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_x2 = (__pyx_v_mxEigenV * __pyx_v_mxEigenV); - /* "MDAnalysis/lib/qcprot.pyx":380 + /* "MDAnalysis/lib/qcprot.pyx":385 * oldg = mxEigenV * x2 = mxEigenV*mxEigenV * b = (x2 + C[2])*mxEigenV # <<<<<<<<<<<<<< @@ -3578,11 +3578,11 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT } else if (unlikely(__pyx_t_18 >= __pyx_pybuffernd_C.diminfo[0].shape)) __pyx_t_5 = 0; if (unlikely(__pyx_t_5 != -1)) { __Pyx_RaiseBufferIndexError(__pyx_t_5); - __PYX_ERR(0, 380, __pyx_L1_error) + __PYX_ERR(0, 385, __pyx_L1_error) } __pyx_v_b = ((__pyx_v_x2 + (*__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_C.rcbuffer->pybuffer.buf, __pyx_t_18, __pyx_pybuffernd_C.diminfo[0].strides))) * __pyx_v_mxEigenV); - /* "MDAnalysis/lib/qcprot.pyx":381 + /* "MDAnalysis/lib/qcprot.pyx":386 * x2 = mxEigenV*mxEigenV * b = (x2 + C[2])*mxEigenV * a = b + C[1] # <<<<<<<<<<<<<< @@ -3597,11 +3597,11 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT } else if (unlikely(__pyx_t_19 >= __pyx_pybuffernd_C.diminfo[0].shape)) __pyx_t_5 = 0; if (unlikely(__pyx_t_5 != -1)) { __Pyx_RaiseBufferIndexError(__pyx_t_5); - __PYX_ERR(0, 381, __pyx_L1_error) + __PYX_ERR(0, 386, __pyx_L1_error) } __pyx_v_a = (__pyx_v_b + (*__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_C.rcbuffer->pybuffer.buf, __pyx_t_19, __pyx_pybuffernd_C.diminfo[0].strides))); - /* "MDAnalysis/lib/qcprot.pyx":382 + /* "MDAnalysis/lib/qcprot.pyx":387 * b = (x2 + C[2])*mxEigenV * a = b + C[1] * delta = ((a*mxEigenV + C[0])/(2.0*x2*mxEigenV + b + a)) # <<<<<<<<<<<<<< @@ -3616,17 +3616,17 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT } else if (unlikely(__pyx_t_20 >= __pyx_pybuffernd_C.diminfo[0].shape)) __pyx_t_5 = 0; if (unlikely(__pyx_t_5 != -1)) { __Pyx_RaiseBufferIndexError(__pyx_t_5); - __PYX_ERR(0, 382, __pyx_L1_error) + __PYX_ERR(0, 387, __pyx_L1_error) } __pyx_t_21 = ((__pyx_v_a * __pyx_v_mxEigenV) + (*__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_C.rcbuffer->pybuffer.buf, __pyx_t_20, __pyx_pybuffernd_C.diminfo[0].strides))); __pyx_t_22 = ((((2.0 * __pyx_v_x2) * __pyx_v_mxEigenV) + __pyx_v_b) + __pyx_v_a); if (unlikely(__pyx_t_22 == 0)) { PyErr_SetString(PyExc_ZeroDivisionError, "float division"); - __PYX_ERR(0, 382, __pyx_L1_error) + __PYX_ERR(0, 387, __pyx_L1_error) } __pyx_v_delta = (__pyx_t_21 / __pyx_t_22); - /* "MDAnalysis/lib/qcprot.pyx":383 + /* "MDAnalysis/lib/qcprot.pyx":388 * a = b + C[1] * delta = ((a*mxEigenV + C[0])/(2.0*x2*mxEigenV + b + a)) * mxEigenV -= delta # <<<<<<<<<<<<<< @@ -3635,7 +3635,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_mxEigenV = (__pyx_v_mxEigenV - __pyx_v_delta); - /* "MDAnalysis/lib/qcprot.pyx":384 + /* "MDAnalysis/lib/qcprot.pyx":389 * delta = ((a*mxEigenV + C[0])/(2.0*x2*mxEigenV + b + a)) * mxEigenV -= delta * if (fabs(mxEigenV - oldg) < fabs((evalprec)*mxEigenV)): # <<<<<<<<<<<<<< @@ -3645,7 +3645,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT __pyx_t_23 = ((fabs((__pyx_v_mxEigenV - __pyx_v_oldg)) < fabs((__pyx_v_evalprec * __pyx_v_mxEigenV))) != 0); if (__pyx_t_23) { - /* "MDAnalysis/lib/qcprot.pyx":385 + /* "MDAnalysis/lib/qcprot.pyx":390 * mxEigenV -= delta * if (fabs(mxEigenV - oldg) < fabs((evalprec)*mxEigenV)): * break # <<<<<<<<<<<<<< @@ -3654,7 +3654,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ goto __pyx_L4_break; - /* "MDAnalysis/lib/qcprot.pyx":384 + /* "MDAnalysis/lib/qcprot.pyx":389 * delta = ((a*mxEigenV + C[0])/(2.0*x2*mxEigenV + b + a)) * mxEigenV -= delta * if (fabs(mxEigenV - oldg) < fabs((evalprec)*mxEigenV)): # <<<<<<<<<<<<<< @@ -3665,7 +3665,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT } __pyx_L4_break:; - /* "MDAnalysis/lib/qcprot.pyx":392 + /* "MDAnalysis/lib/qcprot.pyx":397 * # the fabs() is to guard against extremely small, * # but *negative* numbers due to floating point error * rms = sqrt(fabs(2.0 * (E0 - mxEigenV)/N)) # <<<<<<<<<<<<<< @@ -3675,11 +3675,11 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT __pyx_t_22 = (2.0 * (__pyx_v_E0 - __pyx_v_mxEigenV)); if (unlikely(__pyx_v_N == 0)) { PyErr_SetString(PyExc_ZeroDivisionError, "float division"); - __PYX_ERR(0, 392, __pyx_L1_error) + __PYX_ERR(0, 397, __pyx_L1_error) } __pyx_v_rms = sqrt(fabs((__pyx_t_22 / __pyx_v_N))); - /* "MDAnalysis/lib/qcprot.pyx":394 + /* "MDAnalysis/lib/qcprot.pyx":399 * rms = sqrt(fabs(2.0 * (E0 - mxEigenV)/N)) * * if (rot is None): # <<<<<<<<<<<<<< @@ -3690,7 +3690,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT __pyx_t_24 = (__pyx_t_23 != 0); if (__pyx_t_24) { - /* "MDAnalysis/lib/qcprot.pyx":395 + /* "MDAnalysis/lib/qcprot.pyx":400 * * if (rot is None): * return rms # Don't bother with rotation. # <<<<<<<<<<<<<< @@ -3698,13 +3698,13 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT * a11 = SxxpSyy + Szz-mxEigenV */ __Pyx_XDECREF(__pyx_r); - __pyx_t_1 = PyFloat_FromDouble(__pyx_v_rms); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 395, __pyx_L1_error) + __pyx_t_1 = PyFloat_FromDouble(__pyx_v_rms); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 400, __pyx_L1_error) __Pyx_GOTREF(__pyx_t_1); __pyx_r = __pyx_t_1; __pyx_t_1 = 0; goto __pyx_L0; - /* "MDAnalysis/lib/qcprot.pyx":394 + /* "MDAnalysis/lib/qcprot.pyx":399 * rms = sqrt(fabs(2.0 * (E0 - mxEigenV)/N)) * * if (rot is None): # <<<<<<<<<<<<<< @@ -3713,7 +3713,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ } - /* "MDAnalysis/lib/qcprot.pyx":397 + /* "MDAnalysis/lib/qcprot.pyx":402 * return rms # Don't bother with rotation. * * a11 = SxxpSyy + Szz-mxEigenV # <<<<<<<<<<<<<< @@ -3722,7 +3722,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_a11 = ((__pyx_v_SxxpSyy + __pyx_v_Szz) - __pyx_v_mxEigenV); - /* "MDAnalysis/lib/qcprot.pyx":398 + /* "MDAnalysis/lib/qcprot.pyx":403 * * a11 = SxxpSyy + Szz-mxEigenV * a12 = SyzmSzy # <<<<<<<<<<<<<< @@ -3731,7 +3731,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_a12 = __pyx_v_SyzmSzy; - /* "MDAnalysis/lib/qcprot.pyx":399 + /* "MDAnalysis/lib/qcprot.pyx":404 * a11 = SxxpSyy + Szz-mxEigenV * a12 = SyzmSzy * a13 = - SxzmSzx # <<<<<<<<<<<<<< @@ -3740,7 +3740,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_a13 = (-__pyx_v_SxzmSzx); - /* "MDAnalysis/lib/qcprot.pyx":400 + /* "MDAnalysis/lib/qcprot.pyx":405 * a12 = SyzmSzy * a13 = - SxzmSzx * a14 = SxymSyx # <<<<<<<<<<<<<< @@ -3749,7 +3749,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_a14 = __pyx_v_SxymSyx; - /* "MDAnalysis/lib/qcprot.pyx":401 + /* "MDAnalysis/lib/qcprot.pyx":406 * a13 = - SxzmSzx * a14 = SxymSyx * a21 = SyzmSzy # <<<<<<<<<<<<<< @@ -3758,7 +3758,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_a21 = __pyx_v_SyzmSzy; - /* "MDAnalysis/lib/qcprot.pyx":402 + /* "MDAnalysis/lib/qcprot.pyx":407 * a14 = SxymSyx * a21 = SyzmSzy * a22 = SxxmSyy - Szz-mxEigenV # <<<<<<<<<<<<<< @@ -3767,7 +3767,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_a22 = ((__pyx_v_SxxmSyy - __pyx_v_Szz) - __pyx_v_mxEigenV); - /* "MDAnalysis/lib/qcprot.pyx":403 + /* "MDAnalysis/lib/qcprot.pyx":408 * a21 = SyzmSzy * a22 = SxxmSyy - Szz-mxEigenV * a23 = SxypSyx # <<<<<<<<<<<<<< @@ -3776,7 +3776,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_a23 = __pyx_v_SxypSyx; - /* "MDAnalysis/lib/qcprot.pyx":404 + /* "MDAnalysis/lib/qcprot.pyx":409 * a22 = SxxmSyy - Szz-mxEigenV * a23 = SxypSyx * a24= SxzpSzx # <<<<<<<<<<<<<< @@ -3785,7 +3785,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_a24 = __pyx_v_SxzpSzx; - /* "MDAnalysis/lib/qcprot.pyx":405 + /* "MDAnalysis/lib/qcprot.pyx":410 * a23 = SxypSyx * a24= SxzpSzx * a31 = a13 # <<<<<<<<<<<<<< @@ -3794,7 +3794,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_a31 = __pyx_v_a13; - /* "MDAnalysis/lib/qcprot.pyx":406 + /* "MDAnalysis/lib/qcprot.pyx":411 * a24= SxzpSzx * a31 = a13 * a32 = a23 # <<<<<<<<<<<<<< @@ -3803,7 +3803,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_a32 = __pyx_v_a23; - /* "MDAnalysis/lib/qcprot.pyx":407 + /* "MDAnalysis/lib/qcprot.pyx":412 * a31 = a13 * a32 = a23 * a33 = Syy-Sxx-Szz - mxEigenV # <<<<<<<<<<<<<< @@ -3812,7 +3812,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_a33 = (((__pyx_v_Syy - __pyx_v_Sxx) - __pyx_v_Szz) - __pyx_v_mxEigenV); - /* "MDAnalysis/lib/qcprot.pyx":408 + /* "MDAnalysis/lib/qcprot.pyx":413 * a32 = a23 * a33 = Syy-Sxx-Szz - mxEigenV * a34 = SyzpSzy # <<<<<<<<<<<<<< @@ -3821,7 +3821,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_a34 = __pyx_v_SyzpSzy; - /* "MDAnalysis/lib/qcprot.pyx":409 + /* "MDAnalysis/lib/qcprot.pyx":414 * a33 = Syy-Sxx-Szz - mxEigenV * a34 = SyzpSzy * a41 = a14 # <<<<<<<<<<<<<< @@ -3830,7 +3830,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_a41 = __pyx_v_a14; - /* "MDAnalysis/lib/qcprot.pyx":410 + /* "MDAnalysis/lib/qcprot.pyx":415 * a34 = SyzpSzy * a41 = a14 * a42 = a24 # <<<<<<<<<<<<<< @@ -3839,7 +3839,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_a42 = __pyx_v_a24; - /* "MDAnalysis/lib/qcprot.pyx":411 + /* "MDAnalysis/lib/qcprot.pyx":416 * a41 = a14 * a42 = a24 * a43 = a34 # <<<<<<<<<<<<<< @@ -3848,7 +3848,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_a43 = __pyx_v_a34; - /* "MDAnalysis/lib/qcprot.pyx":412 + /* "MDAnalysis/lib/qcprot.pyx":417 * a42 = a24 * a43 = a34 * a44 = Szz - SxxpSyy - mxEigenV # <<<<<<<<<<<<<< @@ -3857,7 +3857,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_a44 = ((__pyx_v_Szz - __pyx_v_SxxpSyy) - __pyx_v_mxEigenV); - /* "MDAnalysis/lib/qcprot.pyx":413 + /* "MDAnalysis/lib/qcprot.pyx":418 * a43 = a34 * a44 = Szz - SxxpSyy - mxEigenV * a3344_4334 = a33 * a44 - a43 * a34 # <<<<<<<<<<<<<< @@ -3866,7 +3866,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_a3344_4334 = ((__pyx_v_a33 * __pyx_v_a44) - (__pyx_v_a43 * __pyx_v_a34)); - /* "MDAnalysis/lib/qcprot.pyx":414 + /* "MDAnalysis/lib/qcprot.pyx":419 * a44 = Szz - SxxpSyy - mxEigenV * a3344_4334 = a33 * a44 - a43 * a34 * a3244_4234 = a32 * a44-a42*a34 # <<<<<<<<<<<<<< @@ -3875,7 +3875,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_a3244_4234 = ((__pyx_v_a32 * __pyx_v_a44) - (__pyx_v_a42 * __pyx_v_a34)); - /* "MDAnalysis/lib/qcprot.pyx":415 + /* "MDAnalysis/lib/qcprot.pyx":420 * a3344_4334 = a33 * a44 - a43 * a34 * a3244_4234 = a32 * a44-a42*a34 * a3243_4233 = a32 * a43 - a42 * a33 # <<<<<<<<<<<<<< @@ -3884,7 +3884,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_a3243_4233 = ((__pyx_v_a32 * __pyx_v_a43) - (__pyx_v_a42 * __pyx_v_a33)); - /* "MDAnalysis/lib/qcprot.pyx":416 + /* "MDAnalysis/lib/qcprot.pyx":421 * a3244_4234 = a32 * a44-a42*a34 * a3243_4233 = a32 * a43 - a42 * a33 * a3143_4133 = a31 * a43-a41*a33 # <<<<<<<<<<<<<< @@ -3893,7 +3893,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_a3143_4133 = ((__pyx_v_a31 * __pyx_v_a43) - (__pyx_v_a41 * __pyx_v_a33)); - /* "MDAnalysis/lib/qcprot.pyx":417 + /* "MDAnalysis/lib/qcprot.pyx":422 * a3243_4233 = a32 * a43 - a42 * a33 * a3143_4133 = a31 * a43-a41*a33 * a3144_4134 = a31 * a44 - a41 * a34 # <<<<<<<<<<<<<< @@ -3902,7 +3902,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_a3144_4134 = ((__pyx_v_a31 * __pyx_v_a44) - (__pyx_v_a41 * __pyx_v_a34)); - /* "MDAnalysis/lib/qcprot.pyx":418 + /* "MDAnalysis/lib/qcprot.pyx":423 * a3143_4133 = a31 * a43-a41*a33 * a3144_4134 = a31 * a44 - a41 * a34 * a3142_4132 = a31 * a42-a41*a32 # <<<<<<<<<<<<<< @@ -3911,7 +3911,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_a3142_4132 = ((__pyx_v_a31 * __pyx_v_a42) - (__pyx_v_a41 * __pyx_v_a32)); - /* "MDAnalysis/lib/qcprot.pyx":419 + /* "MDAnalysis/lib/qcprot.pyx":424 * a3144_4134 = a31 * a44 - a41 * a34 * a3142_4132 = a31 * a42-a41*a32 * q1 = a22*a3344_4334-a23*a3244_4234+a24*a3243_4233 # <<<<<<<<<<<<<< @@ -3920,7 +3920,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_q1 = (((__pyx_v_a22 * __pyx_v_a3344_4334) - (__pyx_v_a23 * __pyx_v_a3244_4234)) + (__pyx_v_a24 * __pyx_v_a3243_4233)); - /* "MDAnalysis/lib/qcprot.pyx":420 + /* "MDAnalysis/lib/qcprot.pyx":425 * a3142_4132 = a31 * a42-a41*a32 * q1 = a22*a3344_4334-a23*a3244_4234+a24*a3243_4233 * q2 = -a21*a3344_4334+a23*a3144_4134-a24*a3143_4133 # <<<<<<<<<<<<<< @@ -3929,7 +3929,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_q2 = ((((-__pyx_v_a21) * __pyx_v_a3344_4334) + (__pyx_v_a23 * __pyx_v_a3144_4134)) - (__pyx_v_a24 * __pyx_v_a3143_4133)); - /* "MDAnalysis/lib/qcprot.pyx":421 + /* "MDAnalysis/lib/qcprot.pyx":426 * q1 = a22*a3344_4334-a23*a3244_4234+a24*a3243_4233 * q2 = -a21*a3344_4334+a23*a3144_4134-a24*a3143_4133 * q3 = a21*a3244_4234-a22*a3144_4134+a24*a3142_4132 # <<<<<<<<<<<<<< @@ -3938,7 +3938,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_q3 = (((__pyx_v_a21 * __pyx_v_a3244_4234) - (__pyx_v_a22 * __pyx_v_a3144_4134)) + (__pyx_v_a24 * __pyx_v_a3142_4132)); - /* "MDAnalysis/lib/qcprot.pyx":422 + /* "MDAnalysis/lib/qcprot.pyx":427 * q2 = -a21*a3344_4334+a23*a3144_4134-a24*a3143_4133 * q3 = a21*a3244_4234-a22*a3144_4134+a24*a3142_4132 * q4 = -a21*a3243_4233+a22*a3143_4133-a23*a3142_4132 # <<<<<<<<<<<<<< @@ -3947,7 +3947,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_q4 = ((((-__pyx_v_a21) * __pyx_v_a3243_4233) + (__pyx_v_a22 * __pyx_v_a3143_4133)) - (__pyx_v_a23 * __pyx_v_a3142_4132)); - /* "MDAnalysis/lib/qcprot.pyx":424 + /* "MDAnalysis/lib/qcprot.pyx":429 * q4 = -a21*a3243_4233+a22*a3143_4133-a23*a3142_4132 * * qsqr = q1 * q1 + q2 * q2 + q3 * q3 + q4 * q4 # <<<<<<<<<<<<<< @@ -3956,7 +3956,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_qsqr = ((((__pyx_v_q1 * __pyx_v_q1) + (__pyx_v_q2 * __pyx_v_q2)) + (__pyx_v_q3 * __pyx_v_q3)) + (__pyx_v_q4 * __pyx_v_q4)); - /* "MDAnalysis/lib/qcprot.pyx":431 + /* "MDAnalysis/lib/qcprot.pyx":436 * # uncommented, but it is most likely unnecessary. * * if (qsqr < evecprec): # <<<<<<<<<<<<<< @@ -3966,7 +3966,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT __pyx_t_24 = ((__pyx_v_qsqr < __pyx_v_evecprec) != 0); if (__pyx_t_24) { - /* "MDAnalysis/lib/qcprot.pyx":432 + /* "MDAnalysis/lib/qcprot.pyx":437 * * if (qsqr < evecprec): * q1 = a12*a3344_4334 - a13*a3244_4234 + a14*a3243_4233 # <<<<<<<<<<<<<< @@ -3975,7 +3975,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_q1 = (((__pyx_v_a12 * __pyx_v_a3344_4334) - (__pyx_v_a13 * __pyx_v_a3244_4234)) + (__pyx_v_a14 * __pyx_v_a3243_4233)); - /* "MDAnalysis/lib/qcprot.pyx":433 + /* "MDAnalysis/lib/qcprot.pyx":438 * if (qsqr < evecprec): * q1 = a12*a3344_4334 - a13*a3244_4234 + a14*a3243_4233 * q2 = -a11*a3344_4334 + a13*a3144_4134 - a14*a3143_4133 # <<<<<<<<<<<<<< @@ -3984,7 +3984,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_q2 = ((((-__pyx_v_a11) * __pyx_v_a3344_4334) + (__pyx_v_a13 * __pyx_v_a3144_4134)) - (__pyx_v_a14 * __pyx_v_a3143_4133)); - /* "MDAnalysis/lib/qcprot.pyx":434 + /* "MDAnalysis/lib/qcprot.pyx":439 * q1 = a12*a3344_4334 - a13*a3244_4234 + a14*a3243_4233 * q2 = -a11*a3344_4334 + a13*a3144_4134 - a14*a3143_4133 * q3 = a11*a3244_4234 - a12*a3144_4134 + a14*a3142_4132 # <<<<<<<<<<<<<< @@ -3993,7 +3993,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_q3 = (((__pyx_v_a11 * __pyx_v_a3244_4234) - (__pyx_v_a12 * __pyx_v_a3144_4134)) + (__pyx_v_a14 * __pyx_v_a3142_4132)); - /* "MDAnalysis/lib/qcprot.pyx":435 + /* "MDAnalysis/lib/qcprot.pyx":440 * q2 = -a11*a3344_4334 + a13*a3144_4134 - a14*a3143_4133 * q3 = a11*a3244_4234 - a12*a3144_4134 + a14*a3142_4132 * q4 = -a11*a3243_4233 + a12*a3143_4133 - a13*a3142_4132 # <<<<<<<<<<<<<< @@ -4002,7 +4002,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_q4 = ((((-__pyx_v_a11) * __pyx_v_a3243_4233) + (__pyx_v_a12 * __pyx_v_a3143_4133)) - (__pyx_v_a13 * __pyx_v_a3142_4132)); - /* "MDAnalysis/lib/qcprot.pyx":436 + /* "MDAnalysis/lib/qcprot.pyx":441 * q3 = a11*a3244_4234 - a12*a3144_4134 + a14*a3142_4132 * q4 = -a11*a3243_4233 + a12*a3143_4133 - a13*a3142_4132 * qsqr = q1*q1 + q2 *q2 + q3*q3+q4*q4 # <<<<<<<<<<<<<< @@ -4011,7 +4011,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_qsqr = ((((__pyx_v_q1 * __pyx_v_q1) + (__pyx_v_q2 * __pyx_v_q2)) + (__pyx_v_q3 * __pyx_v_q3)) + (__pyx_v_q4 * __pyx_v_q4)); - /* "MDAnalysis/lib/qcprot.pyx":438 + /* "MDAnalysis/lib/qcprot.pyx":443 * qsqr = q1*q1 + q2 *q2 + q3*q3+q4*q4 * * if (qsqr < evecprec): # <<<<<<<<<<<<<< @@ -4021,7 +4021,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT __pyx_t_24 = ((__pyx_v_qsqr < __pyx_v_evecprec) != 0); if (__pyx_t_24) { - /* "MDAnalysis/lib/qcprot.pyx":439 + /* "MDAnalysis/lib/qcprot.pyx":444 * * if (qsqr < evecprec): * a1324_1423 = a13 * a24 - a14 * a23 # <<<<<<<<<<<<<< @@ -4030,7 +4030,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_a1324_1423 = ((__pyx_v_a13 * __pyx_v_a24) - (__pyx_v_a14 * __pyx_v_a23)); - /* "MDAnalysis/lib/qcprot.pyx":440 + /* "MDAnalysis/lib/qcprot.pyx":445 * if (qsqr < evecprec): * a1324_1423 = a13 * a24 - a14 * a23 * a1224_1422 = a12 * a24 - a14 * a22 # <<<<<<<<<<<<<< @@ -4039,7 +4039,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_a1224_1422 = ((__pyx_v_a12 * __pyx_v_a24) - (__pyx_v_a14 * __pyx_v_a22)); - /* "MDAnalysis/lib/qcprot.pyx":441 + /* "MDAnalysis/lib/qcprot.pyx":446 * a1324_1423 = a13 * a24 - a14 * a23 * a1224_1422 = a12 * a24 - a14 * a22 * a1223_1322 = a12 * a23 - a13 * a22 # <<<<<<<<<<<<<< @@ -4048,7 +4048,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_a1223_1322 = ((__pyx_v_a12 * __pyx_v_a23) - (__pyx_v_a13 * __pyx_v_a22)); - /* "MDAnalysis/lib/qcprot.pyx":442 + /* "MDAnalysis/lib/qcprot.pyx":447 * a1224_1422 = a12 * a24 - a14 * a22 * a1223_1322 = a12 * a23 - a13 * a22 * a1124_1421 = a11 * a24 - a14 * a21 # <<<<<<<<<<<<<< @@ -4057,7 +4057,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_a1124_1421 = ((__pyx_v_a11 * __pyx_v_a24) - (__pyx_v_a14 * __pyx_v_a21)); - /* "MDAnalysis/lib/qcprot.pyx":443 + /* "MDAnalysis/lib/qcprot.pyx":448 * a1223_1322 = a12 * a23 - a13 * a22 * a1124_1421 = a11 * a24 - a14 * a21 * a1123_1321 = a11 * a23 - a13 * a21 # <<<<<<<<<<<<<< @@ -4066,7 +4066,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_a1123_1321 = ((__pyx_v_a11 * __pyx_v_a23) - (__pyx_v_a13 * __pyx_v_a21)); - /* "MDAnalysis/lib/qcprot.pyx":444 + /* "MDAnalysis/lib/qcprot.pyx":449 * a1124_1421 = a11 * a24 - a14 * a21 * a1123_1321 = a11 * a23 - a13 * a21 * a1122_1221 = a11 * a22 - a12 * a21 # <<<<<<<<<<<<<< @@ -4075,7 +4075,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_a1122_1221 = ((__pyx_v_a11 * __pyx_v_a22) - (__pyx_v_a12 * __pyx_v_a21)); - /* "MDAnalysis/lib/qcprot.pyx":446 + /* "MDAnalysis/lib/qcprot.pyx":451 * a1122_1221 = a11 * a22 - a12 * a21 * * q1 = a42 * a1324_1423 - a43 * a1224_1422 + a44 * a1223_1322 # <<<<<<<<<<<<<< @@ -4084,7 +4084,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_q1 = (((__pyx_v_a42 * __pyx_v_a1324_1423) - (__pyx_v_a43 * __pyx_v_a1224_1422)) + (__pyx_v_a44 * __pyx_v_a1223_1322)); - /* "MDAnalysis/lib/qcprot.pyx":447 + /* "MDAnalysis/lib/qcprot.pyx":452 * * q1 = a42 * a1324_1423 - a43 * a1224_1422 + a44 * a1223_1322 * q2 = -a41 * a1324_1423 + a43 * a1124_1421 - a44 * a1123_1321 # <<<<<<<<<<<<<< @@ -4093,7 +4093,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_q2 = ((((-__pyx_v_a41) * __pyx_v_a1324_1423) + (__pyx_v_a43 * __pyx_v_a1124_1421)) - (__pyx_v_a44 * __pyx_v_a1123_1321)); - /* "MDAnalysis/lib/qcprot.pyx":448 + /* "MDAnalysis/lib/qcprot.pyx":453 * q1 = a42 * a1324_1423 - a43 * a1224_1422 + a44 * a1223_1322 * q2 = -a41 * a1324_1423 + a43 * a1124_1421 - a44 * a1123_1321 * q3 = a41 * a1224_1422 - a42 * a1124_1421 + a44 * a1122_1221 # <<<<<<<<<<<<<< @@ -4102,7 +4102,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_q3 = (((__pyx_v_a41 * __pyx_v_a1224_1422) - (__pyx_v_a42 * __pyx_v_a1124_1421)) + (__pyx_v_a44 * __pyx_v_a1122_1221)); - /* "MDAnalysis/lib/qcprot.pyx":449 + /* "MDAnalysis/lib/qcprot.pyx":454 * q2 = -a41 * a1324_1423 + a43 * a1124_1421 - a44 * a1123_1321 * q3 = a41 * a1224_1422 - a42 * a1124_1421 + a44 * a1122_1221 * q4 = -a41 * a1223_1322 + a42 * a1123_1321 - a43 * a1122_1221 # <<<<<<<<<<<<<< @@ -4111,7 +4111,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_q4 = ((((-__pyx_v_a41) * __pyx_v_a1223_1322) + (__pyx_v_a42 * __pyx_v_a1123_1321)) - (__pyx_v_a43 * __pyx_v_a1122_1221)); - /* "MDAnalysis/lib/qcprot.pyx":450 + /* "MDAnalysis/lib/qcprot.pyx":455 * q3 = a41 * a1224_1422 - a42 * a1124_1421 + a44 * a1122_1221 * q4 = -a41 * a1223_1322 + a42 * a1123_1321 - a43 * a1122_1221 * qsqr = q1*q1 + q2 *q2 + q3*q3+q4*q4 # <<<<<<<<<<<<<< @@ -4120,7 +4120,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_qsqr = ((((__pyx_v_q1 * __pyx_v_q1) + (__pyx_v_q2 * __pyx_v_q2)) + (__pyx_v_q3 * __pyx_v_q3)) + (__pyx_v_q4 * __pyx_v_q4)); - /* "MDAnalysis/lib/qcprot.pyx":452 + /* "MDAnalysis/lib/qcprot.pyx":457 * qsqr = q1*q1 + q2 *q2 + q3*q3+q4*q4 * * if (qsqr < evecprec): # <<<<<<<<<<<<<< @@ -4130,7 +4130,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT __pyx_t_24 = ((__pyx_v_qsqr < __pyx_v_evecprec) != 0); if (__pyx_t_24) { - /* "MDAnalysis/lib/qcprot.pyx":453 + /* "MDAnalysis/lib/qcprot.pyx":458 * * if (qsqr < evecprec): * q1 = a32 * a1324_1423 - a33 * a1224_1422 + a34 * a1223_1322 # <<<<<<<<<<<<<< @@ -4139,7 +4139,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_q1 = (((__pyx_v_a32 * __pyx_v_a1324_1423) - (__pyx_v_a33 * __pyx_v_a1224_1422)) + (__pyx_v_a34 * __pyx_v_a1223_1322)); - /* "MDAnalysis/lib/qcprot.pyx":454 + /* "MDAnalysis/lib/qcprot.pyx":459 * if (qsqr < evecprec): * q1 = a32 * a1324_1423 - a33 * a1224_1422 + a34 * a1223_1322 * q2 = -a31 * a1324_1423 + a33 * a1124_1421 - a34 * a1123_1321 # <<<<<<<<<<<<<< @@ -4148,7 +4148,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_q2 = ((((-__pyx_v_a31) * __pyx_v_a1324_1423) + (__pyx_v_a33 * __pyx_v_a1124_1421)) - (__pyx_v_a34 * __pyx_v_a1123_1321)); - /* "MDAnalysis/lib/qcprot.pyx":455 + /* "MDAnalysis/lib/qcprot.pyx":460 * q1 = a32 * a1324_1423 - a33 * a1224_1422 + a34 * a1223_1322 * q2 = -a31 * a1324_1423 + a33 * a1124_1421 - a34 * a1123_1321 * q3 = a31 * a1224_1422 - a32 * a1124_1421 + a34 * a1122_1221 # <<<<<<<<<<<<<< @@ -4157,7 +4157,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_q3 = (((__pyx_v_a31 * __pyx_v_a1224_1422) - (__pyx_v_a32 * __pyx_v_a1124_1421)) + (__pyx_v_a34 * __pyx_v_a1122_1221)); - /* "MDAnalysis/lib/qcprot.pyx":456 + /* "MDAnalysis/lib/qcprot.pyx":461 * q2 = -a31 * a1324_1423 + a33 * a1124_1421 - a34 * a1123_1321 * q3 = a31 * a1224_1422 - a32 * a1124_1421 + a34 * a1122_1221 * q4 = -a31 * a1223_1322 + a32 * a1123_1321 - a33 * a1122_1221 # <<<<<<<<<<<<<< @@ -4166,7 +4166,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_q4 = ((((-__pyx_v_a31) * __pyx_v_a1223_1322) + (__pyx_v_a32 * __pyx_v_a1123_1321)) - (__pyx_v_a33 * __pyx_v_a1122_1221)); - /* "MDAnalysis/lib/qcprot.pyx":457 + /* "MDAnalysis/lib/qcprot.pyx":462 * q3 = a31 * a1224_1422 - a32 * a1124_1421 + a34 * a1122_1221 * q4 = -a31 * a1223_1322 + a32 * a1123_1321 - a33 * a1122_1221 * qsqr = q1*q1 + q2 *q2 + q3*q3 + q4*q4 # <<<<<<<<<<<<<< @@ -4175,7 +4175,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_qsqr = ((((__pyx_v_q1 * __pyx_v_q1) + (__pyx_v_q2 * __pyx_v_q2)) + (__pyx_v_q3 * __pyx_v_q3)) + (__pyx_v_q4 * __pyx_v_q4)); - /* "MDAnalysis/lib/qcprot.pyx":459 + /* "MDAnalysis/lib/qcprot.pyx":464 * qsqr = q1*q1 + q2 *q2 + q3*q3 + q4*q4 * * if (qsqr < evecprec): # <<<<<<<<<<<<<< @@ -4185,7 +4185,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT __pyx_t_24 = ((__pyx_v_qsqr < __pyx_v_evecprec) != 0); if (__pyx_t_24) { - /* "MDAnalysis/lib/qcprot.pyx":461 + /* "MDAnalysis/lib/qcprot.pyx":466 * if (qsqr < evecprec): * # if qsqr is still too small, return the identity matrix. # * rot[0] = rot[4] = rot[8] = 1.0 # <<<<<<<<<<<<<< @@ -4200,7 +4200,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT } else if (unlikely(__pyx_t_25 >= __pyx_pybuffernd_rot.diminfo[0].shape)) __pyx_t_5 = 0; if (unlikely(__pyx_t_5 != -1)) { __Pyx_RaiseBufferIndexError(__pyx_t_5); - __PYX_ERR(0, 461, __pyx_L1_error) + __PYX_ERR(0, 466, __pyx_L1_error) } *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_rot.rcbuffer->pybuffer.buf, __pyx_t_25, __pyx_pybuffernd_rot.diminfo[0].strides) = 1.0; __pyx_t_26 = 4; @@ -4211,7 +4211,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT } else if (unlikely(__pyx_t_26 >= __pyx_pybuffernd_rot.diminfo[0].shape)) __pyx_t_5 = 0; if (unlikely(__pyx_t_5 != -1)) { __Pyx_RaiseBufferIndexError(__pyx_t_5); - __PYX_ERR(0, 461, __pyx_L1_error) + __PYX_ERR(0, 466, __pyx_L1_error) } *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_rot.rcbuffer->pybuffer.buf, __pyx_t_26, __pyx_pybuffernd_rot.diminfo[0].strides) = 1.0; __pyx_t_27 = 8; @@ -4222,11 +4222,11 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT } else if (unlikely(__pyx_t_27 >= __pyx_pybuffernd_rot.diminfo[0].shape)) __pyx_t_5 = 0; if (unlikely(__pyx_t_5 != -1)) { __Pyx_RaiseBufferIndexError(__pyx_t_5); - __PYX_ERR(0, 461, __pyx_L1_error) + __PYX_ERR(0, 466, __pyx_L1_error) } *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_rot.rcbuffer->pybuffer.buf, __pyx_t_27, __pyx_pybuffernd_rot.diminfo[0].strides) = 1.0; - /* "MDAnalysis/lib/qcprot.pyx":462 + /* "MDAnalysis/lib/qcprot.pyx":467 * # if qsqr is still too small, return the identity matrix. # * rot[0] = rot[4] = rot[8] = 1.0 * rot[1] = rot[2] = rot[3] = rot[5] = rot[6] = rot[7] = 0.0 # <<<<<<<<<<<<<< @@ -4241,7 +4241,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT } else if (unlikely(__pyx_t_28 >= __pyx_pybuffernd_rot.diminfo[0].shape)) __pyx_t_5 = 0; if (unlikely(__pyx_t_5 != -1)) { __Pyx_RaiseBufferIndexError(__pyx_t_5); - __PYX_ERR(0, 462, __pyx_L1_error) + __PYX_ERR(0, 467, __pyx_L1_error) } *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_rot.rcbuffer->pybuffer.buf, __pyx_t_28, __pyx_pybuffernd_rot.diminfo[0].strides) = 0.0; __pyx_t_29 = 2; @@ -4252,7 +4252,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_rot.diminfo[0].shape)) __pyx_t_5 = 0; if (unlikely(__pyx_t_5 != -1)) { __Pyx_RaiseBufferIndexError(__pyx_t_5); - __PYX_ERR(0, 462, __pyx_L1_error) + __PYX_ERR(0, 467, __pyx_L1_error) } *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_rot.rcbuffer->pybuffer.buf, __pyx_t_29, __pyx_pybuffernd_rot.diminfo[0].strides) = 0.0; __pyx_t_30 = 3; @@ -4263,7 +4263,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_rot.diminfo[0].shape)) __pyx_t_5 = 0; if (unlikely(__pyx_t_5 != -1)) { __Pyx_RaiseBufferIndexError(__pyx_t_5); - __PYX_ERR(0, 462, __pyx_L1_error) + __PYX_ERR(0, 467, __pyx_L1_error) } *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_rot.rcbuffer->pybuffer.buf, __pyx_t_30, __pyx_pybuffernd_rot.diminfo[0].strides) = 0.0; __pyx_t_31 = 5; @@ -4274,7 +4274,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT } else if (unlikely(__pyx_t_31 >= __pyx_pybuffernd_rot.diminfo[0].shape)) __pyx_t_5 = 0; if (unlikely(__pyx_t_5 != -1)) { __Pyx_RaiseBufferIndexError(__pyx_t_5); - __PYX_ERR(0, 462, __pyx_L1_error) + __PYX_ERR(0, 467, __pyx_L1_error) } *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_rot.rcbuffer->pybuffer.buf, __pyx_t_31, __pyx_pybuffernd_rot.diminfo[0].strides) = 0.0; __pyx_t_32 = 6; @@ -4285,7 +4285,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT } else if (unlikely(__pyx_t_32 >= __pyx_pybuffernd_rot.diminfo[0].shape)) __pyx_t_5 = 0; if (unlikely(__pyx_t_5 != -1)) { __Pyx_RaiseBufferIndexError(__pyx_t_5); - __PYX_ERR(0, 462, __pyx_L1_error) + __PYX_ERR(0, 467, __pyx_L1_error) } *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_rot.rcbuffer->pybuffer.buf, __pyx_t_32, __pyx_pybuffernd_rot.diminfo[0].strides) = 0.0; __pyx_t_33 = 7; @@ -4296,11 +4296,11 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT } else if (unlikely(__pyx_t_33 >= __pyx_pybuffernd_rot.diminfo[0].shape)) __pyx_t_5 = 0; if (unlikely(__pyx_t_5 != -1)) { __Pyx_RaiseBufferIndexError(__pyx_t_5); - __PYX_ERR(0, 462, __pyx_L1_error) + __PYX_ERR(0, 467, __pyx_L1_error) } *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_rot.rcbuffer->pybuffer.buf, __pyx_t_33, __pyx_pybuffernd_rot.diminfo[0].strides) = 0.0; - /* "MDAnalysis/lib/qcprot.pyx":464 + /* "MDAnalysis/lib/qcprot.pyx":469 * rot[1] = rot[2] = rot[3] = rot[5] = rot[6] = rot[7] = 0.0 * * return # <<<<<<<<<<<<<< @@ -4311,7 +4311,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; - /* "MDAnalysis/lib/qcprot.pyx":459 + /* "MDAnalysis/lib/qcprot.pyx":464 * qsqr = q1*q1 + q2 *q2 + q3*q3 + q4*q4 * * if (qsqr < evecprec): # <<<<<<<<<<<<<< @@ -4320,7 +4320,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ } - /* "MDAnalysis/lib/qcprot.pyx":452 + /* "MDAnalysis/lib/qcprot.pyx":457 * qsqr = q1*q1 + q2 *q2 + q3*q3+q4*q4 * * if (qsqr < evecprec): # <<<<<<<<<<<<<< @@ -4329,7 +4329,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ } - /* "MDAnalysis/lib/qcprot.pyx":438 + /* "MDAnalysis/lib/qcprot.pyx":443 * qsqr = q1*q1 + q2 *q2 + q3*q3+q4*q4 * * if (qsqr < evecprec): # <<<<<<<<<<<<<< @@ -4338,7 +4338,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ } - /* "MDAnalysis/lib/qcprot.pyx":431 + /* "MDAnalysis/lib/qcprot.pyx":436 * # uncommented, but it is most likely unnecessary. * * if (qsqr < evecprec): # <<<<<<<<<<<<<< @@ -4347,7 +4347,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ } - /* "MDAnalysis/lib/qcprot.pyx":467 + /* "MDAnalysis/lib/qcprot.pyx":472 * * * normq = sqrt(qsqr) # <<<<<<<<<<<<<< @@ -4356,7 +4356,7 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ __pyx_v_normq = sqrt(__pyx_v_qsqr); - /* "MDAnalysis/lib/qcprot.pyx":468 + /* "MDAnalysis/lib/qcprot.pyx":473 * * normq = sqrt(qsqr) * q1 /= normq # <<<<<<<<<<<<<< @@ -4365,11 +4365,11 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ if (unlikely(__pyx_v_normq == 0)) { PyErr_SetString(PyExc_ZeroDivisionError, "float division"); - __PYX_ERR(0, 468, __pyx_L1_error) + __PYX_ERR(0, 473, __pyx_L1_error) } __pyx_v_q1 = (__pyx_v_q1 / __pyx_v_normq); - /* "MDAnalysis/lib/qcprot.pyx":469 + /* "MDAnalysis/lib/qcprot.pyx":474 * normq = sqrt(qsqr) * q1 /= normq * q2 /= normq # <<<<<<<<<<<<<< @@ -4378,11 +4378,11 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ if (unlikely(__pyx_v_normq == 0)) { PyErr_SetString(PyExc_ZeroDivisionError, "float division"); - __PYX_ERR(0, 469, __pyx_L1_error) + __PYX_ERR(0, 474, __pyx_L1_error) } __pyx_v_q2 = (__pyx_v_q2 / __pyx_v_normq); - /* "MDAnalysis/lib/qcprot.pyx":470 + /* "MDAnalysis/lib/qcprot.pyx":475 * q1 /= normq * q2 /= normq * q3 /= normq # <<<<<<<<<<<<<< @@ -4391,11 +4391,11 @@ static PyObject *__pyx_pf_10MDAnalysis_3lib_6qcprot_4FastCalcRMSDAndRotation(CYT */ if (unlikely(__pyx_v_normq == 0)) { PyErr_SetString(PyExc_ZeroDivisionError, "float division"); 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