+01: import numpy as np

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 02: 

 03: cimport cython

 04: from libc.math cimport sqrt

 05: 

+06: DTYPE = np.double

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 08: @cython.boundscheck(False)  # Deactivate bounds checking

 09: @cython.wraparound(False)   # Deactivate negative indexing.

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 12:     Py_ssize_t atom1,

 13:     Py_ssize_t atom2):

 14: 

 15:     cdef double dx, dy, dz

 16: 

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 21: 

 22: @cython.boundscheck(False)

 23: @cython.wraparound(False)

 24: @cython.cdivision(True) # avoide checking the 0 division

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+46:                 if distance(pos_ts, j, k) <= gamma*cm_mod[j,k]:

        __pyx_t_16 = __pyx_v_j;
        __pyx_t_17 = __pyx_v_k;
        __pyx_t_18 = ((__pyx_f_5utils_10q_routines_distance(__pyx_v_pos_ts, __pyx_v_j, __pyx_v_k) <= (__pyx_v_gamma * (*((double *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_cm_mod.data + __pyx_t_16 * __pyx_v_cm_mod.strides[0]) ) + __pyx_t_17 * __pyx_v_cm_mod.strides[1]) ))))) != 0);
        if (__pyx_t_18) {
/* … */
        }
      }
    }

+47:                     tot += 1

          __pyx_v_tot = (__pyx_v_tot + 1.0);

 48: 

+49:         q[i] = tot/total_contacts

    __pyx_t_17 = __pyx_v_i;
    *((double *) ( /* dim=0 */ (__pyx_v_q.data + __pyx_t_17 * __pyx_v_q.strides[0]) )) = (__pyx_v_tot / __pyx_v_total_contacts);
  }

 50: 

+51:     return q

  __Pyx_XDECREF(__pyx_r);
  __pyx_t_5 = __pyx_memoryview_fromslice(__pyx_v_q, 1, (PyObject *(*)(char *)) __pyx_memview_get_double, (int (*)(char *, PyObject *)) __pyx_memview_set_double, 0);; if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 51, __pyx_L1_error)
  __Pyx_GOTREF(__pyx_t_5);
  __pyx_r = __pyx_t_5;
  __pyx_t_5 = 0;
  goto __pyx_L0;