In [70]:

    

%load_ext Cython


    

    




The Cython extension is already loaded. To reload it, use:
  %reload_ext Cython

In [71]:

    

%%cython -lsaxs -I/home/haichit/amber_git/amber/AmberTools/src/saxs/ -L/home/haichit/amber_git/amber/lib/ --cplus --force -lcpptraj -I/home/haichit/amber_git/amber/AmberTools/src/cpptraj/src

## Ctrl - / for uncomment/comment
# cimport _saxs as sx
# from libcpp.vector cimport vector
    
# cdef sx.dx_type dx
# cdef vector[sx.coordinate] vcoords
# from cpython.array cimport array as pyarray
# from pytraj.Frame cimport Frame
# cdef double[:] marr

# sx.read_pdb(b"../tests/tz2.pdb", vcoords)

# cdef double[:] to_memview(vector[sx.coordinate] vcoords):
#     cdef sx.coordinate coord
#     cdef pyarray arr0 = pyarray('d', [])
#     cdef double[:] arr
    
#     for coord in vcoords:
#         pyarray.extend(arr0, pyarray('d', [coord.x, coord.y, coord.z]))
#     arr = arr0
#     return arr

# marr = to_memview(vcoords)
# cdef int n_atoms = int(marr.shape[0]/3)

# frame = Frame(n_atoms)
# frame.set_from_crd(marr)
# print (frame)

# from pytraj.utils import assert_almost_equal
# assert_almost_equal(frame.coords, marr)


    

In [72]:

    

%%cython -lsaxs -I/home/haichit/amber_git/amber/AmberTools/src/saxs/ -L/home/haichit/amber_git/amber/lib/ --cplus --force

cimport _saxs as sx
from libcpp.vector cimport vector
    
cdef sx.dx_type dx
cdef vector[sx.dx_type] v_dx
cdef vector[sx.coordinate] vcoords
from cpython.array cimport array as pyarray

sx.read_dx("../tests/", v_dx)

dx = v_dx[0]

#print (dx)


    

In [73]:

    

%load _saxs.pxd
# distutils: language = c++
from libcpp.string cimport string
from libcpp.vector cimport vector
#from libcpp.complex cimport complex

cdef extern from "saxs.cpp":
    ctypedef struct dx_type:
        string type
        double conc
        vector[double] value
        vector[size_t] n_grids "ngrid"
        vector[double] origin
        vector[double] delta
    
    ctypedef struct coeff_f:
        double a1, b1, a2, b2, a3, b3, a4, b4, c
    
    ctypedef struct coordinate:
        string type        # Atom type
        double x, y, z
        double r
        double B_factor
        size_t nHyd        # Number of hydrogen atoms attached
    
    vector[dx_type] dx
    vector[coordinate] pdb_coord
    
    string dx_dir, pdb_file, outfile, exper
    
    double qcut = 0.5      # Cutoff q
    double anom_f = 0      # f' in anomalous scattering
    double df_on = 0
    double df_off = 0
    double conc_salt = 0   # Bulk concentration of salt
    double conc_wat = 55.34# Water concentration
    double cutoff = 20
    bint expli = 0         # Account for explicit H atoms in pdb file
    bint tight = 0         # Control Lebedev quadrature tight or loose convergence
    bint flex = 0          # Account for flexibility using B-factor in the PDB file
    #bint corr = 0         # Using corrected atomic factor for water as in J Chem Phys 2000, 113, 9149
    bint decomp = 0        # Decomposing intensity into site contributions
    bint off_cutoff = 0
    double dq = 0.01
    unsigned ncpus
    
    # Declare functions to use
    
    void usage ()
    
    
    void read_dx (const string &dx_dir,
                         vector[dx_type] &dx)
    
    
    bint check_dx (const vector[dx_type] &dx)
    
    
    void read_pdb (const string &pdb_file,
                   vector[coordinate] &pdb_coord)
    
    
    void mergeH (vector[coordinate] &pdb_coord)
    
    
    void extreme_pdb (const vector[coordinate] &pdb_coord,
                      coordinate &max,
                      coordinate &min)
    
    
    void read_exp (const string &exper,
                   vector[double] &q)
    
    
    coordinate get_coordinate (const dx_type &dx,
                               size_t index)
    
    
    size_t cal_index (const dx_type &dx,
                      size_t x,
                      size_t y,
                      size_t z)
    
    
    double atom_fact (const coeff_f &atom,
                      double q)
    
    
    void assign_val (const string &type,
                     double q,
                     size_t nHyd,
                     bint expli,
                     double &atomic_factor)
    
    
    vector[size_t] list_cutoff (const dx_type &dx,
                                const vector[coordinate] &pdb_coord,
                                const coordinate &max,
                                const coordinate &min,
                                double cutoff)
    
    
    #complex[double] form_factor (const vector[coordinate] &pdb_coord,
    #                             const coordinate &q_vector,
    #                             double q,
    #                             bint flex,
    #                             bint expli)
    #
    
    #complex[double] grid_factor (const dx_type &dx,
    #                             bint excess,
    #                             double atomic_factor,
    #                             const vector[size_t] &list_cutoff,
    #                             const coordinate &q_vector)
    
    
    dx_type ex_elec (const vector[dx_type] &dx,
                     double anom_f,
                     bint expli)
    
    
    vector[double] cal_I (const vector[dx_type] &dx,
                          bint excess,
                          const vector[coordinate] &pdb_coord,
                          const vector[ vector[size_t] ] &list_cutoff,
                          double q,
                          size_t rule,
                          bint flex,
                          double anom_f,
                          bint expli)


    

    




  File "<ipython-input-73-0c4e9bbd3745>", line 3
    from libcpp.string cimport string
                             ^
SyntaxError: invalid syntax

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