def test_0(self):
print ("use saxs")
pdb = sx.read_pdb("./test.pdb")
v_dx = sx.read_dx("./")
print (pdb)
print (len(v_dx))
d1 = v_dx[0]
print (d1.keys())
print (d1['ngrid'])
v_max, v_min = sx.calc_extreme_pdb(pdb)
print (v_max)
print (v_min)
def test_1(self):
from pytraj import io
import numpy as np
print ("use pytraj")
# load traj
traj = io.load("./test.pdb", "test.pdb")
n_atoms = traj.top.n_atoms
# creat dummy B-factors
b_array = np.zeros(n_atoms)
# create dummy r_array
r_array = np.asarray([atom.gb_radius for atom in traj.top])
#print (r_array[0])
# read pdb for 1st frame
pdb = read_pdb_from_frame(traj.top, traj[0], b_array, r_array)
#print (len(pdb))
#print (pdb[0])
#print (pdb)
# read dx, find all guv.* files in current folder
v_dx = sx.read_dx("./")
# v_dx is a list of dictionary
# in C++ saxs, this is a vector of struct
print (len(v_dx))
d1 = v_dx[0]
print (d1.keys())
# get info
x, y, z = d1['ngrid']
print (x * y * z)
print (d1['conc'])
print (d1['type'])
print (d1['delta'])
print (d1['origin'])
arr0 = np.asarray(d1['value'])
assert arr0.shape[0] == (x * y * z)
# calculate vcoor_max, vcoor_min: dummy example
v_max, v_min = sx.calc_extreme_pdb(pdb)
def test_0(self):
from pytraj import io
import numpy as np
print ("use pytraj")
# load traj
traj = io.load("./test.pdb", "test.pdb")
v_dx = sx.read_dx("./")
# v_dx is a list of dictionary
# in C++ saxs, this is a vector of struct
d1 = v_dx[0]
x, y, z = d1['ngrid']
print (x * y * z)
print (d1['conc'])
print (d1['type'])
print (d1['delta'])
print (d1['origin'])
arr0 = np.asarray(d1['value'])
assert arr0.shape[0] == (x * y * z)
print ("shape of grids = %s %s %s" % (x, y, z))
def test_0(self):
dx = sx.read_dx("./")
d0 = dx[0]
print (d0)