def test_complex():
p = pointsmodelpy.new_pdbmodel()
pointsmodelpy.pdbmodel_add(p,"ff0.pdb")
vp = pointsmodelpy.new_point3dvec()
pointsmodelpy.get_pdbpoints(p,vp);
pointsmodelpy.get_pdb_pr(p,vp)
pointsmodelpy.save_pdb_pr(p,"testcomplex.pr")
iq = iqPy.new_iq(100,0.001, 0.3)
pointsmodelpy.get_pdb_iq(p,iq)
iqPy.OutputIQ(iq,"testcomplex.iq")
a = geoshapespy.new_sphere(10)
lm = pointsmodelpy.new_loresmodel(0.1)
pointsmodelpy.lores_add(lm,a,1.0)
vpcomplex = pointsmodelpy.new_point3dvec();
complex = pointsmodelpy.new_complexmodel()
pointsmodelpy.complexmodel_add(complex,p,"PDB");
pointsmodelpy.complexmodel_add(complex,lm,"LORES");
pointsmodelpy.get_complexpoints(complex,vpcomplex);
pointsmodelpy.get_complex_pr(complex,vpcomplex);
pointsmodelpy.save_complex_pr(complex,"testcomplex1.pr");
iqcomplex = iqPy.new_iq(100,0.001, 0.3)
pointsmodelpy.get_complex_iq(complex,iqcomplex);
iqPy.OutputIQ(iq,"testcomplex1.iq")
def test_lores2d(phi): from sasModeling.pointsmodelpy import pointsmodelpy from sasModeling.iqPy import iqPy from sasModeling.geoshapespy import geoshapespy #lores model is to hold several geometric objects lm = pointsmodelpy.new_loresmodel(0.1) #generate single geometry shape c = geoshapespy.new_cylinder(10,40) geoshapespy.set_center(c,1,1,1) geoshapespy.set_orientation(c,0,0,0) #add single geometry shape to lores model pointsmodelpy.lores_add(lm,c,3.0) #retrieve the points from lores model for sas calculation vp = pointsmodelpy.new_point3dvec() pointsmodelpy.get_lorespoints(lm,vp) #Calculate I(Q) and P(r) 2D pointsmodelpy.distdistribution_xy(lm,vp) pointsmodelpy.outputPR_xy(lm,"out_xy.pr") iq = iqPy.new_iq(100,0.001, 0.3) pointsmodelpy.calculateIQ_2D(lm,iq,phi) iqPy.OutputIQ(iq, "out_xy.iq")
def test_complex3(): pdb = pointsmodelpy.new_pdbmodel() lores = pointsmodelpy.new_loresmodel(0.1) sph = geoshapespy.new_sphere(10) pointsmodelpy.lores_add(lores,sph,1.0) complex = pointsmodelpy.new_complexmodel() pointsmodelpy.complexmodel_add(complex,pdb,"PDB"); pointsmodelpy.complexmodel_add(complex,lores,"LORES") points = pointsmodelpy.new_point3dvec() pointsmodelpy.get_complexpoints(complex,points) pointsmodelpy.get_complex_pr(complex,points); pointsmodelpy.save_complex_pr(complex,"testcomplex3.pr") iqcomplex = iqPy.new_iq(100,0.001, 0.3) pointsmodelpy.get_complex_iq(complex,iqcomplex) iqPy.OutputIQ(iqcomplex,"testcomplex3.iq") print "p(r) is saved in testcomplex3.pr" print "I(Q) is saved in testcomplex3.iq" print "pass"
def test_lores2d(phi):
from sasModeling.pointsmodelpy import pointsmodelpy
from sasModeling.iqPy import iqPy
from sasModeling.geoshapespy import geoshapespy
#lores model is to hold several geometric objects
lm = pointsmodelpy.new_loresmodel(0.1)
#generate single geometry shape
c = geoshapespy.new_cylinder(10, 40)
geoshapespy.set_center(c, 1, 1, 1)
geoshapespy.set_orientation(c, 0, 0, 0)
#add single geometry shape to lores model
pointsmodelpy.lores_add(lm, c, 3.0)
#retrieve the points from lores model for sas calculation
vp = pointsmodelpy.new_point3dvec()
pointsmodelpy.get_lorespoints(lm, vp)
#Calculate I(Q) and P(r) 2D
pointsmodelpy.distdistribution_xy(lm, vp)
pointsmodelpy.outputPR_xy(lm, "out_xy.pr")
iq = iqPy.new_iq(100, 0.001, 0.3)
pointsmodelpy.calculateIQ_2D(lm, iq, phi)
iqPy.OutputIQ(iq, "out_xy.iq")
def test_complex4():
a = geoshapespy.new_sphere(10)
lm = pointsmodelpy.new_loresmodel(0.1)
pointsmodelpy.lores_add(lm, a, 1.0)
vpcomplex = pointsmodelpy.new_point3dvec()
complex = pointsmodelpy.new_complexmodel()
pointsmodelpy.complexmodel_add(complex, lm, "LORES")
pointsmodelpy.get_complexpoints(complex, vpcomplex)
print(pointsmodelpy.get_complex_iq_2D(complex, vpcomplex, 0.1, 0.1))
print(pointsmodelpy.get_complex_iq_2D(complex, vpcomplex, 0.01, 0.1))
def test_complex4():
a = geoshapespy.new_sphere(10)
lm = pointsmodelpy.new_loresmodel(0.1)
pointsmodelpy.lores_add(lm,a,1.0)
vpcomplex = pointsmodelpy.new_point3dvec();
complex = pointsmodelpy.new_complexmodel()
pointsmodelpy.complexmodel_add(complex,lm,"LORES");
pointsmodelpy.get_complexpoints(complex,vpcomplex);
print pointsmodelpy.get_complex_iq_2D(complex,vpcomplex,0.1,0.1);
print pointsmodelpy.get_complex_iq_2D(complex,vpcomplex,0.01,0.1);
def get2d_2():
from math import pi
from Numeric import arange,zeros
from enthought.util.numerix import Float,zeros
from sasModeling.file2array import readfile2array
from sasModeling.pointsmodelpy import pointsmodelpy
from sasModeling.geoshapespy import geoshapespy
lm = pointsmodelpy.new_loresmodel(0.1)
cyn = geoshapespy.new_cylinder(5,20)
geoshapespy.set_orientation(cyn,0,0,90)
pointsmodelpy.lores_add(lm,cyn,1.0)
vp = pointsmodelpy.new_point3dvec()
pointsmodelpy.get_lorespoints(lm,vp)
pointsmodelpy.distdistribution_xy(lm,vp)
value_grid = zeros((100,100),Float)
width, height = value_grid.shape
print(width,height)
I = pointsmodelpy.calculateI_Qxy(lm,0.00001,0.000002)
print(I)
Imax = 0
for i in range(width):
for j in range(height):
qx = float(i-50)/200.0
qy = float(j-50)/200.0
value_grid[i,j] = pointsmodelpy.calculateI_Qxy(lm,qx,qy)
if value_grid[i][j] > Imax:
Imax = value_grid[i][j]
for i in range(width):
for j in range(height):
value_grid[i][j] = value_grid[i][j]/Imax
value_grid[50,50] = 1
return value_grid
def get2d_2():
from math import pi
from Numeric import arange, zeros
from enthought.util.numerix import Float, zeros
from sasModeling.file2array import readfile2array
from sasModeling.pointsmodelpy import pointsmodelpy
from sasModeling.geoshapespy import geoshapespy
lm = pointsmodelpy.new_loresmodel(0.1)
cyn = geoshapespy.new_cylinder(5, 20)
geoshapespy.set_orientation(cyn, 0, 0, 90)
pointsmodelpy.lores_add(lm, cyn, 1.0)
vp = pointsmodelpy.new_point3dvec()
pointsmodelpy.get_lorespoints(lm, vp)
pointsmodelpy.distdistribution_xy(lm, vp)
value_grid = zeros((100, 100), Float)
width, height = value_grid.shape
print(width, height)
I = pointsmodelpy.calculateI_Qxy(lm, 0.00001, 0.000002)
print(I)
Imax = 0
for i in range(width):
for j in range(height):
qx = float(i - 50) / 200.0
qy = float(j - 50) / 200.0
value_grid[i, j] = pointsmodelpy.calculateI_Qxy(lm, qx, qy)
if value_grid[i][j] > Imax:
Imax = value_grid[i][j]
for i in range(width):
for j in range(height):
value_grid[i][j] = value_grid[i][j] / Imax
value_grid[50, 50] = 1
return value_grid
def test_complex2(): pdb = pointsmodelpy.new_pdbmodel() pointsmodelpy.pdbmodel_add(pdb,"ff0.pdb") lores = pointsmodelpy.new_loresmodel(0.1) complex = pointsmodelpy.new_complexmodel() pointsmodelpy.complexmodel_add(complex,pdb,"PDB"); pointsmodelpy.complexmodel_add(complex,lores,"LORES") points = pointsmodelpy.new_point3dvec() pointsmodelpy.get_complexpoints(complex,points) pointsmodelpy.get_complex_pr(complex,points); pointsmodelpy.save_complex_pr(complex,"testcomplex2.pr") iqcomplex = iqPy.new_iq(100,0.001, 0.3) pointsmodelpy.get_complex_iq(complex,iqcomplex) iqPy.OutputIQ(iqcomplex,"testcomplex2.iq") print "p(r) is saved in testcomplex2.pr" print "I(Q) is saved in testcomplex2.iq" print "pass"
# b = geoshapespy.new_sphere(15)
# geoshapespy.set_center(b,15,15,15)
# pointsmodelpy.lores_add(lm,b,2.0)
c = geoshapespy.new_cylinder(10,40)
geoshapespy.set_center(c,1,1,1)
geoshapespy.set_orientation(c,0,0,0)
pointsmodelpy.lores_add(lm,c,3.0)
# d = geoshapespy.new_ellipsoid(10,8,6)
# geoshapespy.set_center(d,3,3,3)
# geoshapespy.set_orientation(c,30,30,30)
# pointsmodelpy.lores_add(lm,d,1.0)
vp = pointsmodelpy.new_point3dvec()
pointsmodelpy.get_lorespoints(lm,vp)
pointsmodelpy.outputPDB(lm,vp,"modelpy.pseudo.pdb")
print "calculating distance distribution"
rmax = pointsmodelpy.get_lores_pr(lm,vp)
print "finish calculating get_lores_pr, and rmax is:", rmax
pointsmodelpy.outputPR(lm,"testlores.pr")
pointsmodelpy.get_lores_iq(lm,iq)
iqPy.OutputIQ(iq, "testlores.iq")
print "Testing get I from a single q"
result = pointsmodelpy.get_lores_i(lm,0.1)
print "The I(0.1) is: %s" % str(result)
if __name__ == "__main__":
from sasModeling.pointsmodelpy import pointsmodelpy
from sasModeling.iqPy import iqPy
from sasModeling.geoshapespy import geoshapespy
a = geoshapespy.new_sphere(10)
lm = pointsmodelpy.new_loresmodel(0.0005)
pointsmodelpy.lores_add(lm, a, 1.0)
b = geoshapespy.new_sphere(20)
geoshapespy.set_center(b, 20, 20, 20)
pointsmodelpy.lores_add(lm, b, -1.0)
vp = pointsmodelpy.new_point3dvec()
pointsmodelpy.get_lorespoints(lm, vp)
pointsmodelpy.get_lores_pr(lm, vp)