def load_d_space(self):
# creates a d_space list with intensities as a second option
crystal = self.entry.crystal(self.crystal_name)
pattern = PowderPattern.from_crystal(crystal)
self.wavelength = PowderPattern.Wavelength.Wavelength_CuKa1
peak_thetas = []
#intents = pattern.intensity
two_t = pattern.two_theta
intents = pattern.intensity # all pattern intensity
intensity = [] # final list of intensities
for i in pattern.tick_marks:
l = i.two_theta # two theta vals
for j, I in zip(two_t, intents):
if abs(l - j) < 0.01:
# compare lists and find peak 2theta values the above assumption may be changed
peak_thetas.append(j) # tick two theta val
intensity.append(
I) # add the intensity of those peaks to a list
break
d_space = [] # list of d_spaces
peak_thetas = np.array(peak_thetas) / 2 # theta vals instead of 2theta
peak_radians = peak_thetas * np.pi / 180 # to radians
for peak in peak_radians:
d = self.wavelength / (2 * np.sin(peak)
) # get the space values in Angstorms
d_space.append(d) # append final values to a list
return d_space, intensity
def load_d_space(self):
# creates a d_space list with intensities as a second option
crystal = self.entry.crystal(self.crystal_name)
pattern = PowderPattern.from_crystal(crystal)
self.wavelength = PowderPattern.Wavelength.Wavelength_CuKa1
peak_thetas = []
#intents = pattern.intensity
two_t = pattern.two_theta
intents = pattern.intensity # all pattern intensity
intensity = [] # final list of intensities
for i in pattern.tick_marks:
l = i.two_theta # two theta vals
for j,I in zip(two_t,intents):
if abs(l-j) < 0.01:
# compare lists and find peak 2theta values the above assumption may be changed
peak_thetas.append(j) # tick two theta val
intensity.append(I) # add the intensity of those peaks to a list
break
d_space = [] # list of d_spaces
peak_thetas = np.array(peak_thetas)/2 # theta vals instead of 2theta
peak_radians = peak_thetas*np.pi/180 # to radians
for peak in peak_radians:
d = self.wavelength/(2*np.sin(peak)) # get the space values in Angstorms
d_space.append(d) # append final values to a list
return d_space,intensity
def calc_powder_from_pdb(self, pdbfile):
crystal = CrystalReader(pdbfile)[0]
print crystal.spacegroup_symbol
print 'angles', crystal.cell_angles[0], crystal.cell_angles[1], crystal.cell_angles[2]
print 'length', crystal.cell_lengths[0], crystal.cell_lengths[1], crystal.cell_lengths[2]
print 'volume', crystal.cell_volume
pattern = PowderPattern.from_crystal(crystal)
pattern.write_xye_file(('./'+pdbfile.replace('.pdb','.xye')))
def load_two_theta(self):
crystal = self.entry.crystal(self.crystal_name)
pattern = PowderPattern.from_crystal(crystal)
return pattern.two_theta
def load_intensities(self):
# loads the intensities of a given crsytal
crystal = self.entry.crystal(self.crystal_name)
pattern = PowderPattern.from_crystal(crystal)
return pattern.intensity
def load_two_theta(self):
crystal = self.entry.crystal(self.crystal_name)
pattern = PowderPattern.from_crystal(crystal)
return pattern.two_theta
def load_intensities(self):
# loads the intensities of a given crsytal
crystal = self.entry.crystal(self.crystal_name)
pattern = PowderPattern.from_crystal(crystal)
return pattern.intensity