def set_lgts(self):
"""Assign scattering lengths.
Assigned the scattering lengths from the lgtfile to the different atom types. If no lgtfile is defined falass
will help the user to build one by working through the atom types in the pdb file and requesting input of the
real and imaginary scattering lengths. This will also occur if a atom type if found in the pdbfile but not in
the given lgts file. falass will write the lgtfile to disk if atom types do not feature in the given lgtfile or
one is written from scratch.
"""
if self.files.lgtfile:
lines = len(self.files.atoms)
print("Setting atoms lengths")
percentage = 0
readwrite.print_update(percentage)
path, extension = os.path.splitext(self.files.lgtfile)
lgtfile_name = path + extension
for i in range(0, len(self.files.atoms)):
percentage_new = np.floor(i / lines * 100)
percentage = readwrite.check_update(percentage, percentage_new)
for j in range(0, len(self.files.atoms[i])):
duplicate = readwrite.check_duplicates(self.files.scat_lens, self.files.atoms[i][j].atom)
if not duplicate:
self.new_file = True
real_scat_len = input('The following atom type has no scattering length given '
'in the lgt file {} \nPlease define a real scattering length for '
'this atom type: '.format(self.files.atoms[i][j].atom))
imag_scat_len = input('\nPlease define a imaginary scattering length for '
'this atom type: '.format(self.files.atoms[i][j].atom))
self.files.scat_lens.append(dataformat.ScatLens(self.files.atoms[i][j].atom, float(real_scat_len),
float(imag_scat_len)))
readwrite.print_update(100)
else:
self.new_file = True
print('There was no lgt file defined, falass will help you define one and save it for future use.')
for i in range(0, len(self.files.atoms)):
for j in range(0, len(self.files.atoms[i])):
duplicate = readwrite.check_duplicates(self.files.scat_lens, self.files.atoms[i][j].atom)
if not duplicate:
real_scat_len = input('The following atom type has no scattering length given '
'in the lgt file {} \nPlease define a real scattering length for '
'this atom type: '.format(self.files.atoms[i][j].atom))
imag_scat_len = input('\nPlease define a imaginary scattering length for '
'this atom type: '.format(self.files.atoms[i][j].atom))
self.files.scat_lens.append(dataformat.ScatLens(self.files.atoms[i][j].atom, float(real_scat_len),
float(imag_scat_len)))
lgtfile_name = input("What should the lgt file be named? ")
path, extension = os.path.splitext(lgtfile_name)
if extension != '.lgt':
lgtfile_name = path + '.lgt'
if self.new_file:
i = 0
while os.path.isfile(lgtfile_name):
i+=1
lgtfile_name = path + '_' + str(i) + '.lgt'
lgtsf = open(lgtfile_name, 'w')
for i in range(0, len(self.files.scat_lens)):
lgtsf.write('{} {} {}\n'.format(self.files.scat_lens[i].atom, self.files.scat_lens[i].real * 1e5,
self.files.scat_lens[i].imag * 1e5))
print('A new lgtfile has been written with the name {}'.format(lgtfile_name))
def test_get_scatlen(self):
atom1 = dataformat.ScatLens('C1', 1.0, 0.0)
atom2 = dataformat.ScatLens('C2', 2.0, 1.0)
atom3 = dataformat.ScatLens('C3', 3.0, 2.0)
array = [atom1, atom2, atom3]
real, imag = sld.get_scatlen('C3', array)
assert_almost_equal(real, 3.0e-5)
assert_almost_equal(imag, 2.0e-5)
return
def test_check_duplicates_false(self):
atom1 = dataformat.ScatLens('C1', 1.0, 0.0)
atom2 = dataformat.ScatLens('C2', 2.0, 1.0)
atom3 = dataformat.ScatLens('C3', 3.0, 2.0)
array = [atom1, atom2, atom3]
check = dataformat.ScatLens('C4', 4.0, 3.0)
bool_ret = readwrite.check_duplicates(array, check.atom)
assert_equal(bool_ret, False)
return
def test_get_scatlen_fail(self):
atom1 = dataformat.ScatLens('C1', 1.0, 0.0)
atom2 = dataformat.ScatLens('C2', 2.0, 1.0)
atom3 = dataformat.ScatLens('C3', 3.0, 2.0)
array = [atom1, atom2, atom3]
with self.assertRaises(ValueError) as context:
sld.get_scatlen('C4', array)
self.assertTrue(
"Attempt to get the scattering length of the atom type {} failed. This should never "
"happen. Please contact the developers".format('C4') in str(
context.exception))
return
def read_lgt(self):
"""Parses .lgt.
Parses the lgtfile. If no lgtfile is defined falass will help the user to build one by working through the
atom types in the pdb file and requesting input of the real and imaginary scattering lengths. This will also
occur if a atom type if found in the pdbfile but not in the given lgts file. falass will write the lgtfile
to disk if atom types do not feature in the given lgtfile or one is written from scratch.
"""
if self.lgtfile:
lines = line_count(self.lgtfile)
print("Reading LGT file")
percentage = 0
print_update(percentage)
file = open(self.lgtfile, 'r')
for i, line in enumerate(file):
percentage_new = np.floor(i / lines * 100)
percentage = check_update(percentage, percentage_new)
line_list = line.split()
duplicate = check_duplicates(self.scat_lens, line_list[0])
if not duplicate:
i = 1
if self.xray:
i *= 2.817940
self.scat_lens.append(
dataformat.ScatLens(line_list[0],
float(line_list[1]) * i,
float(line_list[2]) * i))
print_update(100)
file.close()
else:
raise ValueError("No lgtfile has been defined.")
return
def test_scatlens(self):
a = dataformat.ScatLens('C1', 1., 0.)
assert_equal(a.atom, 'C1')
assert_equal(a.real, 1.0e-5)
assert_equal(a.imag, 0.0)
