def no_images(xds_inp):
firstlast, phi, records = rj_parse_idxref_xds_inp(
open(xds_inp, 'r').readlines())
images = [j for j in range(firstlast[0], firstlast[1] + 1)]
# first run with all images, then define the 'correct' lattice
# as the one which results from this autoindex step.
xds_inp = open('XDS.INP', 'w')
for record in records:
xds_inp.write('%s\n' % record)
xds_inp.write('SPOT_RANGE= %d %d\n' % firstlast)
xds_inp.close()
output = rj_run_job('xds', [], [])
cell = rj_parse_idxref_lp(open('IDXREF.LP', 'r').readlines())
result = lattice_symmetry(cell)
lattice = sort_lattices(result.keys())[-1]
score = result[lattice]['penalty']
metrics = []
for count in range(10):
result = calculate_images(images, phi, count + 1)
xds_inp = open('XDS.INP', 'w')
for record in records:
xds_inp.write('%s\n' % record)
for pair in result:
xds_inp.write('SPOT_RANGE= %d %d\n' % pair)
xds_inp.close()
output = rj_run_job('xds', [], [])
cell = rj_parse_idxref_lp(open('IDXREF.LP', 'r').readlines())
result = lattice_symmetry(cell)
l = sort_lattices(result.keys())[-1]
if l != lattice:
raise RuntimeError, 'cell refinement gave wrong lattice'
metrics.append(result[l]['penalty'])
return metrics, score
def phi_spacing(xds_inp):
firstlast, phi, records = rj_parse_idxref_xds_inp(
open(xds_inp, 'r').readlines())
images = [j for j in range(firstlast[0], firstlast[1] + 1)]
# first run with all images, then define the 'correct' lattice
# as the one which results from this autoindex step.
xds_inp = open('XDS.INP', 'w')
for record in records:
xds_inp.write('%s\n' % record)
xds_inp.write('SPOT_RANGE= %d %d\n' % firstlast)
xds_inp.close()
output = rj_run_job('xds', [], [])
cell = rj_parse_idxref_lp(open('IDXREF.LP', 'r').readlines())
result = lattice_symmetry(cell)
lattice = sort_lattices(result.keys())[-1]
score = result[lattice]['penalty']
metrics = []
spacings = []
phis = [float(j + 1) for j in range(10, 45)]
image_numbers = []
for p in phis:
result = calculate_images(images, phi, p)
if phi * (result[-1][-1] - result[0][0] + 1) > 90.0:
continue
if not result in image_numbers:
image_numbers.append(result)
for result in image_numbers:
spacing = nint(phi * (result[1][0] - result[0][0]))
spacings.append(spacing)
xds_inp = open('XDS.INP', 'w')
for record in records:
xds_inp.write('%s\n' % record)
for pair in result:
xds_inp.write('SPOT_RANGE= %d %d\n' % pair)
xds_inp.close()
output = rj_run_job('xds', [], [])
cell = rj_parse_idxref_lp(open('IDXREF.LP', 'r').readlines())
result = lattice_symmetry(cell)
l = sort_lattices(result.keys())[-1]
if l != lattice:
raise RuntimeError, 'cell refinement gave wrong lattice'
metrics.append(result[l]['penalty'])
return metrics, spacings, score