def read_xds_idxref_lp(idxref_lp_file):
'''Read the XDS IDXREF.LP file and return a dictionary indexed by the
spacegroup number (ASSERT: this is the lowest symmetry spacegroup for
the corresponding lattice) containing unit cell constants and a
penalty. N.B. this also works from CORRECT.LP for the autoindexing
results.'''
# try doing this with regular expression: * int lattice...`
regexp = re.compile(r'^ \*\ ')
results = {}
for record in open(idxref_lp_file, 'r').readlines():
if regexp.match(record):
tokens = record.split()
spacegroup = lattice_to_spacegroup(tokens[2])
cell = tuple(list(map(float, tokens[4:10])))
constrained_cell = constrain_cell(tokens[2][0], cell)
penalty = float(tokens[3])
if spacegroup in results:
if penalty < results[spacegroup][0]:
results[spacegroup] = penalty, constrained_cell
else:
results[spacegroup] = penalty, constrained_cell
if 'DETECTOR COORDINATES (PIXELS) OF DIRECT BEAM' in record:
results['beam centre pixels'] = list(map(float, record.split()[-2:]))
assert('beam centre pixels' in results)
return results
def decide_pointgroup(p1_unit_cell, metadata, input_spacegroup=None):
'''
Run POINTLESS to get the list of allowed pointgroups (N.B. will
insist on triclinic symmetry for this scaling step) then run
pointless on the resulting reflection file to get the idea of the
best pointgroup to use. Then return the correct pointgroup and
cell.
Parameters
----------
p1_unit_cell : tuple
metadata : dict
input_spacegroup : tuple, optional
Returns
-------
returns several values of different types
unit_cell <tuple>, space_group_number <int>
resolution_high <float>
'''
assert (p1_unit_cell)
# write correct input file for the triclinic solution, in the
# working directory
xds_inp = 'P1.INP'
write_xds_inp_correct(metadata, p1_unit_cell, 1, xds_inp, turn_subset=True)
shutil.copyfile(xds_inp, 'XDS.INP')
run_job('xds_par')
shutil.copyfile('CORRECT.LP', 'P1.LP')
# get the list of allowed lattices
results = read_xds_idxref_lp('CORRECT.LP')
# also read out the resolution limit
resolution_high = read_correct_lp_get_resolution('CORRECT.LP')
# run pointless, get the list of suggested lattices and pointgroups
# FIXME should use the program manager for this... yes, this will
# check that the executable is available too!
xdsin = 'XDS_ASCII.HKL'
xmlout = 'pointless.xml'
pointless_log = run_job('pointless_wrapper',
arguments=['xdsin', xdsin, 'xmlout', xmlout],
stdin=['systematicabsences off'])
fout = open('pointless.log', 'w')
for record in pointless_log:
fout.write(record)
fout.close()
# now read the XML file
pointless_results = read_pointless_xml(xmlout)
# select the top solution which is allowed, return this
if input_spacegroup:
sg_accepted = False
input_spacegroup = "".join(input_spacegroup.split())
pointgroup = ersatz_pointgroup(input_spacegroup)
if pointgroup.startswith('H'):
pointgroup = pointgroup.replace('H', 'R')
lattice = spacegroup_to_lattice(input_spacegroup)
for r in pointless_results:
result_sg = "".join(check_spacegroup_name(r[1]).split(' '))
if lattice_to_spacegroup(lattice) in results and \
ersatz_pointgroup(result_sg) == pointgroup:
space_group_number = r[1]
unit_cell = results[lattice_to_spacegroup(r[0])][1]
write('Happy with sg# {}'.format(space_group_number))
write(
'{0[0]:6.2f} {0[1]:6.2f} {0[2]:6.2f} {0[3]:6.2f} {0[4]:6.2f} {0[5]:6.2f}'
.format(unit_cell))
sg_accepted = True
break
if not sg_accepted:
write('No indexing solution for spacegroup {} so ignoring'.format(
input_spacegroup))
input_spacegroup = None
# if input space group obviously nonsense, allow to ignore just warn
if not input_spacegroup:
for r in pointless_results:
if lattice_to_spacegroup(r[0]) in results:
space_group_number = r[1]
unit_cell = results[lattice_to_spacegroup(r[0])][1]
write('Happy with sg# {}'.format(space_group_number))
write(
'{0[0]:6.2f} {0[1]:6.2f} {0[2]:6.2f} {0[3]:6.2f} {0[4]:6.2f} {0[5]:6.2f}'
.format(unit_cell))
break
else:
write('Rejected solution {0[0]} {0[1]:3d}'.format(r))
# this should probably be a proper check...
assert (space_group_number)
# also save the P1 XDS_ASCII.HKL file see
# http://trac.diamond.ac.uk/scientific_software/ticket/1106
shutil.copyfile('XDS_ASCII.HKL', 'XDS_P1.HKL')
return unit_cell, space_group_number, resolution_high
def test_lattice_to_spacegroup(self):
self.assertEqual(lattice_to_spacegroup('aP'), 1)
self.assertEqual(lattice_to_spacegroup('mP'), 3)
self.assertEqual(lattice_to_spacegroup('mC'), 5)
self.assertEqual(lattice_to_spacegroup('mI'), 5)
self.assertEqual(lattice_to_spacegroup('oP'), 16)
self.assertEqual(lattice_to_spacegroup('oC'), 21)
self.assertEqual(lattice_to_spacegroup('oI'), 23)
self.assertEqual(lattice_to_spacegroup('oF'), 22)
self.assertEqual(lattice_to_spacegroup('tP'), 75)
self.assertEqual(lattice_to_spacegroup('tI'), 79)
self.assertEqual(lattice_to_spacegroup('hP'), 143)
self.assertEqual(lattice_to_spacegroup('hR'), 146)
self.assertEqual(lattice_to_spacegroup('hH'), 146)
self.assertEqual(lattice_to_spacegroup('cP'), 195)
self.assertEqual(lattice_to_spacegroup('cF'), 196)
self.assertEqual(lattice_to_spacegroup('cI'), 197)