def mosflm_mtz_to_list(mtz):
'''Run pointless to convert mtz to list of h k l ... and give the
unit cell, then convert this to a list as necessary before returning.'''
hklout = tempfile.mktemp('.hkl', '', os.environ['CCP4_SCR'])
p = Pointless()
p.set_hklin(mtz)
cell = p.sum_mtz(hklout)
hkl = pointless_summedlist_to_list(hklout, cell)
os.remove(hklout)
return hkl
def mosflm_mtz_to_list(mtz):
'''Run pointless to convert mtz to list of h k l ... and give the
unit cell, then convert this to a list as necessary before returning.'''
hklout = tempfile.mktemp('.hkl', '', os.environ['CCP4_SCR'])
p = Pointless()
p.set_hklin(mtz)
cell = p.sum_mtz(hklout)
hkl = pointless_summedlist_to_list(hklout, cell)
os.remove(hklout)
return hkl
def find_blank(hklin):
# first dump to temp. file
hklout = tempfile.mktemp('.hkl', '', os.environ['CCP4_SCR'])
p = Pointless()
p.set_hklin(hklin)
cell = p.sum_mtz(hklout)
if not os.path.isfile(hklout):
Debug.write('Pointless failed:')
Debug.write(''.join(p.get_all_output()))
raise RuntimeError('Pointless failed: %s does not exist' %hklout)
isig = { }
for record in open(hklout, 'r'):
lst = record.split()
if not lst:
continue
batch = int(lst[3])
i, sig = float(lst[4]), float(lst[5])
if not sig:
continue
if not batch in isig:
isig[batch] = []
isig[batch].append(i / sig)
# look at the mean and sd
blank = []
good = []
for batch in sorted(isig):
m, s = meansd(isig[batch])
if m < 1:
blank.append(batch)
else:
good.append(batch)
# finally delete temp file
os.remove(hklout)
return blank, good
def mosflm_mtz_to_list(mtz):
"""Run pointless to convert mtz to list of h k l ... and give the
unit cell, then convert this to a list as necessary before returning."""
try:
with tempfile.NamedTemporaryFile(suffix=".hkl",
dir=os.environ["CCP4_SCR"],
delete=False) as fh:
hklout = fh.name
p = Pointless()
p.set_hklin(mtz)
cell = p.sum_mtz(hklout)
hkl = pointless_summedlist_to_list(hklout, cell)
finally:
os.remove(hklout)
return hkl
def find_blank(hklin):
try:
# first dump to temp. file
with tempfile.NamedTemporaryFile(suffix=".hkl",
dir=os.environ["CCP4_SCR"],
delete=False) as fh:
hklout = fh.name
p = Pointless()
p.set_hklin(hklin)
_ = p.sum_mtz(hklout)
if os.path.getsize(hklout) == 0:
Debug.write("Pointless failed:")
Debug.write("".join(p.get_all_output()))
raise RuntimeError("Pointless failed: no output file written")
isig = {}
with open(hklout, "r") as fh:
for record in fh:
lst = record.split()
if not lst:
continue
batch = int(lst[3])
i, sig = float(lst[4]), float(lst[5])
if not sig:
continue
if not batch in isig:
isig[batch] = []
isig[batch].append(i / sig)
finally:
os.remove(hklout)
# look at the mean and sd
blank = []
good = []
for batch in sorted(isig):
m, s = meansd(isig[batch])
if m < 1:
blank.append(batch)
else:
good.append(batch)
return blank, good
def find_blank(hklin):
# first dump to temp. file
hklout = tempfile.mktemp('.hkl', '', os.environ['CCP4_SCR'])
p = Pointless()
p.set_hklin(hklin)
cell = p.sum_mtz(hklout)
if not os.path.isfile(hklout):
Debug.write('Pointless failed:')
Debug.write(''.join(p.get_all_output()))
raise RuntimeError('Pointless failed: %s does not exist' %hklout)
isig = { }
for record in open(hklout, 'r'):
lst = record.split()
if not lst:
continue
batch = int(lst[3])
i, sig = float(lst[4]), float(lst[5])
if not sig:
continue
if not batch in isig:
isig[batch] = []
isig[batch].append(i / sig)
# look at the mean and sd
blank = []
good = []
for batch in sorted(isig):
m, s = meansd(isig[batch])
if m < 1:
blank.append(batch)
else:
good.append(batch)
# finally delete temp file
os.remove(hklout)
return blank, good
def _decide_space_group_pointless(self):
logger.debug('Deciding space group with pointless')
symmetry = Pointless()
auto_logfiler(symmetry)
self._sorted_mtz = '%i_sorted.mtz' % symmetry.get_xpid()
self._experiments_filename = '%i_experiments_reindexed.json' % symmetry.get_xpid(
)
self._reflections_filename = '%i_reflections_reindexed.pickle' % symmetry.get_xpid(
)
symmetry.set_hklin(self._integrated_combined_mtz)
symmetry.set_hklout(self._sorted_mtz)
symmetry.set_allow_out_of_sequence_files(allow=True)
symmetry.decide_pointgroup()
space_group = sgtbx.space_group_info(
symbol=str(symmetry.get_pointgroup())).group()
cb_op = sgtbx.change_of_basis_op(symmetry.get_reindex_operator())
# reindex to correct bravais setting
self._data_manager.reindex(cb_op=cb_op, space_group=space_group)
self._data_manager.export_experiments(self._experiments_filename)
self._data_manager.export_reflections(self._reflections_filename)
logger.info('Space group determined by pointless: %s' %
space_group.info())
return space_group, cb_op