本文整理汇总了Python中xia2.Handlers.Flags.Flags.get_lattice方法的典型用法代码示例。如果您正苦于以下问题：Python Flags.get_lattice方法的具体用法？Python Flags.get_lattice怎么用？Python Flags.get_lattice使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类xia2.Handlers.Flags.Flags的用法示例。
在下文中一共展示了Flags.get_lattice方法的1个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: setup_from_xinfo_file
# 需要导入模块: from xia2.Handlers.Flags import Flags [as 别名]
# 或者: from xia2.Handlers.Flags.Flags import get_lattice [as 别名]
def setup_from_xinfo_file(self, xinfo_file):
'''Set up this object & all subobjects based on the .xinfo
file contents.'''
settings = PhilIndex.params.xia2.settings
sweep_ids = [sweep.id for sweep in settings.sweep]
sweep_ranges = [sweep.range for sweep in settings.sweep]
if len(sweep_ids) == 0:
sweep_ids = None
sweep_ranges = None
xinfo = XInfo(xinfo_file, sweep_ids=sweep_ids, sweep_ranges=sweep_ranges)
self._name = xinfo.get_project()
crystals = xinfo.get_crystals()
for crystal in crystals.keys():
xc = XCrystal(crystal, self)
if crystals[crystal].has_key('sequence'):
xc.set_aa_sequence(crystals[crystal]['sequence'])
if crystals[crystal].has_key('ha_info'):
if crystals[crystal]['ha_info'] != { }:
xc.set_ha_info(crystals[crystal]['ha_info'])
if crystals[crystal].has_key('scaled_merged_reflection_file'):
xc.set_scaled_merged_reflections(
crystals[crystal]['scaled_merged_reflections'])
if crystals[crystal].has_key('reference_reflection_file'):
xc.set_reference_reflection_file(
crystals[crystal]['reference_reflection_file'])
if crystals[crystal].has_key('freer_file'):
xc.set_freer_file(crystals[crystal]['freer_file'])
# user assigned spacegroup
if crystals[crystal].has_key('user_spacegroup'):
xc.set_user_spacegroup(crystals[crystal]['user_spacegroup'])
elif settings.space_group is not None:
# XXX do we ever actually get here?
xc.set_user_spacegroup(settings.space_group.type().lookup_symbol())
# add a default sample if none present in xinfo file
if len(crystals[crystal]['samples']) == 0:
crystals[crystal]['samples']['X1'] = {}
for sample in crystals[crystal]['samples'].keys():
sample_info = crystals[crystal]['samples'][sample]
xsample = XSample(sample, xc)
xc.add_sample(xsample)
for wavelength in crystals[crystal]['wavelengths'].keys():
# FIXME 29/NOV/06 in here need to be able to cope with
# no wavelength information - this should default to the
# information in the image header (John Cowan pointed
# out that this was untidy - requiring that it agrees
# with the value in the header makes this almost
# useless.)
wave_info = crystals[crystal]['wavelengths'][wavelength]
if not wave_info.has_key('wavelength'):
Debug.write(
'No wavelength value given for wavelength %s' % wavelength)
else:
Debug.write(
'Overriding value for wavelength %s to %8.6f' % \
(wavelength, float(wave_info['wavelength'])))
# handle case where user writes f" in place of f''
if wave_info.has_key('f"') and not \
wave_info.has_key('f\'\''):
wave_info['f\'\''] = wave_info['f"']
xw = XWavelength(wavelength, xc,
wavelength = wave_info.get('wavelength', 0.0),
f_pr = wave_info.get('f\'', 0.0),
f_prpr = wave_info.get('f\'\'', 0.0),
dmin = wave_info.get('dmin', 0.0),
dmax = wave_info.get('dmax', 0.0))
# in here I also need to look and see if we have
# been given any scaled reflection files...
# check to see if we have a user supplied lattice...
if crystals[crystal].has_key('user_spacegroup'):
lattice = Syminfo.get_lattice(
crystals[crystal]['user_spacegroup'])
elif settings.space_group is not None:
# XXX do we ever actually get here?
lattice = Syminfo.get_lattice(
settings.space_group.type().lookup_symbol())
elif Flags.get_lattice():
lattice = Flags.get_lattice()
else:
lattice = None
#.........这里部分代码省略.........