def _parseCif(self, cifFile ):
self.hasRfree = False
self.reflnStatus = False
self.hasAmplitudes = False
cifObject = cif_reader(file_path=cifFile).model()
# For now assume only one dataSet
assert len(cifObject.keys()) == 1,"More than one data set in sf_cif - not sure what to do!"
data = cifObject[ cifObject.keys()[0] ]
# See if any of the _refln.status columns are 'f' - indicating they've been set aside for RFree
if "_refln.status" in data:
self.reflnStatus = True
self.hasRfree = any( map( lambda x: x=='f', data[ "_refln.status" ] ) )
# Need to check we have structure factor amplitudes. For now just check - we
# need to add code to use ctrunctate to convert if we only have intensities
#
# http://mmcif.pdb.org/dictionaries/mmcif_pdbx.dic/Categories/refln.html
if ( "_refln.F_meas" in data or "_refln.F_meas_au" in data ):
self.hasAmplitudes = True
return
def _parseCif(self, cifFile):
self.hasRfree = False
self.reflnStatus = False
self.hasAmplitudes = False
cifObject = cif_reader(file_path=cifFile).model()
# For now assume only one dataSet
assert len(cifObject.keys(
)) == 1, "More than one data set in sf_cif - not sure what to do!"
data = cifObject[cifObject.keys()[0]]
# See if any of the _refln.status columns are 'f' - indicating they've been set aside for RFree
if "_refln.status" in data:
self.reflnStatus = True
self.hasRfree = any(map(lambda x: x == 'f', data["_refln.status"]))
# Need to check we have structure factor amplitudes. For now just check - we
# need to add code to use ctrunctate to convert if we only have intensities
#
# http://mmcif.pdb.org/dictionaries/mmcif_pdbx.dic/Categories/refln.html
if ("_refln.F_meas" in data or "_refln.F_meas_au" in data):
self.hasAmplitudes = True
return
def try_all_readers(file_name):
try: content = mtz.object(file_name=file_name)
except RuntimeError: pass
else: return ("ccp4_mtz", content)
if (detect_binary_file.from_initial_block(file_name=file_name)):
try: content = unpickle_miller_arrays(file_name=file_name)
except KeyboardInterrupt: raise
except Exception: pass
else: return ("cctbx.miller.array", content)
return (None, None)
try: content = cns_reflection_reader.cns_reflection_file(
open(file_name))
except cns_reflection_reader.CNS_input_Error: pass
else: return ("cns_reflection_file", content)
try: content = cns_index_fobs_sigma_reader.reader(
file_name=file_name)
except RuntimeError: pass
else: return ("cns_index_fobs_sigma", content)
try: content = scalepack_merge.reader(
open(file_name))
except scalepack_merge.FormatError: pass
else: return ("scalepack_merge", content)
try: content = scalepack_no_merge.reader(file_name)
except KeyboardInterrupt: raise
except Exception: pass
else: return ("scalepack_no_merge_original_index", content)
try: content = dtrek_reflnlist_reader.reflnlist(
open(file_name))
except KeyboardInterrupt: raise
except Exception: pass
else: return ("dtrek_reflnlist", content)
try: content = shelx_hklf.reader(
file_name=file_name)
except KeyboardInterrupt: raise
except Exception: pass
else: return ("shelx_hklf", content)
try:
content = cif_reader(file_path=file_name)
looks_like_a_reflection_file = False
for block in content.model().values():
if '_refln_index_h' in block or '_refln.index_h' in block:
looks_like_a_reflection_file = True
break
if not looks_like_a_reflection_file:
raise RuntimeError
except KeyboardInterrupt: raise
except Exception: pass
else: return ("cif", content)
try: content = xds_ascii_reader(
open(file_name))
except KeyboardInterrupt: raise
except Exception: pass
else: return ("xds_ascii", content)
try:
content = xds_integrate_hkl_reader()
content.read_file(file_name)
except KeyboardInterrupt: raise
except Exception: pass
else: return ("xds_integrate_hkl", content)
try: content = solve_fpfm_reader(file_name=file_name)
except KeyboardInterrupt: raise
except Exception: pass
else: return ("solve_fpfm", content)
return (None, None)
def try_all_readers(file_name):
try:
content = mtz.object(file_name=file_name)
except RuntimeError:
pass
else:
return ("ccp4_mtz", content)
if (detect_binary_file.from_initial_block(file_name=file_name)):
try:
content = unpickle_miller_arrays(file_name=file_name)
except KeyboardInterrupt:
raise
except Exception:
pass
else:
return ("cctbx.miller.array", content)
return (None, None)
try:
content = cns_reflection_reader.cns_reflection_file(open(file_name))
except cns_reflection_reader.CNS_input_Error:
pass
else:
return ("cns_reflection_file", content)
try:
content = cns_index_fobs_sigma_reader.reader(file_name=file_name)
except RuntimeError:
pass
else:
return ("cns_index_fobs_sigma", content)
try:
content = scalepack_merge.reader(open(file_name))
except scalepack_merge.FormatError:
pass
else:
return ("scalepack_merge", content)
try:
content = scalepack_no_merge.reader(file_name)
except KeyboardInterrupt:
raise
except Exception:
pass
else:
return ("scalepack_no_merge_original_index", content)
try:
content = dtrek_reflnlist_reader.reflnlist(open(file_name))
except KeyboardInterrupt:
raise
except Exception:
pass
else:
return ("dtrek_reflnlist", content)
try:
content = shelx_hklf.reader(file_name=file_name)
except KeyboardInterrupt:
raise
except Exception:
pass
else:
return ("shelx_hklf", content)
try:
content = cif_reader(file_path=file_name)
looks_like_a_reflection_file = False
for block in content.model().values():
if '_refln_index_h' in block or '_refln.index_h' in block:
looks_like_a_reflection_file = True
break
if not looks_like_a_reflection_file:
raise RuntimeError
except KeyboardInterrupt:
raise
except Exception:
pass
else:
return ("cif", content)
try:
content = xds_ascii_reader(open(file_name))
except KeyboardInterrupt:
raise
except Exception:
pass
else:
return ("xds_ascii", content)
try:
content = xds_integrate_hkl_reader()
content.read_file(file_name)
except KeyboardInterrupt:
raise
except Exception:
pass
else:
return ("xds_integrate_hkl", content)
try:
content = solve_fpfm_reader(file_name=file_name)
except KeyboardInterrupt:
raise
except Exception:
pass
else:
return ("solve_fpfm", content)
return (None, None)