def get_year_temperature(filename):
with gzip.open(filename, "r") as fh:
cif = iotbx.cif.reader(file_object=fh)
model = cif.model()
assert len(model) == 1, list(model)
entry = model[list(model)[0]]
year = entry.get("_pdbx_database_status.recvd_initial_deposition_date")
if year and "-" in year:
year = int(year.split("-")[0])
else:
year = False
if entry.get("_exptl.method") != "X-RAY DIFFRACTION":
return year, False
temp = entry.get("_diffrn.ambient_temp")
if not temp:
return year, None
if isinstance(temp, basestring):
return year, parse_temperature(temp)
# scitbx array
templist = filter(None, map(parse_temperature, temp))
if not templist:
return year, None
return year, templist[0]
def __init__(self, file_name):
DetectorImageBase.__init__(self, file_name)
raw = open(file_name, "rb").read()
self.binary_sections = get_binary_sections(raw)
self.header_sections = get_header_sections(raw, self.binary_sections)
assert len(self.binary_sections) == 1
cif = iotbx.cif.fast_reader(input_string=self.header_sections)
self.cif_model = cif.model()
im1 = self.cif_model["image_1"]
self.vendortype = "CBF"
self.readHeader()
def __init__(self, file_name):
DetectorImageBase.__init__(self, file_name)
raw = open(file_name, "rb").read()
self.binary_sections = get_binary_sections(raw)
self.header_sections = get_header_sections(raw, self.binary_sections)
assert len(self.binary_sections)==1
cif = iotbx.cif.fast_reader(input_string=self.header_sections)
self.cif_model = cif.model()
im1 = self.cif_model["image_1"]
self.vendortype = "CBF"
self.readHeader()
def run(args):
dic_path = libtbx.env.find_in_repositories(
relative_path="cbflib/doc/cif_img_1.5.4_28Jul07.dic",
test=op.isfile)
if (dic_path is not None):
cif_dic = iotbx.cif.validation.smart_load_dictionary(file_path=dic_path)
else:
cif_dic = None
for file_name in args:
raw = open(file_name, "rb").read()
pattern = "--CIF-BINARY-FORMAT-SECTION--"
i = raw.find(pattern)
if (i >= 0):
j = raw.rfind(pattern+"--")
sliced = raw[:i] + "\n" + raw[j:]
cif = iotbx.cif.fast_reader(input_string=sliced)
model = cif.model()
for k, v in model.iteritems():
print v["_array_data.data"]
if (cif_dic is not None):
model.validate(cif_dic)
def run(args):
dic_path = libtbx.env.find_in_repositories(
relative_path="cbflib/doc/cif_img_1.5.4_28Jul07.dic",
test=op.isfile)
if (dic_path is not None):
cif_dic = iotbx.cif.validation.smart_load_dictionary(file_path=dic_path)
else:
cif_dic = None
for file_name in args:
raw = open(file_name, "rb").read()
pattern = "--CIF-BINARY-FORMAT-SECTION--"
i = raw.find(pattern)
if (i >= 0):
j = raw.rfind(pattern+"--")
sliced = raw[:i] + "\n" + raw[j:]
cif = iotbx.cif.fast_reader(input_string=sliced)
model = cif.model()
im1 = model["image_1"]
print im1["_array_data.data"]
if (cif_dic is not None):
model.validate(cif_dic)