class xtriage_output(printed_output):
def __init__(self, out):
super(xtriage_output, self).__init__(out)
self.gui_output = True
self._out_orig = self.out
self.out = StringIO()
self._sub_header_to_out = {}
def show_big_header(self, text):
pass
def show_header(self, text):
self._out_orig.write(self.out.getvalue())
self.out = StringIO()
super(xtriage_output, self).show_header(text)
def show_sub_header(self, title):
self._out_orig.write(self.out.getvalue())
self.out = StringIO()
self._current_sub_header = title
assert title not in self._sub_header_to_out
self._sub_header_to_out[title] = self.out
def flush(self):
self._out_orig.write(self.out.getvalue())
self.out.flush()
self._out_orig.flush()
def colorize(source):
"""
write colorized version to "[filename].py.html"
"""
html = StringIO()
Parser(source, html).format(None, None)
html.flush()
html.seek(0)
return html.read()
def colorize(source):
"""
write colorized version to "[filename].py.html"
"""
html = StringIO()
Parser(source, html).format(None, None)
html.flush()
html.seek(0)
return html.read()
class LoggingFramework:
def __init__(self):
self.k = StringIO()
self.current_out = sys.stdout
self.current_err = sys.stderr
sys.stdout = self.k
sys.stderr = self.k
def __del__(self):
sys.stdout = self.current_out
sys.stderr = self.current_err
self.k.flush()
self.k.close()
def getvalue(self): return self.k.getvalue()
def run_call_back(flags,
space_group_info,
max_n_indices=5,
anomalous_flag=True):
if (not flags.Verbose):
out = StringIO()
else:
out = sys.stdout
if (flags.chunk):
chunk_n, chunk_i = [int(i) for i in flags.chunk.split(",")]
else:
chunk_n = 1
chunk_i = 0
if (flags.tag):
if (flags.tag == "internal"):
strudat_contents = strudat.read_all_entries(StringIO(zeolite_edi))
strudat_entries = strudat_contents.entries
else:
atlas_file = libtbx.env.find_in_repositories(
relative_path="phenix_regression/misc/strudat_zeolite_atlas",
test=os.path.isfile)
assert atlas_file is not None
strudat_contents = strudat.read_all_entries(open(atlas_file))
if (not isinstance(flags.tag, str)):
strudat_entries = strudat_contents.entries
else:
strudat_entries = [strudat_contents.get(tag=flags.tag)]
assert strudat_entries[0] is not None
if (flags.isotropic):
use_u_aniso_flags = [False]
elif (flags.anisotropic):
use_u_aniso_flags = [True]
else:
use_u_aniso_flags = [False, True]
if (not flags.tag):
for n_scatterers in range(2, 3 + 1):
for use_u_aniso in use_u_aniso_flags:
xray_structure = random_structure.xray_structure(
space_group_info=space_group_info,
n_scatterers=n_scatterers,
elements="random",
volume_per_atom=100,
general_positions_only=False,
random_f_prime_d_min=1,
random_f_double_prime=anomalous_flag,
use_u_aniso=use_u_aniso,
use_u_iso=not (use_u_aniso),
random_u_iso=True,
random_u_iso_scale=0.3,
random_occupancy=True)
exercise(xray_structure=xray_structure,
anomalous_flag=anomalous_flag,
max_n_indices=max_n_indices,
out=out)
out.flush()
else:
i_structure = count()
for entry in strudat_entries:
if (next(i_structure) % chunk_n != chunk_i): continue
# XXX Not sure why this stderr output is necessary. Disabling to clean
# up t96 output.
# print >> sys.stderr, "strudat tag:", entry.tag
# sys.stderr.flush()
print("strudat tag:", entry.tag, file=out)
out.flush()
for use_u_aniso in use_u_aniso_flags:
xray_structure = entry.as_xray_structure()
xray_structure = random_structure.xray_structure(
space_group_info=xray_structure.space_group_info(),
unit_cell=xray_structure.unit_cell(),
sites_frac=xray_structure.sites_frac(),
elements="random",
random_f_prime_d_min=1,
random_f_double_prime=anomalous_flag,
use_u_aniso=use_u_aniso,
use_u_iso=not (use_u_aniso),
random_u_iso=True,
random_u_iso_scale=0.3,
random_occupancy=True)
exercise(xray_structure=xray_structure,
anomalous_flag=anomalous_flag,
max_n_indices=max_n_indices,
out=out)
out.flush()
if (flags.tag):
return False