def show(self, out=sys.stdout, prefix=" ", show_percentiles=False):
def fs(format, value):
return format_value(format, value, replace_none_with=("(none)"))
maxlen = max([len(label) for label in self.labels])
percentiles = {}
if (show_percentiles):
perc_attr = ["clashscore", "mpscore", "r_work", "r_free"]
stats = dict([(name, getattr(self, name)) for name in perc_attr])
from mmtbx.polygon import get_statistics_percentiles
percentiles = get_statistics_percentiles(self.d_min, stats)
for k, name in enumerate(self.__slots__):
format = "%%s%%-%ds = %%s" % maxlen
if (k < 3):
format += " %%"
percentile_info = ""
if (show_percentiles):
percentile = percentiles.get(name, None)
if (percentile is not None):
format += " (percentile: %s)"
percentile_info = "%.1f" % percentile
else:
format += "%s"
else:
format += "%s"
value = getattr(self, name)
if (value is not None):
print >> out, format % (prefix, self.labels[k],
fs(self.formats[k],
value), percentile_info)
return self
def show (self, out=sys.stdout, prefix=" ", show_percentiles=False) :
def fs (format, value) :
return format_value(format, value, replace_none_with=("(none)"))
maxlen = max([ len(label) for label in self.labels ])
percentiles = {}
if (show_percentiles) :
perc_attr = ["clashscore", "mpscore", "r_work", "r_free"]
stats = dict([ (name, getattr(self, name)) for name in perc_attr ])
from mmtbx.polygon import get_statistics_percentiles
percentiles = get_statistics_percentiles(self.d_min, stats)
for k, name in enumerate(self.__slots__) :
format = "%%s%%-%ds = %%s" % maxlen
if (k < 3) :
format += " %%"
percentile_info = ""
if (show_percentiles) :
percentile = percentiles.get(name, None)
if (percentile is not None) :
format += " (percentile: %s)"
percentile_info = "%.1f" % percentile
else :
format += "%s"
else :
format += "%s"
value = getattr(self, name)
if (value is not None) :
print >> out, format % (prefix, self.labels[k], fs(self.formats[k],
value), percentile_info)
return self
def test_all () :
pr, unused_definitions = polygon.master_params.fetch(sources = [params3],
track_unused_definitions = True)
polygon.polygon(params = pr.extract())
working_phil = polygon.master_params.fetch(source=pr)
percentiles = polygon.get_statistics_percentiles(d_min=1.5,
stats={ "clashscore" : 21, "r_work" : 0.174, "r_free" : 0.19 })
# XXX This will change when the database is updated
assert approx_equal(percentiles['clashscore'], 1.10791, 1.e-4)
def test_all():
pr, unused_definitions = polygon.master_params.fetch(sources=[params3], track_unused_definitions=True)
polygon.polygon(params=pr.extract())
working_phil = polygon.master_params.fetch(source=pr)
percentiles = polygon.get_statistics_percentiles(
d_min=1.5, stats={"clashscore": 21, "r_work": 0.174, "r_free": 0.19}
)
# XXX This will change when the database is updated
assert approx_equal(percentiles["clashscore"], 1.10791, 1.0e-4)
