def example_3():
# show selected characteristics, apply default selection
# d_min comes from the structure that we are comparing against database
pr, unused_definitions = polygon.master_params.fetch(sources = [params2],
track_unused_definitions = True)
polygon.polygon(params = pr.extract(),
d_min = 2.0)
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)
def get_basic_histogram_data (d_min) :
params = polygon.master_params.fetch().extract()
params.polygon.keys_to_show = ["r_work", "r_free",
"bond_rmsd", "angle_rmsd", "adp_mean_all", "clashscore"]
histograms = polygon.polygon(params=params,
d_min=d_min,
show_histograms=False,
extract_gui_data=True)
return histograms
def get_basic_histogram_data(d_min):
params = polygon.master_params.fetch().extract()
params.polygon.keys_to_show = [
"r_work", "r_free", "bond_rmsd", "angle_rmsd", "adp_mean_all",
"clashscore"
]
histograms = polygon.polygon(params=params,
d_min=d_min,
show_histograms=False,
extract_gui_data=True)
return histograms
def get_stats_and_histogram_data (mvd_object, params, debug=False) :
pdb_file = mvd_object.pdb_file
mvd_results = model_vs_data.summarize_results(mvd_object)
fmodel = mvd_object.fmodel
d_min = fmodel.info().d_min
stats = {}
invalid_stats = []
for stat_name in params.polygon.keys_to_show :
value = getattr(mvd_results, stat_name, None)
if value is not None :
print stat_name, value
stats[stat_name] = value
else :
print "Error: got 'None' for %s" % stat_name
invalid_stats.append(stat_name)
for stat_name in invalid_stats :
params.polygon.keys_to_show.remove(stat_name)
histograms = polygon.polygon(params=params,
d_min=d_min,
show_histograms=debug,
extract_gui_data=True)
return stats, histograms
def get_stats_and_histogram_data(mvd_object, params, debug=False):
pdb_file = mvd_object.pdb_file
mvd_results = model_vs_data.summarize_results(mvd_object)
fmodel = mvd_object.fmodel
d_min = fmodel.info().d_min
stats = {}
invalid_stats = []
for stat_name in params.polygon.keys_to_show:
value = getattr(mvd_results, stat_name, None)
if value is not None:
print(stat_name, value)
stats[stat_name] = value
else:
print("Error: got 'None' for %s" % stat_name)
invalid_stats.append(stat_name)
for stat_name in invalid_stats:
params.polygon.keys_to_show.remove(stat_name)
histograms = polygon.polygon(params=params,
d_min=d_min,
show_histograms=debug,
extract_gui_data=True)
return stats, histograms
def example_2():
#
#pr, unused_definitions = polygon.master_params.fetch(sources = [params2],
# track_unused_definitions = True, d_min=1.0)
polygon.polygon(d_min=1.0)
def example_1():
# show selected characteristics, apply pre-defined filters
pr, unused_definitions = polygon.master_params.fetch(
sources=[params1], track_unused_definitions=True)
polygon.polygon(params=pr.extract())
def example_3():
# show selected characteristics, apply default selection
# d_min comes from the structure that we are comparing against database
pr, unused_definitions = polygon.master_params.fetch(sources=[params2], track_unused_definitions=True)
polygon.polygon(params=pr.extract(), d_min=2.0)
def example_2():
#
# pr, unused_definitions = polygon.master_params.fetch(sources = [params2],
# track_unused_definitions = True, d_min=1.0)
polygon.polygon(d_min=1.0)
def example_1():
# show selected characteristics, apply pre-defined filters
pr, unused_definitions = polygon.master_params.fetch(sources=[params1], track_unused_definitions=True)
polygon.polygon(params=pr.extract())