def exercise () :
from mmtbx.command_line import b_factor_statistics
from mmtbx.regression import make_fake_anomalous_data
pdb_file = make_fake_anomalous_data.write_pdb_input_cd_cl(
file_base="tst_b_factor_stats")
out = StringIO()
stats = b_factor_statistics.run(args=[pdb_file], out=out)
assert ("""\
| all : 79 0 7.73 42.64 13.18 None None None |""" in
out.getvalue())
out = StringIO()
stats = b_factor_statistics.run(args=[pdb_file, "selection=element CD"],
out=out)
assert ("""\
| all(noH): 1 0 15.00 15.00 15.00 None None None |""" in
out.getvalue())
print "OK"
def exercise():
from mmtbx.command_line import b_factor_statistics
from mmtbx.regression import make_fake_anomalous_data
pdb_file = make_fake_anomalous_data.write_pdb_input_cd_cl(
file_base="tst_b_factor_stats")
out = StringIO()
stats = b_factor_statistics.run(args=[pdb_file], out=out)
assert ("""\
| all : 79 0 7.73 42.64 13.18 None None None |"""
in out.getvalue())
out = StringIO()
stats = b_factor_statistics.run(args=[pdb_file, "selection=element CD"],
out=out)
assert ("""\
| all(noH): 1 0 15.00 15.00 15.00 None None None |"""
in out.getvalue())
print "OK"
i = self.list3.InsertStringItem(sys.maxint, str(row[0]))
for j, value in enumerate(row[1:]):
self.list3.SetStringItem(i, j + 1, str(value))
p1, p2 = stats.format_plots()
y1, yrange1 = p1
y2, yrange2 = p2
if (not y1.all_eq(0)):
self.plot1.convert_histogram(y1)
if (not y2.all_eq(0)):
self.plot2.convert_histogram(y2)
class adp_histogram(plots.histogram):
def convert_histogram(self, bins):
# XXX flex.histogram has already binned values, so I make new fake values
# that matplotlib then re-bins
values = []
for i, x in enumerate(bins):
values.extend([i] * x)
self.show_histogram(values, len(bins), y_label="# of atoms")
if (__name__ == "__main__"):
from mmtbx.command_line import b_factor_statistics
stats = b_factor_statistics.run(sys.argv[1:])
app = wx.App(0)
frame = ADPStatisticsFrame(None, -1, "ADP statistics")
frame.show_statistics(stats)
frame.Show()
app.MainLoop()
self.list2.SetStringItem(i, j+1, str(value))
for row in t3 :
i = self.list3.InsertStringItem(sys.maxint, str(row[0]))
for j, value in enumerate(row[1:]) :
self.list3.SetStringItem(i, j+1, str(value))
p1, p2 = stats.format_plots()
y1, yrange1 = p1
y2, yrange2 = p2
if (not y1.all_eq(0)) :
self.plot1.convert_histogram(y1)
if (not y2.all_eq(0)) :
self.plot2.convert_histogram(y2)
class adp_histogram (plots.histogram) :
def convert_histogram (self, bins) :
# XXX flex.histogram has already binned values, so I make new fake values
# that matplotlib then re-bins
values = []
for i, x in enumerate(bins) :
values.extend([i] * x)
self.show_histogram(values, len(bins), y_label="# of atoms")
if (__name__ == "__main__") :
from mmtbx.command_line import b_factor_statistics
stats = b_factor_statistics.run(sys.argv[1:])
app = wx.App(0)
frame = ADPStatisticsFrame(None, -1, "ADP statistics")
frame.show_statistics(stats)
frame.Show()
app.MainLoop()