Python run Examples

Example #1

File: tst_b_factor_statistics.py Project: cctbx/cctbx-playground

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"

Example #2

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"

Example #3

File: adp_statistics.py Project: zhuligs/cctbx_project

            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()

Example #4

File: adp_statistics.py Project: cctbx/cctbx-playground

        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()