def exercise () :
for module in ["reduce", "probe", "phenix_regression"] :
if (not libtbx.env.has_module(module)) :
print "%s not available, skipping" % module
return
from mmtbx.command_line import validation_summary
from iotbx import file_reader
import iotbx.pdb.hierarchy
regression_pdb = libtbx.env.find_in_repositories(
relative_path="phenix_regression/pdb/pdb1jxt.ent",
test=os.path.isfile)
out = StringIO()
summary = validation_summary.run(args=[regression_pdb], out=out)
assert approx_equal(summary.clashscore, 13.597, eps=0.001), "clashscore %s is not 13.597(0.0001)" % summary.clashscore
ss = easy_pickle.dumps(summary)
sss = easy_pickle.loads(ss)
out_1 = StringIO()
out_2 = StringIO()
summary.show(out=out_1)
sss.show(out=out_2)
assert out_1.getvalue() == out_2.getvalue()
pdb_in = file_reader.any_file(regression_pdb)
hierarchy = pdb_in.file_object.hierarchy
new_hierarchy = iotbx.pdb.hierarchy.root()
for i in range(5) :
model = hierarchy.only_model().detached_copy()
model.id = str(i+1)
new_hierarchy.append_model(model)
open("tst_validation_summary.pdb", "w").write(new_hierarchy.as_pdb_string())
out2 = StringIO()
summary = validation_summary.run(args=["tst_validation_summary.pdb"],
out=out2)
assert (type(summary).__name__ == 'ensemble')
print "OK"
def exercise():
for module in ["reduce", "probe", "phenix_regression"]:
if not libtbx.env.has_module(module):
print "%s not available, skipping" % module
return
from mmtbx.command_line import validation_summary
from iotbx import file_reader
import iotbx.pdb.hierarchy
regression_pdb = libtbx.env.find_in_repositories(
relative_path="phenix_regression/pdb/pdb1jxt.ent", test=os.path.isfile
)
out = StringIO()
summary = validation_summary.run(args=[regression_pdb], out=out)
assert approx_equal(summary.clashscore, 13.597, eps=0.0001)
ss = easy_pickle.dumps(summary)
sss = easy_pickle.loads(ss)
out_1 = StringIO()
out_2 = StringIO()
summary.show(out=out_1)
sss.show(out=out_2)
assert out_1.getvalue() == out_2.getvalue()
pdb_in = file_reader.any_file(regression_pdb)
hierarchy = pdb_in.file_object.hierarchy
new_hierarchy = iotbx.pdb.hierarchy.root()
for i in range(5):
model = hierarchy.only_model().detached_copy()
model.id = str(i + 1)
new_hierarchy.append_model(model)
open("tst_validation_summary.pdb", "w").write(new_hierarchy.as_pdb_string())
out2 = StringIO()
summary = validation_summary.run(args=["tst_validation_summary.pdb"], out=out2)
assert type(summary).__name__ == "ensemble"
print "OK"
text = wx.StaticText(self, label=label)
sizer.Add(text, 0, style, 5)
def add_control(self,
sizer,
control,
style=wx.LEFT | wx.TOP | wx.BOTTOM
| wx.ALIGN_CENTER_VERTICAL,
spacer=40):
sizer.Add(control, 0, style, 5)
sizer.AddSpacer(spacer)
# =============================================================================
if (__name__ == "__main__"):
result = validation_summary.run(sys.argv[1:])
if (type(result).__name__ != 'ensemble'):
raise Sorry("Not an ensemble, graphics not available.")
app = app.CCTBXApp(0)
frame = wx.Frame(None, -1, "Ensemble validation")
szr = wx.BoxSizer(wx.VERTICAL)
panel = ensemble_validation_panel(frame)
panel.set_ensemble(result)
szr.Add(panel, 1, wx.EXPAND | wx.ALL)
frame.SetSizer(szr)
szr.Fit(panel)
frame.Fit()
panel.OnSelectPlot(None)
frame.Show()
app.MainLoop()
# convenience functions for placing text and widgets
def add_text(self, sizer, label,
style=wx.LEFT|wx.TOP|wx.BOTTOM|wx.ALIGN_CENTER_VERTICAL):
text = wx.StaticText(self, label=label)
sizer.Add(text, 0, style, 5)
def add_control(self, sizer, control,
style=wx.LEFT|wx.TOP|wx.BOTTOM|wx.ALIGN_CENTER_VERTICAL,
spacer=40):
sizer.Add(control, 0, style, 5)
sizer.AddSpacer(spacer)
# =============================================================================
if (__name__ == "__main__") :
result = validation_summary.run(sys.argv[1:])
if (type(result).__name__ != 'ensemble') :
raise Sorry("Not an ensemble, graphics not available.")
app = app.CCTBXApp(0)
frame = wx.Frame(None, -1, "Ensemble validation")
szr = wx.BoxSizer(wx.VERTICAL)
panel = ensemble_validation_panel(frame)
panel.set_ensemble(result)
szr.Add(panel, 1, wx.EXPAND|wx.ALL)
frame.SetSizer(szr)
szr.Fit(panel)
frame.Fit()
panel.OnSelectPlot(None)
frame.Show()
app.MainLoop()