def _set_res(self, event):
if len(self._ref_files) > 0 and len(self._in_files) > 0:
ref = self._ref_files[self._reflections.GetCurrentSelection()]
ins = self._in_files[self._structure.GetCurrentSelection()]
if os.path.exists(ref) and os.path.exists(ins):
hkl = hklf.reader(open(ref))
try:
ma = hkl.as_miller_arrays(crystal_symmetry=crystal_symmetry_from_ins.extract_from(ins))
except:
return
rr = ma[0].resolution_range()
self._res_high.SetValue(str(round(rr[1], 2)))
self._res_low.SetValue(str(round(rr[0], 2)))
ins_obj = Shelx(ins)
self._hydrogens.SetValue(ins_obj.has_hydrogen())
self._residues.Clear()
self._residue_list = []
for r in sorted(ins_obj.residue_list()):
if r not in (ShelxData._r + ['HOH', 'DOD', 'CL', 'MG']) or (r in ['ASP', 'GLU', 'HIS', 'ARG']):
self._residues.Append(r)
self._residue_list.append(r)
def __init__(self, parent, title, rotalyze_data, ins_file):
self.rotalyze_data = rotalyze_data
self._ins = Shelx(ins_file)
self._residue_list = self._ins.residue_list()
self._data_types = ['All', 'Allowed/Outlier', 'Outlier']
self.residue_name = self._residue_list[0]
self.point_type = 'All'
self.plot = None
plots.plot_frame.__init__(self, parent=parent, title=title)
def __init__(self, parent, title, ramalyze_data, ins_file):
self.canvas = None
self.ramalyze_data = ramalyze_data
self._ins = Shelx(ins_file)
self._residue_list = ['*'] + self._ins.residue_list()
self.pos_type = 'general'
self.residue_name = '*'
self.point_type = 'All'
self.types = ["general", "glycine", "cis-proline", "trans-proline", "pre-proline", "isoleucine or valine"]
self._data_types = ['All', 'Allowed/Outlier', 'Outlier']
plots.plot_frame.__init__(self, parent=parent, title=title)
def start_new_refinement(self, title, refln, input, type, cycles, res, resl, options):
id = self._get_next_jobid()
os.mkdir(self._project.root() + '/' + str(id) + '_' + REFINEMENT_TYPES[type])
#root = self._project.root() + '/' + str(id) + '_' + REFINEMENT_TYPES[type] + '/'+ str(id) + '_' + REFINEMENT_TYPES[type].lower()
root = './' + str(id) + '_' + REFINEMENT_TYPES[type] + '/'+ str(id) + '_' + REFINEMENT_TYPES[type].lower()
file = root + '.ins'
print os.getcwd()
shutil.copy2(input, file)
shutil.copy2(refln, root + '.hkl')
if type == FULL_MATRIX:
shutil.copy2(input.replace('.res', '.pdb'), root + '_start.pdb')
print input, file
ins = Shelx(file)
ins.set_type(type, cycles, options)
ins.set_res(res, resl)
ins.set_hklf(refln.find('_F.hkl') > -1)
ins.write()
self._running += 1
self.set_status(str(self._running) + ' Job(s) Running')
self._project.action(REFINEMENT_TYPES[type])
tab = Holder(self._tabs)
tab.start_refinement(type, root, title, res, resl, cycles, input, refln, id, options)
self._tabs.AddPage(tab, str(id) + '_' + REFINEMENT_TYPES[type], True)
tab.SetFocus()
self.GetParent().SetSelection(1)
return id, root
class RotamerFrame(plots.plot_frame):
def __init__(self, parent, title, rotalyze_data, ins_file):
self.rotalyze_data = rotalyze_data
self._ins = Shelx(ins_file)
self._residue_list = self._ins.residue_list()
self._data_types = ['All', 'Allowed/Outlier', 'Outlier']
self.residue_name = self._residue_list[0]
self.point_type = 'All'
self.plot = None
plots.plot_frame.__init__(self, parent=parent, title=title)
def create_plot_panel(self):
self.plot = graphics.rotamer_plot()
self.canvas = FigCanvas(self, -1, self.plot.figure)
self.draw_plot()
return self.canvas
def draw_plot(self):
stats = utils.get_rotarama_data(pos_type='general', convert_to_numpy_array=True)
residue_name = 'GLN'
points, coords = graphics.get_residue_rotamer_data(rotalyze_data=self.rotalyze_data,
residue_name=self.residue_name,
point_type=self.point_type)
self.plot.draw_plot(
stats=stats,
title="Chi1-Chi2 plot for %s" % self.residue_name,
points=points,
xyz=coords,
colormap="Blues",
contours=None)
if self.canvas is not None:
self.canvas.draw()
def draw_top_panel(self):
self.top_panel = wx.Panel(parent=self, style=wx.SUNKEN_BORDER)
self.top_sizer = wx.FlexGridSizer(rows=0, cols=4, vgap=5, hgap=5)
self.top_sizer.Add(wx.StaticText(self, -1, 'Residue Name'), 1, wx.EXPAND|wx.ALL, 5)
self.res_type = wx.ComboBox(self, -1, choices=self._residue_list, style=wx.CB_READONLY)
self.res_type.Bind(wx.EVT_COMBOBOX, self._set_residue_name)
self.top_sizer.Add(self.res_type, 1, wx.EXPAND|wx.ALL, 5)
self.top_sizer.Add(wx.StaticText(self, -1, 'Show Data Points'), 1, wx.EXPAND|wx.ALL, 5)
self.data_type = wx.ComboBox(self, -1, choices=self._data_types, style=wx.CB_READONLY)
self.data_type.Bind(wx.EVT_COMBOBOX, self._set_data_type)
self.top_sizer.Add(self.data_type, 1, wx.EXPAND|wx.ALL, 5)
self.top_panel.SetSizer(self.top_sizer)
def _set_data_type(self, event):
self.point_type = self._data_types[self.data_type.GetCurrentSelection()]
self.draw_plot()
def _set_residue_name(self, event):
self.residue_name = self._residue_list[self.res_type.GetCurrentSelection()]
self.draw_plot()
def OnSave(self, event):
output_file = wx.FileSelector("Saved image name",
default_path='',
default_filename="plot.png",
wildcard="Adobe PDF figure (*.pdf)|*.pdf|" + \
"PNG image (*.png)|*.png|" + \
"Postscript figure (*.ps)|*.ps", flags=wx.SAVE)
if output_file != "" :
self.plot.save_image(output_file)