from __future__ import absolute_import, division, print_function from mmtbx.validation import ramalyze from mmtbx.validation import rotalyze from mmtbx.validation import graphics import mmtbx.validation.utils from wxtbx import utils import wxtbx.plots import wx from math import sqrt, floor from six.moves import range class rotarama_plot(wxtbx.plots.plot_container): hit_test_radius = 3.0 hit_test_minimum_difference = 0.5 def __init__(self, parent, figure_size=(8,8), xyz_shift=None): wxtbx.plots.plot_container.__init__(self, parent=parent, figure_size=figure_size, handle_left_click=True) self.xyz_shift = xyz_shift def show_plot(self, *args, **kwds): if self.disabled : return self.draw_plot(*args, **kwds) self.parent.Refresh() def process_mouse_click(self, mpl_event): (xdata, ydata) = (mpl_event.xdata, mpl_event.ydata) if xdata is None or ydata is None : return False min_dist = self.hit_test_radius closest_point = None for i, (x, y) in enumerate(self._points): dist = sqrt((xdata - x)**2 + (ydata - y)**2) if dist < min_dist : closest_point = i min_dist = dist if closest_point is not None : xyz = self._xyz[closest_point] if (self.xyz_shift is not None): xyz = (xyz[0] + self.xyz_shift[0], xyz[1] + self.xyz_shift[1], xyz[2] + self.xyz_shift[2]) self.parent.zoom_callback(xyz=xyz) class ramalyze_plot(rotarama_plot, ramalyze.ramachandran_plot_mixin): def __init__(self, *args, **kwds): rotarama_plot.__init__(self, *args, **kwds) ramalyze.ramachandran_plot_mixin.__init__(self) class rotalyze_plot(rotarama_plot, rotalyze.rotamer_plot_mixin): def __init__(self, *args, **kwds): rotarama_plot.__init__(self, *args, **kwds) rotalyze.rotamer_plot_mixin.__init__(self) class rotarama_frame(wxtbx.plots.plot_frame): frame_name = "rotarama_frame" show_controls_default = True def __init__(self, parent, title, validation): self._validation = validation wxtbx.plots.plot_frame.__init__(self, parent=parent, title=title, style=wx.DEFAULT_FRAME_STYLE) self._map_cache = {} self._point_cache = {} self._xyz_cache = {} self.OnUpdatePlot(None) def OnDestroy(self, event): if hasattr(self.GetParent(), self.frame_name): setattr(self.GetParent(), self.frame_name, None) def OnUpdatePlot(self, event): pass def zoom_callback(self, **kwds): if getattr(self.GetParent(), "main_window", None) is not None : self.GetParent().main_window.show_gfx_selection(**kwds) class ramalyze_frame(rotarama_frame): frame_name = "rama_frame" def draw_top_panel(self): self.top_panel = wx.Panel(self) szr = wx.BoxSizer(wx.VERTICAL) self.top_panel.SetSizer(szr) grid = wx.FlexGridSizer(cols=4) szr.Add(grid, 0, wx.ALL) grid.Add(utils.bold_text(self.top_panel, "Position type:"), 0, utils.std_sizer_flags, 5) pos_choice = wx.Choice(parent=self.top_panel, choices=ramalyze.res_type_labels) self.Bind(wx.EVT_CHOICE, self.OnUpdatePlot, pos_choice) pos_choice.SetSelection(ramalyze.RAMA_GENERAL) grid.Add(pos_choice, 0, utils.std_sizer_flags, 5) grid.Add(utils.bold_text(self.top_panel, "Residue name:"), 0, utils.std_sizer_flags, 5) aa = ['ALA', 'ARG', 'ASN', 'ASP', 'CYS', 'GLN', 'GLU', 'HIS', 'LEU', 'LYS', 'MET', 'PHE', 'SER', 'THR', 'TRP', 'TYR',] res_choice = wx.Choice(parent=self.top_panel, choices=['*']+aa) res_choice.SetSelection(0) self.Bind(wx.EVT_CHOICE, self.OnUpdatePlot, res_choice) res_choice.Disable() grid.Add(res_choice, 0, utils.std_sizer_flags, 5) grid.Add(utils.bold_text(self.top_panel, "Show data points:"), 0, utils.std_sizer_flags, 5) default = ramalyze.RAMALYZE_ANY pt_choice = wx.Choice(parent=self.top_panel, choices=ramalyze.rama_type_labels) pt_choice.SetSelection(default) self.Bind(wx.EVT_CHOICE, self.OnUpdatePlot, pt_choice) grid.Add(pt_choice, 0, utils.std_sizer_flags, 5) grid.Add(utils.bold_text(self.top_panel, "Color scheme:"), 0, utils.std_sizer_flags, 5) cm_choice = wx.Choice(parent=self.top_panel, choices=wxtbx.plots.colormap_names) cm_choice.SetStringSelection("Blue") self.Bind(wx.EVT_CHOICE, self.OnUpdatePlot, cm_choice) grid.Add(cm_choice, 0, utils.std_sizer_flags, 5) self.choices = [pos_choice, res_choice, pt_choice, cm_choice] self.show_labels = wx.CheckBox(self.top_panel, label="Show labels") self.show_labels.SetValue(True) self.Bind(wx.EVT_CHECKBOX, self.OnUpdatePlot, self.show_labels) grid.Add(self.show_labels, 0, utils.std_sizer_flags, 5) def get_current_state(self): pos_type = self.choices[0].GetSelection() if (pos_type != ramalyze.RAMA_GENERAL): self.choices[1].SetSelection(0) self.choices[1].Disable() else : self.choices[1].Enable() res_type = self.choices[1].GetStringSelection() pt_type = self.choices[2].GetSelection() cm_name = self.choices[3].GetStringSelection() show_labels = self.show_labels.GetValue() return (pos_type, res_type, pt_type, cm_name, show_labels) def create_plot_panel(self): panel = ramalyze_plot(self) return panel def set_plot_type(self, pos_type, res_type="*", pt_type=ramalyze.RAMALYZE_ANY, cm_name='jet', show_labels=True): if not pos_type in self._map_cache : z_data = mmtbx.validation.utils.get_rotarama_data( pos_type=ramalyze.res_types[pos_type], convert_to_numpy_array=True) self._map_cache[pos_type] = z_data if not res_type in self._point_cache : pass title = ramalyze.format_ramachandran_plot_title( position_type=pos_type, residue_type=res_type) points = None coords = None if not (pos_type, res_type, pt_type) in self._point_cache : (points, coords) = self._validation.get_plot_data( position_type=pos_type, residue_name=res_type, point_type=pt_type) self._point_cache[(pos_type, res_type, pt_type)] = points self._xyz_cache[(pos_type, res_type, pt_type)] = coords else : points = self._point_cache[(pos_type, res_type, pt_type)] coords = self._xyz_cache[(pos_type, res_type, pt_type)] contours = ramalyze.get_contours(pos_type) self.plot_panel.show_plot( stats=self._map_cache[pos_type], title=title, points=points, show_labels=show_labels, colormap=wxtbx.plots.colormap_id_dict[cm_name], contours=contours, xyz=coords) def OnUpdatePlot(self, event): (pos_type,res_type,pt_type,cm_name,show_labels) = self.get_current_state() self.set_plot_type(pos_type, res_type, pt_type, cm_name, show_labels) class rotalyze_frame(rotarama_frame): frame_name = "rota_frame" residues = ["Arg", "Asn", "Asp", "Gln", "Glu", "His", "Ile", "Leu", "Lys", "Met", "Phe", "Trp", "Tyr"] def draw_top_panel(self): self.top_panel = wx.Panel(self) szr = wx.BoxSizer(wx.VERTICAL) self.top_panel.SetSizer(szr) grid = wx.FlexGridSizer(cols=4) szr.Add(grid, 0, wx.ALL) grid.Add(utils.bold_text(self.top_panel, "Residue name:"), 0, utils.std_sizer_flags, 5) res_choice = wx.Choice(parent=self.top_panel, choices=self.residues) res_choice.SetSelection(0) self.Bind(wx.EVT_CHOICE, self.OnUpdatePlot, res_choice) grid.Add(res_choice, 0, utils.std_sizer_flags, 5) grid.Add(utils.bold_text(self.top_panel, "Show data points:"), 0, utils.std_sizer_flags, 5) pt_names = ["All", "None", "Outlier"] pt_choice = wx.Choice(self.top_panel, choices=pt_names) pt_choice.SetSelection(0) self.Bind(wx.EVT_CHOICE, self.OnUpdatePlot, pt_choice) grid.Add(pt_choice, 0, utils.std_sizer_flags, 5) grid.Add(utils.bold_text(self.top_panel, "Color scheme:"), 0, utils.std_sizer_flags, 5) cm_choice = wx.Choice(parent=self.top_panel, choices=wxtbx.plots.colormap_names) cm_choice.SetSelection(5) self.Bind(wx.EVT_CHOICE, self.OnUpdatePlot, cm_choice) grid.Add(cm_choice, 0, utils.std_sizer_flags, 5) self.choices = [res_choice, pt_choice, cm_choice] self.show_labels = wx.CheckBox(self.top_panel, label="Show labels") self.show_labels.SetValue(False) self.Bind(wx.EVT_CHECKBOX, self.OnUpdatePlot, self.show_labels) grid.Add(self.show_labels, 0, utils.std_sizer_flags, 5) def get_current_state(self): res_type = self.choices[0].GetStringSelection() pt_type = self.choices[1].GetStringSelection() cm_name = self.choices[2].GetStringSelection() show_labels = self.show_labels.GetValue() return (res_type, pt_type, cm_name, show_labels) def create_plot_panel(self): panel = rotalyze_plot(self) return panel def set_plot_type(self, res_type, pt_type="All", cm_name='jet', show_labels=False): if not res_type in self._map_cache : z_data = mmtbx.validation.utils.get_rotarama_data( residue_type=res_type, db="rota", convert_to_numpy_array=True) self._map_cache[res_type] = z_data title = "Chi1-Chi2 plot for %s" % res_type points = coords = None if (pt_type != "None"): if not (res_type, pt_type) in self._point_cache : (points, coords) = self._validation.get_plot_data( residue_name=res_type.upper(), point_type=pt_type) # shift chi2 values by 180 to fit in contours if (res_type.lower() in ["asp", "phe", "tyr"]): for i in range(len(points)): if (points[i][1] > 180.0): point = list(points[i]) point[1] -= 180.0 points[i] = tuple(point) self._point_cache[(res_type, pt_type)] = points self._xyz_cache[(res_type, pt_type)] = coords else : points = self._point_cache[(res_type, pt_type)] coords = self._xyz_cache[(res_type, pt_type)] extent = y_marks = None if (res_type.lower() in ["asp", "phe", "tyr"]): extent = [0, 360, 0, 180] y_marks = [90] self.plot_panel.show_plot( stats=self._map_cache[res_type], title=title, points=points, show_labels=show_labels, colormap=wxtbx.plots.colormap_id_dict[cm_name], contours=None, xyz=coords, extent=extent, y_marks=y_marks) def OnUpdatePlot(self, event): (res_type,pt_type,cm_name,show_labels) = self.get_current_state() self.set_plot_type(res_type, pt_type, cm_name, show_labels) class multi_criterion_plot(wxtbx.plots.plot_container, graphics.multi_criterion_plot_mixin): def __init__(self, parent, binner, y_limits): self._reset = False graphics.multi_criterion_plot_mixin.__init__(self, binner=binner, y_limits=y_limits) wxtbx.plots.plot_container.__init__(self, parent=parent, figure_size=(16,9), handle_left_click=True) self.figure.subplots_adjust(hspace=0.001) self.canvas.mpl_connect('motion_notify_event', self.OnHover) def show_plot(self, *args, **kwds): if self.disabled : return self.draw_plot(*args, **kwds) self.parent.Refresh() def OnPickRange(self, event): bin = self.choose_range.GetSelection() self.plot_range(bin) def OnHover(self, mpl_event): (xdata, ydata) = (mpl_event.xdata, mpl_event.ydata) if xdata is None or ydata is None : if self._reset : self.parent.residue_status.SetValue("") self._reset = False return False idx = int(floor(xdata)) try : residue = self._current_bin.get_selected(index=idx) except IndexError : pass else : if (residue is not None): self.parent.residue_status.SetValue(residue.id_str()) self._reset = True def process_mouse_click(self, mpl_event): (xdata, ydata) = (mpl_event.xdata, mpl_event.ydata) if xdata is None or ydata is None : return False idx = int(floor(xdata)) selection_string = None xyz = None try : residue = self._current_bin.get_selected(idx) if (residue is not None): selection_string = residue.id_str() xyz = residue.xyz except IndexError : pass else : if ( (selection_string is not None) and (xyz is not None) ): self.parent.zoom_callback(selection_string=selection_string, xyz=xyz) class multi_criterion_frame(wxtbx.plots.plot_frame): show_controls_default = True def __init__(self, parent, title, validation): self._binner = validation.binned_data() self._y_limits = validation.get_y_limits() wxtbx.plots.plot_frame.__init__(self, parent=parent, title=title, style=wx.DEFAULT_FRAME_STYLE) self._map_cache = {} self._point_cache = {} self._xyz_cache = {} self.OnUpdatePlot(None) def create_plot_panel(self): panel = multi_criterion_plot(self, binner=self._binner, y_limits=self._y_limits) return panel def draw_top_panel(self): self.top_panel = wx.Panel(self) szr = wx.BoxSizer(wx.VERTICAL) self.top_panel.SetSizer(szr) grid = wx.FlexGridSizer(cols=4) szr.Add(grid, 0, wx.ALL) grid.Add(utils.bold_text(self.top_panel, "Show residues:"), 0, utils.std_sizer_flags, 5) self.range_choice = wx.Choice(parent=self.top_panel, choices=self._binner.get_ranges()) self.range_choice.SetSelection(0) self.Bind(wx.EVT_CHOICE, self.OnUpdatePlot, self.range_choice) grid.Add(self.range_choice, 0, utils.std_sizer_flags, 5) grid.Add(utils.bold_text(self.top_panel, "Click to zoom residue:"), 0, utils.std_sizer_flags, 5) self.residue_status = wx.TextCtrl(self.top_panel, size=(160,-1), style=wx.TE_READONLY) grid.Add(self.residue_status, 0, utils.std_sizer_flags, 5) def OnUpdatePlot(self, event): bin = self.range_choice.GetSelection() self.plot_panel.plot_range(bin) def zoom_callback(self, **kwds): if getattr(self.GetParent(), "main_window", None) is not None : self.GetParent().main_window.show_gfx_selection(**kwds)