from __future__ import absolute_import, division, print_function from iotbx.data_plots import simple_matplotlib_plot class rotarama_plot_mixin(object): extent = [0, 360, 0, 360] def __init__(self): assert hasattr(self, "figure") self._points = [] self._xyz = [] # only used by Phenix GUI (not offline plotting) self.plot = self.figure.add_subplot(111) self.plot.set_position([0.1, 0.1, 0.85, 0.85]) def draw_plot(self, stats, title, points=None, show_labels=True, colormap='jet', contours=None, xyz=None, extent=None, y_marks=None): import matplotlib.cm self._points = [] self._xyz = [] cm = getattr(matplotlib.cm, colormap) self.plot.clear() if (extent is None): extent = self.extent else : assert (len(extent) == 4) print(extent) self.plot.imshow(stats, origin="lower", cmap=cm, extent=extent) if (contours is not None): self.plot.contour(stats, contours, origin="lower", colors='k', extent=extent) if (y_marks is None): self.set_labels() else : self.set_labels(y_marks=y_marks) self.plot.set_title(title) if (points is not None): if (xyz is not None) : assert (len(xyz) == len(points)) for i, (x, y, label, is_outlier) in enumerate(points): if is_outlier : self.plot.plot((x,),(y,), 'bo', markerfacecolor='red') if show_labels : self.plot.text(x, y, label, color='black') self._points.append((x,y)) if (xyz is not None): self._xyz.append(xyz[i]) else : self.plot.plot((x,),(y,), 'bo', markerfacecolor='white') self.canvas.draw() class ramachandran_plot_mixin(rotarama_plot_mixin): extent = [-179,179,-179,179] def set_labels(self, y_marks=()): self.plot.set_xlabel("Phi") self.plot.set_xticks([-120,-60,0,60,120]) self.plot.set_ylabel("Psi") self.plot.set_yticks([-120,-60,0,60,120]) class rotamer_plot_mixin(rotarama_plot_mixin): def set_labels(self, y_marks=(60,180,300)): self.plot.set_xlabel("Chi1") self.plot.set_xticks([60,180,300]) self.plot.set_ylabel("Chi2") self.plot.set_yticks(list(y_marks)) self.plot.grid(True, color="0.75") class ramachandran_plot(simple_matplotlib_plot, ramachandran_plot_mixin): def __init__(self, *args, **kwds): simple_matplotlib_plot.__init__(self, *args, **kwds) ramachandran_plot_mixin.__init__(self, *args, **kwds) class rotamer_plot(simple_matplotlib_plot, rotamer_plot_mixin): def __init__(self, *args, **kwds): simple_matplotlib_plot.__init__(self, *args, **kwds) rotamer_plot_mixin.__init__(self, *args, **kwds) def get_residue_ramachandran_data(ramalyze_data, position_type, residue_name, point_type): #if (not position_type in ["general", "glycine", "cis-proline", # "trans-proline", "pre-proline", "isoleucine or valine"]): if (not position_type in ["General", "Gly", "cis-Pro", "trans-Pro", "pre-Pro", "Ile/Val"]): raise ValueError("Ramachandran position type '%s' not recognized." % position_type) points, coords = [], [] for i, residue in enumerate(ramalyze_data): (chain_id,resseq,resname,quality,phi,psi,status,pos_name,xyz) = residue if (position_type == "general"): if (((residue_name == '*') or (resname.upper() == residue_name.upper())) and (not resname in ["PRO","GLY","ILE","VAL"])): if ((point_type == "All") or (point_type=="Allowed/Outlier" and status in ["Allowed","OUTLIER"]) or (point_type == "Outlier" and status == "OUTLIER")): points.append((phi, psi, "%s%s" % (chain_id, resseq), (status == "OUTLIER"))) coords.append(xyz) elif (position_type.upper() == pos_name.upper()): if ((point_type == "All") or (point_type=="Allowed/Outlier" and status in ["Allowed","OUTLIER"]) or (point_type == "Outlier" and status == "OUTLIER")): points.append((phi, psi, "%s%s" % (chain_id, resseq), (status == "OUTLIER"))) coords.append(xyz) return (points, coords) def format_ramachandran_plot_title(position_type, residue_type): title = "Ramachandran plot for " if (position_type == "cis-proline"): title += "cis-Proline" elif (position_type == "trans-proline"): title += "trans-Proline" elif (position_type == "glycine"): title += "Glycine" elif (position_type == "pre-proline"): title += "pre-Proline residues" elif (position_type == "isoleucine or valine"): title += "Ile or Val" else : if residue_type == '*' : title += "all non-Pro/Gly residues" else : title += residue_type return title def draw_ramachandran_plot(ramalyze_data, rotarama_data, position_type, file_name, show_labels=True): points, coords = get_residue_ramachandran_data( ramalyze_data=ramalyze_data, position_type=position_type, residue_name='*', point_type="All") p = ramachandran_plot() title = format_ramachandran_plot_title(position_type, '*') # XXX where do these numbers come from? if position_type == "general" : contours = [0.1495, 0.376] else : contours = [0.2115, 0.376] p.draw_plot( stats=rotarama_data, title=title, points=points, xyz=coords, colormap="Blues", contours=contours) p.save_image(file_name) def get_residue_rotamer_data(rotalyze_data, residue_name, point_type): points, coords = [], [] for i, residue in enumerate(rotalyze_data): (chain_id,resseq,resname,quality,chi1,chi2,chi3,chi4,status,xyz)=residue if resname.upper() == residue_name.upper(): if ((point_type == "All") or (point_type=="Outlier" and status=="OUTLIER")): points.append((chi1, chi2, "%s%s" % (chain_id, resseq), (status == "OUTLIER"))) coords.append(xyz) return (points, coords) def draw_rotamer_plot(rotalyze_data, rotarama_data, residue_name, file_name, show_labels=True): points, coords = get_residue_rotamer_data( rotalyze_data=rotalyze_data, residue_name=residue_name, point_type="All") p = rotamer_plot() title = "Chi1-Chi2 plot for %s" % residue_name p.draw_plot( stats=rotarama_data, title=title, points=points, xyz=coords, colormap="Blues", contours=None) p.save_image(file_name)