def load(self): self.manager.d = self self.manager.m = None self.manager.m = None # to also set prevm = None # cmd.delete(self.manager.prevd.obj) # cmd.delete(self.manager.prevd.pid) # print self.manager.d.obj # print self.manager.prevd.obj # sys.exit() cmd.delete("all") cmd.load(self.getloadname(),self.obj,1) cmd.remove(self.obj+" and not chain A") cmd.fetch(self.pid) cmd.remove("het or hydro") cmd.color('gray',self.pid+' and elem C') self.scores['rms'] = cmd.align(self.pid,self.obj+" and chain A")[0] cmd.hide('ev') cmd.show('lines') cmd.show("car") #cmd.disable(self.pid) redopent(self.obj) self.recalc_design_pos() self.read_data_dir('avg_deg') self.read_data_dir('ddG') self.read_data_dir('rot_boltz') self.read_bup() self.read_tot_scores() self.read_res_scores() cmd.orient(self.obj+" or pnt*") self.manager.m = self.remembermm if self.manager.m: self.manager.m.focus() if self.remembermv: cmd.set_view(self.remembermv)
def revert(self): v = cmd.get_view() cmd.remove(self.rdes.obj+" and not chain A") m = cmd.get_model(self.rdes.obj) n = self.oldcrd if not n: cmd.create("tmp12345",self.rnat.sel()) cmd.align("tmp12345",self.rdes.sel()) n = cmd.get_model("tmp12345").atom cmd.delete("tmp12345") di,ni = 0,0 while m.atom[di].resi != str(self.rdes.resi): di += 1 dj = di while m.atom[dj].resi == str(self.rdes.resi): dj += 1 if self.oldcrd: self.oldcrd = None else: self.oldcrd = m.atom[di:dj] m.atom = m.atom[:di] + n + m.atom[dj:] for i in range(di,di+len(n)): m.atom[i].resi = str(self.rdes.resi) m.atom[i].chain = str(self.rdes.chain) cmd.load_model(m,self.rdes.obj,1) cmd.save("tmp.pdb",self.rdes.obj) cmd.delete(self.rdes.obj) cmd.load("tmp.pdb",self.rdes.obj,1) cmd.show('car',self.rdes.obj) cmd.show('lines') redopent(self.rdes.obj) cmd.set_view(v) print "revert removing "+"".join(self.aas)+" from aas!" self.aas = [getaa('A',self.rdes.resi,self.manager.d.obj)]
def save(self,manual=False,savepse=False): sd = "mutalyze_MANUAL_SAVE/" if manual else savedir if not os.path.exists(sd): os.mkdir(sd) redopent(self.obj) sname = self.getsavename(sd) if savepse: cmd.save(sname+".pse") cmd.save (sname+".pdb",self.obj+" or pnt*") with open(sname+".resfile","w") as o: o.write(self.resfile()+"\n") #print "saved pse, pdb, and resfile with notes" self.remembermm = self.manager.m self.remembermv = cmd.get_view()