def default(selection="(all)",_self=cmd): cmd=_self s = tmp_sele cmd.select(s,selection) _prepare(s,_self=cmd) cmd.show("lines",s) cmd.show("nonbonded",s) color=cmd.get_object_color_index(selection) if color<0: util.cbag(selection,_self=cmd) else: util.cnc(selection,_self=cmd) cmd.color(str(color),"("+s+") and elem c")
def default(selection="(all)", _self=cmd): cmd = _self s = tmp_sele cmd.select(s, selection) _prepare(s, _self=cmd) cmd.show("lines", s) cmd.show("nonbonded", s) color = cmd.get_object_color_index(selection) if color < 0: util.cbag(selection, _self=cmd) else: util.cnc(selection, _self=cmd) cmd.color(str(color), "(" + s + ") and elem c")
def setup_alignment_contexts(context_info): # Author: Warren DeLano (list,dict) = context_info[0:2] doc_list = ['\888Legend:'] obj_name_dict = {} for a in list: sf = string.find(a,"_") if sf>=0: object_name = a[0:sf] if not obj_name_dict.has_key(object_name): obj_name_dict[object_name] = 1 col_index = cmd.get_object_color_index(object_name) if col_index>=0: col_tup = cmd.get_color_tuple(col_index) if is_tuple(col_tup): col_int = map(lambda x:int(x*9+0.49999),col_tup) col_str = string.join(map(lambda x:chr(ord('0')+x),col_int),'') doc_list.append("\\"+col_str+object_name+"\\---") key_list = [ 'F1','F2','F3','F4','F5','F6','F7','F8','F9','F10', #,'F11','F12', 'SHFT-F1','SHFT-F2','SHFT-F3','SHFT-F4','SHFT-F5','SHFT-F6','SHFT-F7', 'SHFT-F8','SHFT-F9','SHFT-F10']# ,'SHFT-F11','SHFT-F12'] doc_list.append("") doc_list.append("\\888Toggles:") zoom_context = 1 global labels,ligands,waters,sites,cgos,zooms,dashes labels = 1 ligands = 1 waters = 1 sites = 1 cgos = 0 zooms = 0 dashes = 1 global m4x_sites,m4x_ligands,m4x_waters m4x_sites = "m4x_sites" m4x_ligands = "m4x_ligands" m4x_waters = "m4x_waters" cmd.select(m4x_sites,"none") cmd.select(m4x_ligands,"none") cmd.select(m4x_waters,"none") if len(key_list): key = key_list.pop(0) cmd.set_key(key,toggle_zooms) doc_list.append(key+": Zoom") if len(key_list): key = key_list.pop(0) cmd.set_key(key,toggle_sites) doc_list.append(key+": Sites") if len(key_list): key = key_list.pop(0) cmd.set_key(key,toggle_waters) doc_list.append(key+": Waters") if len(key_list): key = key_list.pop(0) cmd.set_key(key,toggle_dashes) doc_list.append(key+": H-Bonds") if len(key_list): key = key_list.pop(0) cmd.set_key(key,toggle_cgos) doc_list.append(key+": Fits") if len(key_list): key = key_list.pop(0) cmd.set_key(key,toggle_ligands) doc_list.append(key+": Ligands") if len(key_list): key = key_list.pop(0) cmd.set_key(key,toggle_labels) doc_list.append(key+": HB-Dists") for a in list: include_flag = 0 water = a+"_water" ligand = a+"_ligand" site = a+"_site" hbond = a+"_hbond" if cmd.count_atoms(site): if cmd.count_atoms(site+" & m4x_aligned"): include_flag = 1 if cmd.count_atoms(ligand): if cmd.count_atoms(ligand+" & m4x_nearby"): include_flag = 1 if include_flag: name_list = dict[a] if water in name_list: cmd.select(m4x_waters,m4x_waters+"|"+water) if ligand in name_list: cmd.select(m4x_ligands,m4x_ligands+"|"+ligand) if site in name_list: cmd.select(m4x_sites,m4x_sites+"|"+site+ "|((byres (neighbor ("+site+" and name c))) and name n+ca)"+ "|((byres (neighbor ("+site+" and name n))) and name c+ca+o)") cmd.wizard("fedora",doc_list) toggle_cgos(1) toggle_labels(0) toggle_dashes(0) toggle_ligands(1) toggle_sites(0) toggle_waters(0) toggle_cgos(1) cmd.deselect() # cmd.feedback("enable","python","output") cmd.feedback("enable","objectmolecule","results") cmd.set("internal_feedback",1) cmd.set("internal_prompt",0) cmd.feedback("disable","selector","actions") cmd.feedback("disable","scene","actions")
def setup_alignment_contexts(context_info): # Author: Warren DeLano (list, dict) = context_info[0:2] doc_list = ['\888Legend:'] obj_name_dict = {} for a in list: sf = string.find(a, "_") if sf >= 0: object_name = a[0:sf] if not obj_name_dict.has_key(object_name): obj_name_dict[object_name] = 1 col_index = cmd.get_object_color_index(object_name) if col_index >= 0: col_tup = cmd.get_color_tuple(col_index) if is_tuple(col_tup): col_int = map(lambda x: int(x * 9 + 0.49999), col_tup) col_str = string.join( map(lambda x: chr(ord('0') + x), col_int), '') doc_list.append("\\" + col_str + object_name + "\\---") key_list = [ 'F1', 'F2', 'F3', 'F4', 'F5', 'F6', 'F7', 'F8', 'F9', 'F10', #,'F11','F12', 'SHFT-F1', 'SHFT-F2', 'SHFT-F3', 'SHFT-F4', 'SHFT-F5', 'SHFT-F6', 'SHFT-F7', 'SHFT-F8', 'SHFT-F9', 'SHFT-F10' ] # ,'SHFT-F11','SHFT-F12'] doc_list.append("") doc_list.append("\\888Toggles:") zoom_context = 1 global labels, ligands, waters, sites, cgos, zooms, dashes labels = 1 ligands = 1 waters = 1 sites = 1 cgos = 0 zooms = 0 dashes = 1 global m4x_sites, m4x_ligands, m4x_waters m4x_sites = "m4x_sites" m4x_ligands = "m4x_ligands" m4x_waters = "m4x_waters" cmd.select(m4x_sites, "none") cmd.select(m4x_ligands, "none") cmd.select(m4x_waters, "none") if len(key_list): key = key_list.pop(0) cmd.set_key(key, toggle_zooms) doc_list.append(key + ": Zoom") if len(key_list): key = key_list.pop(0) cmd.set_key(key, toggle_sites) doc_list.append(key + ": Sites") if len(key_list): key = key_list.pop(0) cmd.set_key(key, toggle_waters) doc_list.append(key + ": Waters") if len(key_list): key = key_list.pop(0) cmd.set_key(key, toggle_dashes) doc_list.append(key + ": H-Bonds") if len(key_list): key = key_list.pop(0) cmd.set_key(key, toggle_cgos) doc_list.append(key + ": Fits") if len(key_list): key = key_list.pop(0) cmd.set_key(key, toggle_ligands) doc_list.append(key + ": Ligands") if len(key_list): key = key_list.pop(0) cmd.set_key(key, toggle_labels) doc_list.append(key + ": HB-Dists") for a in list: include_flag = 0 water = a + "_water" ligand = a + "_ligand" site = a + "_site" hbond = a + "_hbond" if cmd.count_atoms(site): if cmd.count_atoms(site + " & m4x_aligned"): include_flag = 1 if cmd.count_atoms(ligand): if cmd.count_atoms(ligand + " & m4x_nearby"): include_flag = 1 if include_flag: name_list = dict[a] if water in name_list: cmd.select(m4x_waters, m4x_waters + "|" + water) if ligand in name_list: cmd.select(m4x_ligands, m4x_ligands + "|" + ligand) if site in name_list: cmd.select( m4x_sites, m4x_sites + "|" + site + "|((byres (neighbor (" + site + " and name c))) and name n+ca)" + "|((byres (neighbor (" + site + " and name n))) and name c+ca+o)") cmd.wizard("fedora", doc_list) toggle_cgos(1) toggle_labels(0) toggle_dashes(0) toggle_ligands(1) toggle_sites(0) toggle_waters(0) toggle_cgos(1) cmd.deselect() # cmd.feedback("enable","python","output") cmd.feedback("enable", "objectmolecule", "results") cmd.set("internal_feedback", 1) cmd.set("internal_prompt", 0) cmd.feedback("disable", "selector", "actions") cmd.feedback("disable", "scene", "actions")