add_key_binding("Refine Active Residue", "r", lambda: manual_refine_residues(0)) add_key_binding("Refine Active Residue AA", "x", lambda: refine_active_residue()) add_key_binding("Autofit Rotamer", "j", lambda: auto_fit_rotamer_active_residue()) add_key_binding("Triple Refine", "t", lambda: manual_refine_residues(1)) # add_key_binding("Pepflip", "q", lambda: pepflip_complicado()) add_key_binding("Go To Blob", "g", lambda: blob_under_pointer_to_screen_centre()) add_key_binding("Add Water", "w", lambda: place_typed_atom_at_pointer("Water")) add_key_binding("Eigen-flip Ligand", "e", lambda: flip_active_ligand()) def pepflip_complicado(): done = False try: done = pepflip_intermediate_atoms() if done == 0: pepflip_active_residue() except: pepflip_active_residue() return 1 def add_water_in_blob(): blob_under_pointer_to_screen_centre() place_typed_atom_at_pointer("Water") refine_active_residue() add_key_binding("Add Water +", "W", lambda: add_water_in_blob()) def key_binding_func_1(): active_atom = active_residue() if (not active_atom): print "No active atom" else: imol = active_atom[0] chain_id = active_atom[1] res_no = active_atom[2] ins_code = active_atom[3] atom_name = active_atom[4] alt_conf = active_atom[5] add_terminal_residue(imol, chain_id, res_no, "auto", 1) # let's try to add neighbour-refine and next residue recentering # def key_binding_terminal_residue_complicado(): active_atom = active_residue() if (not active_atom): print "No active atom" else: imol = active_atom[0] chain_id = active_atom[1] res_no = active_atom[2] ins_code = active_atom[3] atom_name = active_atom[4] alt_conf = active_atom[5] # which terminus is this? terminus_type='U' # unknown atoms_prev = residue_info(imol, chain_id, res_no-1, ins_code) atoms_next = residue_info(imol, chain_id, res_no+1, ins_code) # print "atoms_prev", atoms_prev # print "atoms_next", atoms_next if atoms_next == False: terminus_type = 'C' new_res_no = res_no + 1 if atoms_prev == False: terminus_type = 'N' new_res_no = res_no - 1 success = add_terminal_residue(imol, chain_id, res_no, "auto", 1) if success == 1: if terminus_type != 'U': rc_spec = [chain_id, res_no, ins_code] ls = residues_near_residue(imol, rc_spec, 1.9) with_auto_accept([refine_residues, imol, [rc_spec] + ls]) set_go_to_atom_molecule(imol) set_go_to_atom_chain_residue_atom_name(chain_id, new_res_no, ' CA '); # add_key_binding("Add terminal residue", "y", lambda: key_binding_func_1()) add_key_binding("Add terminal residue", "y", lambda: key_binding_terminal_residue_complicado()) def key_binding_func_2(): active_atom = active_residue() if (not active_atom): print "No active atom" else: imol = active_atom[0] chain_id = active_atom[1] res_no = active_atom[2] ins_code = active_atom[3] atom_name = active_atom[4] alt_conf = active_atom[5] fill_partial_residue(imol, chain_id, res_no, ins_code) add_key_binding("Fill Partial", "k", lambda: key_binding_func_2()) def rotamer_dialog_for_ar(): with UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no, aa_ins_code, aa_atom_name, aa_alt_conf]: show_rotamers_dialog(aa_imol, aa_chain_id, aa_res_no, aa_ins_code, aa_alt_conf) add_key_binding("Rotamers dialog for Active Residue", "Q", lambda: rotamer_dialog_for_ar()) def key_binding_func_5(): active_atom = active_residue() if (not active_atom): add_status_bar_text("No active residue") else: imol = active_atom[0] chain_id = active_atom[1] res_no = active_atom[2] ins_code = active_atom[3] atom_name = active_atom[4] alt_conf = active_atom[5] name = get_rotamer_name(imol, chain_id, res_no, ins_code) if (not name): add_status_bar_text("No Name found") else: if (name == ""): add_status_bar_text("No name for this") else: add_status_bar_text("Rotamer name: " + name) add_key_binding("Rotamer name in Status Bar", "~", lambda: key_binding_func_5()) refine_residue_sphere_radius_key = 4.5 # Angstroms add_key_binding("Refine residue in a sphere", "R", lambda: sphere_refine(refine_residue_sphere_radius_key)) def key_binding_func_21(): if not valid_map_molecule_qm(imol_refinement_map()): info_dialog("Must set the refinement map") else: # not using active atom active_atom = active_residue() if (not active_atom): add_status_bar_text("No active residue") else: imol = active_atom[0] chain_id = active_atom[1] res_no = active_atom[2] ins_code = active_atom[3] atom_name = active_atom[4] alt_conf = active_atom[5] rc_spec = [chain_id, res_no, ins_code] ls = residues_near_residue(imol, rc_spec, 1.9) with_auto_accept([refine_residues, imol, [rc_spec] + ls]) add_key_binding("Neighbours Refine", "h", lambda: key_binding_func_21()) add_key_binding("Regularize Residues in sphere", "B", lambda: sphere_regularize(refine_residue_sphere_radius_key)) def edit_chi_angles_key_func(): with UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no, aa_ins_code, aa_atom_name, aa_alt_conf]: edit_chi_angles(aa_imol, aa_chain_id, aa_res_no, aa_ins_code, aa_alt_conf) set_moving_atom_move_chis() set_graphics_edit_current_chi(1) add_key_binding("Edit Chi Angles", "X", lambda: edit_chi_angles_key_func()) def jiggle_fit_residue_key(): with UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no, aa_ins_code, aa_atom_name, aa_alt_conf]: fit_to_map_by_random_jiggle(aa_imol, aa_chain_id, aa_res_no, aa_ins_code, 100, 1.0) add_key_binding("Jiggle Fit", "J", lambda: jiggle_fit_residue_key()) def step_scrollable_map_number(): maps = map_molecule_list() current = scroll_wheel_map() if maps: l = maps.index(current) if (l == len(maps) - 1): new = maps[0] else: new = maps[l+1] set_scroll_wheel_map(new) add_key_binding("Step scrollable map number", "M", lambda: step_scrollable_map_number()) def delete_residue_hydrogens_key(): with UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no, aa_ins_code, aa_atom_name, aa_alt_conf]: delete_residue_hydrogens(aa_imol, aa_chain_id, aa_res_no, aa_ins_code, aa_alt_conf) add_key_binding("Delete Residue Hydrogens", "P", lambda: delete_residue_hydrogens_key()) def key_binding_func_9(): with UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no, aa_ins_code, aa_atom_name, aa_alt_conf]: additional_representation_by_attributes(aa_imol, aa_chain_id, aa_res_no, aa_res_no, aa_ins_code, 2, 2, 0.12, 1) add_key_binding("ball-and-stickify residue", "$", lambda: key_binding_func_9()) add_key_binding("Undo Symmetry View", "V", lambda: undo_symmetry_view()) add_key_binding("Accept Baton Position", "A", lambda: accept_baton_position()) add_key_binding("Cootilus here", "N", lambda: find_nucleic_acids_local(6.0)) def show_chemical_features_func(): set_display_generic_objects_as_solid(1) with UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no, aa_ins_code, aa_atom_name, aa_alt_conf]: show_feats(aa_imol, aa_chain_id, aa_res_no, aa_ins_code) add_key_binding("Show Chemical Features", "T", lambda: show_chemical_features_func()) # Paul's not sure about this one. I likey! # add_key_binding("Delete this water", "D", lambda: delete_atom(*active_residue())) def toggle_contact_dots_func(): def is_dotted_surface_name(name): if name in 'clashes': return True if name in 'big-overlap': return True if name in 'small-overlap': return True if name in 'close-contact': return True if name in 'wide-contact': return True if name in 'H-bond': return True return False n = number_of_generic_objects() objects = {} for i in range(n): if not(is_closed_generic_object_p(i)): name = generic_object_name(i) if is_dotted_surface_name(name): print "name", name, "is dottted surface name" try: objects[name].append(i) except KeyError: objects[name] = [i] print objects for obj in objects: for i in objects[obj]: if generic_object_is_displayed_p(i) == 0: set_display_generic_object_simple(i, 1) else: set_display_generic_object_simple(i, 0) graphics_draw()