# a_rapper_gui.py # Copyright (C) 2008 Bernhard Lohkamp, The University of York # # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program. If not, see . import pygtk, gtk, pango if (os.name == 'nt'): home_dir = os.getenv('COOT_HOME') else: home_dir = os.getenv('HOME') rapper_dir = os.path.join(os.path.normpath(home_dir), "rappermc") rapper_command = "rapper" def rapper_process(): #needed? pass def rename_dir_by_date(dir_name): import time date_str = time.strftime("%Y-%m-%d--%H-%M--%S") new_dir_name = dir_name + date_str # check if exists? os.rename(dir_name, new_dir_name) return new_dir_name # return a string or False # def sequence_string(imol, chain_id, resno_start, resno_end): def all_chars_qm(ls): return all(map(lambda x: x.isalpha(), ls)) if (not coot_utils.valid_model_molecule_qm(imol)): return False else: single_letter_code_list = [] for resno in range(resno_start, resno_end + 1): res_name = coot.residue_name(imol, chain_id, resno, "") single_letter_code_list.append(mutate.three_letter_code2single_letter(res_name)) if (not all_chars_qm): print "bad sequence chars ", single_letter_code_list return False else: return "".join(single_letter_code_list) def rapper_it(imol, chain_id, start_resno, end_resno, sequence, number_of_models): imol_map = coot.imol_refinement_map() if (not coot_utils.valid_map_molecule_qm(imol_map)): print "No valid map molecule given (possibly ambiguous)" else: str = "//" + chain_id + "/" + str(start_no) + \ "-" + str(end_resno) frag_mol = coot.new_molecule_by_atom_selection(imol, str) fragment_pdb = "coot-rapper-fragment-in.pdb" rapper_out_pdb = "rapper_out.pdb" rapper_mode = "model-loops-benchmark" # maybe "ca-trace" perhaps # rapper_mode = "ca-trace" length_for_rapper = 3 # test if (type(sequence) is StringType): sequence_string = sequence else: sequence_string = "AAA" map_file = "coot-rapper.map" whole_pdb_file_name = "rapper-all-atoms.pdb" coot.write_pdb_file(frag_mol, fragment_pdb) coot.write_pdb_file(imol, whole_pdb_file_name) coot.close_molecule(frag_mol) coot.export_map(imol_map, map_file) print "running rapper: ", imol, chain_id, start_resno, end_resno, \ sequence, number_of_models if (os.path.isfile("TESTRUNS")): rename_dir_by_date("TESTRUNS") rapper_command_line_args = [#"params.xml", rapper_mode, "--pdb", fragment_pdb, # "--framework", whole_pdb_file_name, "--pdb-out", rapper_out_pdb, "--map", map_file, "--models", str(number_of_models), "--start", str(start_resno), "--stop", str(end_resno), # "--length", str(length_for_rapper) "--seq", sequence_string, "--mainchain-restraint-threshold", "2.0", "--sidechain-centroid-restraint-threshold", "2.0", "--sidechain-mode", "smart", "--sidechain-radius-reduction", "0.75", "--enforce-mainchain-restraints", "true", "--enforce-sidechain-centroid-restraints", "true", "--edm-fit", "true", "--rapper-dir", rapper_dir] rapper_status = coot_utils.popen_command(rapper_command, rapper_command_line_args, [], "rapper.log", True) print "rapper_status:", rapper_status if (os.path.isfile("TESTRUNS")): new_dir_name = rename_dir_by_date("TESTRUNS") result_pdb_file_name = os.path.join(new_dir_name, "looptest-best.pdb") if (os.path.isfile(result_pdb_file_name)): coot.read_pdb(result_pdb_file_name) else: coot.info_dialog("RAPPER failed - no results") # run rapper, not decided yet how def stop_rapper(): print "stopping rapper process..." def cancel_dialog_func(widget, window): # do something more clever if the rapper process is still running window.destroy() # loop_building_tool is either 'rapper' or 'ARP/wARP' # def a_rapper_gui(loop_building_tool): def rapper_go_func(*args): from types import IntType imol = coot_gui.get_option_menu_active_molecule(option_menu_pdb, model_mol_list) if (not (type(imol) is IntType)): print "bad active model" else: chain_text = entry_chain.get_text() start_resno_text = entry_start_resno.get_text() end_resno_text = entry_end_resno.get_text() text_sequence_buffer = text_sequence.get_buffer() sequence = text_sequence_buffer.get_text() print "BL DEBUG:: input sequence is", sequence number_of_models_text = entry_models.get_text() start_resno = int(start_resno_text) end_resno = int(end_resno_text) number_of_models = int(number_of_models_text) if (not ((type(start_resno) is IntType) and (type(end_resno) is IntType) and (type(number_of_models) is IntType))): print "Something incomprehensible: ", start_resno, end_resno, number_of_models else: if (loop_building_tool == 'rapper'): seq = sequence_string(imol, chain_text, start_resno, end_resno) rapper_it(imol, chain_text, start_resno, end_resno, seq, number_of_models) elif (loop_building_tool == 'ARP/wARP'): # not supprted yet new_start = start_resno - 1 new_end = end_resno + 1 seq = sequence_string(imo, chain_text, new_start, new_end) arp_warp_it(imol, chain_text, [start_resno, end_resno], [new_start, new_end], seq, number_of_models) else: print "INFO:: invalid loop building argument", loop_building_tool window = gtk.Window(gtk.WINDOW_TOPLEVEL) vbox = gtk.VBox(False, 2) pdb_hbox = gtk.HBox(False, 2) chain_hbox = gtk.HBox(False, 2) start_resno_hbox = gtk.HBox(False, 2) end_resno_hbox = gtk.HBox(False, 2) sequence_vbox = gtk.VBox(False, 2) models_hbox = gtk.HBox(False, 2) buttons_hbox = gtk.HBox(False, 2) h_sep = gtk.HSeparator() stop_button = gtk.Button(" Stop ") go_button = gtk.Button(" Go ") cancel_button = gtk.Button(" Cancel ") # pdb label_pdb = gtk.Label("Rebuild fragment of Model: ") option_menu_pdb = gtk.combo_box_new_text() # chain label_chain = gtk.Label("Chain") entry_chain = gtk.Entry() # start resno label_start_resno = gtk.Label("Starting Res Number: ") entry_start_resno = gtk.Entry() # end resno label_end_resno = gtk.Label(" End Res Number: ") entry_end_resno = gtk.Entry() # sequence as it currently is: sequence_as_is_check_button = gtk.CheckButton("As is") # sequence as text label_sequence = gtk.Label("Sequence") text_sequence = gtk.TextView() # number of rapper models label_models = gtk.Label("Number of Models: ") entry_models = gtk.Entry() # model_mol_list = coot_gui.fill_option_menu_with_coordinates_mol_options(option_menu_pdb) #text_sequence.set_usize(-1, 80) # ?? using text view!? pdb_hbox.pack_start(label_pdb, False, False, 2) pdb_hbox.pack_start(option_menu_pdb, False, False, 2) chain_hbox.pack_start(label_chain, False, False, 2) chain_hbox.pack_start(entry_chain, False, False, 2) start_resno_hbox.pack_start(label_start_resno, False, False, 2) start_resno_hbox.pack_start(entry_start_resno, False, False, 2) end_resno_hbox.pack_start(label_end_resno, False, False, 2) end_resno_hbox.pack_start(entry_end_resno, False, False, 2) sequence_vbox.pack_start(label_sequence, False, False, 2) sequence_vbox.pack_start(sequence_as_is_check_button, False, False, 2) sequence_vbox.pack_start(text_sequence, False, False, 2) models_hbox.pack_start(label_models, False, False, 2) models_hbox.pack_start(entry_models, False, False, 2) window.set_title("A Rapper GUI") vbox.pack_start(pdb_hbox, False, False, 2) vbox.pack_start(chain_hbox, False, False, 2) vbox.pack_start(start_resno_hbox, False, False, 2) vbox.pack_start(end_resno_hbox, False, False, 2) vbox.pack_start(sequence_vbox, False, False, 2) vbox.pack_start(models_hbox, False, False, 2) vbox.pack_start(h_sep, False, False, 2) buttons_hbox.pack_start(go_button, True, False, 6) buttons_hbox.pack_start(stop_button, True, False, 6) buttons_hbox.pack_start(cancel_button, True, False, 6) vbox.pack_start(buttons_hbox, True, False, 2) window.add(vbox) entry_models.set_text("2") sequence_as_is_check_button.set_active(True) stop_button.connect("clicked", stop_rapper) cancel_button.connect("clicked", cancel_dialog_func, window) go_button.connect("clicked", rapper_go_func) window.show_all() menu = coot_gui.coot_menubar_menu("Loop") add_simple_coot_menu_menuitem(menu, "RAPPER...", lambda func: a_rapper_gui('rapper')) add_simple_coot_menu_menuitem(menu, "ARP/wARP Loopy...", lambda func: a_rapper_gui('ARP/wARP')) a_rapper_gui()