# what_check.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 . # " 53" -> "53", " " -> "" def strip_leading_spaces(str): return str.lstrip() # consider for coot_utils def go_to_residue_by_spec(imol, spec): def atom_spec_qm(spec): return (len(spec) == 5) # main line coot_utils.set_go_to_atom_molecule(imol) if (atom_spec_qm(spec)): atom_name = spec[3] else: atom_name = " CA " coot_utils.set_go_to_atom_chain_residue_atom_name(spec[0], spec[1], atom_name) # consider for coot_utils def residue_spec_to_string(spec): print("DEBUG:: in residue_spec_to_string() with spec", spec) if len(spec) == 4: return (spec[1] + str(spec[2]) + spec[3]) else: return (spec[0] + str(spec[1]) + spec[2]) # make this internal # # where line is something like " 53 HIS ( 53 ) A12" # ignore xxxxI Cyy # xxxx is 4char resno, I insertion code, C chain id, yy is model number # # return a residue spec, or False # def get_flip_residue(line): l = len(line) if (l < 19): return False else: resno_string = line[11:15] try: resno = int(resno_string) except: return False inscode_pre = line[15:16] if (inscode_pre == " "): inscode = "" else: inscode = inscode_pre chain_id = line[18:19] print("found", resno, inscode, chain_id) return [chain_id, resno, inscode] def convert_to_button_info(problemed_res_list): #print "convert_to_button_info got", problemed_res_list button_label = problemed_res_list[1] problem_string = problemed_res_list[0] action_func = problemed_res_list[2] residue_spec_list = problemed_res_list[3] o = map(lambda x: [problem_string, button_label, action_func, x], residue_spec_list) #print "convert_to_button_info returns", o return o # A problemed-res-list is improper pair where the car is a pair of # string, one describing the problem, and the other being the "fix # it" button label. The cdr is a list of residue specs. # # A problemed_flip_list_list is a list of those things. # def problem_residues2dialog(imol, problemed_res_list_list): if (problemed_res_list_list): def button_list(): ret = [] converted_list = map(convert_to_button_info, problemed_res_list_list) for problemed_list in converted_list: for flip_res_info in problemed_list: flip_res_spec = flip_res_info[3] button_label = flip_res_info[1] action_func = flip_res_info[2] problem_string = flip_res_info[0] ret.append([[problem_string + " " + residue_spec_to_string(flip_res_spec), "go_to_residue_by_spec(" + str(imol) + ", " + str(flip_res_spec) + ")"], [button_label, str(action_func) + "(" + str(imol) + ", " + str(flip_res_spec) + ")"]]) #print "BL DEBUG:: returning button_list", ret return ret coot_gui.dialog_box_of_pairs_of_buttons(imol, "What-Check Report", [270, 300], # buttons is a list of: [[button_1_label, button_1_action,], # [button_2_label, button_2_action]] # The button_1_action function is a string. # The button_2_action function is a string. button_list(), " Close ") # action is either 'gui' (then we get a gui) or 'apply-actions', then the model # modifications are automatically applied. # def parse_check_db(imol, file_name, action): # global my_flip, my_rsr, my_delete_atom, my_rotamer_search def my_flip(imol_local, res_spec): coot.do_180_degree_side_chain_flip(imol_local, res_spec[0], res_spec[1], res_spec[2], "") def my_rsr(imol_local, res_spec): coot_utils.with_auto_accept([refine_zone, imol_local, res_spec[0], res_spec[1], res_spec[1], ""]) # def my_delete_atom(imol, atom_spec): ls = [imol] + atom_spec print("calling delete_atom with args", ls) coot.delete_atom(*ls) # def my_rotamer_search(imol, res_spec): chain_id = res_spec[0] resno = res_spec[1] ins_code = res_spec[2] altloc = "" imol_map = coot.imol_refinement_map() if (coot_utils.valid_map_molecule_qm(imol_map)): print( "rotamer search with imol: %s chain: %s resno: %s inscode: %s" \ %(imol, chain_id, resno, ins_code)) coot.auto_fit_best_rotamer(resno, altloc, ins_code, chain_id, imol, imol_map, 1, 0.01) else: coot.add_status_bar_text("No refinement map available, no rotamer fit") # return False or a residue spec: def line2residue_spec(line): if (len(line) >21): resno_string = line[26:30] try: resno = int(resno_string) except: print("BL WARNING:: no int resno -> return") return False inscode_pre = line[40:41] if (inscode_pre == "_"): inscode = "" else: inscode = inscode_pre chain_id_pre = line[19:20] chain_id = " " if (chain_id_pre == "_") else chain_id_pre return [chain_id, resno, inscode] # return False or an atom_spec # an atom_spec is [chain_id, resno, ins_code, atom_name, alt_conf] # def line2atom_spec(line): if (len(line) > 53): resno_string = line[26:30] try: resno = int(resno_string) except: return False inscode_pre = line[40:41] inscode = "" if (inscode_pre == "_") else inscode_pre chain_id_pre = line[19:20] chain_id = "" if (chain_id_pre == "_") else chain_id_pre atom_name_pre = line[47:51] atom_name = atom_name_pre alt_conf = "" print("found atom name %s resno %s (from %s) inscode %s (%s) chain_id %s" \ %(atom_name, resno, resno_string, inscode_pre, inscode, chain_id)) return [chain_id, resno, inscode, atom_name, alt_conf] def apply_actions(imol, action_list): for action in action_list: func = action[0] baddie_list = action[1] print( "BL DEBUG:: action and baddie_list", action, baddie_list) imol_list = map(lambda x: imol, baddie_list) print( "BL DEBUG:: imol_list", imol_list) print( "applying %s to %s" %(func, baddie_list)) print( "BL DEBUG:: len of lists", len(imol_list), len(baddie_list)) map(func, imol_list, baddie_list) # main line print( "parse_whatcheck_report: parsing output of what-if...") found_flip_table = False found_h2ohbo_table = False found_BMPCHK_table = False found_NAMCHK_table = False found_PLNCHK_table = False h2o_h_bond_less_list = [] plane_list = [] flip_list = [] namchk_list = [] bump_list = [] if (os.path.isfile(file_name)): fin = open(file_name, 'r') lines = fin.readlines() fin.close() for line in lines: line = line.rstrip('\n') # remove trailing \n if (line == "//"): found_flip_table = False found_h2ohbo_table = False found_BMPCHK_table = False found_NAMCHK_table = False found_PLNCHK_table = False if (found_flip_table): if (len(line) > 12): attr_type = line[0:11] if (attr_type == " Name :"): #print "found flip name", line res = line2residue_spec(line) if (res): flip_list.append(res) if (line == "CheckID : HNQCHK"): found_flip_table = True if (found_h2ohbo_table): if (len(line) > 12): attr_type = line[0:11] if (attr_type == " Name :"): #print "found h2obmo name", line atom = line2atom_spec(line) if (atom): h2o_h_bond_less_list.append(atom) if (line == "CheckID : H2OHBO"): found_h2ohbo_table = True if (found_BMPCHK_table): if (len(line) > 12): attr_type = line[0:11] if (attr_type == " Name :"): #print "found bump", line res = line2residue_spec(line) if (res): bump_list.append(res) if (line == "CheckID : BMPCHK"): found_BMPCHK_table = True if (found_NAMCHK_table): if (len(line) > 12): attr_type = line[0:11] if (attr_type == " Name :"): res = line2residue_spec(line) if (res): namchk_list.append(res) if (line == "CheckID : NAMCHK"): found_NAMCHK_table = True if (found_PLNCHK_table): if (len(line) > 12): attr_type = line[0:11] if (attr_type == " Name :"): res = line2residue_spec(line) if (res): plane_list.append(res) if (line == "CheckID : PLNCHK"): found_PLNCHK_table = True #print "Here flip_list is", flip_list #print "Here h2o-h-bond-less-list is", h2o_h_bond_less_list #print "Here bump_list is", bump_list print( "Here plane_list is", plane_list) if (action == 'gui'): problem_residues2dialog(imol, [ ["Needs flipping", "Flip it", "my_flip", flip_list], ["Water with no H-bonds", "Delete it", "my_delete_atom", h2o_h_bond_less_list], ["Has Bumps", "Rotamer Search", "my_rotamer_search", bump_list], ["Nomenclature error", "180 degree flip", "my_flip", namchk_list]]) elif (action == 'apply-actions'): apply_actions(imol, [ # [my_flip, flip_list], # [my_delete_atom, h2o_h_bond_less_list], # [my_rotamer_search, bump_list], [my_rsr, plane_list] # [my_flip, namchk_list] ]) else: print( "INFO:: wrong action input") else: print( "file not found", file_name)