#!/usr/bin/python '''PyMOL plugin that provides show_contacts command and GUI for highlighting good and bad polar contacts. Factored out of clustermols by Matthew Baumgartner. The advantage of this package is it requires many fewer dependencies. ''' from __future__ import print_function import sys,os from pymol import cmd DEBUG=1 def show_contacts(selection,selection2,result="contacts",cutoff=3.6, bigcutoff = 4.0, SC_DEBUG = DEBUG): """ USAGE show_contacts selection, selection2, [result=contacts],[cutoff=3.6],[bigcutoff=4.0] Show various polar contacts, the good, the bad, and the ugly. Edit MPB 6-26-14: The distances are heavy atom distances, so I upped the default cutoff to 4.0 Returns: True/False - if False, something went wrong """ if SC_DEBUG > 4: print('Starting show_contacts') print('selection = "' + selection + '"') print('selection2 = "' + selection2 + '"') result = cmd.get_legal_name(result) #if the group of contacts already exist, delete them cmd.delete(result) # ensure only N and O atoms are in the selection all_don_acc1 = selection + " and (donor or acceptor)" all_don_acc2 = selection2 + " and (donor or acceptor)" if SC_DEBUG > 4: print('all_don_acc1 = "' + all_don_acc1 + '"') print('all_don_acc2 = "' + all_don_acc2 + '"') #if theses selections turn out not to have any atoms in them, pymol throws cryptic errors when calling the dist function like: #'Selector-Error: Invalid selection name' #So for each one, manually perform the selection and then pass the reference to the distance command and at the end, clean up the selections #the return values are the count of the number of atoms all1_sele_count = cmd.select('all_don_acc1_sele', all_don_acc1) all2_sele_count = cmd.select('all_don_acc2_sele', all_don_acc2) #print out some warnings if DEBUG > 3: if not all1_sele_count: print('Warning: all_don_acc1 selection empty!') if not all2_sele_count: print('Warning: all_don_acc2 selection empty!') ######################################## allres = result + "_all" if all1_sele_count and all2_sele_count: cmd.distance(allres, 'all_don_acc1_sele', 'all_don_acc2_sele', bigcutoff, mode = 0) cmd.set("dash_radius", "0.05", allres) cmd.set("dash_color", "purple", allres) cmd.hide("labels", allres) ######################################## #compute good polar interactions according to pymol polres = result + "_polar" if all1_sele_count and all2_sele_count: cmd.distance(polres, 'all_don_acc1_sele', 'all_don_acc2_sele', cutoff, mode = 2) #hopefully this checks angles? Yes cmd.set("dash_radius","0.126",polres) ######################################## #When running distance in mode=2, the cutoff parameter is ignored if set higher then the default of 3.6 #so set it to the passed in cutoff and change it back when you are done. old_h_bond_cutoff_center = cmd.get('h_bond_cutoff_center') # ideal geometry old_h_bond_cutoff_edge = cmd.get('h_bond_cutoff_edge') # minimally acceptable geometry cmd.set('h_bond_cutoff_center', bigcutoff) cmd.set('h_bond_cutoff_edge', bigcutoff) #compute possibly suboptimal polar interactions using the user specified distance pol_ok_res = result + "_polar_ok" if all1_sele_count and all2_sele_count: cmd.distance(pol_ok_res, 'all_don_acc1_sele', 'all_don_acc2_sele', bigcutoff, mode = 2) cmd.set("dash_radius", "0.06", pol_ok_res) #now reset the h_bond cutoffs cmd.set('h_bond_cutoff_center', old_h_bond_cutoff_center) cmd.set('h_bond_cutoff_edge', old_h_bond_cutoff_edge) ######################################## onlyacceptors1 = selection + " and (acceptor and !donor)" onlyacceptors2 = selection2 + " and (acceptor and !donor)" onlydonors1 = selection + " and (!acceptor and donor)" onlydonors2 = selection2 + " and (!acceptor and donor)" #perform the selections onlyacceptors1_sele_count = cmd.select('onlyacceptors1_sele', onlyacceptors1) onlyacceptors2_sele_count = cmd.select('onlyacceptors2_sele', onlyacceptors2) onlydonors1_sele_count = cmd.select('onlydonors1_sele', onlydonors1) onlydonors2_sele_count = cmd.select('onlydonors2_sele', onlydonors2) #print out some warnings if SC_DEBUG > 2: if not onlyacceptors1_sele_count: print('Warning: onlyacceptors1 selection empty!') if not onlyacceptors2_sele_count: print('Warning: onlyacceptors2 selection empty!') if not onlydonors1_sele_count: print('Warning: onlydonors1 selection empty!') if not onlydonors2_sele_count: print('Warning: onlydonors2 selection empty!') accres = result+"_aa" if onlyacceptors1_sele_count and onlyacceptors2_sele_count: aa_dist_out = cmd.distance(accres, 'onlyacceptors1_sele', 'onlyacceptors2_sele', cutoff, 0) if aa_dist_out < 0: print('\n\nCaught a pymol selection error in acceptor-acceptor selection of show_contacts') print('accres:', accres) print('onlyacceptors1', onlyacceptors1) print('onlyacceptors2', onlyacceptors2) return False cmd.set("dash_color","red",accres) cmd.set("dash_radius","0.125",accres) ######################################## donres = result+"_dd" if onlydonors1_sele_count and onlydonors2_sele_count: dd_dist_out = cmd.distance(donres, 'onlydonors1_sele', 'onlydonors2_sele', cutoff, 0) #try to catch the error state if dd_dist_out < 0: print('\n\nCaught a pymol selection error in dd selection of show_contacts') print('donres:', donres) print('onlydonors1', onlydonors1) print('onlydonors2', onlydonors2) print("cmd.distance('" + donres + "', '" + onlydonors1 + "', '" + onlydonors2 + "', " + str(cutoff) + ", 0)") return False cmd.set("dash_color","red",donres) cmd.set("dash_radius","0.125",donres) ########################################################## ##### find the buried unpaired atoms of the receptor ##### ########################################################## #initialize the variable for when CALC_SASA is False unpaired_atoms = '' ## Group cmd.group(result,"%s %s %s %s %s %s" % (polres, allres, accres, donres, pol_ok_res, unpaired_atoms)) ## Clean up the selection objects #if the show_contacts debug level is high enough, don't delete them. if SC_DEBUG < 5: cmd.delete('all_don_acc1_sele') cmd.delete('all_don_acc2_sele') cmd.delete('onlyacceptors1_sele') cmd.delete('onlyacceptors2_sele') cmd.delete('onlydonors1_sele') cmd.delete('onlydonors2_sele') return True cmd.extend('contacts', show_contacts) #contacts to avoid clashing with cluster_mols version ################################################################################# ########################### Start of pymol plugin code ########################## ################################################################################# about_text = '''show_contacts was factored out of the much more full-featured cluster_mols by Dr. Matt Baumgartner (https://pymolwiki.org/index.php/Cluster_mols). It provides an easy way to highlight polar contacts (and clashes) between two selections without requiring the installation of additional dependencies. ''' class Show_Contacts: ''' Tk version of the Plugin GUI ''' def __init__(self, app): parent = app.root self.parent = parent self.app = app import Pmw ############################################################################################ ### Open a window with options to select to loaded objects ### ############################################################################################ self.select_dialog = Pmw.Dialog(parent, buttons = ('Ok','Cancel'), title = 'Show Contacts Plugin', command = self.button_pressed ) self.select_dialog.withdraw() #allow the user to select from objects already loaded in pymol self.select_object_combo_box = Pmw.ComboBox(self.select_dialog.interior(), scrolledlist_items=[], labelpos='w', label_text='Select loaded object:', listbox_height = 2, dropdown=True) self.select_object_combo_box2 = Pmw.ComboBox(self.select_dialog.interior(), scrolledlist_items=[], labelpos='w', label_text='Select loaded object:', listbox_height = 2, dropdown=True) self.select_object_combo_box.grid(column=1, row=0) self.select_object_combo_box2.grid(column=2, row=0) self.populate_ligand_select_list() self.select_dialog.show() def button_pressed(self, result): if hasattr(result,'keycode'): if result.keycode == 36: print('keycode:', result.keycode) elif result == 'Ok' or result == 'Exit' or result == None: s1 = self.select_object_combo_box.get() s2 = self.select_object_combo_box2.get() show_contacts(s1,s2,'%s_%s'%(s1,s2)) self.select_dialog.withdraw() elif result == 'Cancel' or result == None: self.select_dialog.withdraw() def populate_ligand_select_list(self): ''' Go thourgh the loaded objects in PyMOL and add them to the selected list. ''' #get the loaded objects loaded_objects = _get_select_list() self.select_object_combo_box.clear() self.select_object_combo_box2.clear() for ob in loaded_objects: self.select_object_combo_box.insert('end', ob) self.select_object_combo_box2.insert('end', ob) def _get_select_list(): ''' Get either a list of object names, or a list of chain selections ''' loaded_objects = [name for name in cmd.get_names('all', 1) if '_cluster_' not in name] # if single object, try chain selections if len(loaded_objects) == 1: chains = cmd.get_chains(loaded_objects[0]) if len(chains) > 1: loaded_objects = ['{} & chain {}'.format(loaded_objects[0], chain) for chain in chains] return loaded_objects class Show_Contacts_Qt_Dialog(object): ''' Qt version of the Plugin GUI ''' def __init__(self): from pymol.Qt import QtWidgets dialog = QtWidgets.QDialog() self.setupUi(dialog) self.populate_ligand_select_list() dialog.accepted.connect(self.accept) dialog.exec_() def accept(self): s1 = self.select_object_combo_box.currentText() s2 = self.select_object_combo_box2.currentText() show_contacts(s1, s2, '%s_%s' % (s1, s2)) def populate_ligand_select_list(self): loaded_objects = _get_select_list() self.select_object_combo_box.clear() self.select_object_combo_box2.clear() self.select_object_combo_box.addItems(loaded_objects) self.select_object_combo_box2.addItems(loaded_objects) if len(loaded_objects) > 1: self.select_object_combo_box2.setCurrentIndex(1) def setupUi(self, Dialog): # Based on auto-generated code from ui file from pymol.Qt import QtCore, QtWidgets Dialog.resize(400, 50) self.gridLayout = QtWidgets.QGridLayout(Dialog) label = QtWidgets.QLabel("Select loaded object:", Dialog) self.gridLayout.addWidget(label, 0, 0, 1, 1) self.select_object_combo_box = QtWidgets.QComboBox(Dialog) sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Fixed) self.select_object_combo_box.setSizePolicy(sizePolicy) self.select_object_combo_box.setEditable(True) self.gridLayout.addWidget(self.select_object_combo_box, 0, 1, 1, 1) label = QtWidgets.QLabel("Select loaded object:", Dialog) self.gridLayout.addWidget(label, 1, 0, 1, 1) self.select_object_combo_box2 = QtWidgets.QComboBox(Dialog) self.select_object_combo_box2.setSizePolicy(sizePolicy) self.select_object_combo_box2.setEditable(True) self.gridLayout.addWidget(self.select_object_combo_box2, 1, 1, 1, 1) self.buttonBox = QtWidgets.QDialogButtonBox(Dialog) self.buttonBox.setOrientation(QtCore.Qt.Horizontal) self.buttonBox.setStandardButtons(QtWidgets.QDialogButtonBox.Cancel|QtWidgets.QDialogButtonBox.Ok) self.gridLayout.addWidget(self.buttonBox, 2, 0, 1, 2) self.buttonBox.accepted.connect(Dialog.accept) self.buttonBox.rejected.connect(Dialog.reject) def __init__(self): try: from pymol.plugins import addmenuitemqt addmenuitemqt('Show Contacts', Show_Contacts_Qt_Dialog) return except Exception as e: print(e) self.menuBar.addmenuitem('Plugin', 'command', 'Show Contacts', label = 'Show Contacts', command = lambda s=self : Show_Contacts(s))