#!/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. Modified: Marcin Magnus 2020 Source """ from __future__ import print_function import sys import os from pymol import cmd print("""show_contacts ------------------------------------- _polar: good polar interactions according to PyMOL _polar_ok: compute possibly suboptimal polar interactions using the user specified distance _aa: acceptors acceptors _dd: donors donors _all is all ;-) above!""") DEBUG=1 def show_contacts(selection='*', selection2='*', result="contacts", cutoff=3.6, bigcutoff = 4.0, labels=False, 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: #print(allres) #print(cmd.get_distance(allres, 'all_don_acc1_sele', 'all_don_acc2_sele', bigcutoff, mode = 0)) any = cmd.distance(allres, 'all_don_acc1_sele', 'all_don_acc2_sele', bigcutoff, mode = 0) # if any is 0 it seems that there is no distance! if any: cmd.set("dash_radius", "0.05", allres) if not labels: cmd.hide("labels", allres) else: # just do nothing and clena up print('no contacts') cmd.delete('all_don_acc1_sele') cmd.delete('all_don_acc2_sele') cmd.delete(result + "_all") return None ######################################## # 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_color", "marine", allres) #cmd.set('dash_gap', '0') cmd.set("dash_radius","0.2", polres) #"0.126" #cmd.set("dash_color", "marine", allres) if not labels: cmd.hide("labels", 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) if not labels: cmd.hide("labels", 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!') # acceptors acceptors 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) if not labels: cmd.hide("labels", accres) ######################################## # donors donors 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) if not labels: cmd.hide("labels", donres) ########################################################## ##### find the buried unpaired atoms of the receptor ##### ########################################################## #initialize the variable for when CALC_SASA is False unpaired_atoms = '' ## Group print(allres) # contacts_all 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') cmd.disable('contacts_all') cmd.disable('contacts_polar_ok') cmd.disable('contacts_aa') cmd.disable('contacts_dd') 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))