build.rna_tools.tools.PyMOL4RNA.libs.show_contacts.__init__() - Code Metrics - mmagnus/rna-tools - Measure and Improve Code Quality continuously with Scrutinizer

init() A
last analyzed 2025-03-19 22:26 UTC

↳ Parent: build.rna_tools.tools.PyMOL4RNA.libs.show_contacts

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Total Lines	8
Code Lines	8

Duplication

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Ratio	0 %

Importance

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Metric	Value
cc	3
eloc	8
nop	1
dl	0
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rs	10
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#!/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 <https://pymolwiki.org/index.php/Pymol-script-repo>
"""
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))  
        



1			#!/usr/bin/python
2
3			"""
4			PyMOL plugin that provides show_contacts command and GUI
5			for highlighting good and bad polar contacts.
6
7			Factored out of clustermols by Matthew Baumgartner.
8
9			The advantage of this package is it requires many fewer dependencies.
10
11			Modified: Marcin Magnus 2020
12
13			Source <https://pymolwiki.org/index.php/Pymol-script-repo>
14			"""
15			from __future__ import print_function
16
17			import sys
18			import os
19			from pymol import cmd
20
21			print("""show_contacts
22			-------------------------------------
23
24			_polar: good polar interactions according to PyMOL
25			_polar_ok: compute possibly suboptimal polar interactions using the user specified distance
26			_aa: acceptors acceptors
27			_dd: donors donors
28
29			_all is all ;-) above!""")
30
31			DEBUG=1
32
33			def show_contacts(selection='', selection2='',
34			result="contacts",
35			cutoff=3.6,
36			bigcutoff = 4.0,
37			labels=False,
38			SC_DEBUG = DEBUG):
39			"""
40			USAGE
41
42			show_contacts selection, selection2, [result=contacts],[cutoff=3.6],[bigcutoff=4.0]
43
44			Show various polar contacts, the good, the bad, and the ugly.
45
46			Edit MPB 6-26-14: The distances are heavy atom distances, so I upped the default cutoff to 4.0
47
48			Returns:
49			True/False - if False, something went wrong
50			"""
51			if SC_DEBUG > 4:
52			print('Starting show_contacts')
53			print('selection = "' + selection + '"')
54			print('selection2 = "' + selection2 + '"')
55
56			result = cmd.get_legal_name(result)
57
58			#if the group of contacts already exist, delete them
59			cmd.delete(result)
60
61			# ensure only N and O atoms are in the selection
62			all_don_acc1 = selection + " and (donor or acceptor)"
63			all_don_acc2 = selection2 + " and (donor or acceptor)"
64
65			if SC_DEBUG > 4:
66			print('all_don_acc1 = "' + all_don_acc1 + '"')
67			print('all_don_acc2 = "' + all_don_acc2 + '"')
68
69			#if theses selections turn out not to have any atoms in them, pymol throws cryptic errors when calling the dist function like:
70			#'Selector-Error: Invalid selection name'
71			#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
72			#the return values are the count of the number of atoms
73			all1_sele_count = cmd.select('all_don_acc1_sele', all_don_acc1)
74			all2_sele_count = cmd.select('all_don_acc2_sele', all_don_acc2)
75
76			#print out some warnings
77			if DEBUG > 3:
78			if not all1_sele_count:
79			print('Warning: all_don_acc1 selection empty!')
80			if not all2_sele_count:
81			print('Warning: all_don_acc2 selection empty!')
82
83			########################################
84			allres = result + "_all"
85			if all1_sele_count and all2_sele_count:
86			#print(allres)
87			#print(cmd.get_distance(allres, 'all_don_acc1_sele', 'all_don_acc2_sele', bigcutoff, mode = 0))
88			any = cmd.distance(allres, 'all_don_acc1_sele', 'all_don_acc2_sele', bigcutoff, mode = 0)
89			# if any is 0 it seems that there is no distance!
90			if any:
91			cmd.set("dash_radius", "0.05", allres)
92			if not labels:
93			cmd.hide("labels", allres)
94			else:
95			# just do nothing and clena up
96			print('no contacts')
97			cmd.delete('all_don_acc1_sele')
98			cmd.delete('all_don_acc2_sele')
99			cmd.delete(result + "_all")
100			return None
101			########################################
102			# compute good polar interactions according to pymol
103			polres = result + "_polar"
104			if all1_sele_count and all2_sele_count:
105			cmd.distance(polres, 'all_don_acc1_sele', 'all_don_acc2_sele', cutoff, mode = 2) #hopefully this checks angles? Yes
106			#cmd.set("dash_color", "marine", allres)
107			#cmd.set('dash_gap', '0')
108			cmd.set("dash_radius","0.2", polres) #"0.126"
109			#cmd.set("dash_color", "marine", allres)
110			if not labels:
111			cmd.hide("labels", polres)
112
113			########################################
114			# When running distance in mode=2, the cutoff parameter is ignored if set higher then the default of 3.6
115			# so set it to the passed in cutoff and change it back when you are done.
116			old_h_bond_cutoff_center = cmd.get('h_bond_cutoff_center') # ideal geometry
117			old_h_bond_cutoff_edge = cmd.get('h_bond_cutoff_edge') # minimally acceptable geometry
118			cmd.set('h_bond_cutoff_center', bigcutoff)
119			cmd.set('h_bond_cutoff_edge', bigcutoff)
120
121			# compute possibly suboptimal polar interactions using the user specified distance
122			pol_ok_res = result + "_polar_ok"
123			if all1_sele_count and all2_sele_count:
124			cmd.distance(pol_ok_res, 'all_don_acc1_sele', 'all_don_acc2_sele', bigcutoff, mode = 2)
125			cmd.set("dash_radius", "0.06", pol_ok_res)
126			if not labels:
127			cmd.hide("labels", pol_ok_res)
128
129			#now reset the h_bond cutoffs
130			cmd.set('h_bond_cutoff_center', old_h_bond_cutoff_center)
131			cmd.set('h_bond_cutoff_edge', old_h_bond_cutoff_edge)
132
133
134			########################################
135
136			onlyacceptors1 = selection + " and (acceptor and !donor)"
137			onlyacceptors2 = selection2 + " and (acceptor and !donor)"
138			onlydonors1 = selection + " and (!acceptor and donor)"
139			onlydonors2 = selection2 + " and (!acceptor and donor)"
140
141			#perform the selections
142			onlyacceptors1_sele_count = cmd.select('onlyacceptors1_sele', onlyacceptors1)
143			onlyacceptors2_sele_count = cmd.select('onlyacceptors2_sele', onlyacceptors2)
144			onlydonors1_sele_count = cmd.select('onlydonors1_sele', onlydonors1)
145			onlydonors2_sele_count = cmd.select('onlydonors2_sele', onlydonors2)
146
147			#print out some warnings
148			if SC_DEBUG > 2:
149			if not onlyacceptors1_sele_count:
150			print('Warning: onlyacceptors1 selection empty!')
151			if not onlyacceptors2_sele_count:
152			print('Warning: onlyacceptors2 selection empty!')
153			if not onlydonors1_sele_count:
154			print('Warning: onlydonors1 selection empty!')
155			if not onlydonors2_sele_count:
156			print('Warning: onlydonors2 selection empty!')
157
158			# acceptors acceptors
159			accres = result+"_aa"
160			if onlyacceptors1_sele_count and onlyacceptors2_sele_count:
161			aa_dist_out = cmd.distance(accres, 'onlyacceptors1_sele', 'onlyacceptors2_sele', cutoff, 0)
162			if aa_dist_out < 0:
163			print('\n\nCaught a pymol selection error in acceptor-acceptor selection of show_contacts')
164			print('accres:', accres)
165			print('onlyacceptors1', onlyacceptors1)
166			print('onlyacceptors2', onlyacceptors2)
167			return False
168			cmd.set("dash_color","red",accres)
169			cmd.set("dash_radius","0.125",accres)
170			if not labels:
171			cmd.hide("labels", accres)
172
173			########################################
174			# donors donors
175			donres = result+"_dd"
176			if onlydonors1_sele_count and onlydonors2_sele_count:
177			dd_dist_out = cmd.distance(donres, 'onlydonors1_sele', 'onlydonors2_sele', cutoff, 0)
178
179			#try to catch the error state
180			if dd_dist_out < 0:
181			print('\n\nCaught a pymol selection error in dd selection of show_contacts')
182			print('donres:', donres)
183			print('onlydonors1', onlydonors1)
184			print('onlydonors2', onlydonors2)
185			print("cmd.distance('" + donres + "', '" + onlydonors1 + "', '" + onlydonors2 + "', " + str(cutoff) + ", 0)")
186			return False
187
188			cmd.set("dash_color","red",donres)
189			cmd.set("dash_radius","0.125",donres)
190			if not labels:
191			cmd.hide("labels", donres)
192
193			##########################################################
194			##### find the buried unpaired atoms of the receptor #####
195			##########################################################
196
197			#initialize the variable for when CALC_SASA is False
198			unpaired_atoms = ''
199
200			## Group
201			print(allres) # contacts_all
202			cmd.group(result,"%s %s %s %s %s %s" % (polres, allres, accres, donres, pol_ok_res, unpaired_atoms))
203
204			## Clean up the selection objects
205			#if the show_contacts debug level is high enough, don't delete them.
206			if SC_DEBUG < 5:
207			cmd.delete('all_don_acc1_sele')
208			cmd.delete('all_don_acc2_sele')
209			cmd.delete('onlyacceptors1_sele')
210			cmd.delete('onlyacceptors2_sele')
211			cmd.delete('onlydonors1_sele')
212			cmd.delete('onlydonors2_sele')
213
214			cmd.disable('contacts_all')
215			cmd.disable('contacts_polar_ok')
216			cmd.disable('contacts_aa')
217			cmd.disable('contacts_dd')
218			return True
219
220			cmd.extend('contacts', show_contacts) #contacts to avoid clashing with cluster_mols version
221
222
223
224
225
226			#################################################################################
227			########################### Start of pymol plugin code ##########################
228			#################################################################################
229
230
231			about_text = '''show_contacts was factored out of the much more full-featured cluster_mols
232			by Dr. Matt Baumgartner (https://pymolwiki.org/index.php/Cluster_mols). It provides
233			an easy way to highlight polar contacts (and clashes) between two selections without
234			requiring the installation of additional dependencies.
235			'''
236
237			class Show_Contacts:
238			''' Tk version of the Plugin GUI '''
239			def __init__(self, app):
240			parent = app.root
241			self.parent = parent
242
243			self.app = app
244
245			import Pmw
246
247			############################################################################################
248			### Open a window with options to select to loaded objects ###
249			############################################################################################
250
251			self.select_dialog = Pmw.Dialog(parent,
252			buttons = ('Ok','Cancel'),
253			title = 'Show Contacts Plugin',
254			command = self.button_pressed )
255
256			self.select_dialog.withdraw()
257
258
259			#allow the user to select from objects already loaded in pymol
260			self.select_object_combo_box = Pmw.ComboBox(self.select_dialog.interior(),
261			scrolledlist_items=[],
262			labelpos='w',
263			label_text='Select loaded object:',
264			listbox_height = 2,
265			dropdown=True)
266			self.select_object_combo_box2 = Pmw.ComboBox(self.select_dialog.interior(),
267			scrolledlist_items=[],
268			labelpos='w',
269			label_text='Select loaded object:',
270			listbox_height = 2,
271			dropdown=True)
272			self.select_object_combo_box.grid(column=1, row=0)
273			self.select_object_combo_box2.grid(column=2, row=0)
274			self.populate_ligand_select_list()
275			self.select_dialog.show()
276
277
278
279			def button_pressed(self, result):
280			if hasattr(result,'keycode'):
281			if result.keycode == 36:
282			print('keycode:', result.keycode)
283			elif result == 'Ok' or result == 'Exit' or result == None:
284			s1 = self.select_object_combo_box.get()
285			s2 = self.select_object_combo_box2.get()
286			show_contacts(s1,s2,'%s_%s'%(s1,s2))
287			self.select_dialog.withdraw()
288			elif result == 'Cancel' or result == None:
289			self.select_dialog.withdraw()
290
291
292
293
294			def populate_ligand_select_list(self):
295			''' Go thourgh the loaded objects in PyMOL and add them to the selected list. '''
296			#get the loaded objects
297			loaded_objects = _get_select_list()
298
299			self.select_object_combo_box.clear()
300			self.select_object_combo_box2.clear()
301
302			for ob in loaded_objects:
303			self.select_object_combo_box.insert('end', ob)
304			self.select_object_combo_box2.insert('end', ob)
305
306
307			def _get_select_list():
308			'''
309			Get either a list of object names, or a list of chain selections
310			'''
311			loaded_objects = [name for name in cmd.get_names('all', 1) if '_cluster_' not in name]
312
313			# if single object, try chain selections
314			if len(loaded_objects) == 1:
315			chains = cmd.get_chains(loaded_objects[0])
316			if len(chains) > 1:
317			loaded_objects = ['{} & chain {}'.format(loaded_objects[0], chain) for chain in chains]
318
319			return loaded_objects
320
321
322			class Show_Contacts_Qt_Dialog(object):
323			''' Qt version of the Plugin GUI '''
324			def __init__(self):
325			from pymol.Qt import QtWidgets
326			dialog = QtWidgets.QDialog()
327			self.setupUi(dialog)
328			self.populate_ligand_select_list()
329			dialog.accepted.connect(self.accept)
330			dialog.exec_()
331
332			def accept(self):
333			s1 = self.select_object_combo_box.currentText()
334			s2 = self.select_object_combo_box2.currentText()
335			show_contacts(s1, s2, '%s_%s' % (s1, s2))
336
337			def populate_ligand_select_list(self):
338			loaded_objects = _get_select_list()
339
340			self.select_object_combo_box.clear()
341			self.select_object_combo_box2.clear()
342
343			self.select_object_combo_box.addItems(loaded_objects)
344			self.select_object_combo_box2.addItems(loaded_objects)
345
346			if len(loaded_objects) > 1:
347			self.select_object_combo_box2.setCurrentIndex(1)
348
349			def setupUi(self, Dialog):
350			# Based on auto-generated code from ui file
351			from pymol.Qt import QtCore, QtWidgets
352			Dialog.resize(400, 50)
353			self.gridLayout = QtWidgets.QGridLayout(Dialog)
354			label = QtWidgets.QLabel("Select loaded object:", Dialog)
355			self.gridLayout.addWidget(label, 0, 0, 1, 1)
356			self.select_object_combo_box = QtWidgets.QComboBox(Dialog)
357			sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Fixed)
358			self.select_object_combo_box.setSizePolicy(sizePolicy)
359			self.select_object_combo_box.setEditable(True)
360			self.gridLayout.addWidget(self.select_object_combo_box, 0, 1, 1, 1)
361			label = QtWidgets.QLabel("Select loaded object:", Dialog)
362			self.gridLayout.addWidget(label, 1, 0, 1, 1)
363			self.select_object_combo_box2 = QtWidgets.QComboBox(Dialog)
364			self.select_object_combo_box2.setSizePolicy(sizePolicy)
365			self.select_object_combo_box2.setEditable(True)
366			self.gridLayout.addWidget(self.select_object_combo_box2, 1, 1, 1, 1)
367			self.buttonBox = QtWidgets.QDialogButtonBox(Dialog)
368			self.buttonBox.setOrientation(QtCore.Qt.Horizontal)
369			self.buttonBox.setStandardButtons(QtWidgets.QDialogButtonBox.Cancel\|QtWidgets.QDialogButtonBox.Ok)
370			self.gridLayout.addWidget(self.buttonBox, 2, 0, 1, 2)
371			self.buttonBox.accepted.connect(Dialog.accept)
372			self.buttonBox.rejected.connect(Dialog.reject)
373
374
375			def __init__(self):
376			try:
377			from pymol.plugins import addmenuitemqt
378			addmenuitemqt('Show Contacts', Show_Contacts_Qt_Dialog)
379			return
380			except Exception as e:
381			print(e)
382			self.menuBar.addmenuitem('Plugin', 'command', 'Show Contacts', label = 'Show Contacts', command = lambda s=self : Show_Contacts(s))
383
384
385

mmagnus / rna-tools

__init__() A last analyzed 2025-03-19 22:26 UTC

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init() A
last analyzed 2025-03-19 22:26 UTC