Show contacts - Revision history

Cchem: 2 revisions

2019-04-01T03:11:58Z

2 revisions

New page

{{Infobox script-repo
|type = script
|download = [https://github.com/Pymol-Scripts/Pymol-script-repo/blob/master/plugins/show_contacts.py]
|author = [[User:DavidKoes|David Ryan Koes]]
|license = [http://creativecommons.org/licenses/by/4.0/ CC BY 4.0]
}}

== Introduction ==
PyMOL Plugin for displaying polar contacts. Good hydrogen bonds (as determined by PyMOL) are shown in yellow. Electrostatic clashes (donor-donor or acceptor-acceptor) are shown in red. Close (<4.0 A) but not ideal contacts are shown in purple. Cutoffs are configurable. Exports the command `contacts` which takes two selections and an optional name for the generated contacts group. Alternatively, the selections can be chosen using a dialog box accessible from the Plugins menu.

== Usage ==
show_contacts sel1, sel2, result="contacts", cutoff=3.6, bigcutoff=4.0

== Required Arguments ==
* '''sel1''' = first selection
* '''sel2''' = second selection

== Optional Arguments ==
* '''result''' = name of created group containing contacts
* '''cutoff''' = cutoff for good contacts (yellow dashes)
* '''bigcutoff''' = cutoff for suboptimal contacts (purple dashes)

== The Code ==

Copy the following text and save it as show_contacts.py

<source lang="python">
#!/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

import Pmw
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 + '"')

#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:
''' Main Pymol Plugin Class '''
def __init__(self, app):
parent = app.root
self.parent = parent

self.app = app

############################################################################################
### 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 = [ name for name in cmd.get_names('all') if '_cluster_' not in name ]

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 __init__(self):
self.menuBar.addmenuitem('Plugin', 'command', 'Show Contacts', label = 'Show Contacts', command = lambda s=self : Show_Contacts(s))

</source>

[[Category:Script_Library]]
[[Category:Biochemical_Scripts]]
[[Category:Structural_Biology_Scripts]]
[[Category:Plugins]]

Cchem: 2 revisions

2019-03-04T03:58:23Z

2 revisions

New page

{{Infobox script-repo
|type = script
|download = [https://github.com/Pymol-Scripts/Pymol-script-repo/blob/master/plugins/show_contacts.py]
|author = [[User:DavidKoes|David Ryan Koes]]
|license = [http://creativecommons.org/licenses/by/4.0/ CC BY 4.0]
}}

== Introduction ==
PyMOL Plugin for displaying polar contacts. Good hydrogen bonds (as determined by PyMOL) are shown in yellow. Electrostatic clashes (donor-donor or acceptor-acceptor) are shown in red. Close (<4.0 A) but not ideal contacts are shown in purple. Cutoffs are configurable. Exports the command `contacts` which takes two selections and an optional name for the generated contacts group. Alternatively, the selections can be chosen using a dialog box accessible from the Plugins menu.

== Usage ==
show_contacts sel1, sel2, result="contacts", cutoff=3.6, bigcutoff=4.0

== Required Arguments ==
* '''sel1''' = first selection
* '''sel2''' = second selection

== Optional Arguments ==
* '''result''' = name of created group containing contacts
* '''cutoff''' = cutoff for good contacts (yellow dashes)
* '''bigcutoff''' = cutoff for suboptimal contacts (purple dashes)

== The Code ==

Copy the following text and save it as show_contacts.py

<source lang="python">
#!/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
import tkinter.simpledialog
import tkinter.messagebox
import tkinter.filedialog
import Pmw
import tkinter
from tkinter import *
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 + '"')

#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:
''' Main Pymol Plugin Class '''
def __init__(self, app):
parent = app.root
self.parent = parent

self.app = app

############################################################################################
### 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 = [ name for name in cmd.get_names('all') if '_cluster_' not in name ]

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 __init__(self):
self.menuBar.addmenuitem('Plugin', 'command', 'Show Contacts', label = 'Show Contacts', command = lambda s=self : Show_Contacts(s))

</source>

[[Category:Script_Library]]
[[Category:Biochemical_Scripts]]
[[Category:Structural_Biology_Scripts]]
[[Category:Plugins]]