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MainWindow.py
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# coding=utf-8
from __future__ import division
from __future__ import generators
import os
from Tkinter import *
import distutils.spawn # used for find_executable
import sys
from xml.dom.minidom import Document, parse
import imp
from datetime import datetime
import tkFileDialog
import tkMessageBox
import pickle
import Pmw
import urllib2
import urllib
import time
import random
import socket
import json
import re
import webbrowser
import PointDialog
import Manager
try:
from PymolPlugin import PymolPlugin as plugin
PLUGIN = "PyMOL"
except:
import chimera
from ChimeraPlugin import ChimeraPlugin as plugin
PLUGIN = "Chimera"
# Globals:
CONFIGFILE = '.MOLE_PluginSettings.txt'
class MainWindow:
name = "MOLE 2.5"
def __init__(self):
self.plugin_type = PLUGIN
root = Toplevel()
root.title('MOLE 2.5')
root.resizable(0, 0)
self.parent = root
# region Create Frame and NoteBook
self.mainframe = Frame(self.parent, width=463, height=623)
self.mainframe.pack(fill='both', expand=1)
self.mainframe.bind('<<WrongExecutable>>',
lambda e: self.when_error(e, 'Your MOLE 2.0 executable was not found!'))
root.bind('<F5>', (lambda event: self.set_structures(
self.input_structure_box)))
balloon = Pmw.Balloon(self.mainframe)
self.points = {}
# Binary file, Working directory, csa file
self.main_parameters = ['', '', '']
self.notebook = Pmw.NoteBook(self.mainframe)
self.notebook.pack(fill='both', expand=1, padx=10, pady=10)
# endregion
# region self.mainPage / settings
self.mainpage = self.notebook.add('Compute Tunnels')
self.mainpage.focus_set()
input_structure_group = Pmw.Group(
self.mainpage, tag_text='Specify Input Structure')
input_structure_group.pack(fill='both')
starting_point_group = Pmw.Group(
self.mainpage, tag_text='Specify Starting Point')
starting_point_group.pack(fill='both')
if self.plugin_type == "PyMOL":
initialized_structs = ('all',) + plugin.return_tuple_objects()
else:
initialized_structs = ()
self.input_structure_box = Pmw.ScrolledListBox(input_structure_group.interior(), items=initialized_structs,
labelpos='nw', listbox_height=4, listbox_selectmode=EXTENDED,)
self.input_structure_box.component('listbox').configure(
exportselection=0, background='white')
self.input_structure_box.pack(fill='both', expand=0, padx=10, pady=5)
balloon.bind(self.input_structure_box,
'Select one or more structures in which you want to find channels.')
if self.plugin_type == "Chimera":
self.input_structure_box.insert('end', 'all')
if plugin.return_object_list() is not None:
for item in plugin.return_object_list():
self.input_structure_box.insert('end', item)
query = Pmw.Group(input_structure_group.interior(),
tag_text="Not Active Residues")
query.pack(fill='both')
self.query_entry = Entry(query.interior(), width=65)
self.query_entry.config(background='white')
self.query_entry.grid(column=0, row=0, padx=10,
pady=5, sticky=W + E + N + S)
self.query_entry.columnconfigure(0, minsize=65)
self.query_entry.bind(
"<KeyRelease>", lambda event: root.after(2500, self.validate_query))
self.query_entry.bind('<Control-KeyRelease-a>',
lambda event: self.select_all_query_entry())
self.query_entry.focus_set()
balloon.bind(self.query_entry, 'Input not active residues here')
self.query_label = Label(query.interior(),
text='Select atoms/residues not to be included in the calculation using PatternQuery '
'syntax.', width=68)
self.query_label.grid(column=0, row=1, padx=10,
pady=5, sticky=W + E + N + S, columnspan=2)
self.query_help = Label(
query.interior(), text='?', fg="blue", cursor="hand2")
self.query_help.grid(column=1, row=0, padx=[0, 10], pady=5)
self.query_help.bind("<Button-1>", lambda event: webbrowser.open_new("https://webchem.ncbr.muni.cz/Wiki"
"/PatternQuery:UserManual"))
balloon.bind(self.query_help, 'PatternQuery Wiki pages.')
self.is_valid = False
self.start_points_box = Pmw.ScrolledListBox(starting_point_group.interior(), items=(), labelpos='nw',
listbox_height=4, listbox_selectmode=EXTENDED)
self.start_points_box.component('listbox').configure(
exportselection=0, background='white')
self.start_points_box.pack(fill='both', expand=0, padx=10, pady=5)
balloon.bind(self.start_points_box,
'Starting point list. If no starting point is specified, \nMOLE plugin will try to find suitable '
'starting points automatically.\nOtherwise all selected points will be used.')
self.button_box1 = Pmw.ButtonBox(starting_point_group.interior())
self.button_box1.pack(fill='both', expand=0, padx=10, pady=5)
self.button_box1.add('AddStartingPoint', text='Add Starting Point',
command=lambda: self.add_point(self.start_points_box))
self.button_box1.add('RemoveStartingPoint', text='Remove Starting Point',
command=lambda: self.remove_point(self.start_points_box))
self.button_box1.add('RefreshStructures', text='Refresh Structures',
command=lambda: self.set_structures(self.input_structure_box))
self.button_box1.alignbuttons()
property_group = Pmw.Group(self.mainpage, tag_pyclass=None)
property_group.pack(fill='both')
self.overwrite_results = BooleanVar()
self.overwrite_results.set(True)
self.overwrite_results_button = Checkbutton(property_group.interior(), text="Overwrite results",
variable=self.overwrite_results,
onvalue=True, offvalue=False)
self.overwrite_results_button.grid(
column=0, row=0, padx=10, pady=5, sticky=W + E + N + S)
balloon.bind(self.overwrite_results_button,
'If checked MOLE will overwrite old files in output folder. Otherwise, new folder will be '
'created in output folder.')
self.remove_hydrogens = BooleanVar()
self.remove_hydrogens_button = Checkbutton(property_group.interior(), text="Remove hydrogens",
variable=self.remove_hydrogens,
onvalue=True, offvalue=False)
self.remove_hydrogens_button.grid(
column=1, row=0, padx=10, pady=5, sticky=W + E + N + S)
balloon.bind(self.remove_hydrogens_button,
'If checked MOLE will remove all hydrogens from the structure prior to the calculation.')
self.ignore_het = BooleanVar()
self.ignore_het_button = Checkbutton(property_group.interior(), text="Ignore HETeroatoms",
variable=self.ignore_het,
onvalue=True, offvalue=False)
self.ignore_het_button.grid(
column=2, row=0, padx=10, pady=5, sticky=W + E + N + S)
balloon.bind(self.ignore_het_button,
'If checked MOLE will exclude all HETATM entries prior to the calculation.')
self.select_working_directory_button = Button(property_group.interior(), text='Save output to:',
command=self.select_working_directory)
self.select_working_directory_button.grid(
row=1, column=0, sticky=W + E + N + S, padx=10, pady=5)
self.select_working_directory_button.columnconfigure(0, weight=1)
balloon.bind(self.select_working_directory_button,
'Where do you wish to save output from MOLE 2.0 plugin.')
self.working_directory = Pmw.EntryField(
property_group.interior(), labelpos='w')
self.working_directory.component('entry').configure(background='white')
self.working_directory.grid(
row=1, column=1, columnspan=2, sticky=W + E + N + S, padx=10, pady=5)
balloon.bind(self.working_directory,
'Where do you wish to save output from MOLE 2.0 plugin.')
self.generate_csa_selections_button = Button(property_group.interior(), text='Generate CSA sites:',
command=self.CSA_button_click)
self.generate_csa_selections_button.grid(
column=0, row=2, sticky=W + E + N + S, padx=10, pady=5)
balloon.bind(self.generate_csa_selections_button,
'Specify structure by writing its PDB ID and press Generate button.')
self.structure_for_CSA = Pmw.EntryField(
property_group.interior(), labelpos='w')
self.structure_for_CSA.component('entry').configure(background='white')
self.structure_for_CSA.component('entry').bind(
'<Return>', lambda event: self.CSA_button_click())
self.structure_for_CSA.grid(
column=1, row=2, columnspan=2, sticky=W + E + N + S, padx=10, pady=5)
balloon.bind(self.structure_for_CSA,
'Specify structure by writing its PDB ID and press Generate button.')
self.select_CSA_button = Button(property_group.interior(
), text='Select CSA file:', command=self.select_CSA)
self.select_CSA_button.grid(
column=0, row=3, sticky=W + E + N + S, padx=10, pady=5)
balloon.bind(self.select_CSA_button,
'Insert location of CSA.dat file containing CSA database for suggesting active sites as a '
'starting points.')
self.CSA = Pmw.EntryField(property_group.interior(), labelpos='w')
self.CSA.component('entry').configure(background='white')
self.CSA.grid(column=1, columnspan=2, row=3,
sticky=W + E + N + S, padx=10, pady=5)
balloon.bind(self.CSA,
'Insert location of CSA.dat file containing CSA database for suggesting active sites as a '
'starting points.')
self.select_executable_button = Button(property_group.interior(), text='MOLE 2.5 location:',
command=self.select_executable)
self.select_executable_button.grid(
column=0, row=4, sticky=W + E + N + S, padx=10, pady=5)
balloon.bind(self.select_executable_button,
'Select proper path to the MOLE 2.0 command line location')
self.executable = Pmw.EntryField(
property_group.interior(), labelpos='w')
self.executable.component('entry').configure(background='white')
self.executable.grid(column=1, columnspan=2, row=4,
sticky=W + E + N + S, padx=10, pady=5)
balloon.bind(
self.executable, 'Select proper path to the MOLE 2.5 command line location.')
self.compute_tunnels_button = Button(self.mainpage, text='Compute Tunnels', font=("Helvetica", 12, "bold"),
command=lambda b='tunnels': Manager.Manager().construct_params_and_run(self,
b))
self.compute_tunnels_button.pack(
side=BOTTOM, fill='both', expand=0, padx=10, pady=5)
# endregion
# region self.paramsPage / params
self.params_page = self.notebook.add('Settings')
cavity_parameters_group = Pmw.Group(
self.params_page, tag_text='Cavity Parameters')
cavity_parameters_group.pack(fill='both', expand=4)
self.probe_radius = Pmw.Counter(cavity_parameters_group.interior(), labelpos='w', label_text='Probe Radius',
entryfield_value='3', increment=0.1,
entryfield_validate={'validator': 'real', 'separator': '.', 'min': 1.4,
'max': 45},
datatype={'counter': 'real', 'separator': '.'})
self.probe_radius.component('entry').configure(background='white')
balloon.bind(self.probe_radius,
'Radius used for construction of molecular surface.')
self.interior_threshold = Pmw.Counter(cavity_parameters_group.interior(), labelpos='w',
label_text='Interior Threshold',
entryfield_value='1.25', increment=0.1,
entryfield_validate={'validator': 'real', 'separator': '.', 'min': 0.8,
'max': 45.0},
datatype={'counter': 'real', 'separator': '.'})
self.interior_threshold.component(
'entry').configure(background='white')
balloon.bind(self.interior_threshold,
'Lower bound of the tunnel radius.')
self.surface_cover_radius = Pmw.Counter(cavity_parameters_group.interior(), labelpos='w',
label_text='Surface Cover Radius',
entryfield_value='10', increment=0.1,
entryfield_validate={'validator': 'real', 'separator': '.', 'min': 5.0,
'max': 25.0},
datatype={'counter': 'real', 'separator': '.'})
self.surface_cover_radius.component(
'entry').configure(background='white')
balloon.bind(self.surface_cover_radius,
'Determines the density of tunnel exits on the molecular surface.')
self.origin_radius = Pmw.Counter(cavity_parameters_group.interior(), labelpos='w', label_text='Origin Radius',
entryfield_value='5', increment=0.1,
entryfield_validate={'validator': 'real', 'separator': '.', 'min': 0.1,
'max': 10.0},
datatype={'counter': 'real', 'separator': '.'})
self.origin_radius.component('entry').configure(background='white')
balloon.bind(self.origin_radius,
'Better starting points are localized within the defined radius from the original starting point.')
filter_settings = Pmw.Group(
self.params_page, tag_text='Tunnel Parameters')
filter_settings.pack(fill='both', expand=4)
self.bottleneck_radius = Pmw.Counter(filter_settings.interior(), labelpos='w', label_text='Bottleneck Radius',
entryfield_value='1.25', increment=0.1,
entryfield_validate={'validator': 'real', 'separator': '.', 'min': 0.1,
'max': 6.0},
datatype={'counter': 'real', 'separator': '.'})
self.bottleneck_radius.component('entry').configure(background='white')
balloon.bind(self.bottleneck_radius, 'The minimum radius of a tunnel.')
self.bottleneck_length = Pmw.Counter(filter_settings.interior(), labelpos='w', label_text='Bottleneck Length',
entryfield_value='3', increment=0.1,
entryfield_validate={'validator': 'real', 'separator': '.', 'min': 0.0,
'max': 20.0},
datatype={'counter': 'real', 'separator': '.'})
self.bottleneck_length.component('entry').configure(background='white')
balloon.bind(self.bottleneck_length,
'Length of a possible profile narrower than the Bottleneck Radius')
self.cutoff_ratio = Pmw.Counter(filter_settings.interior(), labelpos='w', label_text='Cutoff Ratio',
entryfield_value='0.7', increment=0.05,
entryfield_validate={'validator': 'real', 'separator': '.', 'min': 0.0,
'max': 1.0},
datatype={'counter': 'real', 'separator': '.'})
self.cutoff_ratio.component('entry').configure(background='white')
balloon.bind(self.cutoff_ratio,
'Determines maximum similarity of tunnels centerline. \nIf two tunnels are more similar than the '
'threshold, the longer is discarded.')
# region load executable location from settingsfile
temp_path = os.path.normcase(
str(os.environ['TEMP']) if 'win32' == str.lower(sys.platform) else '/tmp/')
if os.path.exists(CONFIGFILE):
try:
with open(CONFIGFILE, 'r') as f:
self.main_parameters = list(
map(lambda x: os.path.normcase(x), pickle.load(f)))
self.executable.setvalue(self.main_parameters[0])
self.working_directory.setvalue(self.main_parameters[1])
self.CSA.setvalue(self.main_parameters[2])
except:
self.executable.setvalue('')
self.working_directory.setvalue(temp_path)
self.CSA.setvalue('')
else:
self.working_directory.setvalue(temp_path)
self.main_parameters[1] = temp_path
with open(CONFIGFILE, 'w') as f:
pickle.dump(self.main_parameters, f)
# endregion
self.params = (
self.probe_radius, self.interior_threshold, self.surface_cover_radius, self.origin_radius,
self.bottleneck_radius,
self.bottleneck_length, self.cutoff_ratio)
Pmw.alignlabels(self.params)
for counter in self.params:
counter.pack(fill='both', expand=1, padx=10, pady=5)
weight_function_group = Pmw.Group(
self.params_page, tag_text='Weight Function')
weight_function_group.pack(fill='both', expand=0)
self.weight_function = StringVar()
self.voronoi_button = Radiobutton(weight_function_group.interior(), text='Voronoi Scale',
variable=self.weight_function, value="VoronoiScale")
self.voronoi_button.grid(
column=0, row=0, padx=30, pady=5, sticky=W + E + N + S)
balloon.bind(self.voronoi_button,
'Recommended for identification of tunnels leading to the buried active sites')
self.length_radius_button = Radiobutton(weight_function_group.interior(), text='Length + Radius',
variable=self.weight_function, value="LengthAndRadius")
self.length_radius_button.grid(
column=1, row=0, padx=30, pady=5, sticky=W + E + N + S)
balloon.bind(self.length_radius_button,
'Old and universal MOLE 2.0 weight function')
self.length_button = Radiobutton(weight_function_group.interior(), text='Length', variable=self.weight_function,
value="Length")
self.length_button.grid(column=2, row=0, padx=30,
pady=5, sticky=W + E + N + S)
balloon.bind(self.length_button,
'Recommended for identification of transmembrane pores')
self.voronoi_button.invoke()
# endregion
# region self.pathPage / settings
self.path_page = self.notebook.add('Compute Pores')
input_structure_group = Pmw.Group(
self.path_page, tag_text='Specify pores starting points')
input_structure_group.pack(fill='both')
self.path_starting_points_box = Pmw.ScrolledListBox(input_structure_group.interior(), items=(), labelpos='nw',
label_text='Starting Points', listbox_height=4,
listbox_selectmode=EXTENDED)
self.path_starting_points_box.component('listbox').configure(
exportselection=0, background='white')
self.path_starting_points_box.pack(
fill='both', expand=0, padx=10, pady=5)
self.path_starting_points_box.bind(
'<Delete>', lambda event: self.remove_point(self.path_starting_points_box))
balloon.bind(self.path_starting_points_box,
'Starting point list. Every starting point must have coresponding end point.')
self.button_box2 = Pmw.ButtonBox(input_structure_group.interior())
self.button_box2.pack(fill='both', expand=0, padx=10, pady=5)
self.button_box2.add('AddStartingPoint', text='Add Starting Points',
command=lambda: self.add_point(self.path_starting_points_box))
self.button_box2.add('RemoveStartingPoint', text='Remove Starting Points',
command=lambda: self.remove_point(self.path_starting_points_box))
self.button_box2.alignbuttons()
input_structure_group = Pmw.Group(
self.path_page, tag_text='Specify pores end points')
input_structure_group.pack(fill='both')
self.path_end_points_box = Pmw.ScrolledListBox(input_structure_group.interior(), items=(), labelpos='nw',
label_text='End Points', listbox_height=4,
listbox_selectmode=EXTENDED)
self.path_end_points_box.component('listbox').configure(
exportselection=0, background='white')
self.path_end_points_box.bind(
'<Delete>', lambda event: self.remove_point(self.path_end_points_box))
self.path_end_points_box.pack(fill='both', expand=0, padx=10, pady=5)
balloon.bind(self.path_end_points_box,
'End points list. Every end point must have coresponding starting point.')
self.button_box3 = Pmw.ButtonBox(input_structure_group.interior())
self.button_box3.pack(fill='both', expand=0, padx=10, pady=5)
self.button_box3.add('AddEndPoint', text='Add End Points',
command=lambda: self.add_point(self.path_end_points_box))
self.button_box3.add('RemoveEndPoint', text='Remove end points',
command=lambda: self.remove_point(self.path_end_points_box))
self.button_box3.alignbuttons()
self.compute_pores_button = Button(self.path_page, text='Compute Pores', font=("Helvetica", 12, "bold"),
command=lambda b='pores': Manager.Manager().construct_params_and_run(self, b))
self.compute_pores_button.pack(fill='both', expand=0, padx=10, pady=5)
# endregion
# prev set
# region READ
self.read_page = self.notebook.add('Read Channels')
read_group = Pmw.Group(
self.read_page, tag_text='Select a file with previously computed MOLE tunnels/pores')
read_group.pack(fill='both')
self.open_channels_button = Button(read_group.interior(), text='Open computation results',
command=self.open_channels,
font=("Helvetica", 12, "bold"))
self.open_channels_button.pack(fill='both', expand=0, padx=10, pady=5)
# endregion
# region QuickStartGuide
self.guide_page = self.notebook.add('Quick Guide')
guide = Text(self.guide_page, width=72, wrap=WORD)
guide.config(padx=5, pady=8)
guide.tag_configure('big', font=('Arial', 12, 'bold'))
guide.tag_configure('plain_text', font=('Arial', 10))
guide.tag_configure('smaller', font=('Arial', 9))
guide.insert(END, 'Plugin description:\n\n', 'big')
plugin_description = ("The plugin is separated into several tabs The crucial for the calculation are: "
"Compute Tunnels, Settings, and Compute Pores. At first, specify location of output "
"folder and MOLE 2.5 command line executable. Afterwards, select a structure in the "
"'input structure listbox' and starting point from the 'starting point listbox'. "
"Additionally, if you provide a path to the CSA database [1], the plugin will suggest "
"you the potential starting points.\n\n")
guide.insert(END, plugin_description, 'plain_text')
guide.insert(END, "Run:\n\n", 'big')
run_description = ("After selecting one or more structures and one or more starting points by clicking 'Add Starting Point'. Additional "
"search parameters can be adjusted in the Settings tabs. For further info on how to use this "
"please refer the included manual or visit our webpages. Whenever you would feel lost just "
"hover your cursor above any element in order to get tooltip. For more info and news about the "
"MOLE 2.5 visit our webpages.\n")
guide.insert(END, run_description, 'plain_text')
improve_text = ("\n"
"Also if you would like to make a suggestion on how to "
"improve MOLE or send a bug report, please contact authors at [email protected] "
"or the author of this extension directly - [email protected]\n\n")
guide.insert(END, improve_text, 'plain_text')
guide.insert(END, "Happy tunneling! ", 'big')
team_text = ("Mole development team. http://mole.chemi.muni.cz\n\n"
"[1] Furnham,N., Holliday,G.L., De Beer,T.A.P., Jacobsen,J.O.B., Pearson,W.R. and Thornton,J.M. (2014) "
"The Catalytic Site Atlas 2.0: Cataloging catalytic sites and residues identified in enzymes. Nucleic "
"Acids Res., 42, 1–5.")
guide.insert(END, team_text, 'smaller')
guide.config(state=DISABLED)
guide.pack(side=LEFT, fill='both')
# endregion
# region AuthorsPage
self.authors_page = self.notebook.add('Authors')
authors_text_widget = Text(self.authors_page, width=72, height=17)
authors_text_widget.config(padx=5, bg='#52A300', pady=8)
authors_text_widget.tag_configure(
'plain_text', font=('Arial', 10), foreground='white')
authors_text_widget.insert(
END, "If you find this tool useful for your work please cite it as:\n\n", 'plain_text')
cite_text = ("Sehnal D, Svobodova Varekova R, Berka K, Pravda L, Navratilova V,\nBanas P, Ionescu C-M, Otyepka M, "
"Koca J. MOLE2.0: advanced approach for analysis of biomacromolecular channels. Journal of "
"Cheminformatics 2013, 5:39., doi:10.1186/1758-2946-5-39.\n\n"
"If you were using the web server, which is available at http://mole.upol.cz/ please cite it as:\n\n"
"Berka K, Hanak O, Sehnal D, Banas P, Navratilova V, Jaiswal D,Ionescu C-M, Svobodova Varekova R, "
"Koca J, Otyepka M.\nMOLEonline 2.0: interactive web-based analysis of biomacromolecular\nchannels. Nucleic "
"acids research 2012, 40:W222?7., doi:10.1093/nar/gks363")
authors_text_widget.insert(END, cite_text, 'plain_text')
authors_text_widget.config(state=DISABLED)
authors_text_widget.pack(side=LEFT, fill='both')
# endregion
Label(self.mainframe, relief='sunken', anchor=W, justify=LEFT, bg='#52A300', fg='white', font=("Helvetica", 12),
padx=10, pady=10,
text="(c) 2017 CEITEC & NCBR MU & FCH UPOL\nhttp://mole.chemi.muni.cz v. "
"2.5.17.7.11").pack(
fill='both')
self.notebook.setnaturalsize()
self.wd = os.path.realpath(os.path.normcase(self.main_parameters[1]))
self.xml_wd = os.path.realpath(
os.path.normcase(self.main_parameters[1] + "/xml/"))
self.profile_wd = os.path.realpath(
os.path.normcase(self.main_parameters[1] + "/pymol/"))
os.system('xset r off') # for keypress
self.original_view = None
def add_point(self, listbox):
"""
Run add_point window.
:param listbox:
:return:
"""
dialog = PointDialog.PointDialog(
self, self.mainframe, CSA=self.CSA.get())
dialog.activate(geometry='centerscreenalways')
if dialog.return_value is not None:
r = dialog.point_name + " Type: " + \
dialog.return_value[1]['Element']
x = listbox.get()
x += (r,)
listbox.setlist(x)
self.points[dialog.point_name] = dialog.return_value
def select_all_query_entry(self, event=None):
self.query_entry.select_range(0, 'end')
self.query_entry.icursor('end')
def remove_point(self, listbox):
"""
Remove point from listbox
:param listbox:
:return:
"""
x = ()
for i in listbox.get():
if i not in listbox.getvalue():
x += (i,)
listbox.setlist(x)
p = {}
for i in self.points.keys():
if i not in listbox.getvalue() or i[4:5] is '|':
p[i] = self.points[i]
self.points = p
def select_working_directory(self):
"""
Open window for selection wd
:return:
"""
file_path = tkFileDialog.askdirectory(title='Select Output Directory')
file_path = os.path.normcase(file_path)
if file_path != "" and os.access(file_path, os.R_OK and os.W_OK):
try:
with open(os.path.join(file_path, 'testfile.txt'), 'w') as f:
pass
with open(os.path.join(file_path, 'testfile.txt'), 'r') as f:
pass
except:
tkMessageBox.showinfo('Info', 'Selected output directory does not have sufficient permissions to be '
'used.')
return
os.remove(os.path.join(file_path, 'testfile.txt'))
self.working_directory.setvalue(file_path)
try:
self.main_parameters[1] = file_path
with open(CONFIGFILE, 'w') as f:
pickle.dump(self.main_parameters, f)
except:
pass
else:
tkMessageBox.showinfo(
'Info', 'Selected output directory does not have sufficient permissions to be used.')
def select_CSA(self):
"""
Open dialog for CSA file selection.
:return:
"""
file_path = tkFileDialog.askopenfilename(title='Select CSA.dat file',
filetypes=[('CSA.dat file', '.dat'), ('.txt file', '.txt')])
file_path = os.path.normcase(file_path)
if file_path != "":
self.CSA.setvalue(file_path)
try:
self.main_parameters[2] = file_path
with open(CONFIGFILE, 'w') as f:
pickle.dump(self.main_parameters, f)
except:
pass
def select_executable(self):
"""
Open dialog for executable selection.
:return:
"""
file_path = tkFileDialog.askopenfilename(title='Select MOLE 2.0 Executable',
filetypes=[('MOLE 2.0 Executable', '.exe')])
file_path = os.path.normcase(file_path)
if file_path != "":
self.executable.setvalue(file_path)
try:
self.main_parameters[0] = file_path
with open(CONFIGFILE, 'w') as f:
pickle.dump(self.main_parameters, f)
except:
pass
def rename_buttons(self, param):
"""
Rename buttons from tunnels to pores, if necessary.
:param param:
:return:
"""
if param is 'tunnels':
self.compute_tunnels_button.config(text='Compute Tunnels')
else:
self.compute_pores_button.config(text='Compute Pores')
def CSA_button_click(self):
"""
Calls CSA selection.
:return:
"""
Manager.Manager().generate_CSA_selections(self)
def set_state(self, state):
"""
Change state of elements in GUI.
:param state:
:return:
"""
self.generate_csa_selections_button.config(state=state)
self.structure_for_CSA.component('entry').config(state=state)
self.ignore_het_button.config(state=state)
self.overwrite_results_button.config(state=state)
self.compute_tunnels_button.config(state=state)
self.compute_pores_button.config(state=state)
self.select_executable_button.config(state=state)
self.select_working_directory_button.config(state=state)
self.select_CSA_button.config(state=state)
self.CSA.component('entry').config(state=state)
self.executable.component('entry').config(state=state)
self.working_directory.component('entry').config(state=state)
self.remove_hydrogens_button.config(state=state)
for w in self.params:
w.component('entry').config(state=state)
self.button_box1.button(0).config(state=state)
self.button_box1.button(1).config(state=state)
self.button_box1.button(2).config(state=state)
self.button_box2.button(0).config(state=state)
self.button_box2.button(1).config(state=state)
self.button_box3.button(0).config(state=state)
self.button_box3.button(1).config(state=state)
def when_error(self, event, message):
"""
Change state to normal and open tkmessagebox.
:param event:
:param message:
:return:
"""
self.set_state('normal')
tkMessageBox.showinfo('Error', message)
def set_structures(self, listbox):
"""
Fill input structures listbox
:param listbox:
:return:
"""
listbox.clear()
listbox.insert('end', 'all')
for item in plugin.return_object_list():
listbox.insert('end', item)
def get_element(self, selection):
"""
Get element from point structure
:param selection:
:return:
"""
for key in self.points.keys():
if key in selection:
return self.points[key]
return '42'
def open_channels(self):
file_path = tkFileDialog.askopenfilenames(title='Select MOLE tunnel files',
filetypes=[('MOLE tunnels', '.xml .pdb .py')])
if self.plugin_type == "PyMOL":
file_path = self.fix_list(file_path)
for chan_file in file_path:
chan_file = os.path.normcase(chan_file)
extension = os.path.splitext(chan_file)[1].lower()
name = os.path.basename(chan_file).split('.')[0].lower()
if len(extension) < 3:
return
try:
if extension == '.py':
plugin.run(chan_file)
if extension == '.xml':
Manager.Manager().parse_XML_channel(chan_file, name, self)
if extension == '.pdb':
plugin().parse_PDB_channel(chan_file, name)
except Exception, e:
print(e)
@staticmethod
def fix_list(filenames):
# do nothing if already a python list
if isinstance(filenames, list):
return filenames
# http://docs.python.org/library/re.html
# the re should match: {text and white space in brackets} AND anynonwhitespacetokens
# *? is a non-greedy match for any character sequence
# \S is non white space
# split filenames string up into a proper python list
result = re.findall("{.*?}|\S+", filenames)
# remove any {} characters from the start and end of the file names
result = [re.sub("^{|}$", "", i) for i in result]
return result
def group_objects(self, script_path, script_name, structure):
"""
:param script_path:
:param script_name:
:param structure:
:return:
"""
if os.path.exists(script_path):
previous = plugin.return_object_list()
imp.load_source(
structure + str(datetime.now().toordinal()), script_path)
for o in plugin.return_object_list():
if o not in previous:
plugin.return_group(script_name, o)
def when_computation_done(self, out, param):
"""
After computation of tunnels is done, run tunnel script
:param out:
:return:
"""
tkMessageBox.showinfo('Computation is done', out)
self.set_state('normal')
if self.plugin_type == "Chimera":
self.profile_wd = os.path.realpath(
os.path.normcase(self.main_parameters[1] + "/chimera/"))
tunnels_script = os.path.join(self.profile_wd, 'complex.py')
paths_script = os.path.join(self.wd, 'paths.py')
pores_script = os.path.join(self.wd, 'pores.py')
autopores_script = os.path.join(self.wd, 'autopores.py')
dom = parse(os.path.join(self.xml_wd, 'tunnels.xml'))
for e in dom.getElementsByTagName('Exception'):
tkMessageBox.showinfo('Exception', e.getAttribute('Text'))
if self.plugin_type == "PyMOL":
if param == "pores":
self.group_objects(tunnels_script, 'Pores', "MOLE_tunnels")
else:
self.group_objects(tunnels_script, 'Tunnels', "MOLE_pores")
self.group_objects(paths_script, 'Paths', 'MOLE_Paths')
self.group_objects(pores_script, 'Pores', 'MOLE_Pores')
self.group_objects(autopores_script, 'AutoPores', 'MOLE_AutoPores')
plugin().show("cgo", "Interior*")
plugin().set_view(self.original_view)
else:
plugin.run(tunnels_script)
self.set_state('normal')
def validate_query(self, event=None):
"""
Checks internet connection
:param pdb_id:
:return: validation report
"""
if len(self.query_entry.get()) == 0:
return
query = self.strip_white(self.query_entry.get())
query_page = 'http://webchem.ncbr.muni.cz/Platform/PatternQuery/ValidateQuery?query=' + query
query_page = urllib2.quote(query_page, ':/' + '?' + '=')
data_response = False
tries = 0
limit = 5
while tries < limit:
try:
req = urllib2.Request(query_page)
response = urllib2.urlopen(req, None, 5)
except urllib2.HTTPError, e:
if e.code == 404:
self.when_error('', "Could not find server!")
else:
time.sleep(random.randint(1, 2)) # sleep 1-2 seconds
tries += 1
except urllib2.URLError, e:
time.sleep(random.randint(1, 2)) # sleep 1-2 seconds
tries += 1
except socket.timeout, e:
time.sleep(random.randint(1, 2)) # sleep 1-2 seconds
tries += 1
else:
data_response = True
self.isOk = json.load(response)
break
if data_response == False:
self.when_error('', "Check your internet connection!")
return
if 'error' in self.isOk:
self.query_label.config(
text="Invalid query! Error: " + self.isOk['error'])
self.is_valid = False
return
else:
self.query_label.config(text="Valid!")
self.is_valid = True
return
def fill_boxes(self, content):
content1 = tuple(
filter(lambda x: x not in self.start_points_box.get(), content))
content2 = tuple(
filter(lambda x: x not in self.path_starting_points_box.get(), content))
content3 = tuple(
filter(lambda x: x not in self.path_end_points_box.get(), content))
self.start_points_box.setlist(
tuple(self.start_points_box.get()) + content1)
self.path_starting_points_box.setlist(
tuple(self.path_starting_points_box.get()) + content2)
self.path_end_points_box.setlist(
tuple(self.path_end_points_box.get()) + content3)
def strip_white(self, text):
lst = text.split('"')
for i, item in enumerate(lst):
if not i % 2:
lst[i] = re.sub("\s+", "", item)
return str('"'.join(lst))
def __del__(self):
os.system('xset r on')
if PLUGIN == "Chimera":
chimera.dialogs.register(MainWindow.name, MainWindow)
dir, file = os.path.split(__file__)
icon = os.path.join(dir, 'molelogo.png')
chimera.tkgui.app.toolbar.add(
icon, lambda d=chimera.dialogs.display, n=MainWindow.name: d(n), 'MOLE 2.5', None)