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glycosylator_GUI.py
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glycosylator_GUI.py
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#! /usr/bin/env python
'''
----------------------------------------------------------------------------
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>
2016 Thomas Lemmin
----------------------------------------------------------------------------
'''
import Tkinter as tk
import ttk
import Tkconstants, tkFileDialog, tkMessageBox
import Pmw
import os,sys
import sqlite3
import networkx as nx
import matplotlib as mpl
mpl.use('TkAgg')
import matplotlib.backends.tkagg as tkagg
from matplotlib.backends.backend_agg import FigureCanvasAgg
from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg, NavigationToolbar2TkAgg
import numpy as np
SELF_BIN = os.path.dirname(os.path.realpath(sys.argv[0]))
sys.path.insert(0, SELF_BIN + '/support')
import glycosylator as glc
class GlycosylatorGUI(tk.Tk):
""" This Class creates the graphical interface for glycosylator. It is composted of a main window.
In addition, it will create one window for the displaying the database (db_window) and one for uploading a new glycan
Variables:
myGlycosylator: glycosylator instance (for identifying and building glycans)
myDrawer: drawer instance (for displaying glycoprotien and glycans)
user_glycans: dictionary of glycans defined by user. Glycan name as a key and glycan topology as a value
common_glycans: dictionary of common glycans. Glycan name as a key and glycan topology as a value
db_window: database window
selected_glycan: glycan selected by the user
glycan_balloon: Balloon for displaying name of glycan
original_glycans: dictionary of glycans detected in the original glycoprotein. Sequon as a key and glycan tree as a value
original_glycanMolecules: dictionary of glycans Molecules. Sequon as key and Molecule instance as value
linked_glycans: dictionary of built-in glycans. Sequon as a key and glycan tree as a value
linked_glycanMolecules: dictionary of built-in glycans Molecules. Sequon as key and Molecule instance as value
names: dictionary of glycan residue name. Residue id as key and resname as value
"""
def __init__(self):
self.cwd = os.getcwd()
self.myGlycosylator = glc.Glycosylator(SELF_BIN +'/support/toppar_charmm/carbohydrates.rtf', SELF_BIN + '/support/toppar_charmm/carbohydrates.prm')
self.myGlycosylator.builder.Topology.read_topology(SELF_BIN +'/support/topology/DUMMY.top')
self.myDrawer = glc.Drawer()
#database variables
self.user_glycans = {}
self.db_commong = os.path.join(SELF_BIN, 'support/topology/mannose.db')
self.common_glycans = {}
#database window
self.db_window = None
self.selected_canvas = None
self.selection = None
self.selected_glycan = None
self.glycan_balloon = None
#bookkeeping
self.sequon_colors = {}
self.original_glycans = {}
self.original_glycanMolecules = {}
self.linked_glycans = {}
self.linked_glycanMolecules = {}
self.names = {}
#create root window
tk.Tk.__init__(self)
self.title('Glycosylator')
self.geometry('520x520')
self.configure(background='white')
#self.option_readfile('optionDB')
Pmw.initialise(self)
#Pmw.aboutversion('2.0')
#Pmw.aboutcopyright('This program is free software: you can redistribute it and/or modifiy \nit under the terms of the GNU General Public License as published by the Free Software Foundation,\n either version 3 of the License, or any later version.')
#Pmw.aboutcontact('')
#self.about = Pmw.AboutDialog(self, applicationname='Glycosyaltor')
#estimate dpi of screen
mm2in = 1/25.4
pxw = self.winfo_screenwidth()
inw = self.winfo_screenmmwidth() * mm2in
#DPI is usually overestimated by about 30% for an unknown reason
self.dpi = int(pxw/inw*.65)
#self.resizable(False, False)
self.protocol('WM_DELETE_WINDOW', self.save_before_close)
# Create menubar
self.menubar = tk.Menu(master=self, bg="lightgrey", fg="black")
# file menu
self.file_menu = tk.Menu(self.menubar, tearoff=0, bg="lightgrey", fg="black")
self.file_menu.add_command(label="Open glycoprotein", accelerator = "Ctrl+O", command = self.load_glycoprotein)
self.file_menu.add_command(label="Save glycoprotein", accelerator = "Ctrl+S", command = self.save_glycoprotein)
self.file_menu.add_command(label="Export patches", accelerator = "Ctrl+P", command = self.export_patches)
#self.file_menu.add_command(label="Propreties", command = self.set_propreties)
self.menubar.add_cascade(label="File", menu=self.file_menu)
self.config(menu=self.menubar)
# glycan menu
self.gl_menu = tk.Menu(self.menubar, tearoff=0, bg="lightgrey", fg="black")
self.gl_menu.add_command(label="Import glycan library", accelerator = "Ctrl+I", command = self.import_library)
self.gl_menu.add_command(label="Export glycan library", accelerator = "Ctrl+E", command = self.export_library)
self.menubar.add_cascade(label="Glycan library", menu=self.gl_menu)
self.config(menu=self.menubar)
#allow for window to expand
self.columnconfigure(0, weight=6)
self.rowconfigure(0, weight=6)
# Create and layout main frames
self.left_frame = tk.Frame(self, width = 250, height = 500, bg = 'white')
self.right_frame = tk.Frame(self, width = 250, height = 500, bg = 'white')
self.left_frame.grid(column=0, row=0, sticky='NSEW')
self.right_frame.grid(column=1, row=0)
# Create widget for left frame
self.v_scrollbar = tk.Scrollbar(self.left_frame, orient = 'vertical')
self.h_scrollbar = tk.Scrollbar(self.left_frame, orient = 'horizontal')
self.glycoprotein_2D = tk.Canvas(self.left_frame, width = 250, height = 500, bg = 'white', scrollregion=(0, 0, 400, 2000))
self.glycoprotein_2D.configure(yscrollcommand = self.v_scrollbar.set)
self.glycoprotein_2D.configure(xscrollcommand = self.h_scrollbar.set)
self.v_scrollbar.config(command = self.glycoprotein_2D.yview)
self.h_scrollbar.config(command = self.glycoprotein_2D.xview)
self.glycoprotein_2D.bind("<MouseWheel>", self._on_mousewheel)
self.glycoprotein_2D.bind("<Button-4>", self._on_mousewheel)
self.glycoprotein_2D.bind("<Button-5>", self._on_mousewheel)
self.detach_button = tk.Button(self.left_frame, command = self.detach_plot)
self.detach_icon = tk.PhotoImage(file = SELF_BIN + "/icons/detach.gif")
self.detach_button.config(image = self.detach_icon)
#Layout left frame
self.glycoprotein_2D.grid(column = 0, row= 0, sticky='NSEW')
self.detach_button.grid(column = 0, row= 0, sticky='SE')
self.v_scrollbar.grid(column = 1, row = 0, sticky='NS')
self.h_scrollbar.grid(column = 0, row = 1, sticky='EW')
self.left_frame.columnconfigure(0, weight=6)
self.left_frame.rowconfigure(0, weight=6)
# Create widget for right frame
self.glycosylator_logo = tk.PhotoImage(file = SELF_BIN + "/icons/glycosylator_logo.gif")
self.w_logo = tk.Label(self.right_frame, image=self.glycosylator_logo, bg = 'white')
self.chain_label = tk.Label(self.right_frame, text="Chain:", bg = 'white')
options = ['-']
self.chain = tk.StringVar(self.right_frame)
self.chain_menu = tk.OptionMenu(self.right_frame, self.chain, *options, command = self.update_sequons)
self.chain_menu.config(width = 10)
self.chain_menu.configure(state="disabled")
self.sequon_label = tk.Label(self.right_frame, text="Sequon:", bg = 'white')
self.sequon = tk.StringVar(self.right_frame)
self.sequon_menu = tk.OptionMenu(self.right_frame, self.sequon, *options)
self.sequon_menu.config(width = 10)
self.sequon_menu.configure(state="disabled")
self.glycan_label = tk.Label(self.right_frame, text="Click to modify glycan", bg = 'white')
self.glycan_2D = tk.Canvas(self.right_frame, width = 150, height = 150, bg = 'white')
self.glycan_2D.bind("<Button-1>", self.database_window)
self.glycan_name = Pmw.Balloon(self.right_frame)
self.glycan_name.bind(self.glycan_2D, 'No sequon has been selected')
self.undo_button = tk.Button(self.right_frame, command = self.undo_glycan)
self.undo_icon = tk.PhotoImage(file = SELF_BIN + "/icons/undo.gif")
self.undo_button.config(image = self.undo_icon)
self.glycan_name.bind(self.undo_button, 'Undo glycosylation')
self.glycosylate_button = tk.Button(self.right_frame, text="Glycosylate", command = self.glycosylate, width = 10)
# self.glycosylateAll_button = tk.Button(self.right_frame, text="Glycosylate all", width = 10)
self.clashes = tk.Button(self.right_frame, text="Remove clashes", width = 10, command = self.remove_clashes)
# Layout right frame
i = 0
self.w_logo.grid(column = 0, row = i, sticky='N', pady=(1, 65)); i+=1
self.right_frame.rowconfigure(0, weight = 1)
self.chain_label.grid(column = 0, row = i, sticky='W'); i+=1
self.chain_menu.grid(column = 0, row = i); i+=1
self.sequon_label.grid(column = 0, row = i, sticky='W'); i+=1
self.sequon_menu.grid(column = 0, row = i); i+=1
self.glycan_label.grid(column = 0, row = i, sticky='W'); i+=1
self.glycan_2D.grid(column = 0, row = i);
self.undo_button.grid(column = 0, row = i, sticky = 'SE', padx= (5, 10)); i+=1
self.glycosylate_button.grid(column = 0, row = i, pady = (15, 2)); i+=1
# self.glycosylateAll_button.grid(column = 0, row = i, pady = 2); i+=1
self.clashes.grid(column = 0, row = i, pady = 2); i+=1
def save_before_close(self):
"""Do some clean up before destroying main window
"""
if self.db_window:
self.db_window.destroy()
self.destroy()
def detach_plot(self):
"""Opens 2D represenation of glycoprotein in a separate window.
"""
detached = tk.Toplevel(self)
detached.wm_title("Glycoprotein")
fig = mpl.figure.Figure(figsize=(5, 4), dpi=100)
ax = fig.add_subplot(111)
chid = self.chain.get()
l = len(self.myGlycosylator.sequences[chid])
sequons = [k for k in self.myGlycosylator.sequons.keys() if chid in k[:len(chid)]]
trees = self.original_glycans.copy()
trees.update(self.linked_glycans)
self.myDrawer.draw_glycoprotein(l, self.myGlycosylator.get_start_resnum(chid), sequons, ax = ax, axis = 0,
trees = trees, names = self.names, sequon_color = self.sequon_colors)
ax.axis('equal')
ax.axis('off')
canvas = FigureCanvasTkAgg(fig, master=detached)
canvas.show()
canvas.get_tk_widget().pack(side=tk.TOP, fill=tk.BOTH, expand=1)
toolbar = NavigationToolbar2TkAgg(canvas, detached)
toolbar.update()
canvas._tkcanvas.pack(side=tk.TOP, fill=tk.BOTH, expand=1)
def update_sequons(self, chid, *arg):
""" Updates option menu of sequons
Parameters:
chid: selected chain id
"""
sequons = [k for k in self.myGlycosylator.sequons.keys() if chid in k[:len(chid)]]
sequons = glc.alphanum_sort(sequons)
self.sequon_menu['menu'].delete(0, 'end')
self.sequon.set(sequons[0])
for sequon in sequons:
self.sequon_menu['menu'].add_command(label=sequon, command=tk._setit(self.sequon, sequon, self.draw_glycan))
self.draw_glycan(self.sequon)
self.draw_glycoprotein(chid)
def draw_glycan(self, sequon, *arg):
""" Draws 2D representation of glycan of selected sequon
Updates glycan_2D canvas
Parameters:
sequon: id of sequon
"""
fig = mpl.figure.Figure(figsize=(100./self.dpi, 100./self.dpi))
ax = fig.add_subplot(111)
if type(sequon) is not str:
sequon = sequon.get()
if sequon in self.sequon_colors:
color = self.sequon_colors[sequon]
else:
color = [.5, .5, .5]
# Draw protein fragment
self.myDrawer.draw_protein_fragment(ax = ax, sequon_color = color)
# Drawing glycan
glycan = True
if sequon in self.linked_glycans:
root,tree = self.linked_glycans[sequon]
elif sequon in self.original_glycans:
root,tree = self.original_glycans[sequon]
else:
self.myDrawer.draw_protein_fragment(ax = ax)
glycan = False
name = 'Structure: N/A'
if glycan:
self.myDrawer.draw_tree(tree, root, self.names, root_pos = [0, 0], direction = 1, ax = ax, axis = 0)
name = 'Structure: ' + self.myDrawer.tree_to_text(tree, root, self.names, visited = [])
ax.axis('equal')
ax.axis('off')
#ax.set_ylim((-3, 6))
#ax.set_xlim((-3, 3))
# Add to tk window
figure_canvas_agg = FigureCanvasAgg(fig)
figure_canvas_agg.draw()
figure_x, figure_y, figure_w, figure_h = fig.bbox.bounds
figure_w, figure_h = int(figure_w), int(figure_h)
self.glycan_image = tk.PhotoImage(master=self.glycan_2D, width=figure_w, height=figure_h)
self.glycan_2D.create_image(figure_w/2, figure_h/2, image=self.glycan_image)
self.glycan_name.tagunbind(self.right_frame, self.glycan_2D)
self.glycan_name.bind(self.glycan_2D, name)
tkagg.blit(self.glycan_image, figure_canvas_agg.get_renderer()._renderer, colormode=2)
def draw_glycoprotein(self, chid):
"""Draws 2D representation of glycoprotein in right panel
Updates glycoprotein_2D canvas
Parameters:
chid: chain id (string or handle)
"""
fig = mpl.figure.Figure(figsize=(300/self.dpi, 1000/self.dpi), dpi = 100)
ax = fig.add_axes([0, 0, 1, 1])
if type(chid) is not str:
chid = chid.get()
l = len(self.myGlycosylator.sequences[chid])
trees = self.original_glycans.copy()
trees.update(self.linked_glycans)
sequons = [k for k in self.myGlycosylator.sequons.keys() if chid in k[:len(chid)]]
self.myDrawer.draw_glycoprotein(l, self.myGlycosylator.get_start_resnum(chid), sequons, ax = ax, axis = 1,
trees = trees, names = self.names, sequon_color = self.sequon_colors)
ax.axis('equal')
ax.axis('off')
figure_canvas_agg = FigureCanvasAgg(fig)
figure_canvas_agg.draw()
figure_x, figure_y, figure_w, figure_h = fig.bbox.bounds
figure_w, figure_h = int(figure_w), int(figure_h)
# attaching figure to canvas
self.glycoprotein_image = tk.PhotoImage(master=self.glycan_2D, width=figure_w, height=figure_h)
self.glycoprotein_2D.create_image(figure_w/2, figure_h/2, image=self.glycoprotein_image)
tkagg.blit(self.glycoprotein_image, figure_canvas_agg.get_renderer()._renderer, colormode=2)
def load_glycoprotein(self):
"""Open pdb file containing a glycoprotein.
Updates:
- left_panel display glycoprotein
- righ_panel chains, sequons and displayed glycan
"""
filename = tkFileDialog.askopenfilename(initialdir = self.cwd, title = "Select glycoprotein", filetypes = (("pdb files","*.pdb"),("all files","*.*")))
if not filename:
return -1
#Clear previous variable
self.linked_glycans = {}
self.linked_glycanMolecules = {}
self.sequon_colors = {}
#Load new glycoprotein and extract glycans
self.myGlycosylator.load_glycoprotein(filename)
self.original_glycanMolecules = self.myGlycosylator.glycanMolecules.copy()
self.original_glycans = self.myGlycosylator.glycans.copy()
self.names = self.myGlycosylator.names
#Update the option menus
chids = self.myGlycosylator.sequences.keys()
self.chain_menu['menu'].delete(0, 'end')
self.chain.set(chids[0])
for chid in chids:
self.chain_menu['menu'].add_command(label = chid, command = tk._setit(self.chain, chid, self.update_sequons))
self.chain_menu.configure(state="normal")
chid = chids[0]
self.draw_glycoprotein(self.chain.get())
sequons = [k for k in self.myGlycosylator.sequons.keys() if chid in k[:len(chid)]]
sequons = glc.alphanum_sort(sequons)
self.sequon_menu['menu'].delete(0, 'end')
self.sequon.set(sequons[0])
for sequon in sequons:
self.sequon_menu['menu'].add_command(label = sequon, command = tk._setit(self.sequon, sequon, self.draw_glycan))
self.sequon_menu.configure(state="normal")
self.draw_glycan(self.sequon.get())
def save_glycoprotein(self):
"""Dialog for saving a glycoprotein
"""
filename = tkFileDialog.asksaveasfilename(initialdir = self.cwd, defaultextension=".pdb", filetypes = (("pdb files","*.pdb"),("all files","*.*")))
if filename is None:
return
self.myGlycosylator.glycanMolecules.update(self.linked_glycanMolecules)
self.myGlycosylator.write_glycoprotein(filename)
def show_database(self):
"""Make database window visible again
"""
self.db_window.update()
self.db_window.deiconify()
self.selected_glycan = None
def hide_database(self):
"""Hide database window
"""
if self.selected_canvas:
self.selected_canvas.delete(self.selection)
self.selected_canvas = None
self.selection = None
self.db_window.withdraw()
if self.selected_glycan:
root,tree,names = self.build_glycan_tree(self.selected_glycan[1]['UNIT'])
self.glycan_image = self.draw_glycan_in_canvas(self.glycan_2D, tree, root, names)
def select_glycan(self, event = None):
""" Check if a glycan has been selected
"""
if not self.selected_glycan:
tkMessageBox.showerror("Error", "Please select a glycan")
else:
self.hide_database()
def database_window(self, event=None):
"""Window with all databases (common and user defined)
-Notebook with two tabs: one for common glycans and one for user's
"""
if self.db_window:
self.show_database()
return -1
# self.db_window = Pmw.MegaToplevel(self)
self.db_window = tk.Toplevel(self)
self.db_window.wm_title("Glycan Databases")
self.db_window.protocol('WM_DELETE_WINDOW', self.hide_database)
self.glycan_balloon = Pmw.Balloon(self.db_window)
self.db_window.columnconfigure(0, weight=1)
self.db_window.rowconfigure(0, weight=1)
#tabs
self.db_window.bind('<Return>', self.select_glycan)
self.tab_control = ttk.Notebook(self.db_window)
self.tb_commong = tk.Frame(self.tab_control, height = 200)
self.tb_userg = tk.Frame(self.tab_control)
self.tab_control.add(self.tb_commong, text='Common glycans')
self.tab_control.add(self.tb_userg, text='My glycans')
self.button_control = tk.Frame(self.db_window)
self.db_ok = tk.Button(self.button_control, text='OK', command = self.select_glycan)
self.db_cancel = tk.Button(self.button_control, text='cancel', command = self.hide_database)
self.tab_control.grid(column = 0, row = 0, sticky = 'NSEW')
self.tab_control.columnconfigure(0, weight=1)
self.tab_control.rowconfigure(0, weight=1)
self.button_control.grid(column =0, row = 1, sticky = 'E')
self.db_cancel.grid(column = 0, row = 0, sticky = 'E')
self.db_ok.grid(column = 1, row = 0, sticky ='E')
#common glycans tab
self.v_sb_cg = tk.Scrollbar(self.tb_commong, orient = 'vertical')
self.canvas_commong = tk.Canvas(self.tb_commong, width=200, height = 200, scrollregion=(0, 0, 300, 1500), yscrollcommand = self.v_sb_cg.set)
self.v_sb_cg.config(command = self.canvas_commong.yview)
self.canvas_commong.grid(column = 0, row = 0, sticky='NSEW')
self.v_sb_cg.grid(column = 1, row = 0, sticky='NS')
self.tb_commong.columnconfigure(0, weight=1)
self.tb_commong.rowconfigure(0, weight=1)
self.frame_commong = tk.Frame(self.canvas_commong)
self.canvas_commong.create_window((4,4), window=self.frame_commong, anchor="nw",
tags="self.frame_commong")
# self.populate(self.frame_commong)
if not self.common_glycans:
self.hide_database()
self.popup_progress_bar('Importing library...')
self.common_glycans = self.import_glycans(self.db_commong)
self.common_images = []
self.common_canvas = []
self.display_db(self.frame_commong, self.common_glycans, self.common_images, self.common_canvas)
self.popup.destroy()
self.show_database()
self.frame_commong.bind("<Configure>", self._on_frame_configure)
#user glycans tab
self.canvas_userg = tk.Canvas(self.tb_userg)
self.v_sb_ug = tk.Scrollbar(self.tb_userg, orient = 'vertical', command = self.canvas_userg.yview)
self.canvas_userg.config(yscrollcommand = self.v_sb_ug.set)
self.ug_button_frame = tk.Frame(self.tb_userg)
self.tb_userg.columnconfigure(0, weight=1)
self.tb_userg.rowconfigure(0, weight=1)
self.canvas_userg.grid(column = 0, row = 0, sticky = 'NSEW')
self.v_sb_ug.grid(column = 1, row = 0, sticky='NS')
self.ug_button_frame.grid(column = 0, row = 1, sticky= 'SE')
#add buttons for import
self.ug_import = tk.Button(self.ug_button_frame, command = self.import_library)
self.import_icon = tk.PhotoImage(file = SELF_BIN + "/icons/import.gif")
self.ug_import.config(image = self.import_icon)
self.ug_export = tk.Button(self.ug_button_frame, command = self.export_library)
self.export_icon = tk.PhotoImage(file = SELF_BIN + "/icons/export.gif")
self.ug_export.config(image = self.export_icon)
self.ug_add = tk.Button(self.ug_button_frame, command = self.add_glycan_form)
self.add_icon = tk.PhotoImage(file = SELF_BIN + "/icons/add.gif")
self.ug_add.config(image = self.add_icon)
self.ug_delete = tk.Button(self.ug_button_frame, command = self.delete_glycan)
self.delete_icon = tk.PhotoImage(file = SELF_BIN + "/icons/delete.gif")
self.ug_delete.config(image = self.delete_icon)
self.ug_import.grid(column = 0, row = 0)
self.ug_export.grid(column = 1, row = 0)
self.ug_add.grid(column = 2, row = 0)
self.ug_delete.grid(column = 3, row = 0)
self.user_images = []
self.user_canvas = []
self.frame_userg = tk.Frame(self.canvas_userg)
self.canvas_userg.create_window((4,4), window=self.frame_userg, anchor="nw",
tags="self.frame_userg")
self.frame_userg.bind("<Configure>", self._on_frame_configure)
if self.user_glycans:
self.display_db(self.frame_userg, self.user_glycans, self.user_images, self.user_canvas)
def _on_frame_configure(self, event):
'''Reset the scroll region to encompass the inner frame'''
self.canvas_commong.configure(scrollregion=self.canvas_commong.bbox("all"))
self.canvas_userg.configure(scrollregion=self.canvas_userg.bbox("all"))
def _on_mousewheel(self, event):
'''Scroll glycanprotein_2D on mouse wheel'''
if (event.num == 4): delta = -1
elif (event.num == 5): delta = 1
else: delta = event.delta
self.glycoprotein_2D.yview_scroll(delta, "units")
def display_db(self, master, glycans, glycan_images, glycan_canvas):
"""Generates thumbnail images for all glycans in a database
Parameters:
master: master Canvas for drawing
glycans: dictionary of glycans. Names as keys and connectivity topology as values
glycan_images: list for storing generated images
glycan_canvas: list for storing generated canvas
glycan_ttp: list for storing labels for each glycan
"""
i = 0
j = 0
counter = 0
for name in glycans.keys():
# put five images per row
if j and not j%5:
i += 1
j = 0
units = glycans[name]['UNIT']
root,tree,names = self.build_glycan_tree(units)
fig = mpl.figure.Figure(figsize=(70./self.dpi, 70./self.dpi))
ax = fig.add_subplot(111)
self.myDrawer.draw_tree(tree, root, names, root_pos = [0, 0], direction = 1, ax = ax, axis = 0)
ax.axis('equal')
ax.axis('off')
ax.set_ylim((-1, 6))
ax.set_xlim((-3, 3))
# Add to tk window
figure_canvas_agg = FigureCanvasAgg(fig)
figure_canvas_agg.draw()
figure_x, figure_y, figure_w, figure_h = fig.bbox.bounds
figure_w, figure_h = int(figure_w), int(figure_h)
canvas = tk.Canvas(master, width = 100, height = 100)
glycan_image = tk.PhotoImage(master = canvas, width=figure_w, height=figure_h)
canvas.create_image(figure_w/2, figure_h/2, image = glycan_image, tags = counter)
canvas.bind("<Button-1>", self.clicked_glycan)
canvas.bind("<Double-Button-1>", self.select_glycan)
self.glycan_balloon.bind(canvas, 'Name: ' + name + '\nStructure: ' + self.myDrawer.tree_to_text(tree, root, names, visited = []))
tkagg.blit(glycan_image, figure_canvas_agg.get_renderer()._renderer, colormode=2)
canvas.grid(column = j, row = i)
glycan_images.append(glycan_image)
glycan_canvas.append(canvas)
j += 1
counter += 1
def build_glycan_tree(self, glycan):
"""Convert a glycan connectivity tree into a graph for drawing
Parameters:
glycan: list of units form connectivity topology ['UNIT']
Returns:
G: graph representation of glycans
names: dictionary with unit id as key and resname as value
root: id of root unit
"""
G = nx.Graph()
idx = 0
top = {}
names = {}
for unit in glycan:
if not unit[1]:
root = idx
top[' '.join(unit[2])] = idx
names[idx] = unit[0]
idx += 1
for k in top.keys():
e1 = ' '.join(k.split(' ')[:-1])
if e1 != k:
e = (top[k], top[e1])
G.add_edge(top[k], top[e1], patch=k.split(' ')[-1])
#G.add_edge(*e)
else:
G.add_node(top[k])
return root,G,names
def clicked_glycan(self, event):
"""Determines which glycan has been selected from database
The glycan will be highlighted with a red rectangle.
Initializes:
selection: rectangle around the canvas
selected_canvas: selected canvas
selected_glycan: item form glycan dictionary (Key: name, Value: glycan connect topology)
"""
#tab = self.tab_control.tab(self.tab_control.select(), "text")
tab = self.tab_control.index(self.tab_control.select())
item = event.widget.find_closest(event.x, event.y)
idx = int(event.widget.gettags(item)[0])
if self.selected_canvas:
self.selected_canvas.delete(self.selection)
if tab == 0:
self.selected_canvas = self.common_canvas[idx]
self.selected_glycan = self.common_glycans.items()[idx]
elif tab == 1:
self.selected_canvas = self.user_canvas[idx]
self.selected_glycan = self.user_glycans.items()[idx]
self.selection = self.selected_canvas.create_rectangle(0, 0, 100, 100, outline='red', width=6)
def import_library(self):
""" Opens dialog for user to import their library
Update the database windows, if it has already been created.
"""
filename = tkFileDialog.askopenfilename(initialdir = self.cwd, title = "Select glycan library", filetypes = (("db files","*.db"),("all files","*.*")))
if not filename:
return -1
self.user_glycans = self.import_glycans(filename)
if self.db_window:
if self.user_canvas:
self.canvas_userg.delete(all)
self.user_images = []
self.user_canvas = []
self.user_names = []
self.display_db(self.frame_userg, self.user_glycans, self.user_images, self.user_canvas)
def import_glycans(self, filename):
"""Import connectivity topology from sql database
This function will initialize connect_topology
Parameters:
filename: path to database
"""
try:
conn = sqlite3.connect(filename)
except:
print "Error while connecting to the database " + filename
return -1
cursor = conn.cursor()
cursor.execute("SELECT * FROM glycans")
glycans = cursor.fetchall()
connect_topology = {}
for glycan in glycans:
name,tree = glycan
residue = {}
residue['UNIT'] = []
nbr_unit = 0
for unit in tree.split('|'):
unit = unit.split(' ')
nbr_unit += 1
if len(unit) > 2:
residue['UNIT'].append([unit[0],unit[1], unit[2:]])
else:
residue['UNIT'].append([unit[0], ' ', []])
residue['#UNIT'] = nbr_unit
connect_topology[name] = residue
return connect_topology
def export_library(self):
"""Open dialog for user to save their glycan library
"""
filename = tkFileDialog.asksaveasfilename(initialdir = self.cwd, title = "Save glycan library", filetypes = (("db files","*.db"),("all files","*.*")))
self.export_glycans(filename, self.user_glycans)
def export_glycans(self, filename, connect_topology):
"""Export connectivity topology to sql database
This function will export a SQL database with all the user glycans.
"""
try:
conn = sqlite3.connect(filename)
except:
print "Error while connecting to the database " + filename
return -1
cursor = conn.cursor()
tn = 'glycans'
gn = 'glycan_name'
self.selected_glycan[1] = 'glycan_tree'
cursor.execute("DROP TABLE IF EXISTS {tn}".format(tn = tn))
cursor.execute("CREATE TABLE {tn} ({gn} text, {gt} text)".format(tn = tn, gn = gn, gt = gt))
for key in connect_topology.keys():
units = connect_topology[key]['UNIT']
glycan = []
for unit in units:
v = []
v.extend(unit[0:2])
v.extend(unit[2])
glycan.append(' '.join(v))
glycan = '|'.join(glycan)
cursor.execute("INSERT INTO {tn} VALUES (\'{gn}\', \'{gt}\')".format(tn = tn, gn = key, gt = glycan))
conn.commit()
conn.close()
def add_glycan_form(self):
"""Adds a glycan to a library.
Supported format:
pdb
glycosylator topology
"""
self.new_connect_top = {}
self.add_window = tk.Toplevel(self)
self.add_window.wm_title("Add glycan")
#Labels
tk.Label(self.add_window, text = 'File: ').grid(row = 0, column = 0, sticky = 'W')
tk.Label(self.add_window, text = 'Glycan Name: ').grid(row = 1, column = 0, sticky = 'W')
tk.Label(self.add_window, text = 'Structure: ').grid(row = 2, column = 0, sticky = 'W')
#
self.glycan_name_entry = tk.Entry(self.add_window)
self.choose_file = tk.Button(self.add_window, text = 'Choose file', command = self.get_connect_topology)
self.structure_entry = tk.Entry(self.add_window, state = 'disable')
self.glycan_canvas = tk.Canvas(self.add_window, width = 100, height = 100)
self.cancel_glycan_button = tk.Button(self.add_window, text = 'Cancel', command = self.add_window.destroy)
self.add_glycan_button = tk.Button(self.add_window, text = 'Add glycan', command = self.add_glycan)
#Pack
self.choose_file.grid(row = 0, column = 1, sticky = 'E')
self.glycan_name_entry.grid(row = 1, column = 1, sticky = 'E')
self.structure_entry.grid(row = 2, column = 1, sticky = 'E')
self.glycan_canvas.grid(row = 0, column = 2, rowspan = 3, columnspan = 2)
self.cancel_glycan_button.grid(row = 3, column = 2)
self.add_glycan_button.grid(row = 3, column = 3)
# def close_add(self):
def add_glycan(self):
"""Add new glycan to user's database
"""
self.user_glycans[self.glycan_name_entry.get()] = self.new_connect_top
self.add_window.destroy()
for c in self.user_canvas:
self.glycan_name.tagunbind(self.canvas_userg, c)
self.canvas_userg.delete(all)
self.user_images = []
self.user_canvas = []
if self.user_glycans:
self.display_db(self.frame_userg, self.user_glycans, self.user_images, self.user_canvas)
def draw_glycan_in_canvas(self, canvas, tree, root, names, h = 100., w = 100.):
""" Draws a glycan on to a canvas
Parameters:
canvas: tk.Canvas where the image should be drawn
tree: tree representation of the glycan
root: id of root node in tree
names: dictionary with node id as keys and resname as values
h: height of figure in px
w: width of figure in px
Returns:
glycan_image: image instance. This should be saved otherwise the image will be destroyed, thus not displayed.
"""
fig = mpl.figure.Figure(figsize=(h/self.dpi, w/self.dpi))
ax = fig.add_subplot(111)
self.myDrawer.draw_tree(tree, root, names, root_pos = [0, 0], direction = 1, ax = ax, axis = 0)
ax.axis('equal')
ax.axis('off')
ax.set_ylim((-1, 6))
ax.set_xlim((-3, 3))
# Add to tk window
figure_canvas_agg = FigureCanvasAgg(fig)
figure_canvas_agg.draw()
figure_x, figure_y, figure_w, figure_h = fig.bbox.bounds
figure_w, figure_h = int(figure_w), int(figure_h)
glycan_image = tk.PhotoImage(master = canvas, width=figure_w, height=figure_h)
canvas.create_image(figure_w/2, figure_h/2, image = glycan_image)
tkagg.blit(glycan_image, figure_canvas_agg.get_renderer()._renderer, colormode=2)
return glycan_image
def get_connect_topology(self):
"""Dialog window for selecting new glycan. Can be either pdb or topology file
Intialize new_connect_top
"""
filename = tkFileDialog.askopenfilename(initialdir = self.cwd, title = "Select glycan library", filetypes = (("pdb files","*.pdb"), ("topology file", "*.top"), ("all files","*.*")))
if not filename:
return -1
path, file_extension = os.path.splitext(filename)
if file_extension == '.pdb':
glycan = glc.Molecule('glycan')
glycan.read_molecule_from_PDB(filename, update_bonds = False)
self.myGlycosylator.assign_patches(glycan)
connect_tree = self.myGlycosylator.build_connect_topology(glycan)
self.new_connect_top = self.connect_tree_to_topology(connect_tree)
elif file_extension == '.top':
name,self.new_connect_top = self.read_connect_topology(filename)
self.glycan_name_entry.insert(0, name)
root,tree,names = self.build_glycan_tree(self.new_connect_top['UNIT'])
self.new_glycan_image = self.draw_glycan_in_canvas(self.glycan_canvas, tree, root, names, h = 70., w = 70.)
self.structure_entry.configure(state='normal')
self.structure_entry.delete(0, tk.END)
self.structure_entry.insert(0, self.myDrawer.tree_to_text(tree, root, names, visited = []))
self.structure_entry.configure(state='disabled')
def read_connect_topology(self, filename):
"""Reads glycan connect topology from text file
Returns:
resname: name of glycan
residue: dictionary with connect topology
"""
lines = glc.readLinesFromFile(filename)
residue = {}
nbr_units = 0
for line in lines: # Loop through each line
line = line.split('\n')[0].split('!')[0].split() #remove comments and endl
if line:
if line[0] == 'RESI':
residue['UNIT'] = []
resname = line[1]
nbr_units = 0
elif line[0] == 'UNIT':
self.read_unit(line, residue)
nbr_units += 1
residue['#UNIT'] = nbr_units
return resname,residue
def read_unit(self, unit, residue):
"""Reads an unit in glycan connect topology
"""
if len(unit)>2:
residue['UNIT'].append([unit[1], unit[2], unit[3:]])
else:
residue['UNIT'].append([unit[1], '', []])
def connect_tree_to_topology(self, connect_tree):
"""Converts a connect tree to a connect topology
In connect tree the connectivity is represented as a string whereas it is a list in connect topology
"""
connect_topology = {}
units = connect_tree['UNIT']
unit_list = []
n_unit = 0
for unit in units:
unit = filter(None, unit)
n_unit +=1
if len(unit) > 2:
unit_list.append([unit[0], 'C1', unit[2]])
else:
unit_list.append([unit[0], '', ['']])
connect_topology['UNIT'] = unit_list
connect_topology['#UNIT'] = n_unit
return connect_topology
def delete_glycan(self):
"""Delete glycan from database
"""
if not self.selected_glycan:
tkMessageBox.showerror("Error", "Please select a glycan to be deleted")
k,v = self.selected_glycan
del self.user_glycans[k]
for c in self.user_canvas:
self.glycan_name.tagunbind(self.canvas_userg, c)
self.canvas_userg.delete(all)
self.user_images = []
self.user_canvas = []
self.display_db(self.frame_userg, self.user_glycans, self.user_images, self.user_canvas)
def undo_glycan(self):
""" Removes built in glycan
"""
chid = self.chain.get()
sequon = self.sequon.get()
self.sequon_colors[sequon] = [.5, .5, .5]
key = self.sequon.get()
if key in self.linked_glycanMolecules:
del self.linked_glycanMolecules[key]
del self.linked_glycans[key]
self.draw_glycoprotein(chid)
self.draw_glycan(sequon)
def glycosylate(self):
""" Glycosylate sequon with chosen glycan
"""
chid = self.chain.get()
sequon = self.sequon.get()
self.sequon_colors[sequon] = [.7, .1, 0]
key = self.sequon.get()
residue = self.myGlycosylator.get_residue(key)
#Build new glycan
if self.selected_glycan:
self.myGlycosylator.connect_topology['SELECTED'] = self.selected_glycan[1]
#build from current glycan
if key in self.original_glycans:
original_glycan = self.original_glycanMolecules[key].atom_group
r,t = self.original_glycans[key]
connect_tree = self.myGlycosylator.build_connectivity_tree(r, t)
else:
original_glycan = None
connect_tree = None
#Use current glycan
else:
original_glycan = self.original_glycanMolecules[key]
r,t = self.original_glycans[key]
connect_tree = self.myGlycosylator.build_connectivity_tree(r, t)
self.myGlycosylator.connect_topology['SELECTED'] = self.myGlycosylator.build_connect_topology(original_glycan)
original_glycan = original_glycan.atom_group
segname = 'G'+key.split(',')[2]
glycan,bonds = self.myGlycosylator.glycosylate('SELECTED',
template_glycan_tree = connect_tree,
template_glycan = original_glycan,
link_residue=residue, link_patch = 'NGLB', chain = 'G', segname=segname)
new_glycan = glc.Molecule(key)
new_glycan.set_AtomGroup(glycan, bonds = bonds)
self.myGlycosylator.assign_patches(new_glycan)
self.linked_glycanMolecules[key] = new_glycan
self.linked_glycans[key] = [new_glycan.rootRes, new_glycan.interresidue_connectivity]
self.names.update(new_glycan.get_names())
# Update glycoprotein and sequon panels
self.draw_glycoprotein(chid)
self.draw_glycan(sequon)
def remove_clashes(self):
""" Remove clashes from modeled glycans
"""
dihe_parameters = self.myGlycosylator.builder.Parameters.parameters['DIHEDRALS']
vwd_parameters = self.myGlycosylator.builder.Parameters.parameters['NONBONDED']
static_glycans = None
for k in self.original_glycanMolecules:
if k not in self.linked_glycanMolecules:
if static_glycans is not None:
static_glycans += self.original_glycanMolecules[k].atom_group
else:
static_glycans = self.original_glycanMolecules[k].atom_group.copy()
environment = self.myGlycosylator.protein.copy()
environment += static_glycans
#Build topology
self.myGlycosylator.build_glycan_topology(glycanMolecules = self.linked_glycanMolecules, build_all = False)
sampler = glc.Sampler(self.linked_glycanMolecules.values(), environment, dihe_parameters, vwd_parameters)
sampler.remove_clashes_GA()
def _set_propreties(self):
"""Allows user to ajust parameters to improve the rendering of the GUI (size and resolution)
"""
pass
def export_patches(self):
"""Exports a configuration file for CHARMM with all the patches that have to be applied in order to build glycans.
"""
filename = tkFileDialog.asksaveasfilename(initialdir = self.cwd, title = "Save patches", filetypes = (("inp file","*.inp"),("all files","*.*")))
if filename:
patches = self.myGlycosylator.export_patches(self.linked_glycans)
with open(filename, 'w') as f:
f.write('\n'.join(patches))
def popup_progress_bar(self, text):
self.popup = tk.Toplevel(self)
tk.Label(self.popup, text=text).grid(row = 0, column = 0)
progress_bar = ttk.Progressbar(self.popup,mode='indeterminate')
progress_bar.grid(row=1, column=0)
progress_bar.start(1)
self.popup.update()
self.popup.deiconify()
if __name__ == "__main__":
glycogui = GlycosylatorGUI()
glycogui.mainloop()