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
UNIT MAN C1 14bb 14bb 16ab 13ab !Z7 Unit connected with 13ab to Z4 [path from root: 14bb 14bb 16ab]
UNIT MAN C1 14bb 14bb 13ab !Z9 Unit connected with 13ab to Z3 [path from root: 14bb 14bb]
4. The connectivity tree is atomatically guessed based on bonds and patches. This can be used to identify glycan in connectivity tree library
5. A template glycan can be modified to match the defined connectivity tree (e.g Mannose 6: MAN6_1;3,2)
6. A topology tree can also be directly defined as a dictionary
7. A glycan can be built ab initio
"""
import glycosylator as gl
import prody as pd
import os
################################################################################
# 1. Create a glycosylator
myGlycosylator = gl.Glycosylator(os.path.join(gl.GLYCOSYLATOR_PATH, 'support/toppar_charmm/carbohydrates.rtf'),
os.path.join(gl.GLYCOSYLATOR_PATH, 'support/toppar_charmm/carbohydrates.prm'))
# 2. Additional topology files (in this case for building glycans ab initio [DUMMY pathc])
myGlycosylator.builder.Topology.read_topology(os.path.join(gl.GLYCOSYLATOR_PATH, 'support/topology/DUMMY.top'))
# 3. Load glycan connectivity tree library
myGlycosylator.read_connectivity_topology(os.path.join(gl.GLYCOSYLATOR_PATH, 'support/topology/mannose.top'))
################################################################################
# 4. Identify glycan in mannose.top
myMan9 = gl.Molecule('mannose9')
myMan9.read_molecule_from_PDB(os.path.join(gl.GLYCOSYLATOR_PATH, 'support/examples/man9.pdb'), update_bonds=True)
myGlycosylator.assign_patches(myMan9)
print("Identified glycan: " + myGlycosylator.identify_glycan(myMan9))
################################################################################
# 5. Trim man9 down to man6
connect_tree = myGlycosylator.build_connectivity_tree(myMan9.rootRes, myMan9.interresidue_connectivity)
#!usr/bin/env python
"""
demo_polymer.py
The following code will illustrate how to use glycosylator to build a polymer. In this case,
we will build a small peptide.
1. Load glycosylator with topology files for amino acids
"""
import glycosylator as gl
import prody as pd
import os
################################################################################
# 1. Create a glycosylator
myGlycosylator = gl.Glycosylator('peptide.str', 'peptide.prm')
################################################################################
################################################################################
# 2. Define sequence of peptide:
# GLYCSYLATR
peptide_topo = {}
peptide_topo['#UNIT'] = 10
peptide_topo['UNIT'] = [
['GLY', ' ', []], ['LEU', 'C1', ['LINK']], ['TYR', 'C1', ['LINK', 'LINK']],
['CYS', 'C1', ['LINK', 'LINK', 'LINK']],
['SER', 'C1', ['LINK', 'LINK', 'LINK', 'LINK']],
['TYR', 'C1', ['LINK', 'LINK', 'LINK', 'LINK', 'LINK']],
['LEU', 'C1', ['LINK', 'LINK', 'LINK', 'LINK', 'LINK', 'LINK']],
['ALA', 'C1', ['LINK', 'LINK', 'LINK', 'LINK', 'LINK', 'LINK', 'LINK']],
