class NormalModesConfigDialog(TangramBaseDialog):
buttons = ('Run', 'Close')
help = "https://github.com/insilichem/tangram_normalmodes"
VERSION = '0.0.1'
VERSION_URL = "https://api.github.com/repos/insilichem/tangram_normalmodes/releases/latest"
def __init__(self, parent=None, engine='prody', *args, **kwargs):
# GUI init
self.title = 'Calculate Normal Modes with ' + engine.title()
self.parent = parent
self.engine = engine
if engine == 'prody':
self.fill_in_ui = self._fillInUI_Prody
else:
self.fill_in_ui = self._fillInUI_Gaussian
self.lennard_jones = False
self.mass_weighted = False
super(NormalModesConfigDialog, self).__init__(resizable=False,
*args,
**kwargs)
def _fillInUI_Prody(self, parent):
#
# Algorithm selection
#
self.canvas.columnconfigure(1, weight=1)
row = 0
self.ui_algorithms_menu_lbl = tk.Label(self.canvas,
text='Algorithm:',
anchor='e')
self.ui_algorithms_menu = Pmw.OptionMenu(
self.canvas,
items=[
'Full atom', 'Extend from C-alpha', 'Group by residues',
'Group by mass', 'Group by graph'
],
command=self._algorithms_menu_cb)
self.ui_algorithms_param = Pmw.EntryField(self.canvas,
entry_width=3,
validate={
'validator': 'integer',
'min': 1
},
labelpos='w',
label_text='#:')
self.ui_algorithms_param.setvalue(1)
self.ui_algorithms_menu_lbl.grid(row=row,
column=0,
sticky='we',
padx=3,
pady=3)
self.ui_algorithms_menu.grid(row=row,
column=1,
sticky='we',
padx=3,
pady=3,
columnspan=2)
#
# Number of modes & Molecule Minimization
#
row += 1
self.ui_n_modes_lbl = tk.Label(self.canvas,
text='# Modes:',
anchor='e')
self.ui_n_modes = Pmw.EntryField(self.canvas,
entry_width=3,
validate={
'validator': 'integer',
'min': 1
})
self.ui_n_modes.setvalue(20)
self.ui_n_modes_lbl.grid(column=0,
row=row,
sticky='we',
padx=3,
pady=3)
self.ui_n_modes.grid(column=1, row=row, sticky='news', padx=3)
self.ui_minimize_btn = tk.Button(
self.canvas,
text="Minimize",
) #command=lambda: chimera.dialogs.display(mmmdDialog.name))
self.ui_minimize_btn.grid(column=2,
row=row,
sticky='we',
padx=3,
pady=3)
#
# Cutoff
#
row += 1
self.ui_cutoff_lbl = tk.Label(self.canvas, text='Cutoff:', anchor='e')
self.ui_cutoff = Pmw.EntryField(self.canvas,
entry_width=3,
validate={
'validator': 'real',
'min': 4.0
})
self.ui_cutoff.setvalue(15.0)
self.ui_cutoff_lbl.grid(column=0, row=row, sticky='we', padx=3, pady=3)
self.ui_cutoff.grid(column=1, row=row, sticky='news', padx=3)
#
# Cutoff
#
row += 1
self.ui_gamma_lbl = tk.Label(self.canvas, text='Gamma LJ:', anchor='e')
self.ui_gamma = Pmw.EntryField(self.canvas,
entry_width=3,
validate={
'validator': 'real',
'min': 0.0
})
self.ui_gamma.setvalue(1.0)
self.ui_gamma_lbl.grid(column=0, row=row, sticky='we', padx=3, pady=3)
self.ui_gamma.grid(column=1, row=row, sticky='news', padx=3)
#
# Optional Selections: Lennard-Jones and mass-weighted hessian
#
row += 1
self.ui_extra_options = Pmw.Group(self.canvas, tag_text='Options')
self.ui_extra_options.grid(column=0,
row=row,
columnspan=3,
sticky='nsew',
padx=5,
pady=5)
self.ui_extra_options_chk = Pmw.RadioSelect(
self.ui_extra_options.interior(), buttontype='checkbutton')
self.ui_extra_options_chk.add('Mass-Weighted')
self.ui_extra_options_chk.grid(column=0, row=0, sticky='we')
#
# Model selection
#
row += 1
self.ui_molecules_lbl = tk.Label(self.canvas,
text="Select model:",
anchor='e')
self.ui_molecules_lbl.grid(column=0, row=row, padx=3)
self.ui_molecules = MoleculeScrolledListBox(
self.canvas, listbox_selectmode="single")
self.ui_molecules.grid(column=1,
row=row,
columnspan=3,
sticky='nsew',
padx=3,
pady=3)
def _fillInUI_Gaussian(self, parent):
row = 0
parent.columnconfigure(0, weight=1)
self.ui_gaussian_grp = Pmw.Group(self.canvas,
tag_text='Open Gaussian output file')
self.ui_gaussian_grp.grid(column=0,
row=row,
columnspan=2,
sticky='nsew',
padx=5,
pady=5)
self.ui_gaussian_grp.columnconfigure(0, weight=1)
self.ui_gaussian_grp.columnconfigure(1, weight=0)
self.ui_gaussian_file_entry = Pmw.EntryField(
self.ui_gaussian_grp.interior())
self.ui_gaussian_file_entry.pack(side='left',
expand=True,
fill='both',
padx=5,
pady=5)
self.ui_gaussian_btn = tk.Button(self.ui_gaussian_grp.interior(),
text='...',
command=self._load_file)
self.ui_gaussian_btn.pack(side='right', padx=5, pady=5)
def Apply(self):
self.controller = Controller(self)
self.vibrations = self.controller.run()
def Run(self):
self.Apply()
self.Close()
def _load_file(self, *a, **kw):
path = askopenfilename()
if path:
self.ui_gaussian_file_entry.setvalue(path)
def _algorithms_menu_cb(self, *a, **kw):
value = self.ui_algorithms_menu.getvalue()
if value.startswith('Group by'):
self.ui_algorithms_param.grid(row=0, column=2, sticky='ew', padx=5)
if value == 'Group by residues':
self.ui_algorithms_param.configure(label_text='# residues:')
elif value == 'Group by mass':
self.ui_algorithms_param.configure(label_text='# groups:')
else:
self.ui_algorithms_param.grid_forget()
