def addpdb(root, amber_prmtop, messages):
""" Adds PDB information to a topology file """
# Get the name of the file
type_list = [('PDB', '*.pdb'), ('All Files', '*')]
fname = file_chooser('PDB File', type_list)
if not fname: return
widget_list = [('Checkbutton', 'Require all residue names be consistent.'),
('Checkbutton', 'Print element names in %FLAG ELEMENT'),
('Checkbutton', 'Print all insertion codes, even if all are '
'blank.')]
var_list = [StringVar(value='no') for i in range(3)]
description = ('Adds information from the PDB file (e.g., CHAIN IDs) to '
'the topology file')
# Create the window, open it, then wait for it to close
cmd_window = _guiwidgets.ActionWindow('addPDB', amber_prmtop, widget_list,
var_list, description)
cmd_window.wait_window()
# See if we got any variables back
vars_found = True in [bool(v.get()) for v in var_list]
if not vars_found: return
newvars = [fname]
# If we did, pass them through
if var_list[0] == 'yes': newvars.append('strict')
if var_list[1] == 'yes': newvars.append('elem')
if var_list[1] == 'yes': newvars.append('allicodes')
try:
action = actions.addPDB(amber_prmtop, ArgumentList(newvars))
messages.write('%s\n' % action)
action.execute()
except Exception as err:
showerror('Unexpected Error!', '%s: %s' % (type(err).__name__, err))
return
def loadrestrt(root, amber_prmtop, messages):
""" Finds a file to load as a restart """
type_list = [('Inpcrd', '*.inpcrd'), ('Inpcrd', '*.crd'),
('Restart', '*.restrt'), ('Restart', '*.rst7'),
('All Files', '*')]
fname = file_chooser('Amber Coordinate File', type_list)
if fname:
action = actions.loadRestrt(amber_prmtop, ArgumentList(fname))
messages.write('%s\n' % action)
action.execute()
def addcoarsegrain(root, amber_prmtop, messages):
""" Adds coarse graining to topology file via Lula's algo """
# This implementation doesn't exist anywhere yet, so disable it
showerror('Warning', 'This functionality is not implemented in Amber yet!')
return
# We need a file
fname = file_chooser('Coarse Grain Parameter',
[('Coarse Grain Parameters', '*.cgparm'),
('All Files', '*')]
)
if not fname: return
try:
action = actions.addCoarseGrain(amber_prmtop, ArgumentList(fname))
messages.write('%s\n' % action)
action.execute()
except Exception as err:
showerror('Unexpected Error!', '%s: %s' % (type(err).__name__, err))
return
def guiapp():
from parmed import load_file
from parmed.utils.six.moves import tkinter as tk
from parmed.utils.six.moves.tkinter_messagebox import showerror
from optparse import OptionParser
from os.path import exists, split
from parmed.tools.exceptions import ParmError
from parmed import __version__
from parmed.tools.gui.guitools import ParmedApp
from parmed.tools.gui.guifiletools import file_chooser
from parmed.tools.logos import Logo
from parmed.tools.actions import Action
from parmed.tools.parmlist import ParmList
import sys
debug = False
def excepthook(exception_type, exception_value, tb):
""" Default exception handler """
import traceback
if debug: traceback.print_tb(tb)
showerror('Fatal Error','%s: %s' % (exception_type.__name__,
exception_value))
sys.exit(1)
# Launch the root window
root = tk.Tk()
root.resizable(True, True)
# Replace the default excepthook with mine
sys.excepthook = excepthook
# See if we were provided a topology file on the command-line
parser = OptionParser(usage = '%prog [<prmtop>]')
parser.add_option('-d', '--debug', dest='debug', default=False,
action='store_true', help='Show detailed tracebacks ' +
'when an error is detected.')
opt, args = parser.parse_args()
debug = opt.debug
# If the user provided a CL argument, that is the prmtop_name. Otherwise,
# open up a file choosing dialog box to get the input from the user
if len(args) == 0:
prmtop_name = file_chooser('Topology')
elif len(args) == 1:
prmtop_name = args[0]
else:
sys.stderr.write('Unknown command-line options. Ignoring\n')
prmtop_name = file_chooser('Topology')
# If we chose no prmtop file,
if not prmtop_name: raise ParmError('No prmtop chosen!')
# Load the amber prmtop and check for errors
amber_prmtop = ParmList()
parm = load_file(prmtop_name)
amber_prmtop.add_parm(parm)
# Make this overwritable -- the all of the file save boxes will ask the user
# for verification before saving over an existing file. There's no need for
# the AmberParm security layer.
Action.overwrite = True
fname = split(prmtop_name)[1]
root.title('xParmED: Editing/viewing [%s] Choose an operation' % fname)
# Now build the action list on root
app = ParmedApp(root, amber_prmtop)
app.pack(fill=tk.BOTH, expand=1)
root.mainloop()
print('Thank you for using xParmEd!\n%s' % Logo())
def callback():
file_chooser('C4 Parameter File',
extensions=[('All files', '*')], set_var=var)
def guiapp():
from parmed import load_file
from parmed.utils.six.moves import tkinter as tk
from parmed.utils.six.moves.tkinter_messagebox import showerror
from optparse import OptionParser
from os.path import split
from parmed.tools.exceptions import ParmError
from parmed.tools.gui.guitools import ParmedApp
from parmed.tools.gui.guifiletools import file_chooser
from parmed.tools.logos import Logo
from parmed.tools.actions import Action
from parmed.tools.parmlist import ParmList
import sys
debug = False
def excepthook(exception_type, exception_value, tb):
""" Default exception handler """
import traceback
if debug: traceback.print_tb(tb)
showerror('Fatal Error',
'%s: %s' % (exception_type.__name__, exception_value))
sys.exit(1)
# Launch the root window
root = tk.Tk()
root.resizable(True, True)
# Replace the default excepthook with mine
sys.excepthook = excepthook
# See if we were provided a topology file on the command-line
parser = OptionParser(usage='%prog [<prmtop>]')
parser.add_option('-d',
'--debug',
dest='debug',
default=False,
action='store_true',
help='Show detailed tracebacks ' +
'when an error is detected.')
opt, args = parser.parse_args()
debug = opt.debug
# If the user provided a CL argument, that is the prmtop_name. Otherwise,
# open up a file choosing dialog box to get the input from the user
if len(args) == 0:
prmtop_name = file_chooser('Topology')
elif len(args) == 1:
prmtop_name = args[0]
else:
sys.stderr.write('Unknown command-line options. Ignoring\n')
prmtop_name = file_chooser('Topology')
# If we chose no prmtop file,
if not prmtop_name: raise ParmError('No prmtop chosen!')
# Load the amber prmtop and check for errors
amber_prmtop = ParmList()
parm = load_file(prmtop_name)
amber_prmtop.add_parm(parm)
# Make this overwritable -- the all of the file save boxes will ask the user
# for verification before saving over an existing file. There's no need for
# the AmberParm security layer.
Action.overwrite = True
fname = split(prmtop_name)[1]
root.title('xParmED: Editing/viewing [%s] Choose an operation' % fname)
# Now build the action list on root
app = ParmedApp(root, amber_prmtop)
app.pack(fill=tk.BOTH, expand=1)
root.mainloop()
print('Thank you for using xParmEd!\n%s' % Logo())