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 clapp():
# Load system modules.
from argparse import ArgumentParser
import datetime
import os
try:
import readline
except ImportError:
readline = None
import signal
import sys
import warnings
# Load custom modules
from parmed.exceptions import ParmedError
from parmed.tools.logos import Logo
from parmed.tools.exceptions import SeriousParmWarning, InterpreterError
from parmed.tools.parmed_cmd import ParmedCmd
from parmed.tools.actions import Action
from parmed.tools.parmlist import ParmList
from parmed import __version__
# Set up new excepthook to clean up fatal exception printouts
def interrupted(*args, **kwargs):
""" Handle interruptions gracefully """
sys.stdout.write('Interrupted\n')
sys.exit(1)
signal.signal(signal.SIGINT, interrupted)
# Define our own custom warning printer
def _print_warnings(message,
category,
filename,
lineno,
file=None,
line=None):
""" Override the default showwarning method """
if file is None: file = sys.stderr
try:
file.write('%s: %s\n' % (category.__name__, message))
except IOError:
pass
warnings.showwarning = _print_warnings
# Set up parser
parser = ArgumentParser()
parser.add_argument('-v',
'--version',
action='version',
version='%%(prog)s: Version %s' % __version__)
group = parser.add_argument_group('Input Files')
group.add_argument('-i',
'--input',
dest='script',
default=[],
metavar='FILE',
help='''Script with ParmEd commands to execute. Default
reads from stdin. Can be specified multiple times to process multiple
input files.''',
action='append')
group.add_argument('-p',
'--parm',
dest='prmtop',
default=[],
metavar='<prmtop>',
action='append',
help='''List of topology files to
load into ParmEd. Can be specified multiple times to process multiple
topologies.''')
group.add_argument('-c',
'--inpcrd',
dest='inpcrd',
default=[],
metavar='<inpcrd>',
action='append',
help='''List of inpcrd files to
load into ParmEd. They are paired with the topology files in the same
order that each set of files is specified on the command-line.''')
group = parser.add_argument_group('Output Files')
group.add_argument('-O',
'--overwrite',
dest='overwrite',
default=False,
help='Allow ParmEd to overwrite existing files.',
action='store_true')
group.add_argument('-l',
'--logfile',
dest='logfile',
metavar='FILE',
default='parmed.log',
help='''Log file with every command executed
during an interactive ParmEd session. Default is parmed.log''')
group = parser.add_argument_group(
'Interpreter Options', '''These options affect
how the ParmEd interpreter behaves in certain cases.''')
group.add_argument('--prompt',
dest='prompt',
default='>',
metavar='PROMPT',
help='String to use as a command prompt.')
group.add_argument('-n',
'--no-splash',
dest='printlogo',
action='store_false',
help='Prevent printing the greeting logo.',
default=True)
group.add_argument(
'-e',
'--enable-interpreter',
dest='interpreter',
action='store_true',
default=False,
help='''Allow arbitrary single Python commands or blocks of Python code
to be run. By default Python commands will not be run as a safeguard
for your system. Make sure you trust the source of the ParmEd command
before turning this option on.''')
group = parser.add_argument_group(
'Error Handling', '''These options control how
ParmEd handles various errors and warnings that appear occur during the
course of Action execution''')
group.add_argument('-s',
'--strict',
dest='strict',
action='store_true',
default=True,
help='''Prevent scripts from running past unrecognized
input and actions that end with an error. In interactive mode, actions
with unrecognized inputs and failed actions prevent any changes from
being made to the topology, but does not quit the interpreter. This is
the default behavior.''')
group.add_argument(
'-r',
'--relaxed',
dest='strict',
action='store_false',
help='''Scripts ignore unrecognized input and simply skip over failed
actions, executing the rest of the script. Unrecognized input in the
interactive interpreter emits a non-fatal warning.''')
parser.add_argument('prmtop_cl',
nargs='?',
metavar='<prmtop>',
default=None,
help='Topology file to analyze.')
parser.add_argument(
'script_cl',
nargs='?',
metavar='<script>',
default=None,
help='File with a series of ParmEd commands to execute.')
opt = parser.parse_args()
# If the user specified a prmtop and script in the 'old' way, append them to the
# list constructed via the --parm and -i flags -- they come at the end
if opt.script_cl is not None:
opt.script.append(opt.script_cl)
if opt.prmtop_cl is not None:
opt.prmtop.append(opt.prmtop_cl)
# Load the splash screen
if opt.printlogo:
splash = Logo()
print(splash)
# Set our warning filter
if not opt.strict:
warnings.filterwarnings('always', category=SeriousParmWarning)
# Set our overwrite preferences
Action.overwrite = opt.overwrite
amber_prmtop = ParmList()
for i, parm in enumerate(opt.prmtop):
if i < len(opt.inpcrd):
amber_prmtop.add_parm(parm)
amber_prmtop.parm.load_rst7(opt.inpcrd[i])
print('Loaded Amber topology file %s with coordinates from %s\n' %
(parm, opt.inpcrd[i]))
else:
amber_prmtop.add_parm(parm)
print('Loaded Amber topology file %s' % parm)
if len(opt.script) > 0:
# Read from the list of scripts
print(opt.script)
# Make sure that all scripts exist, quitting if we are strict and not all
# scripts exist. Don't do anything until we know that all scripts exist.
for script in opt.script:
if not os.path.exists(script):
warnings.warn('Script file %s cannot be found.' % script,
SeriousParmWarning)
# We have already pre-screened the scripts.
for script in opt.script:
if not os.path.exists(script): continue
print('Reading actions from %s\n' % script)
parmed_commands = ParmedCmd(amber_prmtop, stdin=open(script, 'r'))
parmed_commands.use_rawinput = 0
parmed_commands.interpreter = opt.interpreter
parmed_commands.prompt = ''
# Loop through all of the commands
try:
parmed_commands.cmdloop()
except InterpreterError as err:
sys.exit('%s: %s' % (type(err).__name__, err))
except ParmedError:
# This has already been caught and printed. If it was re-raised,
# then that means we wanted to exit
sys.exit(1)
else:
close_log_file = False
parmed_commands = ParmedCmd(amber_prmtop)
parmed_commands.intro = "Reading input from STDIN..."
parmed_commands.interpreter = opt.interpreter
parmed_commands.prompt = opt.prompt.strip() + ' '
# Set the log file and logging, but only if interactive
if os.isatty(sys.stdin.fileno()):
if os.path.exists(opt.logfile) and readline is not None:
# Load the logfile as a history, and get rid of any timestamps
# from the history
try:
f = open(opt.logfile, 'r')
except IOError:
pass # Do not have permission or something
else:
for line in f:
if line.startswith('# Log started on'): continue
readline.add_history(line.rstrip())
f.close()
try:
logfile = open(opt.logfile, 'a')
except IOError:
print("Could not open logfile. Skip logging", file=sys.stderr)
close_log_file = False
else:
now = datetime.datetime.now()
logfile.write('# Log started on %02d/%02d/%d [mm/dd/yyyy] at '
'%02d:%02d:%02d\n' %
(now.month, now.day, now.year, now.hour,
now.minute, now.second))
parmed_commands.setlog(logfile)
close_log_file = True
# Loop through all of the commands
try:
try:
parmed_commands.cmdloop()
except InterpreterError as err:
sys.exit('%s: %s' % (type(err).__name__, err))
except ParmedError:
# This has already been caught and printed. If it was re-raised,
# then that means we wanted to exit
sys.exit(1)
finally:
if close_log_file:
logfile.close()
print('Done!')
def clapp():
# Load system modules.
from argparse import ArgumentParser
import datetime
import os
try:
import readline
except ImportError:
readline = None
import signal
import sys
import warnings
# Load custom modules
from parmed.exceptions import ParmedError
from parmed.tools.logos import Logo
from parmed.tools.exceptions import SeriousParmWarning, InterpreterError
from parmed.tools.parmed_cmd import ParmedCmd
from parmed.tools.actions import Action
from parmed.tools.parmlist import ParmList
from parmed import __version__
# Set up new excepthook to clean up fatal exception printouts
def interrupted(*args, **kwargs):
""" Handle interruptions gracefully """
sys.stdout.write('Interrupted\n')
sys.exit(1)
signal.signal(signal.SIGINT, interrupted)
# Define our own custom warning printer
def _print_warnings(message, category, filename, lineno, file=None, line=None):
""" Override the default showwarning method """
if file is None: file = sys.stderr
try:
file.write('%s: %s\n' % (category.__name__, message))
except IOError:
pass
warnings.showwarning = _print_warnings
# Set up parser
parser = ArgumentParser()
parser.add_argument('-v', '--version', action='version',
version='%%(prog)s: Version %s' % __version__)
group = parser.add_argument_group('Input Files')
group.add_argument('-i', '--input', dest='script', default=[],
metavar='FILE', help='''Script with ParmEd commands to execute. Default
reads from stdin. Can be specified multiple times to process multiple
input files.''', action='append')
group.add_argument('-p', '--parm', dest='prmtop', default=[],
metavar='<prmtop>', action='append', help='''List of topology files to
load into ParmEd. Can be specified multiple times to process multiple
topologies.''')
group.add_argument('-c', '--inpcrd', dest='inpcrd', default=[],
metavar='<inpcrd>', action='append', help='''List of inpcrd files to
load into ParmEd. They are paired with the topology files in the same
order that each set of files is specified on the command-line.''')
group = parser.add_argument_group('Output Files')
group.add_argument('-O', '--overwrite', dest='overwrite', default=False,
help='Allow ParmEd to overwrite existing files.', action='store_true')
group.add_argument('-l', '--logfile', dest='logfile', metavar='FILE',
default='parmed.log', help='''Log file with every command executed
during an interactive ParmEd session. Default is parmed.log''')
group = parser.add_argument_group('Interpreter Options', '''These options affect
how the ParmEd interpreter behaves in certain cases.''')
group.add_argument('--prompt', dest='prompt', default='>', metavar='PROMPT',
help='String to use as a command prompt.')
group.add_argument('-n', '--no-splash', dest='printlogo', action='store_false',
help='Prevent printing the greeting logo.', default=True)
group.add_argument('-e', '--enable-interpreter', dest='interpreter',
action='store_true', default=False,
help='''Allow arbitrary single Python commands or blocks of Python code
to be run. By default Python commands will not be run as a safeguard
for your system. Make sure you trust the source of the ParmEd command
before turning this option on.''')
group = parser.add_argument_group('Error Handling', '''These options control how
ParmEd handles various errors and warnings that appear occur during the
course of Action execution''')
group.add_argument('-s', '--strict', dest='strict', action='store_true',
default=True, help='''Prevent scripts from running past unrecognized
input and actions that end with an error. In interactive mode, actions
with unrecognized inputs and failed actions prevent any changes from
being made to the topology, but does not quit the interpreter. This is
the default behavior.''')
group.add_argument('-r', '--relaxed', dest='strict', action='store_false',
help='''Scripts ignore unrecognized input and simply skip over failed
actions, executing the rest of the script. Unrecognized input in the
interactive interpreter emits a non-fatal warning.''')
parser.add_argument('prmtop_cl', nargs='?', metavar='<prmtop>', default=None,
help='Topology file to analyze.')
parser.add_argument('script_cl', nargs='?', metavar='<script>', default=None,
help='File with a series of ParmEd commands to execute.')
opt = parser.parse_args()
# If the user specified a prmtop and script in the 'old' way, append them to the
# list constructed via the --parm and -i flags -- they come at the end
if opt.script_cl is not None:
opt.script.append(opt.script_cl)
if opt.prmtop_cl is not None:
opt.prmtop.append(opt.prmtop_cl)
# Load the splash screen
if opt.printlogo:
splash = Logo()
print(splash)
# Set our warning filter
if not opt.strict:
warnings.filterwarnings('always', category=SeriousParmWarning)
# Set our overwrite preferences
Action.overwrite = opt.overwrite
amber_prmtop = ParmList()
for i, parm in enumerate(opt.prmtop):
if i < len(opt.inpcrd):
amber_prmtop.add_parm(parm)
amber_prmtop.parm.load_rst7(opt.inpcrd[i])
print('Loaded Amber topology file %s with coordinates from %s\n' %
(parm, opt.inpcrd[i]))
else:
amber_prmtop.add_parm(parm)
print('Loaded Amber topology file %s' % parm)
if len(opt.script) > 0:
# Read from the list of scripts
print(opt.script)
# Make sure that all scripts exist, quitting if we are strict and not all
# scripts exist. Don't do anything until we know that all scripts exist.
for script in opt.script:
if not os.path.exists(script):
warnings.warn('Script file %s cannot be found.' % script,
SeriousParmWarning)
# We have already pre-screened the scripts.
for script in opt.script:
if not os.path.exists(script): continue
print('Reading actions from %s\n' % script)
parmed_commands = ParmedCmd(amber_prmtop, stdin=open(script, 'r'))
parmed_commands.use_rawinput = 0
parmed_commands.interpreter = opt.interpreter
parmed_commands.prompt = ''
# Loop through all of the commands
try:
parmed_commands.cmdloop()
except InterpreterError as err:
sys.exit('%s: %s' % (type(err).__name__, err))
except ParmedError:
# This has already been caught and printed. If it was re-raised,
# then that means we wanted to exit
sys.exit(1)
else:
close_log_file = False
parmed_commands = ParmedCmd(amber_prmtop)
parmed_commands.intro = "Reading input from STDIN..."
parmed_commands.interpreter = opt.interpreter
parmed_commands.prompt = opt.prompt.strip() + ' '
# Set the log file and logging, but only if interactive
if os.isatty(sys.stdin.fileno()):
if os.path.exists(opt.logfile) and readline is not None:
# Load the logfile as a history, and get rid of any timestamps
# from the history
try:
f = open(opt.logfile, 'r')
except IOError:
pass # Do not have permission or something
else:
for line in f:
if line.startswith('# Log started on'): continue
readline.add_history(line.rstrip())
f.close()
try:
logfile = open(opt.logfile, 'a')
except IOError:
print("Could not open logfile. Skip logging", file=sys.stderr)
close_log_file = False
else:
now = datetime.datetime.now()
logfile.write('# Log started on %02d/%02d/%d [mm/dd/yyyy] at '
'%02d:%02d:%02d\n' % (now.month, now.day, now.year,
now.hour, now.minute, now.second))
parmed_commands.setlog(logfile)
close_log_file = True
# Loop through all of the commands
try:
try:
parmed_commands.cmdloop()
except InterpreterError as err:
sys.exit('%s: %s' % (type(err).__name__, err))
except ParmedError:
# This has already been caught and printed. If it was re-raised,
# then that means we wanted to exit
sys.exit(1)
finally:
if close_log_file:
logfile.close()
print('Done!')
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())