def start_nh():
"""
Starts Nano-Hive server in the background.
Returns 1 if Nano-Hive path is not set or if the path does not exist.
Returns 2 if Nano-Hive config file does not exist.
"""
# Get Nano-Hive executable path from the prefs db.
nanohive_exe = env.prefs[nanohive_path_prefs_key]
if not nanohive_exe:
return 1
if not os.path.exists(nanohive_exe):
return 1
nanohive_config = get_nh_config_filename()
if not nanohive_config:
return 2
args = ["-f", nanohive_config]
# print "start_nh(): args=", args
from processes.Process import Process
arguments = []
for arg in args:
if arg != "":
arguments.append(arg)
nhProcess = Process()
nhProcess.start(nanohive_exe, args)
return 0
def start_nh():
"""
Starts Nano-Hive server in the background.
Returns 1 if Nano-Hive path is not set or if the path does not exist.
Returns 2 if Nano-Hive config file does not exist.
"""
# Get Nano-Hive executable path from the prefs db.
nanohive_exe = env.prefs[nanohive_path_prefs_key]
if not nanohive_exe:
return 1
if not os.path.exists(nanohive_exe):
return 1
nanohive_config = get_nh_config_filename()
if not nanohive_config:
return 2
args = ['-f', nanohive_config]
#print "start_nh(): args=", args
from processes.Process import Process
arguments = []
for arg in args:
if arg != "":
arguments.append(arg)
nhProcess = Process()
nhProcess.start(nanohive_exe, args)
return 0
def verifyPluginUsingVersionFlag(plugin_path, version_flag, vstring):
"""
Verifies a plugin by running it with I{version_flag} as the only
command line argument and matching the output to I{vstring}.
@return: 0 if there is a match. Otherwise, returns 1
@rtype: int
@note: This is only useful if the plug-in supports a version flag arguments.
"""
if not plugin_path:
return 1
if not os.path.exists(plugin_path):
return 1
args = [version_flag]
arguments = []
for arg in args:
if arg != "":
arguments.append(arg)
p = Process()
p.start(plugin_path, arguments)
if not p.waitForFinished (10000): # Wait for 10000 milliseconds = 10 seconds
return 1
output = 'Not vstring'
output = str(p.readAllStandardOutput())
#print "output=", output
#print "vstring=", vstring
if output.find(vstring) == -1:
return 1
else:
return 0 # Match found.
def verify_program(program, version_flag, vstring):
"""
Verifies a program by running it with the version_flag and matching the output to vstring.
Returns 0 if there is a match. Otherwise, returns 1
"""
if not program:
return 1
if not os.path.exists(program):
return 1
args = [version_flag]
from processes.Process import Process
arguments = []
for arg in args:
if arg != "":
arguments.append(arg)
print
print "arguments:", arguments
p = Process()
p.start(program, arguments)
if not p.waitForFinished(10000): # Wait for 10000 milliseconds = 10 seconds
return 1
output = "Not vstring"
output = str(p.readAllStandardOutput())
# print "output=", output
# print "vstring=", vstring
if output.find(vstring) == -1:
return 1
else:
return 0 # Match found.
def verifyPluginUsingVersionFlag(plugin_path, version_flag, vstring):
"""
Verifies a plugin by running it with I{version_flag} as the only
command line argument and matching the output to I{vstring}.
@return: 0 if there is a match. Otherwise, returns 1
@rtype: int
@note: This is only useful if the plug-in supports a version flag arguments.
"""
if not plugin_path:
return 1
if not os.path.exists(plugin_path):
return 1
args = [version_flag]
arguments = []
for arg in args:
if arg != "":
arguments.append(arg)
p = Process()
p.start(plugin_path, arguments)
if not p.waitForFinished(
10000): # Wait for 10000 milliseconds = 10 seconds
return 1
output = 'Not vstring'
output = str(p.readAllStandardOutput())
#print "output=", output
#print "vstring=", vstring
if output.find(vstring) == -1:
return 1
else:
return 0 # Match found.
def verify_program(program, version_flag, vstring):
"""
Verifies a program by running it with the version_flag and matching the output to vstring.
Returns 0 if there is a match. Otherwise, returns 1
"""
if not program:
return 1
if not os.path.exists(program):
return 1
args = [version_flag]
from processes.Process import Process
arguments = []
for arg in args:
if arg != "":
arguments.append(arg)
print
print "arguments:", arguments
p = Process()
p.start(program, arguments)
if not p.waitForFinished (10000): # Wait for 10000 milliseconds = 10 seconds
return 1
output = 'Not vstring'
output = str(p.readAllStandardOutput())
#print "output=", output
#print "vstring=", vstring
if output.find(vstring) == -1:
return 1
else:
return 0 # Match found.
def runGNUplot(self, plotfile):
"""Sends plotfile to GNUplot.
"""
# Make sure plotfile exists
if not os.path.exists(plotfile):
msg = redmsg("Plotfile [" + plotfile + "] is missing. Plot aborted.")
env.history.message(cmd + msg)
return
# filePath = the current directory NE-1 is running from.
filePath = os.path.dirname(os.path.abspath(sys.argv[0]))
# "program" is the full path to the GNUplot executable.
if sys.platform == 'win32':
program = os.path.normpath(filePath + '/../bin/wgnuplot.exe')
else:
program = os.path.normpath('/usr/bin/gnuplot')
# Set environment variables to make gnuplot use a specific AquaTerm on
# Mac. Originally "Huaicai 3/18", fixed by Brian Helfrich May 23, 2007.
#
if sys.platform == 'darwin':
aquaPath = os.path.normpath(filePath + '/../bin/AquaTerm.app')
os.environ['AQUATERM_PATH'] = aquaPath
aquaPath = \
os.path.normpath(filePath + '/../Frameworks/AquaTerm.framework')
os.environ['DYLD_LIBRARY_PATH'] = aquaPath
# Note: I tried using:
# environment.append(QString('AQUATERM_PATH=%s' % aquaPath))
# environment.append(QString('DYLD_LIBRARY_PATH=%s' % aquaPath))
# followed by plotProcess.setEnvironment(environment), but it just
# wouldn't see the AquaTerm library. So, although the above is more
# heavy-handed than just changing the Process environment, at least
# it works.
# Make sure GNUplot executable exists
if not os.path.exists(program):
msg = redmsg("GNUplot executable [" + program + "] is missing. Plot aborted.")
env.history.message(cmd + msg)
return
plotProcess = None
try:
from processes.Process import Process
plotProcess = Process()
# Run gnuplot as a new, separate process.
started = plotProcess.startDetached(program, QStringList(plotfile))
###e It might also be good to pass gnuplot some arg to tell it to ignore ~/.gnuplot. [bruce 060425 guess]
if not started:
env.history.message(redmsg("gnuplot failed to run!"))
else:
env.history.message("Running gnuplot file: " + plotfile)
if debug_gnuplot:
try:
#bruce 060425 debug code; Qt assistant for QProcess says this won't work on Windows (try it there anyway).
pid = plotProcess.pid() # This should work on Windows in Qt 4.2 [mark 2007-05-03]
pid = int(pid) # this is what is predicted to fail on Windows
env.history.message("(debug: gnuplot is %r, its process id is %d)" % (program, pid))
except:
print_compact_traceback("debug: exception printing processIdentifier (might be normal on Windows): ")
pass
pass
except: # We had an exception.
print"exception in GNUplot; continuing: "
if plotProcess:
print ">>> %d" % plotProcess.error()
print "Killing process"
plotProcess.kill()
plotProcess = None
def runGNUplot(self, plotfile):
"""Sends plotfile to GNUplot.
"""
# Make sure plotfile exists
if not os.path.exists(plotfile):
msg = redmsg("Plotfile [" + plotfile + "] is missing. Plot aborted.")
env.history.message(cmd + msg)
return
# filePath = the current directory NE-1 is running from.
filePath = os.path.dirname(os.path.abspath(sys.argv[0]))
# "program" is the full path to the GNUplot executable.
if sys.platform == 'win32':
program = os.path.normpath(filePath + '/../bin/wgnuplot.exe')
else:
program = os.path.normpath(filePath + '/../bin/gnuplot')
# Set environment variables to make gnuplot use a specific AquaTerm on
# Mac. Originally "Huaicai 3/18", fixed by Brian Helfrich May 23, 2007.
#
if sys.platform == 'darwin':
aquaPath = os.path.normpath(filePath + '/../bin/AquaTerm.app')
os.environ['AQUATERM_PATH'] = aquaPath
aquaPath = \
os.path.normpath(filePath + '/../Frameworks/AquaTerm.framework')
os.environ['DYLD_LIBRARY_PATH'] = aquaPath
# Note: I tried using:
# environment.append(QString('AQUATERM_PATH=%s' % aquaPath))
# environment.append(QString('DYLD_LIBRARY_PATH=%s' % aquaPath))
# followed by plotProcess.setEnvironment(environment), but it just
# wouldn't see the AquaTerm library. So, although the above is more
# heavy-handed than just changing the Process environment, at least
# it works.
# Make sure GNUplot executable exists
if not os.path.exists(program):
msg = redmsg("GNUplot executable [" + program + "] is missing. Plot aborted.")
env.history.message(cmd + msg)
return
plotProcess = None
try:
from processes.Process import Process
plotProcess = Process()
# Run gnuplot as a new, separate process.
started = plotProcess.startDetached(program, QStringList(plotfile))
###e It might also be good to pass gnuplot some arg to tell it to ignore ~/.gnuplot. [bruce 060425 guess]
if not started:
env.history.message(redmsg("gnuplot failed to run!"))
else:
env.history.message("Running gnuplot file: " + plotfile)
if debug_gnuplot:
try:
#bruce 060425 debug code; Qt assistant for QProcess says this won't work on Windows (try it there anyway).
pid = plotProcess.pid() # This should work on Windows in Qt 4.2 [mark 2007-05-03]
pid = int(pid) # this is what is predicted to fail on Windows
env.history.message("(debug: gnuplot is %r, its process id is %d)" % (program, pid))
except:
print_compact_traceback("debug: exception printing processIdentifier (might be normal on Windows): ")
pass
pass
except: # We had an exception.
print"exception in GNUplot; continuing: "
if plotProcess:
print ">>> %d" % plotProcess.error()
print "Killing process"
plotProcess.kill()
plotProcess = None
def launch_qutemol(pdb_file):
"""
Launch and load QuteMolX with the PDB file I{pdb_file}.
@param pdb_file: the PDB filename to load
@type pdb_file: string
@return: (errorcode, errortext)
where errorcode is one of the following: ###k
0 = successful
8 = QuteMolX failed for an unknown reason.
@rtype: int, text
"""
plugin_name = "QuteMolX"
plugin_prefs_keys = (qutemol_enabled_prefs_key, qutemol_path_prefs_key)
errorcode, errortext_or_path = \
checkPluginPreferences(plugin_name, plugin_prefs_keys,
insure_executable = True)
if errorcode:
return errorcode, errortext_or_path
program_path = errortext_or_path
workdir, junk_exe = os.path.split(program_path)
# This provides a way to tell NE1 which version of QuteMolX is installed.
if debug_pref("QuteMol 0.4.1 or later",
Choice_boolean_True,
prefs_key = True):
version = "0.4.1"
else:
version = "0.4.0"
# Start QuteMolX.
try:
args = [pdb_file]
if env.debug():
print "Debug: Launching", plugin_name, \
"\n working directory=", workdir, \
"\n program_path=", program_path, \
"\n args are %r" % (args,)
arguments = QStringList()
for arg in args:
if arg != "":
arguments.append(arg)
p = Process()
# QuteMolX must run from the directory its executable lives. Otherwise,
# it has serious problems (but still runs). Mark 2007-06-02.
p.setWorkingDirectory(QString(workdir))
# Tried p.startDetached() so that QuteMolX would be its own process and
# continue to live even if NE1 exits. Unfortunately,
# setWorkingDirectory() doesn't work. Seems like a Qt bug to me.
# Mark 2007-06-02
p.start(program_path, arguments)
except:
print_compact_traceback( "exception in launch_qutemol(): " )
return 8, "%s failed for an unknown reason." % plugin_name
# set an appropriate exitcode and msg
if p.exitStatus() == QProcess.NormalExit:
exitcode = p.exitStatus()
if not exitcode:
msg = plugin_name + " launched."
else:
msg = plugin_name + " had exitcode %r" % exitcode
else:
exitcode = p.exitStatus()
exitcode = -1
msg = "Abnormal exit (or failure to launch)"
if exitcode:
return 8, "Error: " + msg
# this breaks the convention of the other error returns
return 0, plugin_name + " launched." # from launch_qutemol
def launch_povray_or_megapov(
win, info,
povray_ini): #bruce 060707/11 revised this extensively for Mac A8
"""
Try to launch POV-Ray or MegaPOV, as specified in <info> (as returned from decode_povray_prefs, assumed already checked),
on the given <povray_ini> file (which should already exist), and running in the directory of that file
(this is required, since it may contain relative pathnames).
<win> must be the main window object (used for .glpane.is_animating).
Returns (errorcode, errortext), where errorcode is one of the following: ###k
0 = successful
8 = POV-Ray or MegaPOV failed for an unknown reason.
"""
(program_nickname, program_path,
include_dir) = info #e rename this arg renderer_info?
exit = ''
program = program_path
if sys.platform == 'win32':
program = "\"" + program + "\"" # Double quotes needed by Windows. Mark 060602.
if program_nickname == 'POV-Ray':
exit = "/EXIT"
# Later we'll cd to the POV-Ray's INI file directory and use tmp_ini in the POV-Ray command-line.
# This helps us get around POV-Ray's I/O Restrictions. Mark 060529.
workdir, tmp_ini = os.path.split(povray_ini)
# Render scene.
try:
args = [tmp_ini]
if exit:
args += [exit]
if env.debug():
## use env.history.message(_graymsg(msg)) ?
print "debug: Launching %s: \n" % program_nickname,\
"working directory=",workdir,"\n program_path=", program_path, "\n args are %r" % (args,)
arguments = QStringList()
for arg in args:
if arg != "":
arguments.append(arg)
from processes.Process import Process
p = Process()
#bruce 060707: this doesn't take advantage of anything not in QProcess,
# unless it matters that it reads and discards stdout/stderr
# (eg so large output would not block -- unlikely that this matters).
# It doesn't echo stdout/stderr. See also blabout/blaberr in other files. Maybe fix this? ###@@@
p.setWorkingDirectory(workdir)
p.start(program, arguments)
# Put up hourglass cursor to indicate we are busy. Restore the cursor below. Mark 060621.
QApplication.setOverrideCursor(QCursor(Qt.WaitCursor))
win.glpane.is_animating = True # This disables selection [do you mean highlighting? #k] while rendering the image.
import time
msg = "Rendering image"
while p.state() == QProcess.Running:
# Display a message on the status bar that POV-Ray/MegaPOV is rendering.
# I'd much rather display a progressbar and stop button by monitoring the size of the output file.
# This would require the output file to be written in PPM or BMP format, but not PNG format, since
# I don't believe a PNG's final filesize can be predicted.
# Check out monitor_progress_by_file_growth() in runSim.py, which does this. [mark]
time.sleep(0.25)
env.history.statusbar_msg(msg)
env.call_qApp_processEvents()
if 1:
# Update the statusbar message while rendering.
if len(
msg
) > 40: #bruce changed 100 -> 40 in case of short statusbar
msg = "Rendering image"
else:
#msg = msg + "."
msg += "."
except:
#bruce 060707 moved print_compact_traceback earlier, and its import to toplevel (after Windows A8, before Linux/Mac A8)
print_compact_traceback("exception in launch_povray_or_megapov(): ")
QApplication.restoreOverrideCursor()
win.glpane.is_animating = False
return 8, "%s failed for an unknown reason." % program_nickname
#bruce 060707 moved the following outside the above try clause, and revised it (after Windows A8, before Linux/Mac A8)
QApplication.restoreOverrideCursor() # Restore the cursor. Mark 060621.
## env.history.statusbar_msg("Rendering finished!") # this is wrong if it was not a normal exit. [bruce 060707 removed it]
win.glpane.is_animating = False
if 1:
#bruce 060707 added this (after Windows A8, before Linux/Mac A8):
# set an appropriate exitcode and msg
if p.exitStatus() == QProcess.NormalExit:
exitcode = p.exitStatus()
if not exitcode:
msg = "Rendering finished!"
else:
msg = "Rendering program had exitcode %r" % exitcode
# e.g. 126 for Mac failure; same as shell exitcode, which says "cannot execute binary file";
# but /usr/bin/open helps, so we'll try that above (but not in this commit, which is just to
# improve error reporting). ###@@@
# [bruce 060707]
else:
exitcode = p.exitStatus()
exitcode = -1
msg = "Abnormal exit (or failure to launch)"
if exitcode or env.debug():
print msg
env.history.statusbar_msg(msg)
## if env.debug():
## env.history.message(_graymsg(msg)) # not needed, caller prints it
if exitcode:
return 8, "Error: " + msg # this breaks the convention of the other error returns
pass
# Display image in separate window here. [Actually I think this is done in the caller -- bruce 060707 comment]
return 0, "Rendering finished" # from launch_povray_or_megapov
def launch_qutemol(pdb_file):
"""
Launch and load QuteMolX with the PDB file I{pdb_file}.
@param pdb_file: the PDB filename to load
@type pdb_file: string
@return: (errorcode, errortext)
where errorcode is one of the following: ###k
0 = successful
8 = QuteMolX failed for an unknown reason.
@rtype: int, text
"""
plugin_name = "QuteMolX"
plugin_prefs_keys = (qutemol_enabled_prefs_key, qutemol_path_prefs_key)
errorcode, errortext_or_path = \
checkPluginPreferences(plugin_name, plugin_prefs_keys,
insure_executable = True)
if errorcode:
return errorcode, errortext_or_path
program_path = errortext_or_path
workdir, junk_exe = os.path.split(program_path)
# This provides a way to tell NE1 which version of QuteMolX is installed.
if debug_pref("QuteMol 0.4.1 or later",
Choice_boolean_True,
prefs_key=True):
version = "0.4.1"
else:
version = "0.4.0"
# Start QuteMolX.
try:
args = [pdb_file]
if env.debug():
print "Debug: Launching", plugin_name, \
"\n working directory=", workdir, \
"\n program_path=", program_path, \
"\n args are %r" % (args,)
arguments = QStringList()
for arg in args:
if arg != "":
arguments.append(arg)
p = Process()
# QuteMolX must run from the directory its executable lives. Otherwise,
# it has serious problems (but still runs). Mark 2007-06-02.
p.setWorkingDirectory(QString(workdir))
# Tried p.startDetached() so that QuteMolX would be its own process and
# continue to live even if NE1 exits. Unfortunately,
# setWorkingDirectory() doesn't work. Seems like a Qt bug to me.
# Mark 2007-06-02
p.start(program_path, arguments)
except:
print_compact_traceback("exception in launch_qutemol(): ")
return 8, "%s failed for an unknown reason." % plugin_name
# set an appropriate exitcode and msg
if p.exitStatus() == QProcess.NormalExit:
exitcode = p.exitStatus()
if not exitcode:
msg = plugin_name + " launched."
else:
msg = plugin_name + " had exitcode %r" % exitcode
else:
exitcode = p.exitStatus()
exitcode = -1
msg = "Abnormal exit (or failure to launch)"
if exitcode:
return 8, "Error: " + msg
# this breaks the convention of the other error returns
return 0, plugin_name + " launched." # from launch_qutemol
def launch_povray_or_megapov(win, info, povray_ini): #bruce 060707/11 revised this extensively for Mac A8
"""
Try to launch POV-Ray or MegaPOV, as specified in <info> (as returned from decode_povray_prefs, assumed already checked),
on the given <povray_ini> file (which should already exist), and running in the directory of that file
(this is required, since it may contain relative pathnames).
<win> must be the main window object (used for .glpane.is_animating).
Returns (errorcode, errortext), where errorcode is one of the following: ###k
0 = successful
8 = POV-Ray or MegaPOV failed for an unknown reason.
"""
(program_nickname, program_path, include_dir) = info #e rename this arg renderer_info?
exit = ''
program = program_path
if sys.platform == 'win32':
program = "\""+program+"\"" # Double quotes needed by Windows. Mark 060602.
if program_nickname == 'POV-Ray':
exit = "/EXIT"
# Later we'll cd to the POV-Ray's INI file directory and use tmp_ini in the POV-Ray command-line.
# This helps us get around POV-Ray's I/O Restrictions. Mark 060529.
workdir, tmp_ini = os.path.split(povray_ini)
# Render scene.
try:
args = [tmp_ini]
if exit:
args += [exit]
if env.debug():
## use env.history.message(_graymsg(msg)) ?
print "debug: Launching %s: \n" % program_nickname,\
"working directory=",workdir,"\n program_path=", program_path, "\n args are %r" % (args,)
arguments = QStringList()
for arg in args:
if arg != "":
arguments.append(arg)
from processes.Process import Process
p = Process()
#bruce 060707: this doesn't take advantage of anything not in QProcess,
# unless it matters that it reads and discards stdout/stderr
# (eg so large output would not block -- unlikely that this matters).
# It doesn't echo stdout/stderr. See also blabout/blaberr in other files. Maybe fix this? ###@@@
p.setWorkingDirectory(workdir)
p.start(program, arguments)
# Put up hourglass cursor to indicate we are busy. Restore the cursor below. Mark 060621.
QApplication.setOverrideCursor( QCursor(Qt.WaitCursor) )
win.glpane.is_animating = True # This disables selection [do you mean highlighting? #k] while rendering the image.
import time
msg = "Rendering image"
while p.state() == QProcess.Running:
# Display a message on the status bar that POV-Ray/MegaPOV is rendering.
# I'd much rather display a progressbar and stop button by monitoring the size of the output file.
# This would require the output file to be written in PPM or BMP format, but not PNG format, since
# I don't believe a PNG's final filesize can be predicted.
# Check out monitor_progress_by_file_growth() in runSim.py, which does this. [mark]
time.sleep(0.25)
env.history.statusbar_msg(msg)
env.call_qApp_processEvents()
if 1:
# Update the statusbar message while rendering.
if len(msg) > 40: #bruce changed 100 -> 40 in case of short statusbar
msg = "Rendering image"
else:
#msg = msg + "."
msg += "."
except:
#bruce 060707 moved print_compact_traceback earlier, and its import to toplevel (after Windows A8, before Linux/Mac A8)
print_compact_traceback( "exception in launch_povray_or_megapov(): " )
QApplication.restoreOverrideCursor()
win.glpane.is_animating = False
return 8, "%s failed for an unknown reason." % program_nickname
#bruce 060707 moved the following outside the above try clause, and revised it (after Windows A8, before Linux/Mac A8)
QApplication.restoreOverrideCursor() # Restore the cursor. Mark 060621.
## env.history.statusbar_msg("Rendering finished!") # this is wrong if it was not a normal exit. [bruce 060707 removed it]
win.glpane.is_animating = False
if 1:
#bruce 060707 added this (after Windows A8, before Linux/Mac A8):
# set an appropriate exitcode and msg
if p.exitStatus() == QProcess.NormalExit:
exitcode = p.exitStatus()
if not exitcode:
msg = "Rendering finished!"
else:
msg = "Rendering program had exitcode %r" % exitcode
# e.g. 126 for Mac failure; same as shell exitcode, which says "cannot execute binary file";
# but /usr/bin/open helps, so we'll try that above (but not in this commit, which is just to
# improve error reporting). ###@@@
# [bruce 060707]
else:
exitcode = p.exitStatus()
exitcode = -1
msg = "Abnormal exit (or failure to launch)"
if exitcode or env.debug():
print msg
env.history.statusbar_msg(msg)
## if env.debug():
## env.history.message(_graymsg(msg)) # not needed, caller prints it
if exitcode:
return 8, "Error: " + msg # this breaks the convention of the other error returns
pass
# Display image in separate window here. [Actually I think this is done in the caller -- bruce 060707 comment]
return 0, "Rendering finished" # from launch_povray_or_megapov
def run_rosetta(self, movie, args):
"""
Main method that executes the rosetta simulation
@param movie: simulation object
@type movie: L{Movie}
@param args: list of simulation arguments
@type args: list
@note: This method needs to be refactored very badly
"""
self._movie = movie
assert args >= 1
#we have set it up such that the first element in arg[0] is number of simulations
self.numSim = args[0][0]
#set the program path, database path and write the paths.txt in here
#we have set it up such that the third argument in args[0] always have
# the name of the protein we are running rosetta simulation for
#also we say that an error has occurred if we cannot write the resfile.
#not sure if this should be the case
self.errcode = self.set_options_errQ( args[0][2])
if self.errcode: # used to be a local var 'r'
return
#get the starting pdb structure for rosetta simulation
self.sim_input_file = self.sim_input_filename(args[0][2])
if self.sim_input_file is None:
return
#this marks the beginning of the simulation. Although technically we are yet
# to call QProcess, it seems like a good place to set the waitcursor to True
self.set_waitcursor(True)
progressBar = self.win.statusBar().progressBar
# Disable some QActions (menu items/toolbar buttons) while the sim is running.
self.win.disable_QActions_for_sim(True)
try:
self.simProcess = None
#sets up the argument list for running rosetta including the ones
#that were provided in the pop up dialog
backRubArgs = []
if len(args) == 3:
backRubArgs = args[2]
self.setup_sim_args(args[0][1], backRubArgs)
progressBar.setRange(0, 0)
progressBar.reset()
progressBar.show()
env.history.statusbar_msg("Running Rosetta on " + self.sim_input_file[0:len(self.sim_input_file) - 4])
#this is used to name all the files related to this simulation
#we make sure that the pdb id is there in the filename so that it is
#easy to identify for which protein chunk we are running the simulation
rosettaFullBaseFileName = self.tmp_file_prefix
rosettaFullBaseFileInfo = QFileInfo(rosettaFullBaseFileName)
rosettaWorkingDir = rosettaFullBaseFileInfo.dir().absolutePath()
rosettaBaseFileName = rosettaFullBaseFileInfo.fileName()
rosettaProcess = Process()
rosettaProcess.setProcessName("rosetta")
rosettaProcess.redirect_stdout_to_file("%s-rosetta-stdout.txt" %
rosettaFullBaseFileName)
rosettaProcess.redirect_stderr_to_file("%s-rosetta-stderr.txt" %
rosettaFullBaseFileName)
rosettaStdOut = rosettaFullBaseFileName + "-rosetta-stdout.txt"
#rosetta files are all put in RosettaDesignFiles under Nanorex
rosettaProcess.setWorkingDirectory(rosettaWorkingDir)
environmentVariables = rosettaProcess.environment()
rosettaProcess.setEnvironment(environmentVariables)
msg = greenmsg("Starting Rosetta sequence design")
env.history.message(self.cmdname + ": " + msg)
env.history.message("%s: Rosetta files at %s%s%s.*" %
(self.cmdname, rosettaWorkingDir, os.sep,
rosettaFullBaseFileInfo.completeBaseName()))
abortHandler = AbortHandler(self.win.statusBar(), "rosetta")
#main rosetta simulation call
errorCode = rosettaProcess.run(self.program, self._arguments, False, abortHandler)
abortHandler = None
if (errorCode != 0):
if errorCode == -2: # User pressed Abort button in progress dialog.
msg = redmsg("Aborted.")
env.history.message(self.cmdname + ": " + msg)
env.history.statusbar_msg("")
if self.simProcess:
self.simProcess.kill()
else:
#the stdout will tell the user for what other reason,
#the simulation may fail
msg = redmsg("Rosetta sequence design failed. For details check" + rosettaStdOut)
env.history.message(self.cmdname + ": " + msg)
self.errcode = 2;
env.history.statusbar_msg("")
else:
#Error code is not zero but there's in reality error in stdout
#check if that be the case
env.history.statusbar_msg("")
errorInStdOut = self.checkErrorInStdOut(rosettaStdOut)
if errorInStdOut:
msg = redmsg("Rosetta sequence design failed, Rosetta returned %d" % errorCode)
env.history.message(self.cmdname + "," + self.cmd_type + ": " + msg)
env.history.statusbar_msg("")
else:
#bug in rosetta: often for some reason or the other rosetta
#run does not produce an o/p file. One instance is that if
# you already have an output file for this starting structure
#already in the directory rosetta refuses to optimize the
#structue again even if your residue file has changed
#since we remove all related output files before any run on
#the same protein, this is not a possible source of error
#in our case but there can be other similar problems
#Hence we always check the desired output file actually exists
#in the RosettaDesignFiles directory before we actually declare
#that it has been a successful run
if self.cmd_type == "ROSETTA_FIXED_BACKBONE_SEQUENCE_DESIGN":
outputFile = self.outfile + '_0001.pdb'
outPath = os.path.join(os.path.dirname(self.tmp_file_prefix), outputFile)
if os.path.exists(outPath):
#if there's the o/p pdb file, then rosetta design "really"
#succeeded
msg = greenmsg("Rosetta sequence design succeeded")
env.history.message(self.cmdname + "> " + self.cmd_type + ": " + msg)
#find out best score from all the generated outputs
#may be we will do it some day, but for now we only output
#the chunk with the lowest energy (Score)
score, bestSimOutFileName = getScoreFromOutputFile(self.tmp_file_prefix, self.outfile, self.numSim)
chosenOutPath = os.path.join(os.path.dirname(self.tmp_file_prefix), bestSimOutFileName)
insertpdb(self.assy, str(chosenOutPath), None)
#set the secondary structure of the rosetta output protein
#to that of the inpput protein
outProtein = self._set_secondary_structure_of_rosetta_output_protein(bestSimOutFileName)
#update the protein combo box in build protein mode with
#newly created protein chunk
self._updateProteinComboBoxInBuildProteinMode(outProtein)
env.history.statusbar_msg("")
fastaFile = self.outfile + "_design.fasta"
fastaFilePath = os.path.join(os.path.dirname(self.tmp_file_prefix), fastaFile)
#process th fasta file to find the sequence of the protein
#with lowest score
proteinSeqList = processFastaFile(fastaFilePath, bestSimOutFileName, self.sim_input_file[0:len(self.sim_input_file)-4])
#show a pop up dialog to show the best score and most
#optimized sequence
if score is not None and proteinSeqList is not []:
self.showResults(score, proteinSeqList)
else:
#even when there's nothing in stderr or errocode is zero,
#rosetta may not output anything.
msg1 = redmsg("Rosetta sequence design failed. ")
msg2 = redmsg(" %s file was never created by Rosetta." % outputFile)
msg = msg1 + msg2
env.history.message(self.cmdname + ": " + msg)
env.history.statusbar_msg("")
if self.cmd_type == "BACKRUB_PROTEIN_SEQUENCE_DESIGN":
#its important to set thi pref key to False so that if the
#subsequent rosetta run is with fixed backbone then the
#resfile is correctly written
from utilities.prefs_constants import rosetta_backrub_enabled_prefs_key
env.prefs[rosetta_backrub_enabled_prefs_key] = False
#Urmi 20080807: first copy the backrub_low.pdb to a new pdb
#file with the pdb info also added there
outProteinName, outPath = createUniquePDBOutput(self.tmp_file_prefix, self.sim_input_file[0:len(self.sim_input_file)-4], self.win)
if outProteinName is None:
msg1 = redmsg("Rosetta sequence design with backrub motion has failed. ")
msg2 = redmsg(" backrub_low.pdb was never created by Rosetta.")
msg = msg1 + msg2
env.history.message(self.cmdname + "," + self.cmd_type + ": " + msg)
env.history.statusbar_msg("")
else:
env.history.statusbar_msg("")
msg = greenmsg("Rosetta sequence design with backrub motion allowed, succeeded")
env.history.message(self.cmdname + "> " + self.cmd_type + ": " + msg)
insertpdb(self.assy, str(outPath), None)
outProtein = self._set_secondary_structure_of_rosetta_output_protein(outProteinName + ".pdb")
self._updateProteinComboBoxInBuildProteinMode(outProtein)
inProteinName = self.sim_input_file[0:len(self.sim_input_file)-4]
proteinSeqList = getProteinNameAndSeq(inProteinName, outProteinName, self.win)
score = getScoreFromBackrubOutFile(outPath)
if score is not None and proteinSeqList is not []:
self.showResults(score, proteinSeqList)
if self.cmd_type == "ROSETTA_SCORE":
msg = greenmsg("Rosetta scoring has succeeded")
env.history.message(self.cmdname + "> " + self.cmd_type + ": " + msg)
showRosettaScore(self.tmp_file_prefix, self.scorefile, self.win)
except:
print_compact_traceback("bug in simulator-calling code: ")
self.errcode = -11111
self.set_waitcursor(False)
self.win.disable_QActions_for_sim(False)
env.history.statusbar_msg("")
if not self.errcode:
return # success
return # caller should look at self.errcode
def run_using_old_movie_obj_to_hold_sim_params(self, movie, args):
self._movie = movie
assert args >= 1
#for now args has number of simulations
self.numSim = args[0][0]
#set the program path, database path and write the paths.txt in here
self.errcode = self.set_options_errQ( )
if self.errcode: # used to be a local var 'r'
return
self.sim_input_file = self.sim_input_filename(self.part)
if self.sim_input_file is None:
return
self.set_waitcursor(True)
progressBar = self.win.statusBar().progressBar
# Disable some QActions (menu items/toolbar buttons) while the sim is running.
self.win.disable_QActions_for_sim(True)
try: #bruce 050325 added this try/except wrapper, to always restore cursor
self.simProcess = None #bruce 051231
self.setup_sim_args(args)
progressBar.setRange(0, 0)
progressBar.reset()
progressBar.show()
env.history.statusbar_msg("Running Rosetta")
rosettaFullBaseFileName = self.tmp_file_prefix
rosettaFullBaseFileInfo = QFileInfo(rosettaFullBaseFileName)
rosettaWorkingDir = rosettaFullBaseFileInfo.dir().absolutePath()
rosettaBaseFileName = rosettaFullBaseFileInfo.fileName()
rosettaProcess = Process()
rosettaProcess.setProcessName("rosetta")
rosettaProcess.redirect_stdout_to_file("%s-rosetta-stdout.txt" %
rosettaFullBaseFileName)
rosettaProcess.redirect_stderr_to_file("%s-rosetta-stderr.txt" %
rosettaFullBaseFileName)
rosettaStdOut = rosettaFullBaseFileName + "-rosetta-stdout.txt"
rosettaProcess.setWorkingDirectory(rosettaWorkingDir)
environmentVariables = rosettaProcess.environment()
rosettaProcess.setEnvironment(environmentVariables)
msg = greenmsg("Starting Rosetta sequence design")
env.history.message(self.cmdname + ": " + msg)
env.history.message("%s: Rosetta files at %s%s%s.*" %
(self.cmdname, rosettaWorkingDir, os.sep,
rosettaFullBaseFileInfo.completeBaseName()))
abortHandler = AbortHandler(self.win.statusBar(), "rosetta")
errorCode = rosettaProcess.run(self.program, self._arguments, False, abortHandler)
abortHandler = None
if (errorCode != 0):
if errorCode == -2: # User pressed Abort button in progress dialog.
msg = redmsg("Aborted.")
env.history.message(self.cmdname + ": " + msg)
env.history.statusbar_msg("")
if self.simProcess: #bruce 051231 added condition (since won't be there when use_dylib)
self.simProcess.kill()
else:
msg = redmsg("Rosetta sequence design failed. For details check" + rosettaStdOut)
env.history.message(self.cmdname + ": " + msg)
self.errcode = 2;
env.history.statusbar_msg("")
else:
#run has been successful
#open pdb file
env.history.statusbar_msg("")
errorInStdOut = self.checkErrorInStdOut(rosettaStdOut)
if errorInStdOut:
msg = redmsg("Rosetta sequence design failed, Rosetta returned %d" % errorCode)
env.history.message(self.cmdname + ": " + msg)
env.history.statusbar_msg("")
else:
#env.history.message(self.cmdname + ": " + msg)
outputFile = self.outfile + '_0001.pdb'
outPath = os.path.join(os.path.dirname(self.tmp_file_prefix), outputFile)
if os.path.exists(outPath):
msg = greenmsg("Rosetta sequence design succeeded")
env.history.message(self.cmdname + ": " + msg)
#find out best score from all the generated outputs
score, bestSimOutFileName = getScoreFromOutputFile(self.tmp_file_prefix, self.outfile, self.numSim)
chosenOutPath = os.path.join(os.path.dirname(self.tmp_file_prefix), bestSimOutFileName)
insertpdb(self.assy, str(chosenOutPath), None)
env.history.statusbar_msg("")
fastaFile = self.outfile + "_design.fasta"
fastaFilePath = os.path.join(os.path.dirname(self.tmp_file_prefix), fastaFile)
proteinSeqList = processFastaFile(fastaFilePath, bestSimOutFileName, self.sim_input_file[0:len(self.sim_input_file)-4])
#score = getScoreFromOutputFile(outPath)
if score is not None and proteinSeqList is not []:
self.showResults(score, proteinSeqList)
else:
msg1 = redmsg("Rosetta sequence design failed. ")
msg2 = redmsg(" %s file was never created by Rosetta." % outputFile)
msg = msg1 + msg2
env.history.message(self.cmdname + ": " + msg)
env.history.statusbar_msg("")
except:
print_compact_traceback("bug in simulator-calling code: ")
self.errcode = -11111
self.set_waitcursor(False)
self.win.disable_QActions_for_sim(False)
env.history.statusbar_msg("")
if not self.errcode:
return # success
return # caller should look at self.errcode
