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