def run_SortByFront(self):
"""
Run the 2PG Sort algorithm to calculate the Pareto fronts and sorting
@type self: koala.SortByFront.SortByFront
"""
self.path_runs.set_path_execute()
self.path_runs.set_execution_directory()
copy_necessary_files(
self.path_runs.get_path_execute(),
self.path_runs.get_path_execution(),
self.framework.get_framework())
self.framework.set_parameter(
'objective_analisys_dimo_source',
'/home/%s/programs/dimo/DIMO2' % get_logged_user())
self.framework.set_parameter('Local_Execute', self.path_runs.get_path_execution())
self.framework.set_parameter(
'Path_Gromacs_Programs',
get_path_gromacs())
self.framework.set_parameter(
'NativeProtein',
'%s1VII.pdb' % self.path_runs.get_path_execution())
NumberObjective, Fitness_Energy = format_fitness(self.opts.inputFitness)
self.framework.set_parameter('NumberObjective', NumberObjective)
self.framework.set_parameter('Fitness_Energy', Fitness_Energy)
create_configuration_file(
self.path_runs.get_path_execution(), self.framework)
config = 'configuration.conf'
if self.opts.compressedFile == '1':
inputFiles = self.opts.inputPDBs.split(",")
for input_f in inputFiles:
if zipfile.is_zipfile(input_f):
extract_zip_file(input_f, self.path_runs.get_path_execution())
else:
try:
inF = gzip.GzipFile(input_f, 'rb')
f = inF.read()
inF.close()
if f:
extract_gz_file(input_f, self.path_runs.get_path_execution())
except Exception, e:
raise Exception("The input file could not be read.\n%s" % e)
def run_SortByFront(self):
"""
Run the 2PG Sort Method algorithm to calculate the Pareto fronts and sorting
@type self: koala.SortByFront.SortByFront
"""
self.path_runs.set_path_execute()
self.path_runs.set_execution_directory()
copy_necessary_files(
self.path_runs.get_path_execute(),
self.path_runs.get_path_execution(),
self.framework.get_framework())
self.framework.set_parameter(
'objective_analisys_dimo_source',
'/home/%s/programs/dimo/DIMO2' % get_logged_user())
self.framework.set_parameter('Local_Execute', self.path_runs.get_path_execution())
self.framework.set_parameter(
'Path_Gromacs_Programs',
get_path_gromacs())
self.framework.set_parameter(
'NativeProtein',
'%s1VII.pdb' % self.path_runs.get_path_execution())
create_configuration_file(
self.path_runs.get_path_execution(), self.framework)
self.loadMatrixFile(self.opts.inputTxt)
objFile = os.path.join(self.path_runs.get_path_execution(), 'objectivies.txt')
self.framework.set_command(
self.path_runs.get_path_execution(),
'protpred-Gromacs-Sort_Method_by_Front_Dominance')
cl = ['nohup', self.framework.get_command(), objFile, '&']
retProcess = subprocess.Popen(cl, 0, None, None, None, False)
retProcess.wait()
self.getBetterPDBs(self.path_runs.get_path_execution())
result, filesHtml = get_result_files(
self.path_runs.get_path_execution(),
self.opts.toolname)
send_output_files_html(self.opts.htmlfiledir, filesHtml)
send_output_files_html(self.opts.htmlfiledir, [result])
self.makeHtml()
def build_rankingDominance(self):
"""
Create the 2PG Sort configuration file and build the dominance
@type self: koala.DominanceRanking.DominanceRanking
"""
self.path_runs.set_path_execute()
self.path_runs.set_execution_directory()
copy_necessary_files(
self.path_runs.get_path_execute(),
self.path_runs.get_path_execution(),
self.framework.get_framework())
self.framework.set_parameter(
'objective_analisys_dimo_source',
'/home/%s/programs/dimo/DIMO2' % get_logged_user())
self.framework.set_parameter('Local_Execute', self.path_runs.get_path_execution())
self.framework.set_parameter('Path_Gromacs_Programs', get_path_gromacs())
self.framework.set_parameter(
'NativeProtein', '%s1VII.pdb' % self.path_runs.get_path_execution())
self.combinations = format_fitness(self.opts.inputFitness, self.opts.toolname)
if self.opts.compressedFile == '1':
inputFiles = self.opts.inputPDBs.split(",")
for input_f in inputFiles:
if zipfile.is_zipfile(input_f):
extract_zip_file(input_f, self.path_runs.get_path_execution())
else:
try:
inF = gzip.GzipFile(input_f, 'rb')
f = inF.read()
inF.close()
if f:
extract_gz_file(input_f, self.path_runs.get_path_execution())
except Exception, e:
raise Exception("The input file could not be read.\n%s" % e)
def get_path_algorithms(framework):
try:
return "/home/%s/programs/%s/" % (get_logged_user(), framework)
except Exception, e:
show_error_message("Error when getPathAlgorithms\n%s" % e)
def set_path_execute(self):
try:
self.path_execute = "/home/%s/execute/" % get_logged_user()
# self.path_execute = "/dados/%s/execute/" % get_logged_user()
except Exception, e:
show_error_message("Error when getPathExecute\n%s" % e)
def get_path_gromacs():
pathGromacs = "/home/%s/programs/gmx-4.6.5/no_mpi/bin/" % get_logged_user()
return pathGromacs
