class BuildPopulationMEAMT(object):
"""
Execute the MEAMT Build Population algorithm.
"""
sequence = None
path_execute = None
os.environ["GMX_MAXBACKUP"] = "-1"
def __init__(self, opts=None):
"""
@type self: koala.BuildPopulationMEAMT.BuildPopulationMEAMT
@type opts: OptionParser parameters
"""
assert opts is not None
self.opts = opts
self.time_execution = TimeJobExecution()
self.path_runs = PathRuns()
self.framework = Params('MEAMT')
def main(self):
"""
Create the MEAMT Build Population configuration file and begin
the execution to create a initial population.
@type self: koala.BuildPopulationMEAMT.BuildPopulationMEAMT
"""
try:
self.path_runs.set_path_execute()
self.path_runs.set_execution_directory()
print 'create dirs'
self.sequence = create_local_fasta_file(
self.path_runs.get_path_execution(),
self.opts.fromFasta,
self.opts.inputFasta,
self.opts.toolname,
self.framework)
print 'create fasta'
copy_necessary_files(
self.path_runs.get_path_execute(),
self.path_runs.get_path_execution(),
self.framework.get_framework())
print 'copy files'
self.framework.set_command(
self.path_runs.get_path_execution(),
'aemt-pop-up2')
print 'set command'
size = int(self.opts.sizePopulation) / 15
cl = [
self.framework.get_command(),
str(0),
self.opts.sizePopulation,
str(size),
str(size),
str(size),
str(size),
str(size),
str(size),
str(size),
str(size),
str(size),
str(size),
str(size),
str(size),
str(size),
str(size),
str(size),
str(size),
str(0),
str(0),
self.opts.VanderWaalsWeight,
self.opts.ChargeWeight,
str(0),
str(0),
str(0),
str(0),
str(0),
self.opts.SolvWeight,
self.opts.HbondWeight,
os.path.join(self.path_runs.get_path_execution(), "fasta.txt"),
os.path.join(self.path_runs.get_path_execution(), "result.txt"),
os.path.join(self.path_runs.get_path_execution(), "pop_meamt.txt"),
os.path.join(self.path_runs.get_path_execution(), "protein.pdb"),
os.path.join(self.path_runs.get_path_execution(), "saida1.txt"),
os.path.join(self.path_runs.get_path_execution(), "angles.txt"),
str(0),
os.path.join(self.path_runs.get_path_execution(), "meat.txt"),
'&']
print cl
retProcess = subprocess.Popen(cl, 0, None, None, None, False)
retProcess.wait()
path_output, file_output = os.path.split(self.opts.output)
result, html = get_result_files(
self.path_runs.get_path_execution(), self.opts.toolname)
send_output_results(path_output, file_output, result)
except Exception, e:
show_error_message(str(e))
class BuildConformation2PG(object):
"""
Execute the 2PG Build Conformation algorithm.
"""
os.environ["GMX_MAXBACKUP"] = "-1"
def __init__(self, opts=None):
"""
@type self: koala.BuildConformation2PG.BuildConformation2PG
@type opts: OptionParser parameters
"""
assert opts is not None
self.opts = opts
self.path_runs = PathRuns()
self.framework = Params("2PG")
def run_Build_Conformation(self):
"""
Create the 2PG Build Conformation configuration file and begin
the execution to create a initial population.
@type self: koala.BuildConformation2PG.BuildConformation2PG
"""
try:
self.path_runs.set_path_execute()
self.path_runs.set_execution_directory()
self.sequence = create_local_fasta_file(
self.path_runs.get_path_execution(),
self.opts.fromFasta,
self.opts.inputFasta,
self.opts.toolname,
self.framework,
)
copy_necessary_files(
self.path_runs.get_path_execute(), self.path_runs.get_path_execution(), self.framework.get_framework()
)
self.framework.set_parameter("gromacs_energy_min", self.opts.gromacsEnergyMin)
self.framework.set_parameter("SizePopulation", self.opts.sizePopulation)
self.framework.set_parameter("force_field", self.opts.forceField)
self.framework.set_parameter("rotamer_library", self.opts.rotamerLibrary)
if self.opts.forceField == "amber99sb-ildn":
self.framework.set_parameter("c_terminal_charge", self.opts.cTerminal)
self.framework.set_parameter("n_terminal_charge", self.opts.nTerminal)
self.framework.set_parameter(
"SequenceAminoAcidsPathFileName", self.path_runs.get_path_execution() + "fasta.txt"
)
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.framework.set_parameter("Database", "%sDatabase/" % get_path_algorithms("2pg_build_conformation"))
create_configuration_file(self.path_runs.get_path_execution(), self.framework)
self.framework.set_command(self.path_runs.get_path_execution(), "protpred-Gromacs_pop_initial")
config = "configuration.conf"
cl = [self.framework.get_command(), config, "&"]
retProcess = subprocess.Popen(cl, 0, stdout=None, stderr=subprocess.STDOUT, shell=False)
retCode = retProcess.wait()
if retCode != 0:
show_error_message("The 2PG framework finished wrong.\nContact the system administrator.")
path_output, file_output = os.path.split(self.opts.output)
result, html = get_result_files(self.path_runs.get_path_execution(), self.opts.toolname)
send_output_results(path_output, file_output, result)
except Exception, e:
show_error_message(str(e))
