def run_RenameAtoms(self):
"""
Get the PDB file and run the renaming
@type self: koala.CheckPDBStructure.CheckPDBStructure
"""
try:
self.path_runs.set_path_execute()
self.path_runs.set_execution_directory()
self.opts.pdbName = self.opts.pdbName.replace(" ", "-").replace("(", "").replace(")", "")
link_name = os.path.join(self.opts.outputdir, os.path.basename(self.opts.pdbName))
if not os.path.exists(link_name):
os.symlink(self.opts.inputPDB, link_name)
os.system("cp %s %s" % (link_name, self.path_runs.get_path_execution()))
self.rename_atoms_structure(
os.path.join(self.path_runs.get_path_execution(), self.opts.pdbName),
get_path_gromacs(),
self.opts.forceField,
)
path_output, file_output = os.path.split(self.opts.output)
send_output_results(
path_output, file_output, os.path.join(self.path_runs.get_path_execution(), self.opts.pdbName)
)
except Exception, e:
show_error_message(str(e))
def run_SplitPDB(self):
"""
Get the PDB input files and run the splitting
@type self: koala.SplitPDB.SplitPDB
"""
try:
self.path_runs.set_path_execute()
self.path_runs.set_execution_directory()
link_name = os.path.join(self.opts.outputdir, os.path.basename(self.opts.pdbName))
if not os.path.exists(link_name):
os.symlink(self.opts.inputPDB, link_name)
os.system("cp %s %s" % (link_name, self.path_runs.get_path_execution()))
pdbs = parse_pdb(
self.path_runs.get_path_execution(),
os.path.join(self.path_runs.get_path_execution(), self.opts.pdbName))
path_output, file_output = os.path.split(self.opts.output)
send_multiple_outputs(
self.path_runs.get_path_execution(),
pdbs, self.opts.galaxydir,
self.opts.outputID)
if self.opts.createCompressFile == "True":
if compress_files(pdbs, self.path_runs.get_path_execution(), self.opts.toolname):
path_output, file_output = os.path.split(self.opts.outputZip)
send_output_results(
path_output,
file_output,
os.path.join(
self.path_runs.get_path_execution(), '%s.zip' % self.opts.toolname))
except Exception, e:
show_error_message(str(e))
def run_Random(self):
"""
Create the 2PG Random configuration file and begin the execution.
@type self: koala.Random2PG.Random2PG
"""
try:
self.path_runs.set_path_execute()
if self.opts.inputEmail:
email = validate_email(self.opts.inputEmail)
self.path_runs.set_execution_directory(email)
else:
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)
SizePopulation = create_local_pop_file(
self.path_runs.get_path_execution(),
self.opts.inputPop,
self.framework)
if SizePopulation > 1:
show_error_message(
"Error: The population file must contain only one model")
copy_necessary_files(
self.path_runs.get_path_execute(),
self.path_runs.get_path_execution(),
self.framework.get_framework())
self.framework.set_parameter(
'rotamer_library', self.opts.rotamerLibrary)
self.framework.set_parameter(
'StepNumber', self.opts.stepNumber)
self.framework.set_parameter(
'How_Many_Rotation', self.opts.howManyRotation)
self.framework.set_parameter(
'force_field', self.opts.forceField)
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',
'%s/Database/' %
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-Random_Algorithm')
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.")
parse_pdb(
self.path_runs.get_path_execution(),
'random_algorithm_solutions.pdb',
20,
'randomSolution')
if(self.opts.runMinimization == 'true'):
self.do_minimization("randomSolution")
pdbs = list_directory(
self.path_runs.get_path_execution(), 'randomSolution-M*.pdb')
build_images(pdbs, self.path_runs.get_path_execution())
path_output, file_output = os.path.split(self.opts.filehtml)
name, ext = os.path.splitext(self.opts.filehtml)
htmldir = os.path.join(path_output, '%s_files' % name)
if not os.path.exists(htmldir):
os.makedirs(htmldir)
self.opts.htmlfiledir = htmldir
result, filesHtml = get_result_files(
self.path_runs.get_path_execution(),
self.opts.toolname,
'randomSolution-M')
send_output_files_html(self.opts.htmlfiledir, filesHtml)
send_output_files_html(self.opts.htmlfiledir, [result])
if self.opts.createCompressFile == "True":
if compress_files(pdbs, self.path_runs.get_path_execution(), "2PGRandom"):
path_output, file_output = os.path.split(self.opts.outputZip)
send_output_results(
path_output,
file_output,
os.path.join(self.path_runs.get_path_execution(), '2PGRandom.zip'))
self.makeHtml()
if(self.opts.useJmol in ('True', 'true')):
self.makeHtmlWithJMol(pdbs[0])
if(self.opts.inputEmail):
send_email(
'*****@*****.**',
email,
'%s Execution on Galaxy - Cloud USP' % self.opts.toolname,
get_message_email(self.opts.toolname),
[],
'smtp.gmail.com')
except Exception, e:
show_error_message(str(e))
def main(self):
"""
Create the ProtPred-EDA configuration file and begin the execution.
@type self: koala.ProtPredEDA.ProtPredEDA
"""
try:
self.path_runs.set_path_execute()
if self.opts.inputEmail:
email = validate_email(self.opts.inputEmail)
self.path_runs.set_execution_directory(email)
else:
self.path_runs.set_execution_directory()
self.sequence = create_local_fasta_file(
self.path_runs.get_path_execution(),
self.opts.fromFasta,
self.opts.SequenceFile,
self.opts.toolname,
self.framework)
copy_necessary_files(
self.path_runs.get_path_execute(),
self.path_runs.get_path_execution(),
self.framework.get_framework())
# Config
self.framework.set_parameter('OptimMethod', 'rboa')
self.framework.set_parameter('MaxEval', self.opts.MaxEval)
self.framework.set_parameter('Threshold', self.opts.Threshold)
# FitnessPSP
self.framework.set_parameter('VanderWaals', self.opts.VanderWaals)
# ClassColection.setParameter('SASA', self.opts.SASA)
self.framework.set_parameter('Coulomb', self.opts.Coulomb)
self.framework.set_parameter('Solvatation', self.opts.Solvatation)
self.framework.set_parameter('HydrogenBond', self.opts.HydrogenBond)
self.framework.set_parameter('Torsion', self.opts.Torsion)
self.framework.set_parameter('UseAngleDB', self.opts.UseAngleDB)
self.framework.set_parameter('AminoAcidL', self.opts.AminoAcidL)
# rboa
self.framework.set_parameter('PopSize', self.opts.PopSize)
self.framework.set_parameter('SelSize', self.opts.SelSize)
self.framework.set_parameter('MaxParents', self.opts.MaxParents)
self.framework.set_parameter('MixtureComponents', self.opts.MixtureComponents)
create_configuration_file(
self.path_runs.get_path_execution(), self.framework)
self.framework.set_command(
self.path_runs.get_path_execution(),
'protpred')
config = 'input.ini'
cl = [self.framework.get_command(), config, '&']
retProcess = subprocess.Popen(
cl, 0, stdout=None, stderr=None, shell=False)
retCode = retProcess.wait()
if(retCode != 0):
show_error_message(
"The ProtPred-EDA framework finished wrong.\nContact the system administrator.")
copy_files_to_execute_folder(
self.path_runs.get_path_execution(),
'ProtPredEDA_rBOA')
if(self.opts.runMinimization == 'true'):
self.do_minimization("ProtPredEDA_rBOA")
pdbs = sorted(list_directory(self.path_runs.get_path_execution(), '*.pdb'))
build_images(pdbs, self.path_runs.get_path_execution())
path_output, file_output = os.path.split(self.opts.filehtml)
name, ext = os.path.splitext(self.opts.filehtml)
htmldir = os.path.join(path_output, '%s_files' % name)
if not os.path.exists(htmldir):
os.makedirs(htmldir)
self.opts.htmlfiledir = htmldir
result, filesHtml = get_result_files(
self.path_runs.get_path_execution(),
self.opts.toolname)
send_output_results(path_output, file_output, result)
send_output_files_html(self.opts.htmlfiledir, filesHtml)
send_output_files_html(self.opts.htmlfiledir, [result])
if self.opts.createCompressFile == "True":
if compress_files(pdbs, self.path_runs.get_path_execution(), "ProtPredEDA-rBOA"):
path_output, file_output = os.path.split(self.opts.outputZip)
send_output_results(
path_output,
file_output,
os.path.join(
self.path_runs.get_path_execution(), 'ProtPredEDA-rBOA.zip'))
self.makeHtml()
if(self.opts.useJmol in ('True', 'true')):
self.makeHtmlWithJMol(pdbs[0])
if(self.opts.inputEmail):
send_email(
'*****@*****.**',
email,
'%s Execution on Galaxy - Cloud USP' % self.opts.toolname,
get_message_email(self.opts.toolname),
[],
'smtp.gmail.com')
except Exception, e:
show_error_message(str(e))
def run_NSGAII(self):
"""
Create the 2PG NSGA-II configuration file and begin the execution.
@type self: koala.NSGAII2PG.NSGAII2PG
"""
try:
self.path_runs.set_path_execute()
if self.opts.inputEmail:
email = validate_email(self.opts.inputEmail)
self.path_runs.set_execution_directory(email)
else:
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,
)
SizePopulation = create_local_pop_file(
self.path_runs.get_path_execution(), self.opts.inputPop, 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("NumberGeration", self.opts.numberGeration)
self.framework.set_parameter("SizePopulation", SizePopulation)
self.framework.set_parameter(
"SequenceAminoAcidsPathFileName", self.path_runs.get_path_execution() + "fasta.txt"
)
self.framework.set_parameter("How_Many_Rotation", self.opts.howManyRotation)
self.framework.set_parameter("rotamer_library", self.opts.rotamerLibrary)
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"))
NumberObjective, Fitness_Energy = format_fitness(self.opts.inputFitness, self.opts.toolname)
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)
self.framework.set_command(self.path_runs.get_path_execution(), "protpred-Gromacs-NSGA2")
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.")
parse_pdb(
self.path_runs.get_path_execution(),
"pop_NON_DOMINATED_%s.pdb" % self.opts.numberGeration,
20,
"NSGAIISolutions",
)
if self.opts.runMinimization == "true":
self.do_minimization("NSGAIISolutions")
pdbs = list_directory(self.path_runs.get_path_execution(), "NSGAIISolutions-M*.pdb")
build_images(pdbs, self.path_runs.get_path_execution())
path_output, file_output = os.path.split(self.opts.filehtml)
name, ext = os.path.splitext(self.opts.filehtml)
htmldir = os.path.join(path_output, "%s_files" % name)
if not os.path.exists(htmldir):
os.makedirs(htmldir)
self.opts.htmlfiledir = htmldir
result, filesHtml = get_result_files(
self.path_runs.get_path_execution(), self.opts.toolname, "NSGAIISolutions-M"
)
send_output_results(path_output, file_output, result)
send_output_files_html(self.opts.htmlfiledir, filesHtml)
send_output_files_html(self.opts.htmlfiledir, [result])
if self.opts.createCompressFile == "True":
if compress_files(pdbs, self.path_runs.get_path_execution(), "2PGNSGAII"):
path_output, file_output = os.path.split(self.opts.outputZip)
send_output_results(
path_output, file_output, os.path.join(self.path_runs.get_path_execution(), "2PGNSGAII.zip")
)
self.makeHtml()
if self.opts.useJmol in ("True", "true"):
self.makeHtmlWithJMol(pdbs[0])
if self.opts.inputEmail:
send_email(
"*****@*****.**",
email,
"%s Execution on Galaxy - Cloud USP" % self.opts.toolname,
get_message_email(self.opts.toolname),
[],
"smtp.gmail.com",
)
except Exception, e:
show_error_message(str(e))
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))
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))
def main(self):
"""
Create the MEAMT configuration file and begin
the execution to create a initial population.
@type self: koala.MEAMT.MEAMT
"""
try:
self.path_runs.set_path_execute()
if(self.opts.inputEmail):
email = validate_email(self.opts.inputEmail)
self.path_runs.set_execution_directory(email)
else:
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)
SizePopulation = create_local_pop_file(
self.path_runs.get_path_execution(),
self.opts.inputPop,
self.framework)
copy_necessary_files(
self.path_runs.get_path_execute(),
self.path_runs.get_path_execution(),
self.framework.get_framework())
self.framework.set_command(
self.path_runs.get_path_execution(),
'aemt-mo-up2')
size = int(SizePopulation) / 15
cl = [
self.framework.get_command(),
self.opts.numberGeneration,
str(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(), "MEAMT-M1.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"),
'&']
retProcess = subprocess.Popen(
cl, 0, stdout=None, stderr=subprocess.STDOUT, shell=False)
retCode = retProcess.wait()
if(retCode != 0):
show_error_message(
"The MEAMT framework finished wrong.\nContact the system administrator.")
if(self.opts.runMinimization == 'true'):
self.do_minimization()
pdbs = list_directory(self.path_runs.get_path_execution(), '*.pdb')
build_images(pdbs, self.path_runs.get_path_execution())
path_output, file_output = os.path.split(self.opts.filehtml)
name, ext = os.path.splitext(self.opts.filehtml)
htmldir = os.path.join(path_output, '%s_files' % name)
if not os.path.exists(htmldir):
os.makedirs(htmldir)
self.opts.htmlfiledir = htmldir
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])
if self.opts.createCompressFile == "True":
if compress_files(pdbs, self.path_runs.get_path_execution(), "MEAMT"):
path_output, file_output = os.path.split(self.opts.outputZip)
send_output_results(
path_output,
file_output,
os.path.join(self.path_runs.get_path_execution(), 'MEAMT.zip'))
self.makeHtml()
if(self.opts.useJmol == 'true'):
self.makeHtmlWithJMol(pdbs[0])
if(self.opts.inputEmail):
send_email(
'*****@*****.**',
email,
'%s Execution on Galaxy - Cloud USP' % self.opts.toolname,
get_message_email(self.opts.toolname),
[],
'smtp.gmail.com')
except Exception, e:
show_error_message(str(e))
pdbs = list_directory(self.path_runs.get_path_execution(), "*.pdb")
for pdb in pdbs:
self.check_structue_by_pdb2gmx(
os.path.join(self.path_runs.get_path_execution(), pdb),
get_path_gromacs(),
self.opts.forceField)
path_output, file_output = os.path.split(self.opts.output)
pdbs_accepted = list_directory(self.path_runs.get_path_execution(), "*.pdb")
if compress_files(pdbs_accepted, self.path_runs.get_path_execution(), "PDBsChecked"):
send_output_results(
path_output,
file_output,
os.path.join(self.path_runs.get_path_execution(), 'PDBsChecked.zip'))
if(os.path.exists(
os.path.join(self.path_runs.get_path_execution(), self.check_pdb_log))):
send_multiple_outputs(
path_output,
[os.path.join(self.path_runs.get_path_execution(), self.check_pdb_log)],
self.opts.galaxydir,
self.opts.outputID)
except Exception, e:
show_error_message(str(e))
if __name__ == '__main__':
op = optparse.OptionParser()
except Exception, e:
raise Exception("The input file could not be read.\n%s" % e)
else:
copy_pdbs_from_input(
self.path_runs.get_path_execution(),
self.opts.outputdir,
self.opts.inputnames,
self.opts.inputPDBs)
pdbs = list_directory(self.path_runs.get_path_execution(), "*.pdb")
newpdb = merge_pdb(self.path_runs.get_path_execution(), pdbs)
path_output, file_output = os.path.split(self.opts.fileoutput)
send_output_results(path_output, file_output, newpdb)
if __name__ == '__main__':
op = optparse.OptionParser()
op.add_option('-i', '--inputPDBs', default=None)
op.add_option('-k', '--outputdir', default=None)
op.add_option('-z', '--fileoutput', default=None)
op.add_option('-n', '--inputnames', default=None)
op.add_option('-t', '--toolname', default=None)
op.add_option('-g', '--galaxyroot', default=None)
op.add_option('-a', '--datasetID', default=None)
op.add_option('-s', '--compressedFile', default=None)
opts, args = op.parse_args()
if not os.path.exists(opts.outputdir):
os.makedirs(opts.outputdir)
