class SplitPDB(object):
"""
Split the models of a PDB file into new PDB file, where a model corresponds to a new PDB file
"""
def __init__(self, opts=None):
"""
@type self: koala.SplitPDB.SplitPDB
@type opts: OptionParser parameters
"""
assert opts is not None
self.opts = opts
self.path_runs = PathRuns()
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))
class MergePDB(object):
"""
Merge a set of PDB files into models on a single PDB file
"""
methods = []
ignoreoutfiles = ['.pdb']
def __init__(self, opts=None):
"""
@type self: koala.MergePDB.MergePDB
@type opts: OptionParser parameters
"""
assert opts is not None
self.opts = opts
self.path_runs = PathRuns()
def run_MergePDB(self):
"""
Get the input PDB files and run to merge
@type self: koala.MergePDB.MergePDB
"""
self.path_runs.set_path_execute()
self.path_runs.set_execution_directory()
if self.opts.compressedFile == '1':
if zipfile.is_zipfile(opts.inputPDBs):
extract_zip_file(opts.inputPDBs, self.path_runs.get_path_execution())
else:
try:
inF = gzip.GzipFile(opts.inputPDBs, 'rb')
f = inF.read()
inF.close()
if f:
extract_gz_file(opts.inputPDBs, self.path_runs.get_path_execution())
except Exception, e:
raise Exception("The input file could not be read.\n%s" % e)
else:
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 RenameAtoms(object):
"""
Rename the missing atoms of a PDB file according to GROMACS
"""
path_execute = None
os.environ["GMX_MAXBACKUP"] = "-1"
def __init__(self, opts=None):
"""
@type self: koala.RenameAtoms.RenameAtoms
@type opts: OptionParser parameters
"""
assert opts is not None
self.opts = opts
self.path_runs = PathRuns()
def rename_atoms_structure(self, pdbfile, gmx_path, forcefield):
"""
Create a subprocess to rename the atoms of the PDB input file using pdb2gmx
@type self: koala.RenameAtoms.RenameAtoms
@type pdbfile: file
@type gmx_path: string
@type forcefield: string
"""
delete_check_files(self.path_runs.get_path_execution())
program = os.path.join(gmx_path, "pdb2gmx")
process = Popen(
[program, "-f", pdbfile, "-o", pdbfile, "-p", "check.top", "-water", "none", "-ff", forcefield],
stdout=PIPE,
stderr=PIPE,
)
stdout, stderr = process.communicate()
process.wait()
delete_check_files(self.path_runs.get_path_execution())
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))
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))