def run_CalculateRMSD(self):
"""
Get the PDB input files and run the calculation
@type self: koala.CalculateRMSD.CalculateRMSD
"""
try:
self.path_runs.set_path_execute()
self.path_runs.set_execution_directory()
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)
else:
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_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)
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)