def do_minimization(self, pdbPrefix=""):
if not check_pdb(self.path_runs.get_path_execution(), self.opts.galaxyroot):
raise Exception("The script to check the PDBs finished wrong.")
if not prepare_pdb(self.path_runs.get_path_execution(), self.opts.galaxyroot):
raise Exception("The script to prepare the PDBs finished wrong.")
if not residue_renumber(self.path_runs.get_path_execution(), self.opts.galaxyroot):
raise Exception("The script to renumber the residues finished wrong.")
if not minimization(self.path_runs.get_path_execution(), self.opts.galaxyroot, pdbPrefix):
raise Exception("The script of minimization finished wrong.")
else:
copy_pdbs_from_input(
self.path_runs.get_path_execution(),
self.opts.htmlfiledir,
self.opts.inputnames,
self.opts.inputPDBs)
if(self.opts.renameAtoms == 'true'):
if not rename_atoms(
self.path_runs.get_path_execution(),
self.opts.galaxyroot):
raise Exception("The script to rename the atoms finished wrong.")
if(self.opts.checkStructures == 'true'):
if not check_pdb(
self.path_runs.get_path_execution(),
self.opts.galaxyroot):
raise Exception("The script to check the structure finished wrong.")
self.framework.set_command(
self.path_runs.get_path_execution(),
'protpred-Gromacs-Sort_Method_Files_by_Front_Dominance')
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 2PG framework finished wrong.\nContact the system administrator.")