def run_FoldX_AnalyseComplex_And_Agadir(self):
GUM.wait_for_grid_engine_job_to_complete(self.solubis_job_prefix,
'all Solubis jobs to finish')
self.all_mutants_in_Solubis_path = sorted(glob.glob('./*'))
foldx_instance = FoldX()
for mutant_in_Solubis_path in self.all_mutants_in_Solubis_path:
if os.path.isdir(mutant_in_Solubis_path):
mutant_folder_name = mutant_in_Solubis_path.split('/')[-1]
os.chdir(mutant_folder_name)
self._make_backup_of_runscript()
foldx_instance.prepare_for_FoldX_AnalyseComplex(
self.RepairPDB_pdb_name)
print os.getcwd()
# Note: _1_0 is random choice, other two are same.
# cwd is Results/pdbname/Runs/Solubis/mutant_name
relative_path_of_pdb_to_read = './'
relative_path_for_new_fasta_folder_to_write = './'
pdb_name_chain_fasta_dict = GUM.extract_pdb_name_fasta_and_chains_from_pdb(
self.RepairPDB_pdb_name + '_1_0.pdb',
relative_path_of_pdb_to_read)
GUM.write_fasta_to_folder(
pdb_name_chain_fasta_dict,
relative_path_for_new_fasta_folder_to_write)
grid_engine_job_name = self.analyze_complex_job_prefix + mutant_folder_name
agadir_results_path = os.getcwd()
python_script_with_path = self.results_pdb_path + '/../../SourceFiles/Scripts/run_agadir.py ' + \
agadir_results_path
self._run_runscript_on_grid_engine(grid_engine_job_name,
python_script_with_path)
os.chdir('./..') # is this Runs/Solubis folder ?
cwd = os.getcwd() # for debugging
else:
print mutant_in_Solubis_path
def run_yasara_agadir_repair(self):
if not os.path.exists('Results'):
os.makedirs('Results')
for pdb in self.pdb_list:
pdb_name = pdb.split('.')[0]
self._build_results_directory_tree_for_each(pdb)
# current directory Results/pdb
# self._run_yasara_to_organise_pdb(pdb, pdb_name)
self._copy_pdb_foldx_agadir_files_to_new_subdirectories(pdb)
relative_path_of_pdb_to_read = './PDBs/'
relative_path_for_new_fasta_folder_to_write = './'
pdb_name_chain_fasta_dict = GUM.extract_pdb_name_fasta_and_chains_from_pdb(
pdb, relative_path_of_pdb_to_read)
GUM.write_fasta_to_folder(
pdb_name_chain_fasta_dict,
relative_path_for_new_fasta_folder_to_write)
agadir_results_path = self.start_path + '/Results/' + pdb_name
agadir_instance = Agadir(agadir_results_path)
agadir_instance.run_agadir_with_fasta_files('./')
self._run_repair_on_grid_engine(pdb_name)
message_to_print = 'PDBs to be repaired'
GUM.wait_for_grid_engine_job_to_complete(self.repair_job_prefix,
message_to_print)