def prepare_exhaustiveness_run(self, exhaust_vars=None, run_type='exhaustiveness'):
if self.setup_box is False:
print('Please setup simulation box')
sys.exit(0)
self.run_type = run_type
# Vina takes exhaustiveness parameter
if exhaust_vars is None:
self.exhaustiveness = [8, 16, 32, 64, 128, 256, 512, 1024, 2048, 4096]
else:
self.exhaustiveness = exhaust_vars
self.prep_exhaust_run = True
self.run_folder_name = self.receptor_name + '_' + self.molecule_name + '_' + self.run_type
self.sim_folder_run = self.folder_path + os.sep + self.run_folder_name
# Create folder don't forget
# self.directories = self.find_sample_folders(self.folder_path, dir_name=self.run_type)
self.directories = folder_utils.find_folder_in_path(self.folder_path, self.run_folder_name)
print('TADA ', self.directories)
self.json_state_file = self.sim_folder_run + os.sep + self.receptor_name + '_' + self.molecule_name + '_' + self.run_type + '.json'
# This will hold information about run states
if len(self.directories) == 0:
print('Creating folder for vina run\n')
print('Vina run type: {0}'.format(self.run_type))
print(self.sim_folder_run)
folder_utils.create_folder(self.sim_folder_run)
self.folder_exists = True
self.state_data.update({'receptorFile': self.receptor_file,
'ligandFile': self.ligand_file,
'exhaustivenessList': self.exhaustiveness,
'samplesList': self.samples_run,
'folderPath': self.folder_path,
'runType': self.run_type,
'molName': self.molecule_name,
'receptorName': self.receptor_name,
'simRunFolder': self.sim_folder_run,
'directory': self.directories,
'setup': self.setup_box,
'folderCreated': self.folder_exists,
'simStates': {}})
self.prepVinaSim_exhaust()
self.save_state_data_json()
self.load_state_called = False
else:
self.load_state_file = self.json_state_file
self.load_state_called = True
self.load_state_data_json(self.load_state_file)
def prepare_samples_collection_run(self, standard_exhaust=128,
num_samples_run=100,
run_type='samples_run'):
if self.setup_box is False:
print('Please setup simulation box')
sys.exit(0)
self.run_type_samples = run_type
self.prep_samples_run = True
self.samples_exhaust = standard_exhaust
self.samples_run = list(range(1, num_samples_run + 1))
self.run_folder_name_samples = self.receptor_name + '_' + self.molecule_name + '_' + self.run_type_samples
self.sim_folder_run_samples = self.folder_path + os.sep + self.run_folder_name_samples
# Create folder don't forget
# Exhaustiveness for all samples
# self.directories = self.find_sample_folders(self.folder_path, dir_name=self.run_type)
self.directories_samples = folder_utils.find_folder_in_path(self.folder_path, self.run_folder_name_samples)
print('TADA ', self.directories_samples)
self.json_samples_state_file = self.sim_folder_run_samples + os.sep + self.receptor_name + '_' + self.molecule_name + '_' + self.run_type_samples + '.json'
# This will hold information about run states
if len(self.directories_samples) == 0:
print('Creating folder for vina samples run\n')
print('Vina run type: {0}'.format(self.run_type_samples))
print(self.sim_folder_run_samples)
folder_utils.create_folder(self.sim_folder_run_samples)
self.folder_exists_samples = True
self.state_data_samples.update({'receptorFile': self.receptor_file,
'ligandFile': self.ligand_file,
'exhaustivenessList': self.exhaustiveness,
'samples_exhaust': self.samples_exhaust,
'samplesList': self.samples_run,
'folderPath': self.folder_path,
'runType': self.run_type_samples,
'molName': self.molecule_name,
'receptorName': self.receptor_name,
'simRunFolder': self.sim_folder_run_samples,
'directory': self.directories_samples,
'setup': self.setup_box,
'folderCreated': self.folder_exists_samples,
'simStates': {}})
self.prepVinaSim_samples()
self.save_state_data_json(filedata=self.state_data_samples, filename=self.json_samples_state_file)
self.load_state_called_samples = False
self.prep_sample_run = True
else:
self.load_state_file_samples = self.json_samples_state_file
self.load_state_called_samples = True
self.load_samples_state_data_json(self.load_state_file_samples)
self.prep_sample_run = True