def __init__(self,
pymod,
father_protocol,
output_directory=os.path.curdir):
PyMod_protocol.__init__(self, pymod, pymod.domain_analysis_dirpath)
self.father_protocol = father_protocol
self.query_element = self.father_protocol.pymod_element
def __init__(self, pymod, pymod_element):
PyMod_protocol.__init__(self,
pymod,
output_directory=pymod.temp_directory_dirpath)
# Directory in which to save the temporary files.
self.temp_directory = self.pymod.temp_directory_dirpath
self.target_element = pymod_element
self.associate_pdb_file = None
def __init__(self,
pymod,
output_directory=None,
mode=None,
structures_to_fetch=None,
import_mode=None):
PyMod_protocol.__init__(self, pymod, output_directory)
self.mode = mode
self.structures_to_fetch = structures_to_fetch
self.import_mode = import_mode
def __init__(self, pymod):
PyMod_protocol.__init__(self, pymod)
# selected components to be updated/installed
self.selected_comps = []
self.pending_downloads = 0
self.pymod_data_dirpath = os.path.join(
self.pymod.current_pymod_dirpath, self.pymod.data_dirname)
# Path of the file where the download dates will be stored.
self.download_log_filepath = os.path.join(self.pymod_data_dirpath,
data_installer_log_filename)
def quit_protocol(self):
self.remove_psipred_temp_files()
PyMod_protocol.quit_protocol(self)
def __init__(self, pymod, target_sequences=None):
PyMod_protocol.__init__(self, pymod)
self.target_sequences = self.get_pymod_elements(target_sequences)
def quit_protocol(self):
self.finish_blast_search()
PyMod_protocol.quit_protocol(self)
def __init__(self, pymod, pymod_element, output_directory=None):
PyMod_protocol.__init__(self, pymod, output_directory)
self.pymod_element = pymod_element
def __init__(self, pymod, input_cluster_element, *args):
self.input_cluster_element = input_cluster_element
PyMod_protocol.__init__(self, pymod, *args)
def __init__(self, pymod, pymod_element):
PyMod_protocol.__init__(self, pymod)
self.pymod_element = pymod_element