def get_args(self, input_function: t.Callable):
"""
get_args(...) Needs to be called, before filter() can be used. It uses an input function to find all arguments required by a certain instance of a _Filter.
For RingFilter that is a List of all Molecules in the pdb format (CAREFULL: The Molecules need to contain ALL atoms in the Molecules, not just the selected one.)
TODO: What Kind of Error will I get if tools_Rdkit conversion fails?/ Catch it here
Parameters
----------
input_function: function(str)
A function that can get the input
message: str
A string that is displayed if if input function needs to communicate with the user
Returns
-------
NoReturn
Raises
------
BadArgumentException
if the input function does not provide all arguments in the necessary format
"""
input = input_function("A List of Molecules in the PDB FORMAT:")
input = u.check_or_convert_argument(input, list)
molecules_pdb = [u.check_or_convert_argument(i, str) for i in input]
self.molecules_rdk = Rdkit_Functions.parse_pdb_blocks_to_rdkit(
molecules_pdb)
def get_args(self, input_function: t.Callable):
"""
should be overridden by every subclass of _Selection. It will assign all necessart variables using input function.
For MCS_Selection the argument is a list of the Molecules in the pdb format.
Parameters
----------
input_function : t.Callable (str)
a function that will provide the arguments for the selection in the necessary format. Here: Not necessesary. Just pass an 'empty' function or any function at all. It will not be called.
Returns
-------
NoReturn
Raises
------
BadArgumentException:
if the input function does not provide all arguments in the necessary format
"""
input = input_function("A List of Molecules in the PDB FORMAT:")
input = u.check_or_convert_argument(input, list)
molecules_pdb = [u.check_or_convert_argument(i, str) for i in input]
self.molecules_rdk = Rdkit_Functions.parse_pdb_blocks_to_rdkit(
molecules_pdb)
self.update()
def filter(self):
'''
filter should be overridden by every subclass of _Filter. Returns a filtered List of atoms
In the case of Ring Filter: All atoms which are in rings
:return: Filtered atom list
:rtype: t.List[u.Atom]
'''
ids_of_atoms_in_rings = Rdkit_Functions.ring_atom_filter(selected=None, mols=self.molecules_rdk,
selected_mols=None)
return [a for a in self.atoms if a.id in ids_of_atoms_in_rings]
def update(self):
"""
general update function
Returns
-------
NoReturn
"""
print(
"EXECUTING MCS Selection: please Wait - this can take a bit longer.",
mv=5)
mcs_ids = Rdkit_Functions.mcs_selection(self.molecules_rdk)
self.atoms = list(filter(lambda a: a.id in mcs_ids, self.all_atoms))
self.has_finished = True
print("EXECUTING MCS Selection: DONE", mv=5)
def get_args(self, input_function: t.Callable):
"""
get_args(...) Needs to be called, before filter() can be used. It uses an input function to find all arguments required by a certain instance of a _Filter.
For RingFilter that is a List of all Molecules in the pdb format (CAREFULL: The Molecules need to contain ALL atoms in the Molecules, not just the selected one.)
:param input_function: A function that can get the input
:type input_function: function(str)
:param message: A string that is displayed if if input function needs to communicate with the user
:type message: String
:return: -
:rtype: -
:raises: BadArgumentException if the input function does not provide all arguments in the necessary format
"""
input = input_function("A List of Molecules in the PDB FORMAT:")
input = u.check_or_convert_argument(input, list)
molecules_pdb = [u.check_or_convert_argument(i, str) for i in input]
self.molecules_rdk = Rdkit_Functions.parse_pdb_blocks_to_rdkit(molecules_pdb)
def _update(self):
mcs_ids = Rdkit_Functions.mcs_selection(self.molecules_rdk)
self.atoms = list(filter(lambda a: a.id in mcs_ids, self.all_atoms))
self.has_finished = True