def __init__(
self,
main_chain_turns: List[int],
side_chain_turns: List[Union[None, int]],
peptide: Peptide,
) -> None:
"""
Args:
main_chain_turns: A list of integers encoding the turns of the main chain.
side_chain_turns: A list of integers and None encoding the turns of the main chain
or None.
peptide: The peptide we are getting the positions for.
"""
self._main_chain_turns = main_chain_turns
self._side_chain_turns = side_chain_turns
self._main_chain_aminoacid_list = np.array(
list(peptide.get_main_chain.main_chain_residue_sequence))
self._side_chain_aminoacid_list = np.array([
aminoacid.residue_sequence[0] if (aminoacid is not None) else None
for aminoacid in peptide.get_side_chains()
])
self._main_positions = self.generate_main_positions()
self._side_positions = self.generate_side_positions()
def test_peptide_get_side_chains(self):
"""Tests that a side chains are provided."""
main_chain_residue_seq = "SAAAAAAAA"
side_chain_residue_sequences = ["", "", "A", "", "", "A", "", "A", ""]
peptide = Peptide(main_chain_residue_seq, side_chain_residue_sequences)
side_chains = peptide.get_side_chains()
self.assertEqual(side_chains[0], None)
self.assertEqual(side_chains[1], None)
self.assertEqual(side_chains[2].residue_sequence, ["A"])
self.assertEqual(side_chains[3], None)
self.assertEqual(side_chains[4], None)
self.assertEqual(side_chains[5].residue_sequence, ["A"])
self.assertEqual(side_chains[6], None)
self.assertEqual(side_chains[7].residue_sequence, ["A"])
self.assertEqual(side_chains[8], None)