from typing import List
import pyrosetta

class BlueprinterExpected:
    def expected_seq(self):
        """

        :return:
        """
        return ''.join([self.get_expected_aa_from_row(row) for row in self])

    def get_expected_aa_from_row(self, row: List[str]) -> str:
        if len(row) == 0: # impossible
            return ''
        elif len(row) == 3 and row[2] == '.': # "30 K ."
            return row[1]
        elif len(row) == 3:  # "30 K H" ???
            return '*'  # H/L/E/D in lowercase would be ambiguous
        elif len(row) == 4 and row[3] in ('NATAA', 'NATRO'):  # "30 K H NATAA"
            return row[1]
        elif len(row) == 4 and 'PIKAA' in row[3] and len(row[3]) == len('PIKAA ')+1:  # "30 K H PIKAA R"
            return row[3][-1]
        else: # ALLAA etc..
            return '*'

    def show_aligned(self, pose):
        """
        notebook output alignment of pose seq and blueprint expectation
        :param pose:
        :return:
        """
        self.show_seq_aligned(pose.sequence(), self.expected_seq())

    def _show_alignment(self, alignment: list):
        from Bio import pairwise2
        from IPython.display import display, HTML
        formatted = pairwise2.format_alignment(*alignment)
        a, gap, b, score = formatted.strip().split('\n')
        gap = ''.join(['.' if c == '|' else '*' for c in gap])
        display(HTML(f'<div style="font-family:monospace; display: inline-block; white-space: nowrap;">'+
                     f'{a}<br/>{gap.replace(" ", "*")}<br/>{b}<br/>{score}</div>'))
        #ignore pycharm. typehint for display is wrong.

    def show_poses_aligned(self, pose_A, pose_B):
        self.show_seq_aligned(pose_A.sequence(), pose_B.sequence())

    def show_seq_aligned(self, seq_A: str, seq_B:str):
        from Bio import pairwise2
        alignment = pairwise2.align.globalxx(seq_A, seq_B)[0]
        self._show_alignment(alignment)
        return alignment

    def correct(self, pose: pyrosetta.Pose) -> pyrosetta.rosetta.core.select.residue_selector.ResidueSelector:
        """
        This is not a great thing to do. So it is best to relax the neighbours of the vector afterwards.
        If there are valines instead of the intended sequence that is bad.
        Altering the blueprint is required.

        :param pose:
        :return:
        """
        MutateResidue = pyrosetta.rosetta.protocols.simple_moves.MutateResidue
        one2three = pyrosetta.rosetta.protocols.motifs.name3_from_oneletter
        ex_seq = self.expected_seq()
        altered = pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector()
        for i, (expected, current) in enumerate(zip(ex_seq, pose.chain_sequence(1))):
            if expected != current:
                altered.append_index(i + 1)
                MutateResidue(target=i + 1, new_res=one2three(expected)).apply(pose)
        return altered

    def correct_and_relax(self, pose: pyrosetta.Pose):
        altered = self.correct(pose)
        movemap = pyrosetta.MoveMap()
        NeighborhoodResidueSelector = pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector
        neigh_sele = NeighborhoodResidueSelector(altered, distance=15, include_focus_in_subset=True)
        n = neigh_sele.apply(pose)
        movemap.set_bb(allow_bb=n)
        movemap.set_chi(allow_chi=n)
        scorefxn = pyrosetta.get_fa_scorefxn()
        # cartesian
        scorefxn_cart = pyrosetta.create_score_function('ref2015_cart')
        relax = pyrosetta.rosetta.protocols.relax.FastRelax(scorefxn_cart, 5)
        relax.cartesian(True)
        relax.minimize_bond_angles(True)
        relax.minimize_bond_lengths(True)
        relax.set_movemap_disables_packing_of_fixed_chi_positions(True)
        relax.set_movemap(movemap)
        relax.apply(pose)
        # dual
        relax = pyrosetta.rosetta.protocols.relax.FastRelax(scorefxn, 5)
        relax.set_movemap_disables_packing_of_fixed_chi_positions(True)
        relax.set_movemap(movemap)
        relax.apply(pose)






from typing import List
import pyrosetta

class BlueprinterExpected:
    def expected_seq(self):
        """

        :return:
        """
        return ''.join([self.get_expected_aa_from_row(row) for row in self])

    def get_expected_aa_from_row(self, row: List[str]) -> str:
        if len(row) == 0: # impossible
            return ''
        elif len(row) == 3 and row[2] == '.': # "30 K ."
            return row[1]
        elif len(row) == 3:  # "30 K H" ???
            return '*'  # H/L/E/D in lowercase would be ambiguous
        elif len(row) == 4 and row[3] in ('NATAA', 'NATRO'):  # "30 K H NATAA"
            return row[1]
        elif len(row) == 4 and 'PIKAA' in row[3] and len(row[3]) == len('PIKAA ')+1:  # "30 K H PIKAA R"
            return row[3][-1]
        else: # ALLAA etc..
            return '*'

    def show_aligned(self, pose):
        """
        notebook output alignment of pose seq and blueprint expectation
        :param pose:
        :return:
        """
        self.show_seq_aligned(pose.sequence(), self.expected_seq())

    def _show_alignment(self, alignment: list):
        from Bio import pairwise2
        from IPython.display import display, HTML
        formatted = pairwise2.format_alignment(*alignment)
        a, gap, b, score = formatted.strip().split('\n')
        gap = ''.join(['.' if c == '|' else '*' for c in gap])
        display(HTML(f'<div style="font-family:monospace; display: inline-block; white-space: nowrap;">'+
                     f'{a}<br/>{gap.replace(" ", "*")}<br/>{b}<br/>{score}</div>'))
        #ignore pycharm. typehint for display is wrong.

    def show_poses_aligned(self, pose_A, pose_B):
        self.show_seq_aligned(pose_A.sequence(), pose_B.sequence())

    def show_seq_aligned(self, seq_A: str, seq_B:str):
        from Bio import pairwise2
        alignment = pairwise2.align.globalxx(seq_A, seq_B)[0]
        self._show_alignment(alignment)
        return alignment

    def correct(self, pose: pyrosetta.Pose) -> pyrosetta.rosetta.core.select.residue_selector.ResidueSelector:
        """
        This is not a great thing to do. So it is best to relax the neighbours of the vector afterwards.
        If there are valines instead of the intended sequence that is bad.
        Altering the blueprint is required.

        :param pose:
        :return:
        """
        MutateResidue = pyrosetta.rosetta.protocols.simple_moves.MutateResidue
        one2three = pyrosetta.rosetta.protocols.motifs.name3_from_oneletter
        ex_seq = self.expected_seq()
        altered = pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector()
        for i, (expected, current) in enumerate(zip(ex_seq, pose.chain_sequence(1))):
            if expected != current:
                altered.append_index(i + 1)
                MutateResidue(target=i + 1, new_res=one2three(expected)).apply(pose)
        return altered

    def correct_and_relax(self, pose: pyrosetta.Pose):
        altered = self.correct(pose)
        movemap = pyrosetta.MoveMap()
        NeighborhoodResidueSelector = pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector
        neigh_sele = NeighborhoodResidueSelector(altered, distance=15, include_focus_in_subset=True)
        n = neigh_sele.apply(pose)
        movemap.set_bb(allow_bb=n)
        movemap.set_chi(allow_chi=n)
        scorefxn = pyrosetta.get_fa_scorefxn()
        # cartesian
        scorefxn_cart = pyrosetta.create_score_function('ref2015_cart')
        relax = pyrosetta.rosetta.protocols.relax.FastRelax(scorefxn_cart, 5)
        relax.cartesian(True)
        relax.minimize_bond_angles(True)
        relax.minimize_bond_lengths(True)
        relax.set_movemap_disables_packing_of_fixed_chi_positions(True)
        relax.set_movemap(movemap)
        relax.apply(pose)
        # dual
        relax = pyrosetta.rosetta.protocols.relax.FastRelax(scorefxn, 5)
        relax.set_movemap_disables_packing_of_fixed_chi_positions(True)
        relax.set_movemap(movemap)
        relax.apply(pose)






:return: # impossible # "30 K ." # "30 K H" ??? # H/L/E/D in lowercase would be ambiguous # "30 K H NATAA" # "30 K H PIKAA R" # ALLAA etc.. notebook output alignment of pose seq and blueprint expectation         :param pose:         :return: #ignore pycharm. typehint for display is wrong. This is not a great thing to do. So it is best to relax the neighbours of the vector afterwards.         If there are valines instead of the intended sequence that is bad.         Altering the blueprint is required.          :param pose:         :return: # cartesian # dual