




'''simple docstring'''







from typing import Dict, Tuple, overload

import torch
import torch.types
from torch import nn

from . import residue_constants as rc
from .rigid_utils import Rigid, Rotation
from .tensor_utils import batched_gather



@overload
def 					lowerCamelCase__							(			__lowercase    ,      __lowercase    ,      __lowercase							):
     ...



@overload
def 					lowerCamelCase__							(			__lowercase    ,      __lowercase    ,      __lowercase							):
     ...



def 					lowerCamelCase__							(			__lowercase    ,      __lowercase    ,      __lowercase							):
     snake_case :			int					   = aatype == rc.restype_order["""G"""]
     snake_case :			List[Any]					   = rc.atom_order["""CA"""]
     snake_case :			Any					   = rc.atom_order["""CB"""]
     snake_case :			List[str]					   = torch.where(
         is_gly[..., None].expand(*((-1,) * len(is_gly.shape							))    ,      3							)    ,      all_atom_positions[..., ca_idx, :]    ,      all_atom_positions[..., cb_idx, :]    ,      )

     if all_atom_masks is not None:
          snake_case :			Dict					   = torch.where(
              __lowercase    ,      all_atom_masks[..., ca_idx]    ,      all_atom_masks[..., cb_idx]    ,      )
          return pseudo_beta, pseudo_beta_mask
     else:
          return pseudo_beta



def 					lowerCamelCase__							(			__lowercase    ,      __lowercase							):
     snake_case :			List[Any]					   = batched_gather(
         __lowercase    ,      batch["""residx_atom37_to_atom14"""]    ,      dim=-2    ,      no_batch_dims=len(atomaa.shape[:-2]							)    ,      )

     snake_case :			int					   = atomaa_data * batch["""atom37_atom_exists"""][..., None]

     return atomaa_data



def 					lowerCamelCase__							(			__lowercase							):
     snake_case :			int					   = template_feats["""template_aatype"""]
     snake_case :			List[Any]					   = template_feats["""template_torsion_angles_sin_cos"""]
     snake_case :			List[Any]					   = template_feats["""template_alt_torsion_angles_sin_cos"""]
     snake_case :			List[Any]					   = template_feats["""template_torsion_angles_mask"""]
     snake_case :			List[str]					   = torch.cat(
         [
             nn.functional.one_hot(__lowercase    ,      22							),
             torsion_angles_sin_cos.reshape(*torsion_angles_sin_cos.shape[:-2]    ,      14							),
             alt_torsion_angles_sin_cos.reshape(*alt_torsion_angles_sin_cos.shape[:-2]    ,      14							),
             torsion_angles_mask,
         ]    ,      dim=-1    ,      )

     return template_angle_feat



def 					lowerCamelCase__							(			__lowercase    ,      __lowercase    ,      __lowercase    ,      __lowercase    ,      __lowercase = False    ,      __lowercase = 1e-20    ,      __lowercase = 1e8    ,      ):
     snake_case :			Tuple					   = batch["""template_pseudo_beta_mask"""]
     snake_case :			str					   = template_mask[..., None] * template_mask[..., None, :]

     # Compute distogram (this seems to differ slightly from Alg. 5)
     snake_case :			int					   = batch["""template_pseudo_beta"""]
     snake_case :			int					   = torch.sum((tpb[..., None, :] - tpb[..., None, :, :]) ** 2    ,      dim=-1    ,      keepdim=__lowercase							)
     snake_case :			Tuple					   = torch.linspace(__lowercase    ,      __lowercase    ,      __lowercase    ,      device=tpb.device							) ** 2
     snake_case :			List[str]					   = torch.cat([lower[1:], lower.new_tensor([inf]							)]    ,      dim=-1							)
     snake_case :			Optional[Any]					   = ((dgram > lower) * (dgram < upper)).type(dgram.dtype							)

     snake_case :			str					   = [dgram, template_mask_ad[..., None]]

     snake_case :			torch.LongTensor					   = nn.functional.one_hot(
         batch["""template_aatype"""]    ,      rc.restype_num + 2    ,      )

     snake_case :			Any					   = batch["""template_aatype"""].shape[-1]
     to_concat.append(aatype_one_hot[..., None, :, :].expand(*aatype_one_hot.shape[:-2]    ,      __lowercase    ,      -1    ,      -1							)							)
     to_concat.append(aatype_one_hot[..., None, :].expand(*aatype_one_hot.shape[:-2]    ,      -1    ,      __lowercase    ,      -1							)							)

     snake_case   ,		snake_case   ,		snake_case :			Optional[int]					   = [rc.atom_order[a] for a in ["""N""", """CA""", """C"""]]
     snake_case :			List[Any]					   = Rigid.make_transform_from_reference(
         n_xyz=batch["""template_all_atom_positions"""][..., n, :]    ,      ca_xyz=batch["""template_all_atom_positions"""][..., ca, :]    ,      c_xyz=batch["""template_all_atom_positions"""][..., c, :]    ,      eps=__lowercase    ,      )
     snake_case :			Dict					   = rigids.get_trans()[..., None, :, :]
     snake_case :			Any					   = rigids[..., None].invert_apply(__lowercase							)

     snake_case :			Union[str, Any]					   = torch.rsqrt(eps + torch.sum(rigid_vec**2    ,      dim=-1							)							)

     snake_case :			str					   = batch["""template_all_atom_mask"""]
     snake_case :			Tuple					   = t_aa_masks[..., n] * t_aa_masks[..., ca] * t_aa_masks[..., c]
     snake_case :			List[str]					   = template_mask[..., None] * template_mask[..., None, :]

     snake_case :			Union[str, Any]					   = inv_distance_scalar * template_mask_ad
     snake_case :			List[str]					   = rigid_vec * inv_distance_scalar[..., None]

     if not use_unit_vector:
          snake_case :			Optional[int]					   = unit_vector * 0.0

     to_concat.extend(torch.unbind(unit_vector[..., None, :]    ,      dim=-1							)							)
     to_concat.append(template_mask_ad[..., None]							)

     snake_case :			int					   = torch.cat(__lowercase    ,      dim=-1							)
     snake_case :			int					   = act * template_mask_ad[..., None]

     return act



def 					lowerCamelCase__							(			__lowercase							):
     snake_case :			torch.LongTensor					   = nn.functional.one_hot(batch["""extra_msa"""]    ,      23							)
     snake_case :			Optional[Any]					   = [
         msa_ahot,
         batch["""extra_has_deletion"""].unsqueeze(-1							),
         batch["""extra_deletion_value"""].unsqueeze(-1							),
     ]
     return torch.cat(__lowercase    ,      dim=-1							)



def 					lowerCamelCase__							(			__lowercase    ,      __lowercase    ,      __lowercase    ,      __lowercase    ,      ):
     # [*, N, 8, 4, 4]
     snake_case :			Optional[int]					   = rrgdf[aatype, ...]

     # [*, N, 8] transformations, i.e.
     #   One [*, N, 8, 3, 3] rotation matrix and
     #   One [*, N, 8, 3]    translation matrix
     snake_case :			Optional[int]					   = r.from_tensor_axa(__lowercase							)

     snake_case :			int					   = alpha.new_zeros((*((1,) * len(alpha.shape[:-1]							)), 2)							)
     snake_case :			Optional[int]					   = 1

     # [*, N, 8, 2]
     snake_case :			str					   = torch.cat([bb_rot.expand(*alpha.shape[:-2]    ,      -1    ,      -1							), alpha]    ,      dim=-2							)

     # [*, N, 8, 3, 3]
     # Produces rotation matrices of the form:
     # [
     #   [1, 0  , 0  ],
     #   [0, a_2,-a_1],
     #   [0, a_1, a_2]
     # ]
     # This follows the original code rather than the supplement, which uses
     # different indices.

     snake_case :			Dict					   = alpha.new_zeros(default_r.get_rots().get_rot_mats().shape							)
     snake_case :			str					   = 1
     snake_case :			Optional[int]					   = alpha[..., 1]
     snake_case :			Dict					   = -alpha[..., 0]
     snake_case :			str					   = alpha

     snake_case :			Any					   = default_r.compose(Rigid(Rotation(rot_mats=__lowercase							)    ,      __lowercase							)							)

     snake_case :			Union[str, Any]					   = all_frames[..., 5]
     snake_case :			List[Any]					   = all_frames[..., 6]
     snake_case :			Optional[Any]					   = all_frames[..., 7]

     snake_case :			Tuple					   = all_frames[..., 4]
     snake_case :			List[Any]					   = chia_frame_to_bb.compose(__lowercase							)
     snake_case :			Optional[Any]					   = chia_frame_to_bb.compose(__lowercase							)
     snake_case :			Optional[Any]					   = chia_frame_to_bb.compose(__lowercase							)

     snake_case :			str					   = Rigid.cat(
         [
             all_frames[..., :5],
             chia_frame_to_bb.unsqueeze(-1							),
             chia_frame_to_bb.unsqueeze(-1							),
             chia_frame_to_bb.unsqueeze(-1							),
         ]    ,      dim=-1    ,      )

     snake_case :			Optional[Any]					   = r[..., None].compose(__lowercase							)

     return all_frames_to_global







def 					lowerCamelCase__							(			__lowercase    ,      __lowercase    ,      __lowercase    ,      __lowercase    ,      __lowercase    ,      __lowercase    ,      ):
     # [*, N, 14]
     snake_case :			Any					   = group_idx[aatype, ...]

     # [*, N, 14, 8]
     snake_case :			torch.LongTensor					   = nn.functional.one_hot(
         __lowercase    ,      num_classes=default_frames.shape[-3]    ,      )

     # [*, N, 14, 8]
     snake_case :			str					   = r[..., None, :] * group_mask_one_hot

     # [*, N, 14]
     snake_case :			Any					   = t_atoms_to_global.map_tensor_fn(lambda __lowercase							: torch.sum(__lowercase    ,      dim=-1							)							)

     # [*, N, 14, 1]
     snake_case :			Dict					   = atom_mask[aatype, ...].unsqueeze(-1							)

     # [*, N, 14, 3]
     snake_case :			Tuple					   = lit_positions[aatype, ...]
     snake_case :			Dict					   = t_atoms_to_global.apply(__lowercase							)
     snake_case :			Union[str, Any]					   = pred_positions * atom_mask

     return pred_positions









'''simple docstring'''







from .balanced_parentheses import balanced_parentheses
from .stack import Stack



def 					lowerCamelCase__							(			__lowercase							):
     return {"+": 1, "-": 1, "*": 2, "/": 2, "^": 3}.get(__lowercase    ,      -1							)



def 					lowerCamelCase__							(			__lowercase							):
     if not balanced_parentheses(__lowercase							):
          raise ValueError("""Mismatched parentheses"""							)
     snake_case :			Stack[str]					   = Stack()
     snake_case :			List[Any]					   = []
     for char in expression_str:
          if char.isalpha() or char.isdigit():
               postfix.append(__lowercase							)
          elif char == "(":
               stack.push(__lowercase							)
          elif char == ")":
               while not stack.is_empty() and stack.peek() != "(":
                    postfix.append(stack.pop()							)
               stack.pop()
          else:
               while not stack.is_empty() and precedence(__lowercase							) <= precedence(stack.peek()							):
                    postfix.append(stack.pop()							)
               stack.push(__lowercase							)
     while not stack.is_empty():
          postfix.append(stack.pop()							)
     return " ".join(__lowercase							)


if __name__ == "__main__":
      from doctest import testmod

      testmod()
      lowercase			:      Tuple			=					"""a+b*(c^d-e)^(f+g*h)-i"""

      print("""Infix to Postfix Notation demonstration:\n""")
      print("""Infix notation: """ + expression)
      print("""Postfix notation: """ + infix_to_postfix(expression))



