from manim import *


class 	lowerCamelCase_     (   A_ ):






    '''simple docstring'''






    def 			UpperCamelCase__   (	self)       ->	Optional[int]:
        __UpperCamelCase     :Dict			  =		Rectangle(height=0.5 , width=0.5)
        __UpperCamelCase     :Optional[Any]			  =		Rectangle(height=0.46 , width=0.46).set_stroke(width=0)

        __UpperCamelCase     :List[str]			  =		[mem.copy() for i in range(6)]
        __UpperCamelCase     :Any			  =		[mem.copy() for i in range(6)]
        __UpperCamelCase     :Dict			  =		VGroup(*snake_case__).arrange(snake_case__ , buff=0)
        __UpperCamelCase     :Union[str, Any]			  =		VGroup(*snake_case__).arrange(snake_case__ , buff=0)
        __UpperCamelCase     :Any			  =		VGroup(snake_case__ , snake_case__).arrange(snake_case__ , buff=0)
        __UpperCamelCase     :Dict			  =		Text('''CPU''' , font_size=24)
        __UpperCamelCase     :Optional[Any]			  =		Group(snake_case__ , snake_case__).arrange(snake_case__ , buff=0.5 , aligned_edge=snake_case__)
        cpu.move_to([-2.5, -0.5, 0])
        self.add(snake_case__)

        __UpperCamelCase     :Any			  =		[mem.copy() for i in range(1)]
        __UpperCamelCase     :str			  =		VGroup(*snake_case__).arrange(snake_case__ , buff=0)
        __UpperCamelCase     :Tuple			  =		Text('''GPU''' , font_size=24)
        __UpperCamelCase     :List[Any]			  =		Group(snake_case__ , snake_case__).arrange(snake_case__ , buff=0.5 , aligned_edge=snake_case__)
        gpu.align_to(snake_case__ , snake_case__)
        gpu.set_x(gpu.get_x() - 1)

        self.add(snake_case__)

        __UpperCamelCase     :Any			  =		[mem.copy() for i in range(6)]
        __UpperCamelCase     :Tuple			  =		VGroup(*snake_case__).arrange(snake_case__ , buff=0)

        __UpperCamelCase     :int			  =		Text('''Model''' , font_size=24)
        __UpperCamelCase     :List[str]			  =		Group(snake_case__ , snake_case__).arrange(snake_case__ , buff=0.5 , aligned_edge=snake_case__)
        model.move_to([3, -1.0, 0])

        self.play(
            Create(snake_case__ , run_time=1) , Create(snake_case__ , run_time=1) , Create(snake_case__ , run_time=1) , )

        __UpperCamelCase     :List[str]			  =		MarkupText(
            f"""First, an empty model skeleton is loaded\ninto <span fgcolor='{YELLOW}'>memory</span> without using much RAM.""" , font_size=24 , )

        __UpperCamelCase     :List[str]			  =		Square(side_length=2.2)
        key.move_to([-5, 2, 0])

        __UpperCamelCase     :Optional[int]			  =		MarkupText(
            f"""<b>Key:</b>\n\n<span fgcolor='{YELLOW}'>●</span> Empty Model""" , font_size=18 , )

        key_text.move_to([-5, 2.4, 0])

        step_a.move_to([2, 2, 0])
        self.play(Write(snake_case__ , run_time=2.5) , Write(snake_case__) , Write(snake_case__))

        self.add(snake_case__)

        __UpperCamelCase     :str			  =		[]
        __UpperCamelCase     :str			  =		[]
        __UpperCamelCase     :Dict			  =		[]
        for i, rect in enumerate(snake_case__):
            __UpperCamelCase     :int			  =		Rectangle(height=0.46 , width=0.46).set_stroke(width=0.0).set_fill(snake_case__ , opacity=0.7)
            cpu_target.move_to(snake_case__)
            cpu_target.generate_target()
            __UpperCamelCase     :Optional[int]			  =		0.46 / 4
            __UpperCamelCase     :int			  =		0.46 / 3

            if i == 0:
                cpu_target.target.next_to(cpu_left_col_base[0].get_corner(DOWN + LEFT) , buff=0.02 , direction=snake_case__)
                cpu_target.target.set_x(cpu_target.target.get_x() + 0.1)
            elif i == 3:
                cpu_target.target.next_to(cpu_targs[0].target , direction=snake_case__ , buff=0.0)
            else:
                cpu_target.target.next_to(cpu_targs[i - 1].target , direction=snake_case__ , buff=0.0)
            cpu_targs.append(snake_case__)

            first_animations.append(rect.animate(run_time=0.5).set_stroke(snake_case__))
            second_animations.append(MoveToTarget(snake_case__ , run_time=1.5))

        self.play(*snake_case__)
        self.play(*snake_case__)

        self.wait()







from typing import Dict

import numpy as np
import torch

from . import residue_constants as rc
from .tensor_utils import tensor_tree_map, tree_map


def 			UpperCamelCase					(    __lowerCamelCase     : Dict[str, torch.Tensor]    ):
       snake_case       :   List[str]							=      []
       snake_case       :   Optional[int]							=      []
       snake_case       :   Any							=      []

       for rt in rc.restypes:
              snake_case       :   List[Any]							=      rc.restype_name_to_atomaa_names[rc.restype_atoa[rt]]
              restype_atomaa_to_atomaa_list.append([(rc.atom_order[name] if name else 0) for name in atom_names]    )
              snake_case       :   str							=      {name: i for i, name in enumerate(__lowerCamelCase    )}
              restype_atomaa_to_atomaa_list.append(
                  [(atom_name_to_idxaa[name] if name in atom_name_to_idxaa else 0) for name in rc.atom_types]    )

              restype_atomaa_mask_list.append([(1.0 if name else 0.0) for name in atom_names]    )

       # Add dummy mapping for restype 'UNK'
       restype_atomaa_to_atomaa_list.append([0] * 14    )
       restype_atomaa_to_atomaa_list.append([0] * 37    )
       restype_atomaa_mask_list.append([0.0] * 14    )

       snake_case       :   Optional[Any]							=      torch.tensor(
           __lowerCamelCase				,					dtype=torch.intaa				,					device=protein["aatype"].device				,					)
       snake_case       :   List[Any]							=      torch.tensor(
           __lowerCamelCase				,					dtype=torch.intaa				,					device=protein["aatype"].device				,					)
       snake_case       :   int							=      torch.tensor(
           __lowerCamelCase				,					dtype=torch.floataa				,					device=protein["aatype"].device				,					)
       snake_case       :   int							=      protein["aatype"].to(torch.long    )

       # create the mapping for (residx, atom14) --> atom37, i.e. an array
       # with shape (num_res, 14) containing the atom37 indices for this protein
       snake_case       :   List[Any]							=      restype_atomaa_to_atomaa[protein_aatype]
       snake_case       :   str							=      restype_atomaa_mask[protein_aatype]

       snake_case       :   str							=      residx_atomaa_mask
       snake_case       :   Any							=      residx_atomaa_to_atomaa.long()

       # create the gather indices for mapping back
       snake_case       :   List[str]							=      restype_atomaa_to_atomaa[protein_aatype]
       snake_case       :   List[Any]							=      residx_atomaa_to_atomaa.long()

       # create the corresponding mask
       snake_case       :   Union[str, Any]							=      torch.zeros([21, 37]				,					dtype=torch.floataa				,					device=protein["aatype"].device    )
       for restype, restype_letter in enumerate(rc.restypes    ):
              snake_case       :   Optional[int]							=      rc.restype_atoa[restype_letter]
              snake_case       :   Any							=      rc.residue_atoms[restype_name]
              for atom_name in atom_names:
                     snake_case       :   List[Any]							=      rc.atom_order[atom_name]
                     snake_case       :   Optional[Any]							=      1

       snake_case       :   List[Any]							=      restype_atomaa_mask[protein_aatype]
       snake_case       :   int							=      residx_atomaa_mask

       return protein




def 			UpperCamelCase					(    __lowerCamelCase     : Dict[str, torch.Tensor]    ):
       snake_case       :   Dict							=      tree_map(lambda __lowerCamelCase    : torch.tensor(__lowerCamelCase				,					device=batch["aatype"].device    )				,					__lowerCamelCase				,					np.ndarray    )
       snake_case       :   List[str]							=      tensor_tree_map(lambda __lowerCamelCase    : np.array(__lowerCamelCase    )				,					make_atomaa_masks(__lowerCamelCase    )    )
       return out





