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+++ b/data/conda_envs/evalclaw/lib/python3.11/site-packages/transformers/models/esm/openfold_utils/__init__.py
@@ -0,0 +1,8 @@
+from .chunk_utils import chunk_layer
+from .data_transforms import make_atom14_masks
+from .feats import atom14_to_atom37, frames_and_literature_positions_to_atom14_pos, torsion_angles_to_frames
+from .loss import compute_predicted_aligned_error, compute_tm
+from .protein import Protein as OFProtein
+from .protein import to_pdb
+from .rigid_utils import Rigid, Rotation
+from .tensor_utils import dict_multimap, flatten_final_dims, permute_final_dims
diff --git a/data/conda_envs/evalclaw/lib/python3.11/site-packages/transformers/models/esm/openfold_utils/__pycache__/__init__.cpython-311.pyc b/data/conda_envs/evalclaw/lib/python3.11/site-packages/transformers/models/esm/openfold_utils/__pycache__/__init__.cpython-311.pyc
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index 0000000000000000000000000000000000000000..2146a481c8b8eec5f2d33da178eda10d506dcde9
--- /dev/null
+++ b/data/conda_envs/evalclaw/lib/python3.11/site-packages/transformers/models/esm/openfold_utils/chunk_utils.py
@@ -0,0 +1,398 @@
+# Copyright 2021 AlQuraishi Laboratory
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+import logging
+import math
+from collections.abc import Callable, Iterable, Sequence
+from functools import partial
+from typing import Any
+
+import torch
+
+from .tensor_utils import tensor_tree_map, tree_map
+
+
+def _fetch_dims(tree: dict | list | tuple | torch.Tensor) -> list[tuple[int, ...]]:
+    shapes = []
+    if isinstance(tree, dict):
+        for v in tree.values():
+            shapes.extend(_fetch_dims(v))
+    elif isinstance(tree, (list, tuple)):
+        for t in tree:
+            shapes.extend(_fetch_dims(t))
+    elif isinstance(tree, torch.Tensor):
+        shapes.append(tree.shape)
+    else:
+        raise TypeError("Not supported")
+
+    return shapes
+
+
+@torch.jit.ignore
+def _flat_idx_to_idx(flat_idx: int, dims: tuple[int, ...]) -> tuple[int, ...]:
+    idx = []
+    for d in reversed(dims):
+        idx.append(flat_idx % d)
+        flat_idx = flat_idx // d
+
+    return tuple(reversed(idx))
+
+
+@torch.jit.ignore
+def _get_minimal_slice_set(
+    start: Sequence[int],
+    end: Sequence[int],
+    dims: Sequence[int],
+    start_edges: Sequence[bool] | None = None,
+    end_edges: Sequence[bool] | None = None,
+) -> list[tuple[slice, ...]]:
+    """
+    Produces an ordered sequence of tensor slices that, when used in sequence on a tensor with shape dims, yields
+    tensors that contain every leaf in the contiguous range [start, end]. Care is taken to yield a short sequence of
+    slices, and perhaps even the shortest possible (I'm pretty sure it's the latter).
+
+    end is INCLUSIVE.
+    """
+
+    # start_edges and end_edges both indicate whether, starting from any given
+    # dimension, the start/end index is at the top/bottom edge of the
+    # corresponding tensor, modeled as a tree
+    def reduce_edge_list(l: list[bool]) -> None:
+        tally = True
+        for i in range(len(l)):
+            reversed_idx = -1 * (i + 1)
+            l[reversed_idx] &= tally
+            tally = l[reversed_idx]
+
+    if start_edges is None:
+        start_edges = [s == 0 for s in start]
+        reduce_edge_list(start_edges)
+    if end_edges is None:
+        end_edges = [e == (d - 1) for e, d in zip(end, dims)]
+        reduce_edge_list(end_edges)
+
+    # Base cases. Either start/end are empty and we're done, or the final,
+    # one-dimensional tensor can be simply sliced
+    if len(start) == 0:
+        return [()]
+    elif len(start) == 1:
+        return [(slice(start[0], end[0] + 1),)]
+
+    slices: list[tuple[slice, ...]] = []
+    path_list: list[slice] = []
+
+    # Dimensions common to start and end can be selected directly
+    for s, e in zip(start, end):
+        if s == e:
+            path_list.append(slice(s, s + 1))
+        else:
+            break
+
+    path: tuple[slice, ...] = tuple(path_list)
+    divergence_idx = len(path)
+
+    # start == end, and we're done
+    if divergence_idx == len(dims):
+        return [path]
+
+    def upper() -> tuple[tuple[slice, ...], ...]:
+        assert start_edges is not None
+        assert end_edges is not None
+
+        sdi = start[divergence_idx]
+        return tuple(
+            path + (slice(sdi, sdi + 1),) + s
+            for s in _get_minimal_slice_set(
+                start[divergence_idx + 1 :],
+                [d - 1 for d in dims[divergence_idx + 1 :]],
+                dims[divergence_idx + 1 :],
+                start_edges=start_edges[divergence_idx + 1 :],
+                end_edges=[True for _ in end_edges[divergence_idx + 1 :]],
+            )
+        )
+
+    def lower() -> tuple[tuple[slice, ...], ...]:
+        assert start_edges is not None
+        assert end_edges is not None
+
+        edi = end[divergence_idx]
+        return tuple(
+            path + (slice(edi, edi + 1),) + s
+            for s in _get_minimal_slice_set(
+                [0 for _ in start[divergence_idx + 1 :]],
+                end[divergence_idx + 1 :],
+                dims[divergence_idx + 1 :],
+                start_edges=[True for _ in start_edges[divergence_idx + 1 :]],
+                end_edges=end_edges[divergence_idx + 1 :],
+            )
+        )
+
+    # If both start and end are at the edges of the subtree rooted at
+    # divergence_idx, we can just select the whole subtree at once
+    if start_edges[divergence_idx] and end_edges[divergence_idx]:
+        slices.append(path + (slice(start[divergence_idx], end[divergence_idx] + 1),))
+    # If just start is at the edge, we can grab almost all of the subtree,
+    # treating only the ragged bottom edge as an edge case
+    elif start_edges[divergence_idx]:
+        slices.append(path + (slice(start[divergence_idx], end[divergence_idx]),))
+        slices.extend(lower())
+    # Analogous to the previous case, but the top is ragged this time
+    elif end_edges[divergence_idx]:
+        slices.extend(upper())
+        slices.append(path + (slice(start[divergence_idx] + 1, end[divergence_idx] + 1),))
+    # If both sides of the range are ragged, we need to handle both sides
+    # separately. If there's contiguous meat in between them, we can index it
+    # in one big chunk
+    else:
+        slices.extend(upper())
+        middle_ground = end[divergence_idx] - start[divergence_idx]
+        if middle_ground > 1:
+            slices.append(path + (slice(start[divergence_idx] + 1, end[divergence_idx]),))
+        slices.extend(lower())
+
+    return slices
+
+
+@torch.jit.ignore
+def _chunk_slice(t: torch.Tensor, flat_start: int, flat_end: int, no_batch_dims: int) -> torch.Tensor:
+    """
+    Equivalent to
+
+        t.reshape((-1,) + t.shape[no_batch_dims:])[flat_start:flat_end]
+
+    but without the need for the initial reshape call, which can be memory-intensive in certain situations. The only
+    reshape operations in this function are performed on sub-tensors that scale with (flat_end - flat_start), the chunk
+    size.
+    """
+
+    batch_dims = t.shape[:no_batch_dims]
+    start_idx = list(_flat_idx_to_idx(flat_start, batch_dims))
+    # _get_minimal_slice_set is inclusive
+    end_idx = list(_flat_idx_to_idx(flat_end - 1, batch_dims))
+
+    # Get an ordered list of slices to perform
+    slices = _get_minimal_slice_set(
+        start_idx,
+        end_idx,
+        batch_dims,
+    )
+
+    sliced_tensors = [t[s] for s in slices]
+
+    return torch.cat([s.view((-1,) + t.shape[no_batch_dims:]) for s in sliced_tensors])
+
+
+def chunk_layer(
+    layer: Callable,
+    inputs: dict[str, Any],
+    chunk_size: int,
+    no_batch_dims: int,
+    low_mem: bool = False,
+    _out: Any = None,
+    _add_into_out: bool = False,
+) -> Any:
+    """
+    Implements the "chunking" procedure described in section 1.11.8.
+
+    Layer outputs and inputs are assumed to be simple "pytrees," consisting only of (arbitrarily nested) lists, tuples,
+    and dicts with torch.Tensor leaves.
+
+    Args:
+        layer:
+            The layer to be applied chunk-wise
+        inputs:
+            A (non-nested) dictionary of keyworded inputs. All leaves must be tensors and must share the same batch
+            dimensions.
+        chunk_size:
+            The number of sub-batches per chunk. If multiple batch dimensions are specified, a "sub-batch" is defined
+            as a single indexing of all batch dimensions simultaneously (s.t. the number of sub-batches is the product
+            of the batch dimensions).
+        no_batch_dims:
+            How many of the initial dimensions of each input tensor can be considered batch dimensions.
+        low_mem:
+            Avoids flattening potentially large input tensors. Unnecessary in most cases, and is ever so slightly
+            slower than the default setting.
+    Returns:
+        The reassembled output of the layer on the inputs.
+    """
+    if not (len(inputs) > 0):
+        raise ValueError("Must provide at least one input")
+
+    initial_dims = [shape[:no_batch_dims] for shape in _fetch_dims(inputs)]
+    orig_batch_dims = tuple(max(s) for s in zip(*initial_dims))
+
+    def _prep_inputs(t: torch.Tensor) -> torch.Tensor:
+        if not low_mem:
+            if sum(t.shape[:no_batch_dims]) != no_batch_dims:
+                t = t.expand(orig_batch_dims + t.shape[no_batch_dims:])
+            t = t.reshape(-1, *t.shape[no_batch_dims:])
+        else:
+            t = t.expand(orig_batch_dims + t.shape[no_batch_dims:])
+        return t
+
+    prepped_inputs: dict[str, Any] = tensor_tree_map(_prep_inputs, inputs)
+    prepped_outputs = None
+    if _out is not None:
+        prepped_outputs = tensor_tree_map(lambda t: t.view([-1] + list(t.shape[no_batch_dims:])), _out)
+
+    flat_batch_dim = 1
+    for d in orig_batch_dims:
+        flat_batch_dim *= d
+
+    no_chunks = flat_batch_dim // chunk_size + (flat_batch_dim % chunk_size != 0)
+
+    def _select_chunk(t: torch.Tensor) -> torch.Tensor:
+        return t[i : i + chunk_size] if t.shape[0] != 1 else t
+
+    i = 0
+    out = prepped_outputs
+    for _ in range(no_chunks):
+        # Chunk the input
+        if not low_mem:
+            select_chunk = _select_chunk
+        else:
+            select_chunk = partial(
+                _chunk_slice,
+                flat_start=i,
+                flat_end=min(flat_batch_dim, i + chunk_size),
+                no_batch_dims=len(orig_batch_dims),
+            )
+
+        chunks: dict[str, Any] = tensor_tree_map(select_chunk, prepped_inputs)
+
+        # Run the layer on the chunk
+        output_chunk = layer(**chunks)
+
+        # Allocate space for the output
+        if out is None:
+            out = tensor_tree_map(lambda t: t.new_zeros((flat_batch_dim,) + t.shape[1:]), output_chunk)
+
+        # Put the chunk in its pre-allocated space
+        if isinstance(output_chunk, dict):
+
+            def assign(d1: dict, d2: dict) -> None:
+                for k, v in d1.items():
+                    if isinstance(v, dict):
+                        assign(v, d2[k])
+                    else:
+                        if _add_into_out:
+                            v[i : i + chunk_size] += d2[k]
+                        else:
+                            v[i : i + chunk_size] = d2[k]
+
+            assign(out, output_chunk)
+        elif isinstance(output_chunk, tuple):
+            for x1, x2 in zip(out, output_chunk):
+                if _add_into_out:
+                    x1[i : i + chunk_size] += x2
+                else:
+                    x1[i : i + chunk_size] = x2
+        elif isinstance(output_chunk, torch.Tensor):
+            if _add_into_out:
+                out[i : i + chunk_size] += output_chunk
+            else:
+                out[i : i + chunk_size] = output_chunk
+        else:
+            raise TypeError("Not supported")
+
+        i += chunk_size
+
+    out = tensor_tree_map(lambda t: t.view(orig_batch_dims + t.shape[1:]), out)
+
+    return out
+
+
+class ChunkSizeTuner:
+    def __init__(
+        self,
+        # Heuristically, runtimes for most of the modules in the network
+        # plateau earlier than this on all GPUs I've run the model on.
+        max_chunk_size: int = 512,
+    ):
+        self.max_chunk_size = max_chunk_size
+        self.cached_chunk_size: int | None = None
+        self.cached_arg_data: tuple | None = None
+
+    def _determine_favorable_chunk_size(self, fn: Callable, args: tuple, min_chunk_size: int) -> int:
+        logging.info("Tuning chunk size...")
+
+        if min_chunk_size >= self.max_chunk_size:
+            return min_chunk_size
+
+        candidates: list[int] = [2**l for l in range(int(math.log2(self.max_chunk_size)) + 1)]
+        candidates = [c for c in candidates if c > min_chunk_size]
+        candidates = [min_chunk_size] + candidates
+        candidates[-1] += 4
+
+        def test_chunk_size(chunk_size: int) -> bool:
+            try:
+                with torch.no_grad():
+                    fn(*args, chunk_size=chunk_size)
+                return True
+            except RuntimeError:
+                return False
+
+        min_viable_chunk_size_index = 0
+        i = len(candidates) - 1
+        while i > min_viable_chunk_size_index:
+            viable = test_chunk_size(candidates[i])
+            if not viable:
+                i = (min_viable_chunk_size_index + i) // 2
+            else:
+                min_viable_chunk_size_index = i
+                i = (i + len(candidates) - 1) // 2
+
+        return candidates[min_viable_chunk_size_index]
+
+    def _compare_arg_caches(self, ac1: Iterable, ac2: Iterable) -> bool:
+        consistent = True
+        for a1, a2 in zip(ac1, ac2):
+            assert type(ac1) is type(ac2)
+            if isinstance(ac1, (list, tuple)):
+                consistent &= self._compare_arg_caches(a1, a2)
+            elif isinstance(ac1, dict):
+                a1_items = [v for _, v in sorted(a1.items(), key=lambda x: x[0])]
+                a2_items = [v for _, v in sorted(a2.items(), key=lambda x: x[0])]
+                consistent &= self._compare_arg_caches(a1_items, a2_items)
+            else:
+                consistent &= a1 == a2
+
+        return consistent
+
+    def tune_chunk_size(
+        self,
+        representative_fn: Callable,
+        args: tuple,
+        min_chunk_size: int,
+    ) -> int:
+        consistent = True
+        arg_data: tuple = tree_map(lambda a: a.shape if isinstance(a, torch.Tensor) else a, args, object)
+        if self.cached_arg_data is not None:
+            # If args have changed shape/value, we need to re-tune
+            assert len(self.cached_arg_data) == len(arg_data)
+            consistent = self._compare_arg_caches(self.cached_arg_data, arg_data)
+        else:
+            # Otherwise, we can reuse the precomputed value
+            consistent = False
+
+        if not consistent:
+            self.cached_chunk_size = self._determine_favorable_chunk_size(
+                representative_fn,
+                args,
+                min_chunk_size,
+            )
+            self.cached_arg_data = arg_data
+
+        assert self.cached_chunk_size is not None
+
+        return self.cached_chunk_size
diff --git a/data/conda_envs/evalclaw/lib/python3.11/site-packages/transformers/models/esm/openfold_utils/data_transforms.py b/data/conda_envs/evalclaw/lib/python3.11/site-packages/transformers/models/esm/openfold_utils/data_transforms.py
new file mode 100644
index 0000000000000000000000000000000000000000..bcd67aacab8e5ee6d141166d1ec7fa94cba84e6d
--- /dev/null
+++ b/data/conda_envs/evalclaw/lib/python3.11/site-packages/transformers/models/esm/openfold_utils/data_transforms.py
@@ -0,0 +1,90 @@
+# Copyright 2021 AlQuraishi Laboratory
+# Copyright 2021 DeepMind Technologies Limited
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
+import numpy as np
+import torch
+
+from . import residue_constants as rc
+from .tensor_utils import tensor_tree_map, tree_map
+
+
+def make_atom14_masks(protein: dict[str, torch.Tensor]) -> dict[str, torch.Tensor]:
+    """Construct denser atom positions (14 dimensions instead of 37)."""
+    restype_atom14_to_atom37_list = []
+    restype_atom37_to_atom14_list = []
+    restype_atom14_mask_list = []
+
+    for rt in rc.restypes:
+        atom_names = rc.restype_name_to_atom14_names[rc.restype_1to3[rt]]
+        restype_atom14_to_atom37_list.append([(rc.atom_order[name] if name else 0) for name in atom_names])
+        atom_name_to_idx14 = {name: i for i, name in enumerate(atom_names)}
+        restype_atom37_to_atom14_list.append([(atom_name_to_idx14.get(name, 0)) for name in rc.atom_types])
+
+        restype_atom14_mask_list.append([(1.0 if name else 0.0) for name in atom_names])
+
+    # Add dummy mapping for restype 'UNK'
+    restype_atom14_to_atom37_list.append([0] * 14)
+    restype_atom37_to_atom14_list.append([0] * 37)
+    restype_atom14_mask_list.append([0.0] * 14)
+
+    restype_atom14_to_atom37 = torch.tensor(
+        restype_atom14_to_atom37_list,
+        dtype=torch.int32,
+        device=protein["aatype"].device,
+    )
+    restype_atom37_to_atom14 = torch.tensor(
+        restype_atom37_to_atom14_list,
+        dtype=torch.int32,
+        device=protein["aatype"].device,
+    )
+    restype_atom14_mask = torch.tensor(
+        restype_atom14_mask_list,
+        dtype=torch.float32,
+        device=protein["aatype"].device,
+    )
+    protein_aatype = 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
+    residx_atom14_to_atom37 = restype_atom14_to_atom37[protein_aatype]
+    residx_atom14_mask = restype_atom14_mask[protein_aatype]
+
+    protein["atom14_atom_exists"] = residx_atom14_mask
+    protein["residx_atom14_to_atom37"] = residx_atom14_to_atom37.long()
+
+    # create the gather indices for mapping back
+    residx_atom37_to_atom14 = restype_atom37_to_atom14[protein_aatype]
+    protein["residx_atom37_to_atom14"] = residx_atom37_to_atom14.long()
+
+    # create the corresponding mask
+    restype_atom37_mask = torch.zeros([21, 37], dtype=torch.float32, device=protein["aatype"].device)
+    for restype, restype_letter in enumerate(rc.restypes):
+        restype_name = rc.restype_1to3[restype_letter]
+        atom_names = rc.residue_atoms[restype_name]
+        for atom_name in atom_names:
+            atom_type = rc.atom_order[atom_name]
+            restype_atom37_mask[restype, atom_type] = 1
+
+    residx_atom37_mask = restype_atom37_mask[protein_aatype]
+    protein["atom37_atom_exists"] = residx_atom37_mask
+
+    return protein
+
+
+def make_atom14_masks_np(batch: dict[str, torch.Tensor]) -> dict[str, np.ndarray]:
+    batch = tree_map(lambda n: torch.tensor(n, device=batch["aatype"].device), batch, np.ndarray)
+    out = tensor_tree_map(lambda t: np.array(t), make_atom14_masks(batch))
+    return out
diff --git a/data/conda_envs/evalclaw/lib/python3.11/site-packages/transformers/models/esm/openfold_utils/feats.py b/data/conda_envs/evalclaw/lib/python3.11/site-packages/transformers/models/esm/openfold_utils/feats.py
new file mode 100644
index 0000000000000000000000000000000000000000..366f3c47d9466d0c5556b6eb7c365393785a82aa
--- /dev/null
+++ b/data/conda_envs/evalclaw/lib/python3.11/site-packages/transformers/models/esm/openfold_utils/feats.py
@@ -0,0 +1,253 @@
+# Copyright 2021 AlQuraishi Laboratory
+# Copyright 2021 DeepMind Technologies Limited
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from typing import 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 pseudo_beta_fn(aatype: torch.Tensor, all_atom_positions: torch.Tensor, all_atom_masks: None) -> torch.Tensor: ...
+
+
+@overload
+def pseudo_beta_fn(
+    aatype: torch.Tensor, all_atom_positions: torch.Tensor, all_atom_masks: torch.Tensor
+) -> tuple[torch.Tensor, torch.Tensor]: ...
+
+
+def pseudo_beta_fn(aatype, all_atom_positions, all_atom_masks):
+    is_gly = aatype == rc.restype_order["G"]
+    ca_idx = rc.atom_order["CA"]
+    cb_idx = rc.atom_order["CB"]
+    pseudo_beta = 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:
+        pseudo_beta_mask = torch.where(
+            is_gly,
+            all_atom_masks[..., ca_idx],
+            all_atom_masks[..., cb_idx],
+        )
+        return pseudo_beta, pseudo_beta_mask
+    else:
+        return pseudo_beta
+
+
+def atom14_to_atom37(atom14: torch.Tensor, batch: dict[str, torch.Tensor]) -> torch.Tensor:
+    atom37_data = batched_gather(
+        atom14,
+        batch["residx_atom37_to_atom14"],
+        dim=-2,
+        no_batch_dims=len(atom14.shape[:-2]),
+    )
+
+    atom37_data = atom37_data * batch["atom37_atom_exists"][..., None]
+
+    return atom37_data
+
+
+def build_template_angle_feat(template_feats: dict[str, torch.Tensor]) -> torch.Tensor:
+    template_aatype = template_feats["template_aatype"]
+    torsion_angles_sin_cos = template_feats["template_torsion_angles_sin_cos"]
+    alt_torsion_angles_sin_cos = template_feats["template_alt_torsion_angles_sin_cos"]
+    torsion_angles_mask = template_feats["template_torsion_angles_mask"]
+    template_angle_feat = torch.cat(
+        [
+            nn.functional.one_hot(template_aatype, 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 build_template_pair_feat(
+    batch: dict[str, torch.Tensor],
+    min_bin: torch.types.Number,
+    max_bin: torch.types.Number,
+    no_bins: int,
+    use_unit_vector: bool = False,
+    eps: float = 1e-20,
+    inf: float = 1e8,
+) -> torch.Tensor:
+    template_mask = batch["template_pseudo_beta_mask"]
+    template_mask_2d = template_mask[..., None] * template_mask[..., None, :]
+
+    # Compute distogram (this seems to differ slightly from Alg. 5)
+    tpb = batch["template_pseudo_beta"]
+    dgram = torch.sum((tpb[..., None, :] - tpb[..., None, :, :]) ** 2, dim=-1, keepdim=True)
+    lower = torch.linspace(min_bin, max_bin, no_bins, device=tpb.device) ** 2
+    upper = torch.cat([lower[1:], lower.new_tensor([inf])], dim=-1)
+    dgram = ((dgram > lower) * (dgram < upper)).type(dgram.dtype)
+
+    to_concat = [dgram, template_mask_2d[..., None]]
+
+    aatype_one_hot: torch.LongTensor = nn.functional.one_hot(
+        batch["template_aatype"],
+        rc.restype_num + 2,
+    )
+
+    n_res = batch["template_aatype"].shape[-1]
+    to_concat.append(aatype_one_hot[..., None, :, :].expand(*aatype_one_hot.shape[:-2], n_res, -1, -1))
+    to_concat.append(aatype_one_hot[..., None, :].expand(*aatype_one_hot.shape[:-2], -1, n_res, -1))
+
+    n, ca, c = [rc.atom_order[a] for a in ["N", "CA", "C"]]
+    rigids = 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=eps,
+    )
+    points = rigids.get_trans()[..., None, :, :]
+    rigid_vec = rigids[..., None].invert_apply(points)
+
+    inv_distance_scalar = torch.rsqrt(eps + torch.sum(rigid_vec**2, dim=-1))
+
+    t_aa_masks = batch["template_all_atom_mask"]
+    template_mask = t_aa_masks[..., n] * t_aa_masks[..., ca] * t_aa_masks[..., c]
+    template_mask_2d = template_mask[..., None] * template_mask[..., None, :]
+
+    inv_distance_scalar = inv_distance_scalar * template_mask_2d
+    unit_vector = rigid_vec * inv_distance_scalar[..., None]
+
+    if not use_unit_vector:
+        unit_vector = unit_vector * 0.0
+
+    to_concat.extend(torch.unbind(unit_vector[..., None, :], dim=-1))
+    to_concat.append(template_mask_2d[..., None])
+
+    act = torch.cat(to_concat, dim=-1)
+    act = act * template_mask_2d[..., None]
+
+    return act
+
+
+def build_extra_msa_feat(batch: dict[str, torch.Tensor]) -> torch.Tensor:
+    msa_1hot: torch.LongTensor = nn.functional.one_hot(batch["extra_msa"], 23)
+    msa_feat = [
+        msa_1hot,
+        batch["extra_has_deletion"].unsqueeze(-1),
+        batch["extra_deletion_value"].unsqueeze(-1),
+    ]
+    return torch.cat(msa_feat, dim=-1)
+
+
+def torsion_angles_to_frames(
+    r: Rigid,
+    alpha: torch.Tensor,
+    aatype: torch.Tensor,
+    rrgdf: torch.Tensor,
+) -> Rigid:
+    # [*, N, 8, 4, 4]
+    default_4x4 = rrgdf[aatype, ...]
+
+    # [*, N, 8] transformations, i.e.
+    #   One [*, N, 8, 3, 3] rotation matrix and
+    #   One [*, N, 8, 3]    translation matrix
+    default_r = r.from_tensor_4x4(default_4x4)
+
+    bb_rot = alpha.new_zeros((*((1,) * len(alpha.shape[:-1])), 2))
+    bb_rot[..., 1] = 1
+
+    # [*, N, 8, 2]
+    alpha = 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.
+
+    all_rots = alpha.new_zeros(default_r.get_rots().get_rot_mats().shape)
+    all_rots[..., 0, 0] = 1
+    all_rots[..., 1, 1] = alpha[..., 1]
+    all_rots[..., 1, 2] = -alpha[..., 0]
+    all_rots[..., 2, 1:] = alpha
+
+    all_frames = default_r.compose(Rigid(Rotation(rot_mats=all_rots), None))
+
+    chi2_frame_to_frame = all_frames[..., 5]
+    chi3_frame_to_frame = all_frames[..., 6]
+    chi4_frame_to_frame = all_frames[..., 7]
+
+    chi1_frame_to_bb = all_frames[..., 4]
+    chi2_frame_to_bb = chi1_frame_to_bb.compose(chi2_frame_to_frame)
+    chi3_frame_to_bb = chi2_frame_to_bb.compose(chi3_frame_to_frame)
+    chi4_frame_to_bb = chi3_frame_to_bb.compose(chi4_frame_to_frame)
+
+    all_frames_to_bb = Rigid.cat(
+        [
+            all_frames[..., :5],
+            chi2_frame_to_bb.unsqueeze(-1),
+            chi3_frame_to_bb.unsqueeze(-1),
+            chi4_frame_to_bb.unsqueeze(-1),
+        ],
+        dim=-1,
+    )
+
+    all_frames_to_global = r[..., None].compose(all_frames_to_bb)
+
+    return all_frames_to_global
+
+
+def frames_and_literature_positions_to_atom14_pos(
+    r: Rigid,
+    aatype: torch.Tensor,
+    default_frames: torch.Tensor,
+    group_idx: torch.Tensor,
+    atom_mask: torch.Tensor,
+    lit_positions: torch.Tensor,
+) -> torch.Tensor:
+    # [*, N, 14]
+    group_mask = group_idx[aatype, ...]
+
+    # [*, N, 14, 8]
+    group_mask_one_hot: torch.LongTensor = nn.functional.one_hot(
+        group_mask,
+        num_classes=default_frames.shape[-3],
+    )
+
+    # [*, N, 14, 8]
+    t_atoms_to_global = r[..., None, :] * group_mask_one_hot
+
+    # [*, N, 14]
+    t_atoms_to_global = t_atoms_to_global.map_tensor_fn(lambda x: torch.sum(x, dim=-1))
+
+    # [*, N, 14, 1]
+    atom_mask = atom_mask[aatype, ...].unsqueeze(-1)
+
+    # [*, N, 14, 3]
+    lit_positions = lit_positions[aatype, ...]
+    pred_positions = t_atoms_to_global.apply(lit_positions)
+    pred_positions = pred_positions * atom_mask
+
+    return pred_positions
diff --git a/data/conda_envs/evalclaw/lib/python3.11/site-packages/transformers/models/esm/openfold_utils/loss.py b/data/conda_envs/evalclaw/lib/python3.11/site-packages/transformers/models/esm/openfold_utils/loss.py
new file mode 100644
index 0000000000000000000000000000000000000000..1ca0e64306ba9ee0db0b10370e06b92c75451862
--- /dev/null
+++ b/data/conda_envs/evalclaw/lib/python3.11/site-packages/transformers/models/esm/openfold_utils/loss.py
@@ -0,0 +1,104 @@
+# Copyright 2021 AlQuraishi Laboratory
+# Copyright 2021 DeepMind Technologies Limited
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
+import torch
+
+
+def _calculate_bin_centers(boundaries: torch.Tensor) -> torch.Tensor:
+    step = boundaries[1] - boundaries[0]
+    bin_centers = boundaries + step / 2
+    bin_centers = torch.cat([bin_centers, (bin_centers[-1] + step).unsqueeze(-1)], dim=0)
+    return bin_centers
+
+
+def _calculate_expected_aligned_error(
+    alignment_confidence_breaks: torch.Tensor,
+    aligned_distance_error_probs: torch.Tensor,
+) -> tuple[torch.Tensor, torch.Tensor]:
+    bin_centers = _calculate_bin_centers(alignment_confidence_breaks)
+    return (
+        torch.sum(aligned_distance_error_probs * bin_centers, dim=-1),
+        bin_centers[-1],
+    )
+
+
+def compute_predicted_aligned_error(
+    logits: torch.Tensor,
+    max_bin: int = 31,
+    no_bins: int = 64,
+    **kwargs,
+) -> dict[str, torch.Tensor]:
+    """Computes aligned confidence metrics from logits.
+
+    Args:
+      logits: [*, num_res, num_res, num_bins] the logits output from
+        PredictedAlignedErrorHead.
+      max_bin: Maximum bin value
+      no_bins: Number of bins
+    Returns:
+      aligned_confidence_probs: [*, num_res, num_res, num_bins] the predicted
+        aligned error probabilities over bins for each residue pair.
+      predicted_aligned_error: [*, num_res, num_res] the expected aligned distance
+        error for each pair of residues.
+      max_predicted_aligned_error: [*] the maximum predicted error possible.
+    """
+    boundaries = torch.linspace(0, max_bin, steps=(no_bins - 1), device=logits.device)
+
+    aligned_confidence_probs = torch.nn.functional.softmax(logits, dim=-1)
+    predicted_aligned_error, max_predicted_aligned_error = _calculate_expected_aligned_error(
+        alignment_confidence_breaks=boundaries,
+        aligned_distance_error_probs=aligned_confidence_probs,
+    )
+
+    return {
+        "aligned_confidence_probs": aligned_confidence_probs,
+        "predicted_aligned_error": predicted_aligned_error,
+        "max_predicted_aligned_error": max_predicted_aligned_error,
+    }
+
+
+def compute_tm(
+    logits: torch.Tensor,
+    residue_weights: torch.Tensor | None = None,
+    max_bin: int = 31,
+    no_bins: int = 64,
+    eps: float = 1e-8,
+    **kwargs,
+) -> torch.Tensor:
+    if residue_weights is None:
+        residue_weights = logits.new_ones(logits.shape[-2])
+
+    boundaries = torch.linspace(0, max_bin, steps=(no_bins - 1), device=logits.device)
+
+    bin_centers = _calculate_bin_centers(boundaries)
+    torch.sum(residue_weights)
+    n = logits.shape[-2]
+    clipped_n = max(n, 19)
+
+    d0 = 1.24 * (clipped_n - 15) ** (1.0 / 3) - 1.8
+
+    probs = torch.nn.functional.softmax(logits, dim=-1)
+
+    tm_per_bin = 1.0 / (1 + (bin_centers**2) / (d0**2))
+    predicted_tm_term = torch.sum(probs * tm_per_bin, dim=-1)
+
+    normed_residue_mask = residue_weights / (eps + residue_weights.sum())
+    per_alignment = torch.sum(predicted_tm_term * normed_residue_mask, dim=-1)
+
+    weighted = per_alignment * residue_weights
+
+    argmax = (weighted == torch.max(weighted)).nonzero()[0]
+    return per_alignment[tuple(argmax)]
diff --git a/data/conda_envs/evalclaw/lib/python3.11/site-packages/transformers/models/esm/openfold_utils/protein.py b/data/conda_envs/evalclaw/lib/python3.11/site-packages/transformers/models/esm/openfold_utils/protein.py
new file mode 100644
index 0000000000000000000000000000000000000000..0c347119a49d227cf7f9e7e0572850e9d29a4200
--- /dev/null
+++ b/data/conda_envs/evalclaw/lib/python3.11/site-packages/transformers/models/esm/openfold_utils/protein.py
@@ -0,0 +1,330 @@
+# Copyright 2021 AlQuraishi Laboratory
+# Copyright 2021 DeepMind Technologies Limited
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""Protein data type."""
+
+import dataclasses
+import re
+import string
+from collections.abc import Iterator, Mapping, Sequence
+from typing import Any
+
+import numpy as np
+
+from . import residue_constants
+
+
+FeatureDict = Mapping[str, np.ndarray]
+ModelOutput = Mapping[str, Any]  # Is a nested dict.
+PICO_TO_ANGSTROM = 0.01
+
+
+@dataclasses.dataclass(frozen=True)
+class Protein:
+    """Protein structure representation."""
+
+    # Cartesian coordinates of atoms in angstroms. The atom types correspond to
+    # residue_constants.atom_types, i.e. the first three are N, CA, CB.
+    atom_positions: np.ndarray  # [num_res, num_atom_type, 3]
+
+    # Amino-acid type for each residue represented as an integer between 0 and
+    # 20, where 20 is 'X'.
+    aatype: np.ndarray  # [num_res]
+
+    # Binary float mask to indicate presence of a particular atom. 1.0 if an atom
+    # is present and 0.0 if not. This should be used for loss masking.
+    atom_mask: np.ndarray  # [num_res, num_atom_type]
+
+    # Residue index as used in PDB. It is not necessarily continuous or 0-indexed.
+    residue_index: np.ndarray  # [num_res]
+
+    # B-factors, or temperature factors, of each residue (in sq. angstroms units),
+    # representing the displacement of the residue from its ground truth mean
+    # value.
+    b_factors: np.ndarray  # [num_res, num_atom_type]
+
+    # Chain indices for multi-chain predictions
+    chain_index: np.ndarray | None = None
+
+    # Optional remark about the protein. Included as a comment in output PDB
+    # files
+    remark: str | None = None
+
+    # Templates used to generate this protein (prediction-only)
+    parents: Sequence[str] | None = None
+
+    # Chain corresponding to each parent
+    parents_chain_index: Sequence[int] | None = None
+
+
+def from_proteinnet_string(proteinnet_str: str) -> Protein:
+    tag_re = r"(\[[A-Z]+\]\n)"
+    tags: list[str] = [tag.strip() for tag in re.split(tag_re, proteinnet_str) if len(tag) > 0]
+    groups: Iterator[tuple[str, list[str]]] = zip(tags[0::2], [l.split("\n") for l in tags[1::2]])
+
+    atoms: list[str] = ["N", "CA", "C"]
+    aatype = None
+    atom_positions = None
+    atom_mask = None
+    for g in groups:
+        if g[0] == "[PRIMARY]":
+            seq = g[1][0].strip()
+            # Replace unknown residues with "X" (strings are immutable, so convert to list first)
+            seq = [char if char in residue_constants.restypes else "X" for char in seq]
+            aatype = np.array(
+                [residue_constants.restype_order.get(res_symbol, residue_constants.restype_num) for res_symbol in seq]
+            )
+        elif g[0] == "[TERTIARY]":
+            tertiary: list[list[float]] = []
+            for axis in range(3):
+                tertiary.append(list(map(float, g[1][axis].split())))
+            tertiary_np = np.array(tertiary)
+            atom_positions = np.zeros((len(tertiary[0]) // 3, residue_constants.atom_type_num, 3)).astype(np.float32)
+            for i, atom in enumerate(atoms):
+                atom_positions[:, residue_constants.atom_order[atom], :] = np.transpose(tertiary_np[:, i::3])
+            atom_positions *= PICO_TO_ANGSTROM
+        elif g[0] == "[MASK]":
+            mask = np.array(list(map({"-": 0, "+": 1}.get, g[1][0].strip())))
+            atom_mask = np.zeros(
+                (
+                    len(mask),
+                    residue_constants.atom_type_num,
+                )
+            ).astype(np.float32)
+            for i, atom in enumerate(atoms):
+                atom_mask[:, residue_constants.atom_order[atom]] = 1
+            atom_mask *= mask[..., None]
+
+    assert aatype is not None
+
+    return Protein(
+        atom_positions=atom_positions,
+        atom_mask=atom_mask,
+        aatype=aatype,
+        residue_index=np.arange(len(aatype)),
+        b_factors=None,
+    )
+
+
+def get_pdb_headers(prot: Protein, chain_id: int = 0) -> list[str]:
+    pdb_headers: list[str] = []
+
+    remark = prot.remark
+    if remark is not None:
+        pdb_headers.append(f"REMARK {remark}")
+
+    parents = prot.parents
+    parents_chain_index = prot.parents_chain_index
+    if parents is not None and parents_chain_index is not None:
+        parents = [p for i, p in zip(parents_chain_index, parents) if i == chain_id]
+
+    if parents is None or len(parents) == 0:
+        parents = ["N/A"]
+
+    pdb_headers.append(f"PARENT {' '.join(parents)}")
+
+    return pdb_headers
+
+
+def add_pdb_headers(prot: Protein, pdb_str: str) -> str:
+    """Add pdb headers to an existing PDB string. Useful during multi-chain
+    recycling
+    """
+    out_pdb_lines: list[str] = []
+    lines = pdb_str.split("\n")
+
+    remark = prot.remark
+    if remark is not None:
+        out_pdb_lines.append(f"REMARK {remark}")
+
+    parents_per_chain: list[list[str]]
+    if prot.parents is not None and len(prot.parents) > 0:
+        parents_per_chain = []
+        if prot.parents_chain_index is not None:
+            parent_dict: dict[str, list[str]] = {}
+            for p, i in zip(prot.parents, prot.parents_chain_index):
+                parent_dict.setdefault(str(i), [])
+                parent_dict[str(i)].append(p)
+
+            max_idx = max(int(chain_idx) for chain_idx in parent_dict)
+            for i in range(max_idx + 1):
+                chain_parents = parent_dict.get(str(i), ["N/A"])
+                parents_per_chain.append(chain_parents)
+        else:
+            parents_per_chain.append(list(prot.parents))
+    else:
+        parents_per_chain = [["N/A"]]
+
+    def make_parent_line(p: Sequence[str]) -> str:
+        return f"PARENT {' '.join(p)}"
+
+    out_pdb_lines.append(make_parent_line(parents_per_chain[0]))
+
+    chain_counter = 0
+    for i, l in enumerate(lines):
+        if "PARENT" not in l and "REMARK" not in l:
+            out_pdb_lines.append(l)
+        if "TER" in l and "END" not in lines[i + 1]:
+            chain_counter += 1
+            if not chain_counter >= len(parents_per_chain):
+                chain_parents = parents_per_chain[chain_counter]
+            else:
+                chain_parents = ["N/A"]
+
+            out_pdb_lines.append(make_parent_line(chain_parents))
+
+    return "\n".join(out_pdb_lines)
+
+
+def to_pdb(prot: Protein) -> str:
+    """Converts a `Protein` instance to a PDB string.
+
+    Args:
+      prot: The protein to convert to PDB.
+
+    Returns:
+      PDB string.
+    """
+    restypes = residue_constants.restypes + ["X"]
+
+    def res_1to3(r: int) -> str:
+        return residue_constants.restype_1to3.get(restypes[r], "UNK")
+
+    atom_types = residue_constants.atom_types
+
+    pdb_lines: list[str] = []
+
+    atom_mask = prot.atom_mask
+    aatype = prot.aatype
+    atom_positions = prot.atom_positions
+    residue_index = prot.residue_index.astype(np.int32)
+    b_factors = prot.b_factors
+    chain_index = prot.chain_index
+
+    if np.any(aatype > residue_constants.restype_num):
+        raise ValueError("Invalid aatypes.")
+
+    headers = get_pdb_headers(prot)
+    if len(headers) > 0:
+        pdb_lines.extend(headers)
+
+    n = aatype.shape[0]
+    atom_index = 1
+    prev_chain_index = 0
+    chain_tags = string.ascii_uppercase
+    chain_tag = None
+    # Add all atom sites.
+    for i in range(n):
+        res_name_3 = res_1to3(aatype[i])
+        for atom_name, pos, mask, b_factor in zip(atom_types, atom_positions[i], atom_mask[i], b_factors[i]):
+            if mask < 0.5:
+                continue
+
+            record_type = "ATOM"
+            name = atom_name if len(atom_name) == 4 else f" {atom_name}"
+            alt_loc = ""
+            insertion_code = ""
+            occupancy = 1.00
+            element = atom_name[0]  # Protein supports only C, N, O, S, this works.
+            charge = ""
+
+            chain_tag = "A"
+            if chain_index is not None:
+                chain_tag = chain_tags[chain_index[i]]
+
+            # PDB is a columnar format, every space matters here!
+            atom_line = (
+                f"{record_type:<6}{atom_index:>5} {name:<4}{alt_loc:>1}"
+                f"{res_name_3:>3} {chain_tag:>1}"
+                f"{residue_index[i]:>4}{insertion_code:>1}   "
+                f"{pos[0]:>8.3f}{pos[1]:>8.3f}{pos[2]:>8.3f}"
+                f"{occupancy:>6.2f}{b_factor:>6.2f}          "
+                f"{element:>2}{charge:>2}"
+            )
+            pdb_lines.append(atom_line)
+            atom_index += 1
+
+        should_terminate = i == n - 1
+        if chain_index is not None:
+            if i != n - 1 and chain_index[i + 1] != prev_chain_index:
+                should_terminate = True
+                prev_chain_index = chain_index[i + 1]
+
+        if should_terminate:
+            # Close the chain.
+            chain_end = "TER"
+            chain_termination_line = (
+                f"{chain_end:<6}{atom_index:>5}      {res_1to3(aatype[i]):>3} {chain_tag:>1}{residue_index[i]:>4}"
+            )
+            pdb_lines.append(chain_termination_line)
+            atom_index += 1
+
+            if i != n - 1:
+                # "prev" is a misnomer here. This happens at the beginning of
+                # each new chain.
+                pdb_lines.extend(get_pdb_headers(prot, prev_chain_index))
+
+    pdb_lines.append("END")
+    pdb_lines.append("")
+    return "\n".join(pdb_lines)
+
+
+def ideal_atom_mask(prot: Protein) -> np.ndarray:
+    """Computes an ideal atom mask.
+
+    `Protein.atom_mask` typically is defined according to the atoms that are reported in the PDB. This function
+    computes a mask according to heavy atoms that should be present in the given sequence of amino acids.
+
+    Args:
+      prot: `Protein` whose fields are `numpy.ndarray` objects.
+
+    Returns:
+      An ideal atom mask.
+    """
+    return residue_constants.STANDARD_ATOM_MASK[prot.aatype]
+
+
+def from_prediction(
+    features: FeatureDict,
+    result: ModelOutput,
+    b_factors: np.ndarray | None = None,
+    chain_index: np.ndarray | None = None,
+    remark: str | None = None,
+    parents: Sequence[str] | None = None,
+    parents_chain_index: Sequence[int] | None = None,
+) -> Protein:
+    """Assembles a protein from a prediction.
+
+    Args:
+      features: Dictionary holding model inputs.
+      result: Dictionary holding model outputs.
+      b_factors: (Optional) B-factors to use for the protein.
+      chain_index: (Optional) Chain indices for multi-chain predictions
+      remark: (Optional) Remark about the prediction
+      parents: (Optional) List of template names
+    Returns:
+      A protein instance.
+    """
+    return Protein(
+        aatype=features["aatype"],
+        atom_positions=result["final_atom_positions"],
+        atom_mask=result["final_atom_mask"],
+        residue_index=features["residue_index"] + 1,
+        b_factors=b_factors if b_factors is not None else np.zeros_like(result["final_atom_mask"]),
+        chain_index=chain_index,
+        remark=remark,
+        parents=parents,
+        parents_chain_index=parents_chain_index,
+    )
diff --git a/data/conda_envs/evalclaw/lib/python3.11/site-packages/transformers/models/esm/openfold_utils/residue_constants.py b/data/conda_envs/evalclaw/lib/python3.11/site-packages/transformers/models/esm/openfold_utils/residue_constants.py
new file mode 100644
index 0000000000000000000000000000000000000000..e92e65d29bfb2e7a0ad640e71d983c1c467d3a54
--- /dev/null
+++ b/data/conda_envs/evalclaw/lib/python3.11/site-packages/transformers/models/esm/openfold_utils/residue_constants.py
@@ -0,0 +1,979 @@
+# Copyright 2021 AlQuraishi Laboratory
+# Copyright 2021 DeepMind Technologies Limited
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""Constants used in AlphaFold."""
+
+import collections
+import copy
+import functools
+from collections.abc import Mapping, Sequence
+from importlib import resources
+
+import numpy as np
+
+
+# Internal import (35fd).
+
+
+# Distance from one CA to next CA [trans configuration: omega = 180].
+ca_ca = 3.80209737096
+
+# Format: The list for each AA type contains chi1, chi2, chi3, chi4 in
+# this order (or a relevant subset from chi1 onwards). ALA and GLY don't have
+# chi angles so their chi angle lists are empty.
+chi_angles_atoms: dict[str, list[list[str]]] = {
+    "ALA": [],
+    # Chi5 in arginine is always 0 +- 5 degrees, so ignore it.
+    "ARG": [["N", "CA", "CB", "CG"], ["CA", "CB", "CG", "CD"], ["CB", "CG", "CD", "NE"], ["CG", "CD", "NE", "CZ"]],
+    "ASN": [["N", "CA", "CB", "CG"], ["CA", "CB", "CG", "OD1"]],
+    "ASP": [["N", "CA", "CB", "CG"], ["CA", "CB", "CG", "OD1"]],
+    "CYS": [["N", "CA", "CB", "SG"]],
+    "GLN": [["N", "CA", "CB", "CG"], ["CA", "CB", "CG", "CD"], ["CB", "CG", "CD", "OE1"]],
+    "GLU": [["N", "CA", "CB", "CG"], ["CA", "CB", "CG", "CD"], ["CB", "CG", "CD", "OE1"]],
+    "GLY": [],
+    "HIS": [["N", "CA", "CB", "CG"], ["CA", "CB", "CG", "ND1"]],
+    "ILE": [["N", "CA", "CB", "CG1"], ["CA", "CB", "CG1", "CD1"]],
+    "LEU": [["N", "CA", "CB", "CG"], ["CA", "CB", "CG", "CD1"]],
+    "LYS": [["N", "CA", "CB", "CG"], ["CA", "CB", "CG", "CD"], ["CB", "CG", "CD", "CE"], ["CG", "CD", "CE", "NZ"]],
+    "MET": [["N", "CA", "CB", "CG"], ["CA", "CB", "CG", "SD"], ["CB", "CG", "SD", "CE"]],
+    "PHE": [["N", "CA", "CB", "CG"], ["CA", "CB", "CG", "CD1"]],
+    "PRO": [["N", "CA", "CB", "CG"], ["CA", "CB", "CG", "CD"]],
+    "SER": [["N", "CA", "CB", "OG"]],
+    "THR": [["N", "CA", "CB", "OG1"]],
+    "TRP": [["N", "CA", "CB", "CG"], ["CA", "CB", "CG", "CD1"]],
+    "TYR": [["N", "CA", "CB", "CG"], ["CA", "CB", "CG", "CD1"]],
+    "VAL": [["N", "CA", "CB", "CG1"]],
+}
+
+# If chi angles given in fixed-length array, this matrix determines how to mask
+# them for each AA type. The order is as per restype_order (see below).
+chi_angles_mask: list[list[float]] = [
+    [0.0, 0.0, 0.0, 0.0],  # ALA
+    [1.0, 1.0, 1.0, 1.0],  # ARG
+    [1.0, 1.0, 0.0, 0.0],  # ASN
+    [1.0, 1.0, 0.0, 0.0],  # ASP
+    [1.0, 0.0, 0.0, 0.0],  # CYS
+    [1.0, 1.0, 1.0, 0.0],  # GLN
+    [1.0, 1.0, 1.0, 0.0],  # GLU
+    [0.0, 0.0, 0.0, 0.0],  # GLY
+    [1.0, 1.0, 0.0, 0.0],  # HIS
+    [1.0, 1.0, 0.0, 0.0],  # ILE
+    [1.0, 1.0, 0.0, 0.0],  # LEU
+    [1.0, 1.0, 1.0, 1.0],  # LYS
+    [1.0, 1.0, 1.0, 0.0],  # MET
+    [1.0, 1.0, 0.0, 0.0],  # PHE
+    [1.0, 1.0, 0.0, 0.0],  # PRO
+    [1.0, 0.0, 0.0, 0.0],  # SER
+    [1.0, 0.0, 0.0, 0.0],  # THR
+    [1.0, 1.0, 0.0, 0.0],  # TRP
+    [1.0, 1.0, 0.0, 0.0],  # TYR
+    [1.0, 0.0, 0.0, 0.0],  # VAL
+]
+
+# The following chi angles are pi periodic: they can be rotated by a multiple
+# of pi without affecting the structure.
+chi_pi_periodic: list[list[float]] = [
+    [0.0, 0.0, 0.0, 0.0],  # ALA
+    [0.0, 0.0, 0.0, 0.0],  # ARG
+    [0.0, 0.0, 0.0, 0.0],  # ASN
+    [0.0, 1.0, 0.0, 0.0],  # ASP
+    [0.0, 0.0, 0.0, 0.0],  # CYS
+    [0.0, 0.0, 0.0, 0.0],  # GLN
+    [0.0, 0.0, 1.0, 0.0],  # GLU
+    [0.0, 0.0, 0.0, 0.0],  # GLY
+    [0.0, 0.0, 0.0, 0.0],  # HIS
+    [0.0, 0.0, 0.0, 0.0],  # ILE
+    [0.0, 0.0, 0.0, 0.0],  # LEU
+    [0.0, 0.0, 0.0, 0.0],  # LYS
+    [0.0, 0.0, 0.0, 0.0],  # MET
+    [0.0, 1.0, 0.0, 0.0],  # PHE
+    [0.0, 0.0, 0.0, 0.0],  # PRO
+    [0.0, 0.0, 0.0, 0.0],  # SER
+    [0.0, 0.0, 0.0, 0.0],  # THR
+    [0.0, 0.0, 0.0, 0.0],  # TRP
+    [0.0, 1.0, 0.0, 0.0],  # TYR
+    [0.0, 0.0, 0.0, 0.0],  # VAL
+    [0.0, 0.0, 0.0, 0.0],  # UNK
+]
+
+# Atoms positions relative to the 8 rigid groups, defined by the pre-omega, phi,
+# psi and chi angles:
+# 0: 'backbone group',
+# 1: 'pre-omega-group', (empty)
+# 2: 'phi-group', (currently empty, because it defines only hydrogens)
+# 3: 'psi-group',
+# 4,5,6,7: 'chi1,2,3,4-group'
+# The atom positions are relative to the axis-end-atom of the corresponding
+# rotation axis. The x-axis is in direction of the rotation axis, and the y-axis
+# is defined such that the dihedral-angle-definiting atom (the last entry in
+# chi_angles_atoms above) is in the xy-plane (with a positive y-coordinate).
+# format: [atomname, group_idx, rel_position]
+rigid_group_atom_positions: dict[str, list[tuple[str, int, tuple[float, float, float]]]] = {
+    "ALA": [
+        ("N", 0, (-0.525, 1.363, 0.000)),
+        ("CA", 0, (0.000, 0.000, 0.000)),
+        ("C", 0, (1.526, -0.000, -0.000)),
+        ("CB", 0, (-0.529, -0.774, -1.205)),
+        ("O", 3, (0.627, 1.062, 0.000)),
+    ],
+    "ARG": [
+        ("N", 0, (-0.524, 1.362, -0.000)),
+        ("CA", 0, (0.000, 0.000, 0.000)),
+        ("C", 0, (1.525, -0.000, -0.000)),
+        ("CB", 0, (-0.524, -0.778, -1.209)),
+        ("O", 3, (0.626, 1.062, 0.000)),
+        ("CG", 4, (0.616, 1.390, -0.000)),
+        ("CD", 5, (0.564, 1.414, 0.000)),
+        ("NE", 6, (0.539, 1.357, -0.000)),
+        ("NH1", 7, (0.206, 2.301, 0.000)),
+        ("NH2", 7, (2.078, 0.978, -0.000)),
+        ("CZ", 7, (0.758, 1.093, -0.000)),
+    ],
+    "ASN": [
+        ("N", 0, (-0.536, 1.357, 0.000)),
+        ("CA", 0, (0.000, 0.000, 0.000)),
+        ("C", 0, (1.526, -0.000, -0.000)),
+        ("CB", 0, (-0.531, -0.787, -1.200)),
+        ("O", 3, (0.625, 1.062, 0.000)),
+        ("CG", 4, (0.584, 1.399, 0.000)),
+        ("ND2", 5, (0.593, -1.188, 0.001)),
+        ("OD1", 5, (0.633, 1.059, 0.000)),
+    ],
+    "ASP": [
+        ("N", 0, (-0.525, 1.362, -0.000)),
+        ("CA", 0, (0.000, 0.000, 0.000)),
+        ("C", 0, (1.527, 0.000, -0.000)),
+        ("CB", 0, (-0.526, -0.778, -1.208)),
+        ("O", 3, (0.626, 1.062, -0.000)),
+        ("CG", 4, (0.593, 1.398, -0.000)),
+        ("OD1", 5, (0.610, 1.091, 0.000)),
+        ("OD2", 5, (0.592, -1.101, -0.003)),
+    ],
+    "CYS": [
+        ("N", 0, (-0.522, 1.362, -0.000)),
+        ("CA", 0, (0.000, 0.000, 0.000)),
+        ("C", 0, (1.524, 0.000, 0.000)),
+        ("CB", 0, (-0.519, -0.773, -1.212)),
+        ("O", 3, (0.625, 1.062, -0.000)),
+        ("SG", 4, (0.728, 1.653, 0.000)),
+    ],
+    "GLN": [
+        ("N", 0, (-0.526, 1.361, -0.000)),
+        ("CA", 0, (0.000, 0.000, 0.000)),
+        ("C", 0, (1.526, 0.000, 0.000)),
+        ("CB", 0, (-0.525, -0.779, -1.207)),
+        ("O", 3, (0.626, 1.062, -0.000)),
+        ("CG", 4, (0.615, 1.393, 0.000)),
+        ("CD", 5, (0.587, 1.399, -0.000)),
+        ("NE2", 6, (0.593, -1.189, -0.001)),
+        ("OE1", 6, (0.634, 1.060, 0.000)),
+    ],
+    "GLU": [
+        ("N", 0, (-0.528, 1.361, 0.000)),
+        ("CA", 0, (0.000, 0.000, 0.000)),
+        ("C", 0, (1.526, -0.000, -0.000)),
+        ("CB", 0, (-0.526, -0.781, -1.207)),
+        ("O", 3, (0.626, 1.062, 0.000)),
+        ("CG", 4, (0.615, 1.392, 0.000)),
+        ("CD", 5, (0.600, 1.397, 0.000)),
+        ("OE1", 6, (0.607, 1.095, -0.000)),
+        ("OE2", 6, (0.589, -1.104, -0.001)),
+    ],
+    "GLY": [
+        ("N", 0, (-0.572, 1.337, 0.000)),
+        ("CA", 0, (0.000, 0.000, 0.000)),
+        ("C", 0, (1.517, -0.000, -0.000)),
+        ("O", 3, (0.626, 1.062, -0.000)),
+    ],
+    "HIS": [
+        ("N", 0, (-0.527, 1.360, 0.000)),
+        ("CA", 0, (0.000, 0.000, 0.000)),
+        ("C", 0, (1.525, 0.000, 0.000)),
+        ("CB", 0, (-0.525, -0.778, -1.208)),
+        ("O", 3, (0.625, 1.063, 0.000)),
+        ("CG", 4, (0.600, 1.370, -0.000)),
+        ("CD2", 5, (0.889, -1.021, 0.003)),
+        ("ND1", 5, (0.744, 1.160, -0.000)),
+        ("CE1", 5, (2.030, 0.851, 0.002)),
+        ("NE2", 5, (2.145, -0.466, 0.004)),
+    ],
+    "ILE": [
+        ("N", 0, (-0.493, 1.373, -0.000)),
+        ("CA", 0, (0.000, 0.000, 0.000)),
+        ("C", 0, (1.527, -0.000, -0.000)),
+        ("CB", 0, (-0.536, -0.793, -1.213)),
+        ("O", 3, (0.627, 1.062, -0.000)),
+        ("CG1", 4, (0.534, 1.437, -0.000)),
+        ("CG2", 4, (0.540, -0.785, -1.199)),
+        ("CD1", 5, (0.619, 1.391, 0.000)),
+    ],
+    "LEU": [
+        ("N", 0, (-0.520, 1.363, 0.000)),
+        ("CA", 0, (0.000, 0.000, 0.000)),
+        ("C", 0, (1.525, -0.000, -0.000)),
+        ("CB", 0, (-0.522, -0.773, -1.214)),
+        ("O", 3, (0.625, 1.063, -0.000)),
+        ("CG", 4, (0.678, 1.371, 0.000)),
+        ("CD1", 5, (0.530, 1.430, -0.000)),
+        ("CD2", 5, (0.535, -0.774, 1.200)),
+    ],
+    "LYS": [
+        ("N", 0, (-0.526, 1.362, -0.000)),
+        ("CA", 0, (0.000, 0.000, 0.000)),
+        ("C", 0, (1.526, 0.000, 0.000)),
+        ("CB", 0, (-0.524, -0.778, -1.208)),
+        ("O", 3, (0.626, 1.062, -0.000)),
+        ("CG", 4, (0.619, 1.390, 0.000)),
+        ("CD", 5, (0.559, 1.417, 0.000)),
+        ("CE", 6, (0.560, 1.416, 0.000)),
+        ("NZ", 7, (0.554, 1.387, 0.000)),
+    ],
+    "MET": [
+        ("N", 0, (-0.521, 1.364, -0.000)),
+        ("CA", 0, (0.000, 0.000, 0.000)),
+        ("C", 0, (1.525, 0.000, 0.000)),
+        ("CB", 0, (-0.523, -0.776, -1.210)),
+        ("O", 3, (0.625, 1.062, -0.000)),
+        ("CG", 4, (0.613, 1.391, -0.000)),
+        ("SD", 5, (0.703, 1.695, 0.000)),
+        ("CE", 6, (0.320, 1.786, -0.000)),
+    ],
+    "PHE": [
+        ("N", 0, (-0.518, 1.363, 0.000)),
+        ("CA", 0, (0.000, 0.000, 0.000)),
+        ("C", 0, (1.524, 0.000, -0.000)),
+        ("CB", 0, (-0.525, -0.776, -1.212)),
+        ("O", 3, (0.626, 1.062, -0.000)),
+        ("CG", 4, (0.607, 1.377, 0.000)),
+        ("CD1", 5, (0.709, 1.195, -0.000)),
+        ("CD2", 5, (0.706, -1.196, 0.000)),
+        ("CE1", 5, (2.102, 1.198, -0.000)),
+        ("CE2", 5, (2.098, -1.201, -0.000)),
+        ("CZ", 5, (2.794, -0.003, -0.001)),
+    ],
+    "PRO": [
+        ("N", 0, (-0.566, 1.351, -0.000)),
+        ("CA", 0, (0.000, 0.000, 0.000)),
+        ("C", 0, (1.527, -0.000, 0.000)),
+        ("CB", 0, (-0.546, -0.611, -1.293)),
+        ("O", 3, (0.621, 1.066, 0.000)),
+        ("CG", 4, (0.382, 1.445, 0.0)),
+        # ('CD', 5, (0.427, 1.440, 0.0)),
+        ("CD", 5, (0.477, 1.424, 0.0)),  # manually made angle 2 degrees larger
+    ],
+    "SER": [
+        ("N", 0, (-0.529, 1.360, -0.000)),
+        ("CA", 0, (0.000, 0.000, 0.000)),
+        ("C", 0, (1.525, -0.000, -0.000)),
+        ("CB", 0, (-0.518, -0.777, -1.211)),
+        ("O", 3, (0.626, 1.062, -0.000)),
+        ("OG", 4, (0.503, 1.325, 0.000)),
+    ],
+    "THR": [
+        ("N", 0, (-0.517, 1.364, 0.000)),
+        ("CA", 0, (0.000, 0.000, 0.000)),
+        ("C", 0, (1.526, 0.000, -0.000)),
+        ("CB", 0, (-0.516, -0.793, -1.215)),
+        ("O", 3, (0.626, 1.062, 0.000)),
+        ("CG2", 4, (0.550, -0.718, -1.228)),
+        ("OG1", 4, (0.472, 1.353, 0.000)),
+    ],
+    "TRP": [
+        ("N", 0, (-0.521, 1.363, 0.000)),
+        ("CA", 0, (0.000, 0.000, 0.000)),
+        ("C", 0, (1.525, -0.000, 0.000)),
+        ("CB", 0, (-0.523, -0.776, -1.212)),
+        ("O", 3, (0.627, 1.062, 0.000)),
+        ("CG", 4, (0.609, 1.370, -0.000)),
+        ("CD1", 5, (0.824, 1.091, 0.000)),
+        ("CD2", 5, (0.854, -1.148, -0.005)),
+        ("CE2", 5, (2.186, -0.678, -0.007)),
+        ("CE3", 5, (0.622, -2.530, -0.007)),
+        ("NE1", 5, (2.140, 0.690, -0.004)),
+        ("CH2", 5, (3.028, -2.890, -0.013)),
+        ("CZ2", 5, (3.283, -1.543, -0.011)),
+        ("CZ3", 5, (1.715, -3.389, -0.011)),
+    ],
+    "TYR": [
+        ("N", 0, (-0.522, 1.362, 0.000)),
+        ("CA", 0, (0.000, 0.000, 0.000)),
+        ("C", 0, (1.524, -0.000, -0.000)),
+        ("CB", 0, (-0.522, -0.776, -1.213)),
+        ("O", 3, (0.627, 1.062, -0.000)),
+        ("CG", 4, (0.607, 1.382, -0.000)),
+        ("CD1", 5, (0.716, 1.195, -0.000)),
+        ("CD2", 5, (0.713, -1.194, -0.001)),
+        ("CE1", 5, (2.107, 1.200, -0.002)),
+        ("CE2", 5, (2.104, -1.201, -0.003)),
+        ("OH", 5, (4.168, -0.002, -0.005)),
+        ("CZ", 5, (2.791, -0.001, -0.003)),
+    ],
+    "VAL": [
+        ("N", 0, (-0.494, 1.373, -0.000)),
+        ("CA", 0, (0.000, 0.000, 0.000)),
+        ("C", 0, (1.527, -0.000, -0.000)),
+        ("CB", 0, (-0.533, -0.795, -1.213)),
+        ("O", 3, (0.627, 1.062, -0.000)),
+        ("CG1", 4, (0.540, 1.429, -0.000)),
+        ("CG2", 4, (0.533, -0.776, 1.203)),
+    ],
+}
+
+# A list of atoms (excluding hydrogen) for each AA type. PDB naming convention.
+residue_atoms: dict[str, list[str]] = {
+    "ALA": ["C", "CA", "CB", "N", "O"],
+    "ARG": ["C", "CA", "CB", "CG", "CD", "CZ", "N", "NE", "O", "NH1", "NH2"],
+    "ASP": ["C", "CA", "CB", "CG", "N", "O", "OD1", "OD2"],
+    "ASN": ["C", "CA", "CB", "CG", "N", "ND2", "O", "OD1"],
+    "CYS": ["C", "CA", "CB", "N", "O", "SG"],
+    "GLU": ["C", "CA", "CB", "CG", "CD", "N", "O", "OE1", "OE2"],
+    "GLN": ["C", "CA", "CB", "CG", "CD", "N", "NE2", "O", "OE1"],
+    "GLY": ["C", "CA", "N", "O"],
+    "HIS": ["C", "CA", "CB", "CG", "CD2", "CE1", "N", "ND1", "NE2", "O"],
+    "ILE": ["C", "CA", "CB", "CG1", "CG2", "CD1", "N", "O"],
+    "LEU": ["C", "CA", "CB", "CG", "CD1", "CD2", "N", "O"],
+    "LYS": ["C", "CA", "CB", "CG", "CD", "CE", "N", "NZ", "O"],
+    "MET": ["C", "CA", "CB", "CG", "CE", "N", "O", "SD"],
+    "PHE": ["C", "CA", "CB", "CG", "CD1", "CD2", "CE1", "CE2", "CZ", "N", "O"],
+    "PRO": ["C", "CA", "CB", "CG", "CD", "N", "O"],
+    "SER": ["C", "CA", "CB", "N", "O", "OG"],
+    "THR": ["C", "CA", "CB", "CG2", "N", "O", "OG1"],
+    "TRP": ["C", "CA", "CB", "CG", "CD1", "CD2", "CE2", "CE3", "CZ2", "CZ3", "CH2", "N", "NE1", "O"],
+    "TYR": ["C", "CA", "CB", "CG", "CD1", "CD2", "CE1", "CE2", "CZ", "N", "O", "OH"],
+    "VAL": ["C", "CA", "CB", "CG1", "CG2", "N", "O"],
+}
+
+# Naming swaps for ambiguous atom names.
+# Due to symmetries in the amino acids the naming of atoms is ambiguous in
+# 4 of the 20 amino acids.
+# (The LDDT paper lists 7 amino acids as ambiguous, but the naming ambiguities
+# in LEU, VAL and ARG can be resolved by using the 3d constellations of
+# the 'ambiguous' atoms and their neighbours)
+# TODO: ^ interpret this
+residue_atom_renaming_swaps: dict[str, dict[str, str]] = {
+    "ASP": {"OD1": "OD2"},
+    "GLU": {"OE1": "OE2"},
+    "PHE": {"CD1": "CD2", "CE1": "CE2"},
+    "TYR": {"CD1": "CD2", "CE1": "CE2"},
+}
+
+# Van der Waals radii [Angstroem] of the atoms (from Wikipedia)
+van_der_waals_radius: dict[str, float] = {
+    "C": 1.7,
+    "N": 1.55,
+    "O": 1.52,
+    "S": 1.8,
+}
+
+Bond = collections.namedtuple("Bond", ["atom1_name", "atom2_name", "length", "stddev"])
+BondAngle = collections.namedtuple(
+    "BondAngle",
+    ["atom1_name", "atom2_name", "atom3name", "angle_rad", "stddev"],
+)
+
+
+def map_structure_with_atom_order(in_list: list, first_call: bool = True) -> list:
+    # Maps strings in a nested list structure to their corresponding index in atom_order
+    if first_call:
+        in_list = copy.deepcopy(in_list)
+    for i in range(len(in_list)):
+        if isinstance(in_list[i], list):
+            in_list[i] = map_structure_with_atom_order(in_list[i], first_call=False)
+        elif isinstance(in_list[i], str):
+            in_list[i] = atom_order[in_list[i]]
+        else:
+            raise TypeError("Unexpected type when mapping nested lists!")
+    return in_list
+
+
+@functools.cache
+def load_stereo_chemical_props() -> tuple[
+    Mapping[str, list[Bond]],
+    Mapping[str, list[Bond]],
+    Mapping[str, list[BondAngle]],
+]:
+    """Load stereo_chemical_props.txt into a nice structure.
+
+    Load literature values for bond lengths and bond angles and translate bond angles into the length of the opposite
+    edge of the triangle ("residue_virtual_bonds").
+
+    Returns:
+      residue_bonds: dict that maps resname --> list of Bond tuples residue_virtual_bonds: dict that maps resname -->
+      list of Bond tuples residue_bond_angles: dict that maps resname --> list of BondAngle tuples
+    """
+    # TODO: this file should be downloaded in a setup script
+    stereo_chemical_props = resources.read_text("openfold.resources", "stereo_chemical_props.txt")
+
+    lines_iter = iter(stereo_chemical_props.splitlines())
+    # Load bond lengths.
+    residue_bonds: dict[str, list[Bond]] = {}
+    next(lines_iter)  # Skip header line.
+    for line in lines_iter:
+        if line.strip() == "-":
+            break
+        bond, resname, bond_length, stddev = line.split()
+        atom1, atom2 = bond.split("-")
+        if resname not in residue_bonds:
+            residue_bonds[resname] = []
+        residue_bonds[resname].append(Bond(atom1, atom2, float(bond_length), float(stddev)))
+    residue_bonds["UNK"] = []
+
+    # Load bond angles.
+    residue_bond_angles: dict[str, list[BondAngle]] = {}
+    next(lines_iter)  # Skip empty line.
+    next(lines_iter)  # Skip header line.
+    for line in lines_iter:
+        if line.strip() == "-":
+            break
+        bond, resname, angle_degree, stddev_degree = line.split()
+        atom1, atom2, atom3 = bond.split("-")
+        if resname not in residue_bond_angles:
+            residue_bond_angles[resname] = []
+        residue_bond_angles[resname].append(
+            BondAngle(
+                atom1,
+                atom2,
+                atom3,
+                float(angle_degree) / 180.0 * np.pi,
+                float(stddev_degree) / 180.0 * np.pi,
+            )
+        )
+    residue_bond_angles["UNK"] = []
+
+    def make_bond_key(atom1_name: str, atom2_name: str) -> str:
+        """Unique key to lookup bonds."""
+        return "-".join(sorted([atom1_name, atom2_name]))
+
+    # Translate bond angles into distances ("virtual bonds").
+    residue_virtual_bonds: dict[str, list[Bond]] = {}
+    for resname, bond_angles in residue_bond_angles.items():
+        # Create a fast lookup dict for bond lengths.
+        bond_cache: dict[str, Bond] = {}
+        for b in residue_bonds[resname]:
+            bond_cache[make_bond_key(b.atom1_name, b.atom2_name)] = b
+        residue_virtual_bonds[resname] = []
+        for ba in bond_angles:
+            bond1 = bond_cache[make_bond_key(ba.atom1_name, ba.atom2_name)]
+            bond2 = bond_cache[make_bond_key(ba.atom2_name, ba.atom3name)]
+
+            # Compute distance between atom1 and atom3 using the law of cosines
+            # c^2 = a^2 + b^2 - 2ab*cos(gamma).
+            gamma = ba.angle_rad
+            length = np.sqrt(bond1.length**2 + bond2.length**2 - 2 * bond1.length * bond2.length * np.cos(gamma))
+
+            # Propagation of uncertainty assuming uncorrelated errors.
+            dl_outer = 0.5 / length
+            dl_dgamma = (2 * bond1.length * bond2.length * np.sin(gamma)) * dl_outer
+            dl_db1 = (2 * bond1.length - 2 * bond2.length * np.cos(gamma)) * dl_outer
+            dl_db2 = (2 * bond2.length - 2 * bond1.length * np.cos(gamma)) * dl_outer
+            stddev = np.sqrt(
+                (dl_dgamma * ba.stddev) ** 2 + (dl_db1 * bond1.stddev) ** 2 + (dl_db2 * bond2.stddev) ** 2
+            )
+            residue_virtual_bonds[resname].append(Bond(ba.atom1_name, ba.atom3name, length, stddev))
+
+    return (residue_bonds, residue_virtual_bonds, residue_bond_angles)
+
+
+# Between-residue bond lengths for general bonds (first element) and for Proline
+# (second element).
+between_res_bond_length_c_n: tuple[float, float] = (1.329, 1.341)
+between_res_bond_length_stddev_c_n: tuple[float, float] = (0.014, 0.016)
+
+# Between-residue cos_angles.
+between_res_cos_angles_c_n_ca: tuple[float, float] = (-0.5203, 0.0353)  # degrees: 121.352 +- 2.315
+between_res_cos_angles_ca_c_n: tuple[float, float] = (-0.4473, 0.0311)  # degrees: 116.568 +- 1.995
+
+# This mapping is used when we need to store atom data in a format that requires
+# fixed atom data size for every residue (e.g. a numpy array).
+atom_types: list[str] = [
+    "N",
+    "CA",
+    "C",
+    "CB",
+    "O",
+    "CG",
+    "CG1",
+    "CG2",
+    "OG",
+    "OG1",
+    "SG",
+    "CD",
+    "CD1",
+    "CD2",
+    "ND1",
+    "ND2",
+    "OD1",
+    "OD2",
+    "SD",
+    "CE",
+    "CE1",
+    "CE2",
+    "CE3",
+    "NE",
+    "NE1",
+    "NE2",
+    "OE1",
+    "OE2",
+    "CH2",
+    "NH1",
+    "NH2",
+    "OH",
+    "CZ",
+    "CZ2",
+    "CZ3",
+    "NZ",
+    "OXT",
+]
+atom_order: dict[str, int] = {atom_type: i for i, atom_type in enumerate(atom_types)}
+atom_type_num = len(atom_types)  # := 37.
+
+# A compact atom encoding with 14 columns
+# pylint: disable=line-too-long
+restype_name_to_atom14_names: dict[str, list[str]] = {
+    "ALA": ["N", "CA", "C", "O", "CB", "", "", "", "", "", "", "", "", ""],
+    "ARG": ["N", "CA", "C", "O", "CB", "CG", "CD", "NE", "CZ", "NH1", "NH2", "", "", ""],
+    "ASN": ["N", "CA", "C", "O", "CB", "CG", "OD1", "ND2", "", "", "", "", "", ""],
+    "ASP": ["N", "CA", "C", "O", "CB", "CG", "OD1", "OD2", "", "", "", "", "", ""],
+    "CYS": ["N", "CA", "C", "O", "CB", "SG", "", "", "", "", "", "", "", ""],
+    "GLN": ["N", "CA", "C", "O", "CB", "CG", "CD", "OE1", "NE2", "", "", "", "", ""],
+    "GLU": ["N", "CA", "C", "O", "CB", "CG", "CD", "OE1", "OE2", "", "", "", "", ""],
+    "GLY": ["N", "CA", "C", "O", "", "", "", "", "", "", "", "", "", ""],
+    "HIS": ["N", "CA", "C", "O", "CB", "CG", "ND1", "CD2", "CE1", "NE2", "", "", "", ""],
+    "ILE": ["N", "CA", "C", "O", "CB", "CG1", "CG2", "CD1", "", "", "", "", "", ""],
+    "LEU": ["N", "CA", "C", "O", "CB", "CG", "CD1", "CD2", "", "", "", "", "", ""],
+    "LYS": ["N", "CA", "C", "O", "CB", "CG", "CD", "CE", "NZ", "", "", "", "", ""],
+    "MET": ["N", "CA", "C", "O", "CB", "CG", "SD", "CE", "", "", "", "", "", ""],
+    "PHE": ["N", "CA", "C", "O", "CB", "CG", "CD1", "CD2", "CE1", "CE2", "CZ", "", "", ""],
+    "PRO": ["N", "CA", "C", "O", "CB", "CG", "CD", "", "", "", "", "", "", ""],
+    "SER": ["N", "CA", "C", "O", "CB", "OG", "", "", "", "", "", "", "", ""],
+    "THR": ["N", "CA", "C", "O", "CB", "OG1", "CG2", "", "", "", "", "", "", ""],
+    "TRP": ["N", "CA", "C", "O", "CB", "CG", "CD1", "CD2", "NE1", "CE2", "CE3", "CZ2", "CZ3", "CH2"],
+    "TYR": ["N", "CA", "C", "O", "CB", "CG", "CD1", "CD2", "CE1", "CE2", "CZ", "OH", "", ""],
+    "VAL": ["N", "CA", "C", "O", "CB", "CG1", "CG2", "", "", "", "", "", "", ""],
+    "UNK": ["", "", "", "", "", "", "", "", "", "", "", "", "", ""],
+}
+# pylint: enable=line-too-long
+
+
+# This is the standard residue order when coding AA type as a number.
+# Reproduce it by taking 3-letter AA codes and sorting them alphabetically.
+restypes: list[str] = [
+    "A",
+    "R",
+    "N",
+    "D",
+    "C",
+    "Q",
+    "E",
+    "G",
+    "H",
+    "I",
+    "L",
+    "K",
+    "M",
+    "F",
+    "P",
+    "S",
+    "T",
+    "W",
+    "Y",
+    "V",
+]
+restype_order: dict[str, int] = {restype: i for i, restype in enumerate(restypes)}
+restype_num = len(restypes)  # := 20.
+unk_restype_index = restype_num  # Catch-all index for unknown restypes.
+
+restypes_with_x: list[str] = restypes + ["X"]
+restype_order_with_x: dict[str, int] = {restype: i for i, restype in enumerate(restypes_with_x)}
+
+
+def sequence_to_onehot(sequence: str, mapping: Mapping[str, int], map_unknown_to_x: bool = False) -> np.ndarray:
+    """Maps the given sequence into a one-hot encoded matrix.
+
+    Args:
+      sequence: An amino acid sequence.
+      mapping: A dictionary mapping amino acids to integers.
+      map_unknown_to_x: If True, any amino acid that is not in the mapping will be
+        mapped to the unknown amino acid 'X'. If the mapping doesn't contain amino acid 'X', an error will be thrown.
+        If False, any amino acid not in the mapping will throw an error.
+
+    Returns:
+      A numpy array of shape (seq_len, num_unique_aas) with one-hot encoding of the sequence.
+
+    Raises:
+      ValueError: If the mapping doesn't contain values from 0 to
+        num_unique_aas - 1 without any gaps.
+    """
+    num_entries = max(mapping.values()) + 1
+
+    if sorted(set(mapping.values())) != list(range(num_entries)):
+        raise ValueError(
+            "The mapping must have values from 0 to num_unique_aas-1 without any gaps. Got: %s"
+            % sorted(mapping.values())
+        )
+
+    one_hot_arr = np.zeros((len(sequence), num_entries), dtype=np.int32)
+
+    for aa_index, aa_type in enumerate(sequence):
+        if map_unknown_to_x:
+            if aa_type.isalpha() and aa_type.isupper():
+                aa_id = mapping.get(aa_type, mapping["X"])
+            else:
+                raise ValueError(f"Invalid character in the sequence: {aa_type}")
+        else:
+            aa_id = mapping[aa_type]
+        one_hot_arr[aa_index, aa_id] = 1
+
+    return one_hot_arr
+
+
+restype_1to3: dict[str, str] = {
+    "A": "ALA",
+    "R": "ARG",
+    "N": "ASN",
+    "D": "ASP",
+    "C": "CYS",
+    "Q": "GLN",
+    "E": "GLU",
+    "G": "GLY",
+    "H": "HIS",
+    "I": "ILE",
+    "L": "LEU",
+    "K": "LYS",
+    "M": "MET",
+    "F": "PHE",
+    "P": "PRO",
+    "S": "SER",
+    "T": "THR",
+    "W": "TRP",
+    "Y": "TYR",
+    "V": "VAL",
+}
+
+
+# NB: restype_3to1 differs from Bio.PDB.protein_letters_3to1 by being a simple
+# 1-to-1 mapping of 3 letter names to one letter names. The latter contains
+# many more, and less common, three letter names as keys and maps many of these
+# to the same one letter name (including 'X' and 'U' which we don't use here).
+restype_3to1: dict[str, str] = {v: k for k, v in restype_1to3.items()}
+
+# Define a restype name for all unknown residues.
+unk_restype = "UNK"
+
+resnames: list[str] = [restype_1to3[r] for r in restypes] + [unk_restype]
+resname_to_idx: dict[str, int] = {resname: i for i, resname in enumerate(resnames)}
+
+
+# The mapping here uses hhblits convention, so that B is mapped to D, J and O
+# are mapped to X, U is mapped to C, and Z is mapped to E. Other than that the
+# remaining 20 amino acids are kept in alphabetical order.
+# There are 2 non-amino acid codes, X (representing any amino acid) and
+# "-" representing a missing amino acid in an alignment.  The id for these
+# codes is put at the end (20 and 21) so that they can easily be ignored if
+# desired.
+HHBLITS_AA_TO_ID: dict[str, int] = {
+    "A": 0,
+    "B": 2,
+    "C": 1,
+    "D": 2,
+    "E": 3,
+    "F": 4,
+    "G": 5,
+    "H": 6,
+    "I": 7,
+    "J": 20,
+    "K": 8,
+    "L": 9,
+    "M": 10,
+    "N": 11,
+    "O": 20,
+    "P": 12,
+    "Q": 13,
+    "R": 14,
+    "S": 15,
+    "T": 16,
+    "U": 1,
+    "V": 17,
+    "W": 18,
+    "X": 20,
+    "Y": 19,
+    "Z": 3,
+    "-": 21,
+}
+
+# Partial inversion of HHBLITS_AA_TO_ID.
+ID_TO_HHBLITS_AA: dict[int, str] = {
+    0: "A",
+    1: "C",  # Also U.
+    2: "D",  # Also B.
+    3: "E",  # Also Z.
+    4: "F",
+    5: "G",
+    6: "H",
+    7: "I",
+    8: "K",
+    9: "L",
+    10: "M",
+    11: "N",
+    12: "P",
+    13: "Q",
+    14: "R",
+    15: "S",
+    16: "T",
+    17: "V",
+    18: "W",
+    19: "Y",
+    20: "X",  # Includes J and O.
+    21: "-",
+}
+
+restypes_with_x_and_gap: list[str] = restypes + ["X", "-"]
+MAP_HHBLITS_AATYPE_TO_OUR_AATYPE: tuple[int, ...] = tuple(
+    restypes_with_x_and_gap.index(ID_TO_HHBLITS_AA[i]) for i in range(len(restypes_with_x_and_gap))
+)
+
+
+def _make_standard_atom_mask() -> np.ndarray:
+    """Returns [num_res_types, num_atom_types] mask array."""
+    # +1 to account for unknown (all 0s).
+    mask = np.zeros([restype_num + 1, atom_type_num], dtype=np.int32)
+    for restype, restype_letter in enumerate(restypes):
+        restype_name = restype_1to3[restype_letter]
+        atom_names = residue_atoms[restype_name]
+        for atom_name in atom_names:
+            atom_type = atom_order[atom_name]
+            mask[restype, atom_type] = 1
+    return mask
+
+
+STANDARD_ATOM_MASK = _make_standard_atom_mask()
+
+
+# A one hot representation for the first and second atoms defining the axis
+# of rotation for each chi-angle in each residue.
+def chi_angle_atom(atom_index: int) -> np.ndarray:
+    """Define chi-angle rigid groups via one-hot representations."""
+    chi_angles_index = {}
+    one_hots = []
+
+    for k, v in chi_angles_atoms.items():
+        indices = [atom_types.index(s[atom_index]) for s in v]
+        indices.extend([-1] * (4 - len(indices)))
+        chi_angles_index[k] = indices
+
+    for r in restypes:
+        res3 = restype_1to3[r]
+        one_hot = np.eye(atom_type_num)[chi_angles_index[res3]]
+        one_hots.append(one_hot)
+
+    one_hots.append(np.zeros([4, atom_type_num]))  # Add zeros for residue `X`.
+    one_hot = np.stack(one_hots, axis=0)
+    one_hot = np.transpose(one_hot, [0, 2, 1])
+
+    return one_hot
+
+
+chi_atom_1_one_hot = chi_angle_atom(1)
+chi_atom_2_one_hot = chi_angle_atom(2)
+
+# An array like chi_angles_atoms but using indices rather than names.
+chi_angles_atom_indices_list: list[list[list[str]]] = [chi_angles_atoms[restype_1to3[r]] for r in restypes]
+chi_angles_atom_indices_ours: list = map_structure_with_atom_order(chi_angles_atom_indices_list)
+chi_angles_atom_indices = np.array(
+    [chi_atoms + ([[0, 0, 0, 0]] * (4 - len(chi_atoms))) for chi_atoms in chi_angles_atom_indices_list]
+)
+
+# Mapping from (res_name, atom_name) pairs to the atom's chi group index
+# and atom index within that group.
+chi_groups_for_atom: dict[tuple[str, str], list[tuple[int, int]]] = collections.defaultdict(list)
+for res_name, chi_angle_atoms_for_res in chi_angles_atoms.items():
+    for chi_group_i, chi_group in enumerate(chi_angle_atoms_for_res):
+        for atom_i, atom in enumerate(chi_group):
+            chi_groups_for_atom[(res_name, atom)].append((chi_group_i, atom_i))
+chi_groups_for_atom = dict(chi_groups_for_atom)
+
+
+def _make_rigid_transformation_4x4(ex: np.ndarray, ey: np.ndarray, translation: np.ndarray) -> np.ndarray:
+    """Create a rigid 4x4 transformation matrix from two axes and transl."""
+    # Normalize ex.
+    ex_normalized = ex / np.linalg.norm(ex)
+
+    # make ey perpendicular to ex
+    ey_normalized = ey - np.dot(ey, ex_normalized) * ex_normalized
+    ey_normalized /= np.linalg.norm(ey_normalized)
+
+    # compute ez as cross product
+    eznorm = np.cross(ex_normalized, ey_normalized)
+    m = np.stack([ex_normalized, ey_normalized, eznorm, translation]).transpose()
+    m = np.concatenate([m, [[0.0, 0.0, 0.0, 1.0]]], axis=0)
+    return m
+
+
+# create an array with (restype, atomtype) --> rigid_group_idx
+# and an array with (restype, atomtype, coord) for the atom positions
+# and compute affine transformation matrices (4,4) from one rigid group to the
+# previous group
+restype_atom37_to_rigid_group = np.zeros([21, 37], dtype=int)
+restype_atom37_mask = np.zeros([21, 37], dtype=np.float32)
+restype_atom37_rigid_group_positions = np.zeros([21, 37, 3], dtype=np.float32)
+restype_atom14_to_rigid_group = np.zeros([21, 14], dtype=int)
+restype_atom14_mask = np.zeros([21, 14], dtype=np.float32)
+restype_atom14_rigid_group_positions = np.zeros([21, 14, 3], dtype=np.float32)
+restype_rigid_group_default_frame = np.zeros([21, 8, 4, 4], dtype=np.float32)
+
+
+def _make_rigid_group_constants() -> None:
+    """Fill the arrays above."""
+    for restype, restype_letter in enumerate(restypes):
+        resname = restype_1to3[restype_letter]
+        for atomname, group_idx, atom_position in rigid_group_atom_positions[resname]:
+            atomtype = atom_order[atomname]
+            restype_atom37_to_rigid_group[restype, atomtype] = group_idx
+            restype_atom37_mask[restype, atomtype] = 1
+            restype_atom37_rigid_group_positions[restype, atomtype, :] = atom_position
+
+            atom14idx = restype_name_to_atom14_names[resname].index(atomname)
+            restype_atom14_to_rigid_group[restype, atom14idx] = group_idx
+            restype_atom14_mask[restype, atom14idx] = 1
+            restype_atom14_rigid_group_positions[restype, atom14idx, :] = atom_position
+
+    for restype, restype_letter in enumerate(restypes):
+        resname = restype_1to3[restype_letter]
+        atom_positions: dict[str, np.ndarray] = {
+            name: np.array(pos) for name, _, pos in rigid_group_atom_positions[resname]
+        }
+
+        # backbone to backbone is the identity transform
+        restype_rigid_group_default_frame[restype, 0, :, :] = np.eye(4)
+
+        # pre-omega-frame to backbone (currently dummy identity matrix)
+        restype_rigid_group_default_frame[restype, 1, :, :] = np.eye(4)
+
+        # phi-frame to backbone
+        mat = _make_rigid_transformation_4x4(
+            ex=atom_positions["N"] - atom_positions["CA"],
+            ey=np.array([1.0, 0.0, 0.0]),
+            translation=atom_positions["N"],
+        )
+        restype_rigid_group_default_frame[restype, 2, :, :] = mat
+
+        # psi-frame to backbone
+        mat = _make_rigid_transformation_4x4(
+            ex=atom_positions["C"] - atom_positions["CA"],
+            ey=atom_positions["CA"] - atom_positions["N"],
+            translation=atom_positions["C"],
+        )
+        restype_rigid_group_default_frame[restype, 3, :, :] = mat
+
+        # chi1-frame to backbone
+        if chi_angles_mask[restype][0]:
+            base_atom_names = chi_angles_atoms[resname][0]
+            base_atom_positions = [atom_positions[name] for name in base_atom_names]
+            mat = _make_rigid_transformation_4x4(
+                ex=base_atom_positions[2] - base_atom_positions[1],
+                ey=base_atom_positions[0] - base_atom_positions[1],
+                translation=base_atom_positions[2],
+            )
+            restype_rigid_group_default_frame[restype, 4, :, :] = mat
+
+        # chi2-frame to chi1-frame
+        # chi3-frame to chi2-frame
+        # chi4-frame to chi3-frame
+        # luckily all rotation axes for the next frame start at (0,0,0) of the
+        # previous frame
+        for chi_idx in range(1, 4):
+            if chi_angles_mask[restype][chi_idx]:
+                axis_end_atom_name = chi_angles_atoms[resname][chi_idx][2]
+                axis_end_atom_position = atom_positions[axis_end_atom_name]
+                mat = _make_rigid_transformation_4x4(
+                    ex=axis_end_atom_position,
+                    ey=np.array([-1.0, 0.0, 0.0]),
+                    translation=axis_end_atom_position,
+                )
+                restype_rigid_group_default_frame[restype, 4 + chi_idx, :, :] = mat
+
+
+_make_rigid_group_constants()
+
+
+def make_atom14_dists_bounds(
+    overlap_tolerance: float = 1.5,
+    bond_length_tolerance_factor: int = 15,
+) -> dict[str, np.ndarray]:
+    """compute upper and lower bounds for bonds to assess violations."""
+    restype_atom14_bond_lower_bound = np.zeros([21, 14, 14], np.float32)
+    restype_atom14_bond_upper_bound = np.zeros([21, 14, 14], np.float32)
+    restype_atom14_bond_stddev = np.zeros([21, 14, 14], np.float32)
+    residue_bonds, residue_virtual_bonds, _ = load_stereo_chemical_props()
+    for restype, restype_letter in enumerate(restypes):
+        resname = restype_1to3[restype_letter]
+        atom_list = restype_name_to_atom14_names[resname]
+
+        # create lower and upper bounds for clashes
+        for atom1_idx, atom1_name in enumerate(atom_list):
+            if not atom1_name:
+                continue
+            atom1_radius = van_der_waals_radius[atom1_name[0]]
+            for atom2_idx, atom2_name in enumerate(atom_list):
+                if (not atom2_name) or atom1_idx == atom2_idx:
+                    continue
+                atom2_radius = van_der_waals_radius[atom2_name[0]]
+                lower = atom1_radius + atom2_radius - overlap_tolerance
+                upper = 1e10
+                restype_atom14_bond_lower_bound[restype, atom1_idx, atom2_idx] = lower
+                restype_atom14_bond_lower_bound[restype, atom2_idx, atom1_idx] = lower
+                restype_atom14_bond_upper_bound[restype, atom1_idx, atom2_idx] = upper
+                restype_atom14_bond_upper_bound[restype, atom2_idx, atom1_idx] = upper
+
+        # overwrite lower and upper bounds for bonds and angles
+        for b in residue_bonds[resname] + residue_virtual_bonds[resname]:
+            atom1_idx = atom_list.index(b.atom1_name)
+            atom2_idx = atom_list.index(b.atom2_name)
+            lower = b.length - bond_length_tolerance_factor * b.stddev
+            upper = b.length + bond_length_tolerance_factor * b.stddev
+            restype_atom14_bond_lower_bound[restype, atom1_idx, atom2_idx] = lower
+            restype_atom14_bond_lower_bound[restype, atom2_idx, atom1_idx] = lower
+            restype_atom14_bond_upper_bound[restype, atom1_idx, atom2_idx] = upper
+            restype_atom14_bond_upper_bound[restype, atom2_idx, atom1_idx] = upper
+            restype_atom14_bond_stddev[restype, atom1_idx, atom2_idx] = b.stddev
+            restype_atom14_bond_stddev[restype, atom2_idx, atom1_idx] = b.stddev
+    return {
+        "lower_bound": restype_atom14_bond_lower_bound,  # shape (21,14,14)
+        "upper_bound": restype_atom14_bond_upper_bound,  # shape (21,14,14)
+        "stddev": restype_atom14_bond_stddev,  # shape (21,14,14)
+    }
+
+
+restype_atom14_ambiguous_atoms = np.zeros((21, 14), dtype=np.float32)
+restype_atom14_ambiguous_atoms_swap_idx: np.ndarray = np.tile(np.arange(14, dtype=int), (21, 1))
+
+
+def _make_atom14_ambiguity_feats() -> None:
+    for res, pairs in residue_atom_renaming_swaps.items():
+        res_idx = restype_order[restype_3to1[res]]
+        for atom1, atom2 in pairs.items():
+            atom1_idx = restype_name_to_atom14_names[res].index(atom1)
+            atom2_idx = restype_name_to_atom14_names[res].index(atom2)
+            restype_atom14_ambiguous_atoms[res_idx, atom1_idx] = 1
+            restype_atom14_ambiguous_atoms[res_idx, atom2_idx] = 1
+            restype_atom14_ambiguous_atoms_swap_idx[res_idx, atom1_idx] = atom2_idx
+            restype_atom14_ambiguous_atoms_swap_idx[res_idx, atom2_idx] = atom1_idx
+
+
+_make_atom14_ambiguity_feats()
+
+
+def aatype_to_str_sequence(aatype: Sequence[int]) -> str:
+    return "".join([restypes_with_x[aatype[i]] for i in range(len(aatype))])
diff --git a/data/conda_envs/evalclaw/lib/python3.11/site-packages/transformers/models/esm/openfold_utils/rigid_utils.py b/data/conda_envs/evalclaw/lib/python3.11/site-packages/transformers/models/esm/openfold_utils/rigid_utils.py
new file mode 100644
index 0000000000000000000000000000000000000000..8f21ccfd1a34e57db4b2fcaff5d44b1665d971f0
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+++ b/data/conda_envs/evalclaw/lib/python3.11/site-packages/transformers/models/esm/openfold_utils/rigid_utils.py
@@ -0,0 +1,1243 @@
+# Copyright 2021 AlQuraishi Laboratory
+# Copyright 2021 DeepMind Technologies Limited
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from __future__ import annotations
+
+from collections.abc import Callable, Sequence
+from functools import cache
+from typing import Any
+
+import numpy as np
+import torch
+
+
+def rot_matmul(a: torch.Tensor, b: torch.Tensor) -> torch.Tensor:
+    """
+    Performs matrix multiplication of two rotation matrix tensors. Written out by hand to avoid AMP downcasting.
+
+    Args:
+        a: [*, 3, 3] left multiplicand
+        b: [*, 3, 3] right multiplicand
+    Returns:
+        The product ab
+    """
+
+    def row_mul(i: int) -> torch.Tensor:
+        return torch.stack(
+            [
+                a[..., i, 0] * b[..., 0, 0] + a[..., i, 1] * b[..., 1, 0] + a[..., i, 2] * b[..., 2, 0],
+                a[..., i, 0] * b[..., 0, 1] + a[..., i, 1] * b[..., 1, 1] + a[..., i, 2] * b[..., 2, 1],
+                a[..., i, 0] * b[..., 0, 2] + a[..., i, 1] * b[..., 1, 2] + a[..., i, 2] * b[..., 2, 2],
+            ],
+            dim=-1,
+        )
+
+    return torch.stack(
+        [
+            row_mul(0),
+            row_mul(1),
+            row_mul(2),
+        ],
+        dim=-2,
+    )
+
+
+def rot_vec_mul(r: torch.Tensor, t: torch.Tensor) -> torch.Tensor:
+    """
+    Applies a rotation to a vector. Written out by hand to avoid transfer to avoid AMP downcasting.
+
+    Args:
+        r: [*, 3, 3] rotation matrices
+        t: [*, 3] coordinate tensors
+    Returns:
+        [*, 3] rotated coordinates
+    """
+    x, y, z = torch.unbind(t, dim=-1)
+    return torch.stack(
+        [
+            r[..., 0, 0] * x + r[..., 0, 1] * y + r[..., 0, 2] * z,
+            r[..., 1, 0] * x + r[..., 1, 1] * y + r[..., 1, 2] * z,
+            r[..., 2, 0] * x + r[..., 2, 1] * y + r[..., 2, 2] * z,
+        ],
+        dim=-1,
+    )
+
+
+@cache
+def identity_rot_mats(
+    batch_dims: tuple[int, ...],
+    dtype: torch.dtype | None = None,
+    device: torch.device | None = None,
+    requires_grad: bool = True,
+) -> torch.Tensor:
+    rots = torch.eye(3, dtype=dtype, device=device, requires_grad=requires_grad)
+    rots = rots.view(*((1,) * len(batch_dims)), 3, 3)
+    rots = rots.expand(*batch_dims, -1, -1)
+    rots = rots.contiguous()
+
+    return rots
+
+
+@cache
+def identity_trans(
+    batch_dims: tuple[int, ...],
+    dtype: torch.dtype | None = None,
+    device: torch.device | None = None,
+    requires_grad: bool = True,
+) -> torch.Tensor:
+    trans = torch.zeros((*batch_dims, 3), dtype=dtype, device=device, requires_grad=requires_grad)
+    return trans
+
+
+@cache
+def identity_quats(
+    batch_dims: tuple[int, ...],
+    dtype: torch.dtype | None = None,
+    device: torch.device | None = None,
+    requires_grad: bool = True,
+) -> torch.Tensor:
+    quat = torch.zeros((*batch_dims, 4), dtype=dtype, device=device, requires_grad=requires_grad)
+
+    with torch.no_grad():
+        quat[..., 0] = 1
+
+    return quat
+
+
+_quat_elements: list[str] = ["a", "b", "c", "d"]
+_qtr_keys: list[str] = [l1 + l2 for l1 in _quat_elements for l2 in _quat_elements]
+_qtr_ind_dict: dict[str, int] = {key: ind for ind, key in enumerate(_qtr_keys)}
+
+
+def _to_mat(pairs: list[tuple[str, int]]) -> np.ndarray:
+    mat = np.zeros((4, 4))
+    for key, value in pairs:
+        ind = _qtr_ind_dict[key]
+        mat[ind // 4][ind % 4] = value
+
+    return mat
+
+
+_QTR_MAT = np.zeros((4, 4, 3, 3))
+_QTR_MAT[..., 0, 0] = _to_mat([("aa", 1), ("bb", 1), ("cc", -1), ("dd", -1)])
+_QTR_MAT[..., 0, 1] = _to_mat([("bc", 2), ("ad", -2)])
+_QTR_MAT[..., 0, 2] = _to_mat([("bd", 2), ("ac", 2)])
+_QTR_MAT[..., 1, 0] = _to_mat([("bc", 2), ("ad", 2)])
+_QTR_MAT[..., 1, 1] = _to_mat([("aa", 1), ("bb", -1), ("cc", 1), ("dd", -1)])
+_QTR_MAT[..., 1, 2] = _to_mat([("cd", 2), ("ab", -2)])
+_QTR_MAT[..., 2, 0] = _to_mat([("bd", 2), ("ac", -2)])
+_QTR_MAT[..., 2, 1] = _to_mat([("cd", 2), ("ab", 2)])
+_QTR_MAT[..., 2, 2] = _to_mat([("aa", 1), ("bb", -1), ("cc", -1), ("dd", 1)])
+
+
+def quat_to_rot(quat: torch.Tensor) -> torch.Tensor:
+    """
+    Converts a quaternion to a rotation matrix.
+
+    Args:
+        quat: [*, 4] quaternions
+    Returns:
+        [*, 3, 3] rotation matrices
+    """
+    # [*, 4, 4]
+    quat = quat[..., None] * quat[..., None, :]
+
+    # [4, 4, 3, 3]
+    mat = _get_quat("_QTR_MAT", dtype=quat.dtype, device=quat.device)
+
+    # [*, 4, 4, 3, 3]
+    shaped_qtr_mat = mat.view((1,) * len(quat.shape[:-2]) + mat.shape)
+    quat = quat[..., None, None] * shaped_qtr_mat
+
+    # [*, 3, 3]
+    return torch.sum(quat, dim=(-3, -4))
+
+
+def rot_to_quat(rot: torch.Tensor) -> torch.Tensor:
+    if rot.shape[-2:] != (3, 3):
+        raise ValueError("Input rotation is incorrectly shaped")
+
+    [[xx, xy, xz], [yx, yy, yz], [zx, zy, zz]] = [[rot[..., i, j] for j in range(3)] for i in range(3)]
+
+    k = [
+        [
+            xx + yy + zz,
+            zy - yz,
+            xz - zx,
+            yx - xy,
+        ],
+        [
+            zy - yz,
+            xx - yy - zz,
+            xy + yx,
+            xz + zx,
+        ],
+        [
+            xz - zx,
+            xy + yx,
+            yy - xx - zz,
+            yz + zy,
+        ],
+        [
+            yx - xy,
+            xz + zx,
+            yz + zy,
+            zz - xx - yy,
+        ],
+    ]
+
+    _, vectors = torch.linalg.eigh((1.0 / 3.0) * torch.stack([torch.stack(t, dim=-1) for t in k], dim=-2))
+    return vectors[..., -1]
+
+
+_QUAT_MULTIPLY = np.zeros((4, 4, 4))
+_QUAT_MULTIPLY[:, :, 0] = [[1, 0, 0, 0], [0, -1, 0, 0], [0, 0, -1, 0], [0, 0, 0, -1]]
+
+_QUAT_MULTIPLY[:, :, 1] = [[0, 1, 0, 0], [1, 0, 0, 0], [0, 0, 0, 1], [0, 0, -1, 0]]
+
+_QUAT_MULTIPLY[:, :, 2] = [[0, 0, 1, 0], [0, 0, 0, -1], [1, 0, 0, 0], [0, 1, 0, 0]]
+
+_QUAT_MULTIPLY[:, :, 3] = [[0, 0, 0, 1], [0, 0, 1, 0], [0, -1, 0, 0], [1, 0, 0, 0]]
+
+_QUAT_MULTIPLY_BY_VEC = _QUAT_MULTIPLY[:, 1:, :]
+
+_CACHED_QUATS: dict[str, np.ndarray] = {
+    "_QTR_MAT": _QTR_MAT,
+    "_QUAT_MULTIPLY": _QUAT_MULTIPLY,
+    "_QUAT_MULTIPLY_BY_VEC": _QUAT_MULTIPLY_BY_VEC,
+}
+
+
+@cache
+def _get_quat(quat_key: str, dtype: torch.dtype, device: torch.device) -> torch.Tensor:
+    return torch.tensor(_CACHED_QUATS[quat_key], dtype=dtype, device=device)
+
+
+def quat_multiply(quat1: torch.Tensor, quat2: torch.Tensor) -> torch.Tensor:
+    """Multiply a quaternion by another quaternion."""
+    mat = _get_quat("_QUAT_MULTIPLY", dtype=quat1.dtype, device=quat1.device)
+    reshaped_mat = mat.view((1,) * len(quat1.shape[:-1]) + mat.shape)
+    return torch.sum(reshaped_mat * quat1[..., :, None, None] * quat2[..., None, :, None], dim=(-3, -2))
+
+
+def quat_multiply_by_vec(quat: torch.Tensor, vec: torch.Tensor) -> torch.Tensor:
+    """Multiply a quaternion by a pure-vector quaternion."""
+    mat = _get_quat("_QUAT_MULTIPLY_BY_VEC", dtype=quat.dtype, device=quat.device)
+    reshaped_mat = mat.view((1,) * len(quat.shape[:-1]) + mat.shape)
+    return torch.sum(reshaped_mat * quat[..., :, None, None] * vec[..., None, :, None], dim=(-3, -2))
+
+
+def invert_rot_mat(rot_mat: torch.Tensor) -> torch.Tensor:
+    return rot_mat.transpose(-1, -2)
+
+
+def invert_quat(quat: torch.Tensor) -> torch.Tensor:
+    quat_prime = quat.clone()
+    quat_prime[..., 1:] *= -1
+    inv = quat_prime / torch.sum(quat**2, dim=-1, keepdim=True)
+    return inv
+
+
+class Rotation:
+    """
+    A 3D rotation. Depending on how the object is initialized, the rotation is represented by either a rotation matrix
+    or a quaternion, though both formats are made available by helper functions. To simplify gradient computation, the
+    underlying format of the rotation cannot be changed in-place. Like Rigid, the class is designed to mimic the
+    behavior of a torch Tensor, almost as if each Rotation object were a tensor of rotations, in one format or another.
+    """
+
+    def __init__(
+        self,
+        rot_mats: torch.Tensor | None = None,
+        quats: torch.Tensor | None = None,
+        normalize_quats: bool = True,
+    ):
+        """
+        Args:
+            rot_mats:
+                A [*, 3, 3] rotation matrix tensor. Mutually exclusive with quats
+            quats:
+                A [*, 4] quaternion. Mutually exclusive with rot_mats. If normalize_quats is not True, must be a unit
+                quaternion
+            normalize_quats:
+                If quats is specified, whether to normalize quats
+        """
+        if (rot_mats is None and quats is None) or (rot_mats is not None and quats is not None):
+            raise ValueError("Exactly one input argument must be specified")
+
+        if (rot_mats is not None and rot_mats.shape[-2:] != (3, 3)) or (quats is not None and quats.shape[-1] != 4):
+            raise ValueError("Incorrectly shaped rotation matrix or quaternion")
+
+        # Force full-precision
+        if quats is not None:
+            quats = quats.to(dtype=torch.float32)
+        if rot_mats is not None:
+            rot_mats = rot_mats.to(dtype=torch.float32)
+
+        if quats is not None and normalize_quats:
+            quats = quats / torch.linalg.norm(quats, dim=-1, keepdim=True)
+
+        self._rot_mats = rot_mats
+        self._quats = quats
+
+    @staticmethod
+    def identity(
+        shape,
+        dtype: torch.dtype | None = None,
+        device: torch.device | None = None,
+        requires_grad: bool = True,
+        fmt: str = "quat",
+    ) -> Rotation:
+        """
+        Returns an identity Rotation.
+
+        Args:
+            shape:
+                The "shape" of the resulting Rotation object. See documentation for the shape property
+            dtype:
+                The torch dtype for the rotation
+            device:
+                The torch device for the new rotation
+            requires_grad:
+                Whether the underlying tensors in the new rotation object should require gradient computation
+            fmt:
+                One of "quat" or "rot_mat". Determines the underlying format of the new object's rotation
+        Returns:
+            A new identity rotation
+        """
+        if fmt == "rot_mat":
+            rot_mats = identity_rot_mats(
+                shape,
+                dtype,
+                device,
+                requires_grad,
+            )
+            return Rotation(rot_mats=rot_mats, quats=None)
+        elif fmt == "quat":
+            quats = identity_quats(shape, dtype, device, requires_grad)
+            return Rotation(rot_mats=None, quats=quats, normalize_quats=False)
+        else:
+            raise ValueError(f"Invalid format: f{fmt}")
+
+    # Magic methods
+
+    def __getitem__(self, index: Any) -> Rotation:
+        """
+        Allows torch-style indexing over the virtual shape of the rotation object. See documentation for the shape
+        property.
+
+        Args:
+            index:
+                A torch index. E.g. (1, 3, 2), or (slice(None,))
+        Returns:
+            The indexed rotation
+        """
+        if type(index) is not tuple:
+            index = (index,)
+
+        if self._rot_mats is not None:
+            rot_mats = self._rot_mats[index + (slice(None), slice(None))]
+            return Rotation(rot_mats=rot_mats)
+        elif self._quats is not None:
+            quats = self._quats[index + (slice(None),)]
+            return Rotation(quats=quats, normalize_quats=False)
+        else:
+            raise ValueError("Both rotations are None")
+
+    def __mul__(self, right: torch.Tensor) -> Rotation:
+        """
+        Pointwise left multiplication of the rotation with a tensor. Can be used to e.g. mask the Rotation.
+
+        Args:
+            right:
+                The tensor multiplicand
+        Returns:
+            The product
+        """
+        if not (isinstance(right, torch.Tensor)):
+            raise TypeError("The other multiplicand must be a Tensor")
+
+        if self._rot_mats is not None:
+            rot_mats = self._rot_mats * right[..., None, None]
+            return Rotation(rot_mats=rot_mats, quats=None)
+        elif self._quats is not None:
+            quats = self._quats * right[..., None]
+            return Rotation(rot_mats=None, quats=quats, normalize_quats=False)
+        else:
+            raise ValueError("Both rotations are None")
+
+    def __rmul__(self, left: torch.Tensor) -> Rotation:
+        """
+        Reverse pointwise multiplication of the rotation with a tensor.
+
+        Args:
+            left:
+                The left multiplicand
+        Returns:
+            The product
+        """
+        return self.__mul__(left)
+
+    # Properties
+
+    @property
+    def shape(self) -> torch.Size:
+        """
+        Returns the virtual shape of the rotation object. This shape is defined as the batch dimensions of the
+        underlying rotation matrix or quaternion. If the Rotation was initialized with a [10, 3, 3] rotation matrix
+        tensor, for example, the resulting shape would be [10].
+
+        Returns:
+            The virtual shape of the rotation object
+        """
+        if self._rot_mats is not None:
+            return self._rot_mats.shape[:-2]
+        elif self._quats is not None:
+            return self._quats.shape[:-1]
+        else:
+            raise ValueError("Both rotations are None")
+
+    @property
+    def dtype(self) -> torch.dtype:
+        """
+        Returns the dtype of the underlying rotation.
+
+        Returns:
+            The dtype of the underlying rotation
+        """
+        if self._rot_mats is not None:
+            return self._rot_mats.dtype
+        elif self._quats is not None:
+            return self._quats.dtype
+        else:
+            raise ValueError("Both rotations are None")
+
+    @property
+    def device(self) -> torch.device:
+        """
+        The device of the underlying rotation
+
+        Returns:
+            The device of the underlying rotation
+        """
+        if self._rot_mats is not None:
+            return self._rot_mats.device
+        elif self._quats is not None:
+            return self._quats.device
+        else:
+            raise ValueError("Both rotations are None")
+
+    @property
+    def requires_grad(self) -> bool:
+        """
+        Returns the requires_grad property of the underlying rotation
+
+        Returns:
+            The requires_grad property of the underlying tensor
+        """
+        if self._rot_mats is not None:
+            return self._rot_mats.requires_grad
+        elif self._quats is not None:
+            return self._quats.requires_grad
+        else:
+            raise ValueError("Both rotations are None")
+
+    def get_rot_mats(self) -> torch.Tensor:
+        """
+        Returns the underlying rotation as a rotation matrix tensor.
+
+        Returns:
+            The rotation as a rotation matrix tensor
+        """
+        if self._rot_mats is not None:
+            return self._rot_mats
+        elif self._quats is not None:
+            return quat_to_rot(self._quats)
+        else:
+            raise ValueError("Both rotations are None")
+
+    def get_quats(self) -> torch.Tensor:
+        """
+        Returns the underlying rotation as a quaternion tensor.
+
+        Depending on whether the Rotation was initialized with a quaternion, this function may call torch.linalg.eigh.
+
+        Returns:
+            The rotation as a quaternion tensor.
+        """
+        if self._rot_mats is not None:
+            return rot_to_quat(self._rot_mats)
+        elif self._quats is not None:
+            return self._quats
+        else:
+            raise ValueError("Both rotations are None")
+
+    def get_cur_rot(self) -> torch.Tensor:
+        """
+        Return the underlying rotation in its current form
+
+        Returns:
+            The stored rotation
+        """
+        if self._rot_mats is not None:
+            return self._rot_mats
+        elif self._quats is not None:
+            return self._quats
+        else:
+            raise ValueError("Both rotations are None")
+
+    # Rotation functions
+
+    def compose_q_update_vec(self, q_update_vec: torch.Tensor, normalize_quats: bool = True) -> Rotation:
+        """
+        Returns a new quaternion Rotation after updating the current object's underlying rotation with a quaternion
+        update, formatted as a [*, 3] tensor whose final three columns represent x, y, z such that (1, x, y, z) is the
+        desired (not necessarily unit) quaternion update.
+
+        Args:
+            q_update_vec:
+                A [*, 3] quaternion update tensor
+            normalize_quats:
+                Whether to normalize the output quaternion
+        Returns:
+            An updated Rotation
+        """
+        quats = self.get_quats()
+        new_quats = quats + quat_multiply_by_vec(quats, q_update_vec)
+        return Rotation(
+            rot_mats=None,
+            quats=new_quats,
+            normalize_quats=normalize_quats,
+        )
+
+    def compose_r(self, r: Rotation) -> Rotation:
+        """
+        Compose the rotation matrices of the current Rotation object with those of another.
+
+        Args:
+            r:
+                An update rotation object
+        Returns:
+            An updated rotation object
+        """
+        r1 = self.get_rot_mats()
+        r2 = r.get_rot_mats()
+        new_rot_mats = rot_matmul(r1, r2)
+        return Rotation(rot_mats=new_rot_mats, quats=None)
+
+    def compose_q(self, r: Rotation, normalize_quats: bool = True) -> Rotation:
+        """
+        Compose the quaternions of the current Rotation object with those of another.
+
+        Depending on whether either Rotation was initialized with quaternions, this function may call
+        torch.linalg.eigh.
+
+        Args:
+            r:
+                An update rotation object
+        Returns:
+            An updated rotation object
+        """
+        q1 = self.get_quats()
+        q2 = r.get_quats()
+        new_quats = quat_multiply(q1, q2)
+        return Rotation(rot_mats=None, quats=new_quats, normalize_quats=normalize_quats)
+
+    def apply(self, pts: torch.Tensor) -> torch.Tensor:
+        """
+        Apply the current Rotation as a rotation matrix to a set of 3D coordinates.
+
+        Args:
+            pts:
+                A [*, 3] set of points
+        Returns:
+            [*, 3] rotated points
+        """
+        rot_mats = self.get_rot_mats()
+        return rot_vec_mul(rot_mats, pts)
+
+    def invert_apply(self, pts: torch.Tensor) -> torch.Tensor:
+        """
+        The inverse of the apply() method.
+
+        Args:
+            pts:
+                A [*, 3] set of points
+        Returns:
+            [*, 3] inverse-rotated points
+        """
+        rot_mats = self.get_rot_mats()
+        inv_rot_mats = invert_rot_mat(rot_mats)
+        return rot_vec_mul(inv_rot_mats, pts)
+
+    def invert(self) -> Rotation:
+        """
+        Returns the inverse of the current Rotation.
+
+        Returns:
+            The inverse of the current Rotation
+        """
+        if self._rot_mats is not None:
+            return Rotation(rot_mats=invert_rot_mat(self._rot_mats), quats=None)
+        elif self._quats is not None:
+            return Rotation(
+                rot_mats=None,
+                quats=invert_quat(self._quats),
+                normalize_quats=False,
+            )
+        else:
+            raise ValueError("Both rotations are None")
+
+    # "Tensor" stuff
+
+    def unsqueeze(self, dim: int) -> Rotation:
+        """
+        Analogous to torch.unsqueeze. The dimension is relative to the shape of the Rotation object.
+
+        Args:
+            dim: A positive or negative dimension index.
+        Returns:
+            The unsqueezed Rotation.
+        """
+        if dim >= len(self.shape):
+            raise ValueError("Invalid dimension")
+
+        if self._rot_mats is not None:
+            rot_mats = self._rot_mats.unsqueeze(dim if dim >= 0 else dim - 2)
+            return Rotation(rot_mats=rot_mats, quats=None)
+        elif self._quats is not None:
+            quats = self._quats.unsqueeze(dim if dim >= 0 else dim - 1)
+            return Rotation(rot_mats=None, quats=quats, normalize_quats=False)
+        else:
+            raise ValueError("Both rotations are None")
+
+    @staticmethod
+    def cat(rs: Sequence[Rotation], dim: int) -> Rotation:
+        """
+        Concatenates rotations along one of the batch dimensions. Analogous to torch.cat().
+
+        Note that the output of this operation is always a rotation matrix, regardless of the format of input
+        rotations.
+
+        Args:
+            rs:
+                A list of rotation objects
+            dim:
+                The dimension along which the rotations should be concatenated
+        Returns:
+            A concatenated Rotation object in rotation matrix format
+        """
+        rot_mats = torch.cat(
+            [r.get_rot_mats() for r in rs],
+            dim=dim if dim >= 0 else dim - 2,
+        )
+
+        return Rotation(rot_mats=rot_mats, quats=None)
+
+    def map_tensor_fn(self, fn: Callable[[torch.Tensor], torch.Tensor]) -> Rotation:
+        """
+        Apply a Tensor -> Tensor function to underlying rotation tensors, mapping over the rotation dimension(s). Can
+        be used e.g. to sum out a one-hot batch dimension.
+
+        Args:
+            fn:
+                A Tensor -> Tensor function to be mapped over the Rotation
+        Returns:
+            The transformed Rotation object
+        """
+        if self._rot_mats is not None:
+            rot_mats = self._rot_mats.view(self._rot_mats.shape[:-2] + (9,))
+            rot_mats = torch.stack(list(map(fn, torch.unbind(rot_mats, dim=-1))), dim=-1)
+            rot_mats = rot_mats.view(rot_mats.shape[:-1] + (3, 3))
+            return Rotation(rot_mats=rot_mats, quats=None)
+        elif self._quats is not None:
+            quats = torch.stack(list(map(fn, torch.unbind(self._quats, dim=-1))), dim=-1)
+            return Rotation(rot_mats=None, quats=quats, normalize_quats=False)
+        else:
+            raise ValueError("Both rotations are None")
+
+    def cuda(self) -> Rotation:
+        """
+        Analogous to the cuda() method of torch Tensors
+
+        Returns:
+            A copy of the Rotation in CUDA memory
+        """
+        if self._rot_mats is not None:
+            return Rotation(rot_mats=self._rot_mats.cuda(), quats=None)
+        elif self._quats is not None:
+            return Rotation(rot_mats=None, quats=self._quats.cuda(), normalize_quats=False)
+        else:
+            raise ValueError("Both rotations are None")
+
+    def to(self, device: torch.device | None, dtype: torch.dtype | None) -> Rotation:
+        """
+        Analogous to the to() method of torch Tensors
+
+        Args:
+            device:
+                A torch device
+            dtype:
+                A torch dtype
+        Returns:
+            A copy of the Rotation using the new device and dtype
+        """
+        if self._rot_mats is not None:
+            return Rotation(
+                rot_mats=self._rot_mats.to(device=device, dtype=dtype),
+                quats=None,
+            )
+        elif self._quats is not None:
+            return Rotation(
+                rot_mats=None,
+                quats=self._quats.to(device=device, dtype=dtype),
+                normalize_quats=False,
+            )
+        else:
+            raise ValueError("Both rotations are None")
+
+    def detach(self) -> Rotation:
+        """
+        Returns a copy of the Rotation whose underlying Tensor has been detached from its torch graph.
+
+        Returns:
+            A copy of the Rotation whose underlying Tensor has been detached from its torch graph
+        """
+        if self._rot_mats is not None:
+            return Rotation(rot_mats=self._rot_mats.detach(), quats=None)
+        elif self._quats is not None:
+            return Rotation(
+                rot_mats=None,
+                quats=self._quats.detach(),
+                normalize_quats=False,
+            )
+        else:
+            raise ValueError("Both rotations are None")
+
+
+class Rigid:
+    """
+    A class representing a rigid transformation. Little more than a wrapper around two objects: a Rotation object and a
+    [*, 3] translation Designed to behave approximately like a single torch tensor with the shape of the shared batch
+    dimensions of its component parts.
+    """
+
+    def __init__(self, rots: Rotation | None, trans: torch.Tensor | None):
+        """
+        Args:
+            rots: A [*, 3, 3] rotation tensor
+            trans: A corresponding [*, 3] translation tensor
+        """
+        # (we need device, dtype, etc. from at least one input)
+
+        batch_dims, dtype, device, requires_grad = None, None, None, None
+        if trans is not None:
+            batch_dims = trans.shape[:-1]
+            dtype = trans.dtype
+            device = trans.device
+            requires_grad = trans.requires_grad
+        elif rots is not None:
+            batch_dims = rots.shape
+            dtype = rots.dtype
+            device = rots.device
+            requires_grad = rots.requires_grad
+        else:
+            raise ValueError("At least one input argument must be specified")
+
+        if rots is None:
+            rots = Rotation.identity(
+                batch_dims,
+                dtype,
+                device,
+                requires_grad,
+            )
+        elif trans is None:
+            trans = identity_trans(
+                batch_dims,
+                dtype,
+                device,
+                requires_grad,
+            )
+
+        assert rots is not None
+        assert trans is not None
+
+        if (rots.shape != trans.shape[:-1]) or (rots.device != trans.device):
+            raise ValueError("Rots and trans incompatible")
+
+        # Force full precision. Happens to the rotations automatically.
+        trans = trans.to(dtype=torch.float32)
+
+        self._rots = rots
+        self._trans = trans
+
+    @staticmethod
+    def identity(
+        shape: tuple[int, ...],
+        dtype: torch.dtype | None = None,
+        device: torch.device | None = None,
+        requires_grad: bool = True,
+        fmt: str = "quat",
+    ) -> Rigid:
+        """
+        Constructs an identity transformation.
+
+        Args:
+            shape:
+                The desired shape
+            dtype:
+                The dtype of both internal tensors
+            device:
+                The device of both internal tensors
+            requires_grad:
+                Whether grad should be enabled for the internal tensors
+        Returns:
+            The identity transformation
+        """
+        return Rigid(
+            Rotation.identity(shape, dtype, device, requires_grad, fmt=fmt),
+            identity_trans(shape, dtype, device, requires_grad),
+        )
+
+    def __getitem__(self, index: Any) -> Rigid:
+        """
+        Indexes the affine transformation with PyTorch-style indices. The index is applied to the shared dimensions of
+        both the rotation and the translation.
+
+        E.g.::
+
+            r = Rotation(rot_mats=torch.rand(10, 10, 3, 3), quats=None) t = Rigid(r, torch.rand(10, 10, 3)) indexed =
+            t[3, 4:6] assert(indexed.shape == (2,)) assert(indexed.get_rots().shape == (2,))
+            assert(indexed.get_trans().shape == (2, 3))
+
+        Args:
+            index: A standard torch tensor index. E.g. 8, (10, None, 3),
+            or (3, slice(0, 1, None))
+        Returns:
+            The indexed tensor
+        """
+        if type(index) is not tuple:
+            index = (index,)
+
+        return Rigid(
+            self._rots[index],
+            self._trans[index + (slice(None),)],
+        )
+
+    def __mul__(self, right: torch.Tensor) -> Rigid:
+        """
+        Pointwise left multiplication of the transformation with a tensor. Can be used to e.g. mask the Rigid.
+
+        Args:
+            right:
+                The tensor multiplicand
+        Returns:
+            The product
+        """
+        if not (isinstance(right, torch.Tensor)):
+            raise TypeError("The other multiplicand must be a Tensor")
+
+        new_rots = self._rots * right
+        new_trans = self._trans * right[..., None]
+
+        return Rigid(new_rots, new_trans)
+
+    def __rmul__(self, left: torch.Tensor) -> Rigid:
+        """
+        Reverse pointwise multiplication of the transformation with a tensor.
+
+        Args:
+            left:
+                The left multiplicand
+        Returns:
+            The product
+        """
+        return self.__mul__(left)
+
+    @property
+    def shape(self) -> torch.Size:
+        """
+        Returns the shape of the shared dimensions of the rotation and the translation.
+
+        Returns:
+            The shape of the transformation
+        """
+        return self._trans.shape[:-1]
+
+    @property
+    def device(self) -> torch.device:
+        """
+        Returns the device on which the Rigid's tensors are located.
+
+        Returns:
+            The device on which the Rigid's tensors are located
+        """
+        return self._trans.device
+
+    def get_rots(self) -> Rotation:
+        """
+        Getter for the rotation.
+
+        Returns:
+            The rotation object
+        """
+        return self._rots
+
+    def get_trans(self) -> torch.Tensor:
+        """
+        Getter for the translation.
+
+        Returns:
+            The stored translation
+        """
+        return self._trans
+
+    def compose_q_update_vec(self, q_update_vec: torch.Tensor) -> Rigid:
+        """
+        Composes the transformation with a quaternion update vector of shape [*, 6], where the final 6 columns
+        represent the x, y, and z values of a quaternion of form (1, x, y, z) followed by a 3D translation.
+
+        Args:
+            q_vec: The quaternion update vector.
+        Returns:
+            The composed transformation.
+        """
+        q_vec, t_vec = q_update_vec[..., :3], q_update_vec[..., 3:]
+        new_rots = self._rots.compose_q_update_vec(q_vec)
+
+        trans_update = self._rots.apply(t_vec)
+        new_translation = self._trans + trans_update
+
+        return Rigid(new_rots, new_translation)
+
+    def compose(self, r: Rigid) -> Rigid:
+        """
+        Composes the current rigid object with another.
+
+        Args:
+            r:
+                Another Rigid object
+        Returns:
+            The composition of the two transformations
+        """
+        new_rot = self._rots.compose_r(r._rots)
+        new_trans = self._rots.apply(r._trans) + self._trans
+        return Rigid(new_rot, new_trans)
+
+    def apply(self, pts: torch.Tensor) -> torch.Tensor:
+        """
+        Applies the transformation to a coordinate tensor.
+
+        Args:
+            pts: A [*, 3] coordinate tensor.
+        Returns:
+            The transformed points.
+        """
+        rotated = self._rots.apply(pts)
+        return rotated + self._trans
+
+    def invert_apply(self, pts: torch.Tensor) -> torch.Tensor:
+        """
+        Applies the inverse of the transformation to a coordinate tensor.
+
+        Args:
+            pts: A [*, 3] coordinate tensor
+        Returns:
+            The transformed points.
+        """
+        pts = pts - self._trans
+        return self._rots.invert_apply(pts)
+
+    def invert(self) -> Rigid:
+        """
+        Inverts the transformation.
+
+        Returns:
+            The inverse transformation.
+        """
+        rot_inv = self._rots.invert()
+        trn_inv = rot_inv.apply(self._trans)
+
+        return Rigid(rot_inv, -1 * trn_inv)
+
+    def map_tensor_fn(self, fn: Callable[[torch.Tensor], torch.Tensor]) -> Rigid:
+        """
+        Apply a Tensor -> Tensor function to underlying translation and rotation tensors, mapping over the
+        translation/rotation dimensions respectively.
+
+        Args:
+            fn:
+                A Tensor -> Tensor function to be mapped over the Rigid
+        Returns:
+            The transformed Rigid object
+        """
+        new_rots = self._rots.map_tensor_fn(fn)
+        new_trans = torch.stack(list(map(fn, torch.unbind(self._trans, dim=-1))), dim=-1)
+
+        return Rigid(new_rots, new_trans)
+
+    def to_tensor_4x4(self) -> torch.Tensor:
+        """
+        Converts a transformation to a homogeneous transformation tensor.
+
+        Returns:
+            A [*, 4, 4] homogeneous transformation tensor
+        """
+        tensor = self._trans.new_zeros((*self.shape, 4, 4))
+        tensor[..., :3, :3] = self._rots.get_rot_mats()
+        tensor[..., :3, 3] = self._trans
+        tensor[..., 3, 3] = 1
+        return tensor
+
+    @staticmethod
+    def from_tensor_4x4(t: torch.Tensor) -> Rigid:
+        """
+        Constructs a transformation from a homogeneous transformation tensor.
+
+        Args:
+            t: [*, 4, 4] homogeneous transformation tensor
+        Returns:
+            T object with shape [*]
+        """
+        if t.shape[-2:] != (4, 4):
+            raise ValueError("Incorrectly shaped input tensor")
+
+        rots = Rotation(rot_mats=t[..., :3, :3], quats=None)
+        trans = t[..., :3, 3]
+
+        return Rigid(rots, trans)
+
+    def to_tensor_7(self) -> torch.Tensor:
+        """
+        Converts a transformation to a tensor with 7 final columns, four for the quaternion followed by three for the
+        translation.
+
+        Returns:
+            A [*, 7] tensor representation of the transformation
+        """
+        tensor = self._trans.new_zeros((*self.shape, 7))
+        tensor[..., :4] = self._rots.get_quats()
+        tensor[..., 4:] = self._trans
+
+        return tensor
+
+    @staticmethod
+    def from_tensor_7(t: torch.Tensor, normalize_quats: bool = False) -> Rigid:
+        if t.shape[-1] != 7:
+            raise ValueError("Incorrectly shaped input tensor")
+
+        quats, trans = t[..., :4], t[..., 4:]
+
+        rots = Rotation(rot_mats=None, quats=quats, normalize_quats=normalize_quats)
+
+        return Rigid(rots, trans)
+
+    @staticmethod
+    def from_3_points(
+        p_neg_x_axis: torch.Tensor, origin: torch.Tensor, p_xy_plane: torch.Tensor, eps: float = 1e-8
+    ) -> Rigid:
+        """
+        Implements algorithm 21. Constructs transformations from sets of 3 points using the Gram-Schmidt algorithm.
+
+        Args:
+            p_neg_x_axis: [*, 3] coordinates
+            origin: [*, 3] coordinates used as frame origins
+            p_xy_plane: [*, 3] coordinates
+            eps: Small epsilon value
+        Returns:
+            A transformation object of shape [*]
+        """
+        p_neg_x_axis_unbound = torch.unbind(p_neg_x_axis, dim=-1)
+        origin_unbound = torch.unbind(origin, dim=-1)
+        p_xy_plane_unbound = torch.unbind(p_xy_plane, dim=-1)
+
+        e0 = [c1 - c2 for c1, c2 in zip(origin_unbound, p_neg_x_axis_unbound)]
+        e1 = [c1 - c2 for c1, c2 in zip(p_xy_plane_unbound, origin_unbound)]
+
+        denom = torch.sqrt(sum(c * c for c in e0) + eps * torch.ones_like(e0[0]))
+        e0 = [c / denom for c in e0]
+        dot = sum((c1 * c2 for c1, c2 in zip(e0, e1)))
+        e1 = [c2 - c1 * dot for c1, c2 in zip(e0, e1)]
+        denom = torch.sqrt(sum(c * c for c in e1) + eps * torch.ones_like(e1[0]))
+        e1 = [c / denom for c in e1]
+        e2 = [
+            e0[1] * e1[2] - e0[2] * e1[1],
+            e0[2] * e1[0] - e0[0] * e1[2],
+            e0[0] * e1[1] - e0[1] * e1[0],
+        ]
+
+        rots = torch.stack([c for tup in zip(e0, e1, e2) for c in tup], dim=-1)
+        rots = rots.reshape(rots.shape[:-1] + (3, 3))
+
+        rot_obj = Rotation(rot_mats=rots, quats=None)
+
+        return Rigid(rot_obj, torch.stack(origin_unbound, dim=-1))
+
+    def unsqueeze(self, dim: int) -> Rigid:
+        """
+        Analogous to torch.unsqueeze. The dimension is relative to the shared dimensions of the rotation/translation.
+
+        Args:
+            dim: A positive or negative dimension index.
+        Returns:
+            The unsqueezed transformation.
+        """
+        if dim >= len(self.shape):
+            raise ValueError("Invalid dimension")
+        rots = self._rots.unsqueeze(dim)
+        trans = self._trans.unsqueeze(dim if dim >= 0 else dim - 1)
+
+        return Rigid(rots, trans)
+
+    @staticmethod
+    def cat(ts: Sequence[Rigid], dim: int) -> Rigid:
+        """
+        Concatenates transformations along a new dimension.
+
+        Args:
+            ts:
+                A list of T objects
+            dim:
+                The dimension along which the transformations should be concatenated
+        Returns:
+            A concatenated transformation object
+        """
+        rots = Rotation.cat([t._rots for t in ts], dim)
+        trans = torch.cat([t._trans for t in ts], dim=dim if dim >= 0 else dim - 1)
+
+        return Rigid(rots, trans)
+
+    def apply_rot_fn(self, fn: Callable[[Rotation], Rotation]) -> Rigid:
+        """
+        Applies a Rotation -> Rotation function to the stored rotation object.
+
+        Args:
+            fn: A function of type Rotation -> Rotation
+        Returns:
+            A transformation object with a transformed rotation.
+        """
+        return Rigid(fn(self._rots), self._trans)
+
+    def apply_trans_fn(self, fn: Callable[[torch.Tensor], torch.Tensor]) -> Rigid:
+        """
+        Applies a Tensor -> Tensor function to the stored translation.
+
+        Args:
+            fn:
+                A function of type Tensor -> Tensor to be applied to the translation
+        Returns:
+            A transformation object with a transformed translation.
+        """
+        return Rigid(self._rots, fn(self._trans))
+
+    def scale_translation(self, trans_scale_factor: float) -> Rigid:
+        """
+        Scales the translation by a constant factor.
+
+        Args:
+            trans_scale_factor:
+                The constant factor
+        Returns:
+            A transformation object with a scaled translation.
+        """
+        return self.apply_trans_fn(lambda t: t * trans_scale_factor)
+
+    def stop_rot_gradient(self) -> Rigid:
+        """
+        Detaches the underlying rotation object
+
+        Returns:
+            A transformation object with detached rotations
+        """
+        return self.apply_rot_fn(lambda r: r.detach())
+
+    @staticmethod
+    def make_transform_from_reference(
+        n_xyz: torch.Tensor, ca_xyz: torch.Tensor, c_xyz: torch.Tensor, eps: float = 1e-20
+    ) -> Rigid:
+        """
+        Returns a transformation object from reference coordinates.
+
+        Note that this method does not take care of symmetries. If you provide the atom positions in the non-standard
+        way, the N atom will end up not at [-0.527250, 1.359329, 0.0] but instead at [-0.527250, -1.359329, 0.0]. You
+        need to take care of such cases in your code.
+
+        Args:
+            n_xyz: A [*, 3] tensor of nitrogen xyz coordinates.
+            ca_xyz: A [*, 3] tensor of carbon alpha xyz coordinates.
+            c_xyz: A [*, 3] tensor of carbon xyz coordinates.
+        Returns:
+            A transformation object. After applying the translation and rotation to the reference backbone, the
+            coordinates will approximately equal to the input coordinates.
+        """
+        translation = -1 * ca_xyz
+        n_xyz = n_xyz + translation
+        c_xyz = c_xyz + translation
+
+        c_x, c_y, c_z = [c_xyz[..., i] for i in range(3)]
+        norm = torch.sqrt(eps + c_x**2 + c_y**2)
+        sin_c1 = -c_y / norm
+        cos_c1 = c_x / norm
+
+        c1_rots = sin_c1.new_zeros((*sin_c1.shape, 3, 3))
+        c1_rots[..., 0, 0] = cos_c1
+        c1_rots[..., 0, 1] = -1 * sin_c1
+        c1_rots[..., 1, 0] = sin_c1
+        c1_rots[..., 1, 1] = cos_c1
+        c1_rots[..., 2, 2] = 1
+
+        norm = torch.sqrt(eps + c_x**2 + c_y**2 + c_z**2)
+        sin_c2 = c_z / norm
+        cos_c2 = torch.sqrt(c_x**2 + c_y**2) / norm
+
+        c2_rots = sin_c2.new_zeros((*sin_c2.shape, 3, 3))
+        c2_rots[..., 0, 0] = cos_c2
+        c2_rots[..., 0, 2] = sin_c2
+        c2_rots[..., 1, 1] = 1
+        c2_rots[..., 2, 0] = -1 * sin_c2
+        c2_rots[..., 2, 2] = cos_c2
+
+        c_rots = rot_matmul(c2_rots, c1_rots)
+        n_xyz = rot_vec_mul(c_rots, n_xyz)
+
+        _, n_y, n_z = [n_xyz[..., i] for i in range(3)]
+        norm = torch.sqrt(eps + n_y**2 + n_z**2)
+        sin_n = -n_z / norm
+        cos_n = n_y / norm
+
+        n_rots = sin_c2.new_zeros((*sin_c2.shape, 3, 3))
+        n_rots[..., 0, 0] = 1
+        n_rots[..., 1, 1] = cos_n
+        n_rots[..., 1, 2] = -1 * sin_n
+        n_rots[..., 2, 1] = sin_n
+        n_rots[..., 2, 2] = cos_n
+
+        rots = rot_matmul(n_rots, c_rots)
+
+        rots = rots.transpose(-1, -2)
+        translation = -1 * translation
+
+        rot_obj = Rotation(rot_mats=rots, quats=None)
+
+        return Rigid(rot_obj, translation)
+
+    def cuda(self) -> Rigid:
+        """
+        Moves the transformation object to GPU memory
+
+        Returns:
+            A version of the transformation on GPU
+        """
+        return Rigid(self._rots.cuda(), self._trans.cuda())
diff --git a/data/conda_envs/evalclaw/lib/python3.11/site-packages/transformers/models/esm/openfold_utils/tensor_utils.py b/data/conda_envs/evalclaw/lib/python3.11/site-packages/transformers/models/esm/openfold_utils/tensor_utils.py
new file mode 100644
index 0000000000000000000000000000000000000000..1362fa8de1c79a14f20501a551afa41145a39349
--- /dev/null
+++ b/data/conda_envs/evalclaw/lib/python3.11/site-packages/transformers/models/esm/openfold_utils/tensor_utils.py
@@ -0,0 +1,140 @@
+# Copyright 2021 AlQuraishi Laboratory
+# Copyright 2021 DeepMind Technologies Limited
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from collections.abc import Callable
+from functools import partial
+from typing import Any, TypeVar, overload
+
+import torch
+import torch.nn as nn
+import torch.types
+
+
+def add(m1: torch.Tensor, m2: torch.Tensor, inplace: bool) -> torch.Tensor:
+    # The first operation in a checkpoint can't be in-place, but it's
+    # nice to have in-place addition during inference. Thus...
+    if not inplace:
+        m1 = m1 + m2
+    else:
+        m1 += m2
+
+    return m1
+
+
+def permute_final_dims(tensor: torch.Tensor, inds: list[int]) -> torch.Tensor:
+    zero_index = -1 * len(inds)
+    first_inds = list(range(len(tensor.shape[:zero_index])))
+    return tensor.permute(first_inds + [zero_index + i for i in inds])
+
+
+def flatten_final_dims(t: torch.Tensor, no_dims: int) -> torch.Tensor:
+    return t.reshape(t.shape[:-no_dims] + (-1,))
+
+
+def masked_mean(mask: torch.Tensor, value: torch.Tensor, dim: int, eps: float = 1e-4) -> torch.Tensor:
+    mask = mask.expand(*value.shape)
+    return torch.sum(mask * value, dim=dim) / (eps + torch.sum(mask, dim=dim))
+
+
+def pts_to_distogram(
+    pts: torch.Tensor, min_bin: torch.types.Number = 2.3125, max_bin: torch.types.Number = 21.6875, no_bins: int = 64
+) -> torch.Tensor:
+    boundaries = torch.linspace(min_bin, max_bin, no_bins - 1, device=pts.device)
+    dists = torch.sqrt(torch.sum((pts.unsqueeze(-2) - pts.unsqueeze(-3)) ** 2, dim=-1))
+    return torch.bucketize(dists, boundaries)
+
+
+def dict_multimap(fn: Callable[[list], Any], dicts: list[dict]) -> dict:
+    first = dicts[0]
+    new_dict = {}
+    for k, v in first.items():
+        all_v = [d[k] for d in dicts]
+        if isinstance(v, dict):
+            new_dict[k] = dict_multimap(fn, all_v)
+        else:
+            new_dict[k] = fn(all_v)
+
+    return new_dict
+
+
+def one_hot(x: torch.Tensor, v_bins: torch.Tensor) -> torch.Tensor:
+    reshaped_bins = v_bins.view(((1,) * len(x.shape)) + (len(v_bins),))
+    diffs = x[..., None] - reshaped_bins
+    am = torch.argmin(torch.abs(diffs), dim=-1)
+    return nn.functional.one_hot(am, num_classes=len(v_bins)).float()
+
+
+def batched_gather(data: torch.Tensor, inds: torch.Tensor, dim: int = 0, no_batch_dims: int = 0) -> torch.Tensor:
+    ranges: list[slice | torch.Tensor] = []
+    for i, s in enumerate(data.shape[:no_batch_dims]):
+        r = torch.arange(s)
+        r = r.view(*(*((1,) * i), -1, *((1,) * (len(inds.shape) - i - 1))))
+        ranges.append(r)
+
+    remaining_dims: list[slice | torch.Tensor] = [slice(None) for _ in range(len(data.shape) - no_batch_dims)]
+    remaining_dims[dim - no_batch_dims if dim >= 0 else dim] = inds
+    ranges.extend(remaining_dims)
+    # Matt note: Editing this to get around the behaviour of using a list as an array index changing
+    # in recent Numpy versions
+    return data[tuple(ranges)]
+
+
+T = TypeVar("T")
+
+
+def dict_map(
+    fn: Callable[[T], Any], dic: dict[Any, dict | list | tuple | T], leaf_type: type[T]
+) -> dict[Any, dict | list | tuple | Any]:
+    new_dict: dict[Any, dict | list | tuple | Any] = {}
+    for k, v in dic.items():
+        if isinstance(v, dict):
+            new_dict[k] = dict_map(fn, v, leaf_type)
+        else:
+            new_dict[k] = tree_map(fn, v, leaf_type)
+
+    return new_dict
+
+
+@overload
+def tree_map(fn: Callable[[T], Any], tree: T, leaf_type: type[T]) -> Any: ...
+
+
+@overload
+def tree_map(fn: Callable[[T], Any], tree: dict, leaf_type: type[T]) -> dict: ...
+
+
+@overload
+def tree_map(fn: Callable[[T], Any], tree: list, leaf_type: type[T]) -> list: ...
+
+
+@overload
+def tree_map(fn: Callable[[T], Any], tree: tuple, leaf_type: type[T]) -> tuple: ...
+
+
+def tree_map(fn, tree, leaf_type):
+    if isinstance(tree, dict):
+        return dict_map(fn, tree, leaf_type)
+    elif isinstance(tree, list):
+        return [tree_map(fn, x, leaf_type) for x in tree]
+    elif isinstance(tree, tuple):
+        return tuple(tree_map(fn, x, leaf_type) for x in tree)
+    elif isinstance(tree, leaf_type):
+        return fn(tree)
+    else:
+        print(type(tree))
+        raise TypeError("Not supported")
+
+
+tensor_tree_map = partial(tree_map, leaf_type=torch.Tensor)
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