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# 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 functools import partial
import logging
from typing import Tuple, List, Callable, Any, Dict, Sequence, Optional
import torch
import torch.nn as nn
def add(m1, m2, inplace):
# 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]):
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):
return t.reshape(t.shape[:-no_dims] + (-1,))
def masked_mean(mask, value, dim, eps=1e-4):
mask = mask.expand(*value.shape)
return torch.sum(mask * value, dim=dim) / (eps + torch.sum(mask, dim=dim))
def pts_to_distogram(pts, min_bin=2.3125, max_bin=21.6875, no_bins=64):
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, dicts):
first = dicts[0]
new_dict = {}
for k, v in first.items():
all_v = [d[k] for d in dicts]
if type(v) is dict:
new_dict[k] = dict_multimap(fn, all_v)
else:
new_dict[k] = fn(all_v)
return new_dict
def one_hot(x, v_bins):
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, inds, dim=0, no_batch_dims=0):
ranges = []
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 = [
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)
return data[ranges]
# With tree_map, a poor man's JAX tree_map
def dict_map(fn, dic, leaf_type):
new_dict = {}
for k, v in dic.items():
if type(v) is dict:
new_dict[k] = dict_map(fn, v, leaf_type)
else:
new_dict[k] = tree_map(fn, v, leaf_type)
return new_dict
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 ValueError("Not supported")
tensor_tree_map = partial(tree_map, leaf_type=torch.Tensor)
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