多次运用集成函数处理蛋白质特征数据
wrap_ensemble_fn函数实现对蛋白质特征的多次集成函数操作（如多次抽样sample_msa等）
主要函数
tree.map_structure：
fn_output_signature = tree.map_structure( tf.TensorSpec.from_tensor, tensors_0)
tf.map_fn：用于在张量的每个元素上应用一个函数。
tensors = tf.map_fn(
lambda x: wrap_ensemble_fn(tensors, x),
tf.range(num_ensemble),
parallel_iterations=1,
fn_output_signature=fn_output_signature)
import copy
import tensorflow.compat.v1 as tf
import tree
import pickle
import numpy as np
import ml_collections
NUM_RES = 'num residues placeholder'
NUM_MSA_SEQ = 'msa placeholder'
NUM_EXTRA_SEQ = 'extra msa placeholder'
NUM_TEMPLATES = 'num templates placeholder'
CONFIG = ml_collections.ConfigDict({
'data': {
'common': {
'masked_msa': {
'profile_prob': 0.1,
'same_prob': 0.1,
'uniform_prob': 0.1
},
'max_extra_msa': 1024,
'msa_cluster_features': True,
'num_recycle': 3,
'reduce_msa_clusters_by_max_templates': False,
'resample_msa_in_recycling': True,
'template_features': [
'template_all_atom_positions', 'template_sum_probs',
'template_aatype', 'template_all_atom_masks',
'template_domain_names'
],
'unsupervised_features': [
'aatype', 'residue_index', 'sequence', 'msa', 'domain_name',
'num_alignments', 'seq_length', 'between_segment_residues',
'deletion_matrix'
],
'use_templates': False,
},
'eval': {
'feat': {
'aatype': [NUM_RES],
'all_atom_mask': [NUM_RES, None],
'all_atom_positions': [NUM_RES, None, None],
'alt_chi_angles': [NUM_RES, None],
'atom14_alt_gt_exists': [NUM_RES, None],
'atom14_alt_gt_positions': [NUM_RES, None, None],
'atom14_atom_exists': [NUM_RES, None],
'atom14_atom_is_ambiguous': [NUM_RES, None],
'atom14_gt_exists': [NUM_RES, None],
'atom14_gt_positions': [NUM_RES, None, None],
'atom37_atom_exists': [NUM_RES, None],
'backbone_affine_mask': [NUM_RES],
'backbone_affine_tensor': [NUM_RES, None],
'bert_mask': [NUM_MSA_SEQ, NUM_RES],
'chi_angles': [NUM_RES, None],
'chi_mask': [NUM_RES, None],
'extra_deletion_value': [NUM_EXTRA_SEQ, NUM_RES],
'extra_has_deletion': [NUM_EXTRA_SEQ, NUM_RES],
'extra_msa': [NUM_EXTRA_SEQ, NUM_RES],
'extra_msa_mask': [NUM_EXTRA_SEQ, NUM_RES],
'extra_msa_row_mask': [NUM_EXTRA_SEQ],
'is_distillation': [],
'msa_feat': [NUM_MSA_SEQ, NUM_RES, None],
'msa_mask': [NUM_MSA_SEQ, NUM_RES],
'msa_row_mask': [NUM_MSA_SEQ],
'pseudo_beta': [NUM_RES, None],
'pseudo_beta_mask': [NUM_RES],
'random_crop_to_size_seed': [None],
'residue_index': [NUM_RES],
'residx_atom14_to_atom37': [NUM_RES, None],
'residx_atom37_to_atom14': [NUM_RES, None],
'resolution': [],
'rigidgroups_alt_gt_frames': [NUM_RES, None, None],
'rigidgroups_group_exists': [NUM_RES, None],
'rigidgroups_group_is_ambiguous': [NUM_RES, None],
'rigidgroups_gt_exists': [NUM_RES, None],
'rigidgroups_gt_frames': [NUM_RES, None, None],
'seq_length': [],
'seq_mask': [NUM_RES],
'target_feat': [NUM_RES, None],
'template_aatype': [NUM_TEMPLATES, NUM_RES],
'template_all_atom_masks': [NUM_TEMPLATES, NUM_RES, None],
'template_all_atom_positions': [
NUM_TEMPLATES, NUM_RES, None, None],
'template_backbone_affine_mask': [NUM_TEMPLATES, NUM_RES],
'template_backbone_affine_tensor': [
NUM_TEMPLATES, NUM_RES, None],
'template_mask': [NUM_TEMPLATES],
'template_pseudo_beta': [NUM_TEMPLATES, NUM_RES, None],
'template_pseudo_beta_mask': [NUM_TEMPLATES, NUM_RES],
'template_sum_probs': [NUM_TEMPLATES, None],
'true_msa': [NUM_MSA_SEQ, NUM_RES]
},
'fixed_size': True,
'subsample_templates': True, # We want top templates.
'masked_msa_replace_fraction': 0.15,
'max_msa_clusters': 512,
'max_templates': 4,
'num_ensemble': 1,
'crop_size': 100,
},
},
'model': {
'embeddings_and_evoformer': {
'evoformer_num_block': 48,
'evoformer': {
'msa_row_attention_with_pair_bias': {
'dropout_rate': 0.15,
'gating': True,
'num_head': 8,
'orientation': 'per_row',
'shared_dropout': True
},
'msa_column_attention': {
'dropout_rate': 0.0,
'gating': True,
'num_head': 8,
'orientation': 'per_column',
'shared_dropout': True
},
'msa_transition': {
'dropout_rate': 0.0,
'num_intermediate_factor': 4,
'orientation': 'per_row',
'shared_dropout': True
},
'outer_product_mean': {
'first': False,
'chunk_size': 128,
'dropout_rate': 0.0,
'num_outer_channel': 32,
'orientation': 'per_row',
'shared_dropout': True
},
'triangle_attention_starting_node': {
'dropout_rate': 0.25,
'gating': True,
'num_head': 4,
'orientation': 'per_row',
'shared_dropout': True
},
'triangle_attention_ending_node': {
'dropout_rate': 0.25,
'gating': True,
'num_head': 4,
'orientation': 'per_column',
'shared_dropout': True
},
'triangle_multiplication_outgoing': {
'dropout_rate': 0.25,
'equation': 'ikc,jkc->ijc',
'num_intermediate_channel': 128,
'orientation': 'per_row',
'shared_dropout': True,
'fuse_projection_weights': False,
},
'triangle_multiplication_incoming': {
'dropout_rate': 0.25,
'equation': 'kjc,kic->ijc',
'num_intermediate_channel': 128,
'orientation': 'per_row',
'shared_dropout': True,
'fuse_projection_weights': False,
},
'pair_transition': {
'dropout_rate': 0.0,
'num_intermediate_factor': 4,
'orientation': 'per_row',
'shared_dropout': True
}
},
'extra_msa_channel': 64,
'extra_msa_stack_num_block': 4,
'max_relative_feature': 32,
'msa_channel': 256,
'pair_channel': 128,
'prev_pos': {
'min_bin': 3.25,
'max_bin': 20.75,
'num_bins': 15
},
'recycle_features': True,
'recycle_pos': True,
'seq_channel': 384,
'template': {
'attention': {
'gating': False,
'key_dim': 64,
'num_head': 4,
'value_dim': 64
},
'dgram_features': {
'min_bin': 3.25,
'max_bin': 50.75,
'num_bins': 39
},
'embed_torsion_angles': False,
'enabled': False,
'template_pair_stack': {
'num_block': 2,
'triangle_attention_starting_node': {
'dropout_rate': 0.25,
'gating': True,
'key_dim': 64,
'num_head': 4,
'orientation': 'per_row',
'shared_dropout': True,
'value_dim': 64
},
'triangle_attention_ending_node': {
'dropout_rate': 0.25,
'gating': True,
'key_dim': 64,
'num_head': 4,
'orientation': 'per_column',
'shared_dropout': True,
'value_dim': 64
},
'triangle_multiplication_outgoing': {
'dropout_rate': 0.25,
'equation': 'ikc,jkc->ijc',
'num_intermediate_channel': 64,
'orientation': 'per_row',
'shared_dropout': True,
'fuse_projection_weights': False,
},
'triangle_multiplication_incoming': {
'dropout_rate': 0.25,
'equation': 'kjc,kic->ijc',
'num_intermediate_channel': 64,
'orientation': 'per_row',
'shared_dropout': True,
'fuse_projection_weights': False,
},
'pair_transition': {
'dropout_rate': 0.0,
'num_intermediate_factor': 2,
'orientation': 'per_row',
'shared_dropout': True
}
},
'max_templates': 4,
'subbatch_size': 128,
'use_template_unit_vector': False,
}
},
'global_config': {
'deterministic': False,
'multimer_mode': False,
'subbatch_size': 4,
'use_remat': False,
'zero_init': True,
'eval_dropout': False,
},
'heads': {
'distogram': {
'first_break': 2.3125,
'last_break': 21.6875,
'num_bins': 64,
'weight': 0.3
},
'predicted_aligned_error': {
# `num_bins - 1` bins uniformly space the
# [0, max_error_bin A] range.
# The final bin covers [max_error_bin A, +infty]
# 31A gives bins with 0.5A width.
'max_error_bin': 31.,
'num_bins': 64,
'num_channels': 128,
'filter_by_resolution': True,
'min_resolution': 0.1,
'max_resolution': 3.0,
'weight': 0.0,
},
'experimentally_resolved': {
'filter_by_resolution': True,
'max_resolution': 3.0,
'min_resolution': 0.1,
'weight': 0.01
},
'structure_module': {
'num_layer': 8,
'fape': {
'clamp_distance': 10.0,
'clamp_type': 'relu',
'loss_unit_distance': 10.0
},
'angle_norm_weight': 0.01,
'chi_weight': 0.5,
'clash_overlap_tolerance': 1.5,
'compute_in_graph_metrics': True,
'dropout': 0.1,
'num_channel': 384,
'num_head': 12,
'num_layer_in_transition': 3,
'num_point_qk': 4,
'num_point_v': 8,
'num_scalar_qk': 16,
'num_scalar_v': 16,
'position_scale': 10.0,
'sidechain': {
'atom_clamp_distance': 10.0,
'num_channel': 128,
'num_residual_block': 2,
'weight_frac': 0.5,
'length_scale': 10.,
},
'structural_violation_loss_weight': 1.0,
'violation_tolerance_factor': 12.0,
'weight': 1.0
},
'predicted_lddt': {
'filter_by_resolution': True,
'max_resolution': 3.0,
'min_resolution': 0.1,
'num_bins': 50,
'num_channels': 128,
'weight': 0.01
},
'masked_msa': {
'num_output': 23,
'weight': 2.0
},
},
'num_recycle': 3,
'resample_msa_in_recycling': True
},
})
_MSA_FEATURE_NAMES = [
'msa', 'deletion_matrix', 'msa_mask', 'msa_row_mask', 'bert_mask',
'true_msa'
]
class SeedMaker(object):
"""Return unique seeds."""
def __init__(self, initial_seed=0):
self.next_seed = initial_seed
def __call__(self):
i = self.next_seed
self.next_seed += 1
return i
def shape_list(x):
"""Return list of dimensions of a tensor, statically where possible.
Like `x.shape.as_list()` but with tensors instead of `None`s.
Args:
x: A tensor.
Returns:
A list with length equal to the rank of the tensor. The n-th element of the
list is an integer when that dimension is statically known otherwise it is
the n-th element of `tf.shape(x)`.
"""
x = tf.convert_to_tensor(x)
# If unknown rank, return dynamic shape
if x.get_shape().dims is None:
return tf.shape(x)
static = x.get_shape().as_list()
shape = tf.shape(x)
ret = []
for i in range(len(static)):
dim = static[i]
if dim is None:
dim = shape[i]
ret.append(dim)
return ret
def shaped_categorical(probs, epsilon=1e-10):
ds = shape_list(probs)
num_classes = ds[-1]
counts = tf.random.categorical(
tf.reshape(tf.log(probs + epsilon), [-1, num_classes]),
1,
dtype=tf.int32)
return tf.reshape(counts, ds[:-1])
def data_transforms_curry1(f):
"""Supply all arguments but the first."""
def fc(*args, **kwargs):
return lambda x: f(x, *args, **kwargs)
return fc
@data_transforms_curry1
def sample_msa(protein, max_seq, keep_extra):
"""Sample MSA randomly, remaining sequences are stored as `extra_*`.
Args:
protein: batch to sample msa from.
max_seq: number of sequences to sample.
keep_extra: When True sequences not sampled are put into fields starting
with 'extra_*'.
Returns:
Protein with sampled msa.
"""
num_seq = tf.shape(protein['msa'])[0]
# 索引0的序列为查询序列
shuffled = tf.random_shuffle(tf.range(1, num_seq))
index_order = tf.concat([[0], shuffled], axis=0)
num_sel = tf.minimum(max_seq, num_seq)
# tf.split函数将张量沿指定轴进行切分，
# 第一张量大小为num_sel，第二张量大小为num_seq - num_sel
sel_seq, not_sel_seq = tf.split(index_order, [num_sel, num_seq - num_sel])
for k in _MSA_FEATURE_NAMES:
if k in protein:
if keep_extra:
# tf.gather 按索引从输入张量中收集元素的函数
protein['extra_' + k] = tf.gather(protein[k], not_sel_seq)
protein[k] = tf.gather(protein[k], sel_seq)
return protein
@data_transforms_curry1
def make_masked_msa(protein, config, replace_fraction):
"""Create data for BERT on raw MSA."""
# Add a random amino acid uniformly
random_aa = tf.constant([0.05] * 20 + [0., 0.], dtype=tf.float32)
# 构建随机随机出现某一氨基酸的概率，和MSA中氨基酸的保守性有关
categorical_probs = (
config.uniform_prob * random_aa +
config.profile_prob * protein['hhblits_profile'] +
config.same_prob * tf.one_hot(protein['msa'], 22))
#print(tf.reduce_sum(categorical_probs, axis=-1)) # 都为0.3
# Put all remaining probability on [MASK] which is a new column
pad_shapes = [[0, 0] for _ in range(len(categorical_probs.shape))]
pad_shapes[-1][1] = 1
# mask_prob ： 0.7， 其他prob加在一起0.3
mask_prob = 1. - config.profile_prob - config.same_prob - config.uniform_prob
assert mask_prob >= 0.
# categorical_probs张量后填充mask_prob值，代表MSA每一个位置的概率（20种氨基酸+gap+X+mask）
categorical_probs = tf.pad(
categorical_probs, pad_shapes, constant_values=mask_prob)
#print(tf.reduce_sum(categorical_probs, axis=-1)) # 都为0.3
sh = shape_list(protein['msa'])
# 0-1均匀分布中随机抽样，形状为sh，通过和replace_fraction（0.15）比较,产生随机mask位置
mask_position = tf.random.uniform(sh) < replace_fraction
##抽样，注意随机性产生的方式，抽到mask概率最大，而抽到其他氨基酸概率的大小和其在MSA中的保守性有关
bert_msa = shaped_categorical(categorical_probs)
## 大概0.15的概率用随机氨基酸代替，随机氨基酸中有0.7的概率是mask，还有0.3的概率抽到其他氨基酸，
## 氨基酸在此位置越保守，抽到的可能性越大
## bert_msa中大概有0.7*0.15的mask，还有混杂着错误和正确的氨基酸
bert_msa = tf.where(mask_position, bert_msa, protein['msa'])
# Mix real and masked MSA
protein['bert_mask'] = tf.cast(mask_position, tf.float32)
protein['true_msa'] = protein['msa']
protein['msa'] = bert_msa
return protein
@data_transforms_curry1
def nearest_neighbor_clusters(protein, gap_agreement_weight=0.):
"""Assign each extra MSA sequence to its nearest neighbor in sampled MSA."""
# Determine how much weight we assign to each agreement. In theory, we could
# use a full blosum matrix here, but right now let's just down-weight gap
# agreement because it could be spurious.
# Never put weight on agreeing on BERT mask
# 除了gap权重为0，其他（restype+X+mask）权重为1
weights = tf.concat([
tf.ones(21),
gap_agreement_weight * tf.ones(1),
np.zeros(1)], 0)
# Make agreement score as weighted Hamming distance
# 增加一个维度
sample_one_hot = (protein['msa_mask'][:, :, None] *
tf.one_hot(protein['msa'], 23))
extra_one_hot = (protein['extra_msa_mask'][:, :, None] *
tf.one_hot(protein['extra_msa'], 23))
num_seq, num_res, _ = shape_list(sample_one_hot)
extra_num_seq, _, _ = shape_list(extra_one_hot)
# Compute tf.einsum('mrc,nrc,c->mn', sample_one_hot, extra_one_hot, weights)
# in an optimized fashion to avoid possible memory or computation blowup.
# 判断extra msa序列与MSA sample序列的相似度,相同的氨基酸越多，越相似。
# 没有考虑氨基酸的性质，可以改进
# 注意氨基酸的权重（weights）
agreement = tf.matmul(
tf.reshape(extra_one_hot, [extra_num_seq, num_res * 23]),
tf.reshape(sample_one_hot * weights, [num_seq, num_res * 23]),
transpose_b=True)
# Assign each sequence in the extra sequences to the closest MSA sample
# 对extra msa中每一条序列，取相似度最高的MSA sample序列
protein['extra_cluster_assignment'] = tf.argmax(
agreement, axis=1, output_type=tf.int32)
return protein
@data_transforms_curry1
def summarize_clusters(protein):
"""Produce profile and deletion_matrix_mean within each cluster."""
num_seq = shape_list(protein['msa'])[0]
def csum(x):
return tf.math.unsorted_segment_sum(
x, protein['extra_cluster_assignment'], num_seq)
mask = protein['extra_msa_mask']
mask_counts = 1e-6 + protein['msa_mask'] + csum(mask) # Include center
# 结果张量[num_seq, num_resi]，第一行表示和msa中的0号序列是最近邻序列的extr_msa之和，以此类推
msa_sum = csum(mask[:, :, None] * tf.one_hot(protein['extra_msa'], 23))
msa_sum += tf.one_hot(protein['msa'], 23) # Original sequence
protein['cluster_profile'] = msa_sum / mask_counts[:, :, None]
del msa_sum
# 每条msa序列的最近邻序列的extr_msa，在不同位置deletion数统计
# del_sum [num_seq, num_resi]，第一行表示和msa中的0号序列是最近邻序列的extr_msa,不同位置deletion数，以此类推
del_sum = csum(mask * protein['extra_deletion_matrix'])
del_sum += protein['deletion_matrix'] # Original sequence
protein['cluster_deletion_mean'] = del_sum / mask_counts
del del_sum
return protein
@data_transforms_curry1
def crop_extra_msa(protein, max_extra_msa):
"""MSA features are cropped so only `max_extra_msa` sequences are kept."""
num_seq = tf.shape(protein['extra_msa'])[0]
num_sel = tf.minimum(max_extra_msa, num_seq)
select_indices = tf.random_shuffle(tf.range(0, num_seq))[:num_sel]
for k in _MSA_FEATURE_NAMES:
if 'extra_' + k in protein:
protein['extra_' + k] = tf.gather(protein['extra_' + k], select_indices)
return protein
@data_transforms_curry1
def make_msa_feat(protein):
"""Create and concatenate MSA features."""
# Whether there is a domain break. Always zero for chains, but keeping
# for compatibility with domain datasets.
has_break = tf.clip_by_value(
tf.cast(protein['between_segment_residues'], tf.float32),
0, 1)
aatype_1hot = tf.one_hot(protein['aatype'], 21, axis=-1)
target_feat = [
tf.expand_dims(has_break, axis=-1),
aatype_1hot, # Everyone gets the original sequence.
]
msa_1hot = tf.one_hot(protein['msa'], 23, axis=-1)
has_deletion = tf.clip_by_value(protein['deletion_matrix'], 0., 1.)
deletion_value = tf.atan(protein['deletion_matrix'] / 3.) * (2. / np.pi)
msa_feat = [
msa_1hot,
tf.expand_dims(has_deletion, axis=-1),
tf.expand_dims(deletion_value, axis=-1),
]
if 'cluster_profile' in protein:
deletion_mean_value = (
tf.atan(protein['cluster_deletion_mean'] / 3.) * (2. / np.pi))
msa_feat.extend([
protein['cluster_profile'],
tf.expand_dims(deletion_mean_value, axis=-1),
])
if 'extra_deletion_matrix' in protein:
protein['extra_has_deletion'] = tf.clip_by_value(
protein['extra_deletion_matrix'], 0., 1.)
protein['extra_deletion_value'] = tf.atan(
protein['extra_deletion_matrix'] / 3.) * (2. / np.pi)
protein['msa_feat'] = tf.concat(msa_feat, axis=-1)
protein['target_feat'] = tf.concat(target_feat, axis=-1)
return protein
@data_transforms_curry1
def select_feat(protein, feature_list):
return {k: v for k, v in protein.items() if k in feature_list}
@data_transforms_curry1
def random_crop_to_size(protein, crop_size, max_templates, shape_schema,
subsample_templates=False):
"""Crop randomly to `crop_size`, or keep as is if shorter than that."""
seq_length = protein['seq_length']
if 'template_mask' in protein:
num_templates = tf.cast(
shape_list(protein['template_mask'])[0], tf.int32)
else:
num_templates = tf.constant(0, dtype=tf.int32)
num_res_crop_size = tf.math.minimum(seq_length, crop_size)
# Ensures that the cropping of residues and templates happens in the same way
# across ensembling iterations.
# Do not use for randomness that should vary in ensembling.
seed_maker = SeedMaker(initial_seed=protein['random_crop_to_size_seed'])
if subsample_templates:
templates_crop_start = tf.random.stateless_uniform(
shape=(), minval=0, maxval=num_templates + 1, dtype=tf.int32,
seed=seed_maker())
else:
templates_crop_start = 0
num_templates_crop_size = tf.math.minimum(
num_templates - templates_crop_start, max_templates)
num_res_crop_start = tf.random.stateless_uniform(
shape=(), minval=0, maxval=seq_length - num_res_crop_size + 1,
dtype=tf.int32, seed=seed_maker())
## 产生随机打乱的索引，用于所有需要裁剪的模版特征
# tf.argsort 函数用于返回张量中元素的排序索引
# tf.random.stateless_uniform：生成指定形状的服从均匀分布的随机张量
# 生成num_templates个指定形状的服从均匀分布的随机张量，形状为shape=(num_templates,)。
# 注：num_templates为标量，作为shape时，变成list[num_templates]
templates_select_indices = tf.argsort(tf.random.stateless_uniform(
[num_templates], seed=seed_maker()))
for k, v in protein.items():
if k not in shape_schema or (
'template' not in k and NUM_RES not in shape_schema[k]):
continue
# randomly permute the templates before cropping them.
if k.startswith('template') and subsample_templates:
v = tf.gather(v, templates_select_indices)
crop_sizes = []
crop_starts = []
# zip函数把维度说明和维度值绑定
# shape_schema[k]维度说明（placeholder）列表 ，shape_list(v)维度值
for i, (dim_size, dim) in enumerate(zip(shape_schema[k],shape_list(v))):
is_num_res = (dim_size == NUM_RES)
if i == 0 and k.startswith('template'):
crop_size = num_templates_crop_size
crop_start = templates_crop_start
else:
crop_start = num_res_crop_start if is_num_res else 0
crop_size = (num_res_crop_size if is_num_res else
(-1 if dim is None else dim))
crop_sizes.append(crop_size)
crop_starts.append(crop_start)
protein[k] = tf.slice(v, crop_starts, crop_sizes)
protein['seq_length'] = num_res_crop_size
return protein
@data_transforms_curry1
def make_fixed_size(protein, shape_schema, msa_cluster_size, extra_msa_size,
num_res, num_templates=0):
"""Guess at the MSA and sequence dimensions to make fixed size."""
pad_size_map = {
NUM_RES: num_res,
NUM_MSA_SEQ: msa_cluster_size,
NUM_EXTRA_SEQ: extra_msa_size,
NUM_TEMPLATES: num_templates,
}
for k, v in protein.items():
# Don't transfer this to the accelerator.
if k == 'extra_cluster_assignment':
continue
shape = v.shape.as_list()
# 特征维度placeholder
schema = shape_schema[k]
assert len(shape) == len(schema), (
f'Rank mismatch between shape and shape schema for {k}: '
f'{shape} vs {schema}')
# 特征张量不同维度的填充尺寸（pad_size）。需要填充的维度尺寸由pad_size_map决定。
# 字典get方法，键不存在时返回的None,这时列表取 s1 for (s1, s2) in zip(shape, schema)
pad_size = [
pad_size_map.get(s2, None) or s1 for (s1, s2) in zip(shape, schema)
]
# 在张量的后面填充，需要填充0的数目为填充尺寸减去现有的尺寸（p - tf.shape(v)[i]）
padding = [(0, p - tf.shape(v)[i]) for i, p in enumerate(pad_size)]
if padding:
protein[k] = tf.pad(
v, padding, name=f'pad_to_fixed_{k}')
protein[k].set_shape(pad_size)
return protein
def ensembled_map_fns(data_config):
"""Input pipeline functions that can be ensembled and averaged."""
common_cfg = data_config.common
eval_cfg = data_config.eval
map_fns = []
if common_cfg.reduce_msa_clusters_by_max_templates:
pad_msa_clusters = eval_cfg.max_msa_clusters - eval_cfg.max_templates
else:
pad_msa_clusters = eval_cfg.max_msa_clusters
max_msa_clusters = pad_msa_clusters
max_extra_msa = common_cfg.max_extra_msa
map_fns.append(sample_msa(max_msa_clusters,keep_extra=True))
if 'masked_msa' in common_cfg:
# Masked MSA should come *before* MSA clustering so that
# the clustering and full MSA profile do not leak information about
# the masked locations and secret corrupted locations.
map_fns.append(make_masked_msa(common_cfg.masked_msa,
eval_cfg.masked_msa_replace_fraction))
if common_cfg.msa_cluster_features:
map_fns.append(nearest_neighbor_clusters())
map_fns.append(summarize_clusters())
# Crop after creating the cluster profiles.
if max_extra_msa:
map_fns.append(crop_extra_msa(max_extra_msa))
else:
map_fns.append(delete_extra_msa)
map_fns.append(make_msa_feat())
crop_feats = dict(eval_cfg.feat)
if eval_cfg.fixed_size:
map_fns.append(select_feat(list(crop_feats)))
map_fns.append(random_crop_to_size(
eval_cfg.crop_size,
eval_cfg.max_templates,
crop_feats,
eval_cfg.subsample_templates))
map_fns.append(make_fixed_size(
crop_feats,
pad_msa_clusters,
common_cfg.max_extra_msa,
eval_cfg.crop_size,
eval_cfg.max_templates))
else:
map_fns.append(crop_templates(eval_cfg.max_templates))
return map_fns
@data_transforms_curry1
def compose(x, fs):
for f in fs:
x = f(x)
return x
### 得到配置数据
data_config = CONFIG.data
eval_cfg = data_config.eval
common_cfg = data_config.common
crop_feats = dict(eval_cfg.feat)
#pad_msa_clusters = eval_cfg.max_msa_clusters
shape_schema = crop_feats
num_ensemble = eval_cfg.num_ensemble
def wrap_ensemble_fn(data, i):
"""Function to be mapped over the ensemble dimension."""
d = data.copy()
fns = ensembled_map_fns(data_config)
fn = compose(fns)
d['ensemble_index'] = i
return fn(d)
### 读入数据，蛋白质特征已经过nonensembled函数处理
with open("Human_HBB_tensor_dict_nonensembled.pkl",'rb') as f:
Human_HBB_tensor = pickle.load(f)
protein = copy.deepcopy(Human_HBB_tensor)
#加上protein['deletion_matrix']特征，不然会报错
protein['deletion_matrix'] = tf.cast(protein['deletion_matrix_int'], dtype=tf.float32)
protein_0 = wrap_ensemble_fn(protein, tf.constant(0))
if data_config.common.resample_msa_in_recycling:
# Separate batch per ensembling & recycling step.
num_ensemble *= data_config.common.num_recycle + 1
if isinstance(num_ensemble, tf.Tensor) or num_ensemble > 1:
fn_output_signature = tree.map_structure(
tf.TensorSpec.from_tensor, protein_0)
#tf.map_fn 在处理两个结构不具有相同嵌套结构的情况时，
#可以使用 fn_output_signature 参数来指定输出函数的签名，
#从而显式指定输出的结构。
protein = tf.map_fn(
lambda x: wrap_ensemble_fn(protein, x),
tf.range(num_ensemble),
parallel_iterations=1,
fn_output_signature=fn_output_signature)
else:
# 增加一个维度
protein = tree.map_structure(lambda x: x[None],
protein_0)
print(f"ensembled函数处理前:")
print(f"特征数:{len(Human_HBB_tensor)}")
print(f"特征:{Human_HBB_tensor.keys()}")
print(Human_HBB_tensor['aatype'].shape)
#print(Human_HBB_tensor['aatype'])
print(f"ensembled函数处理后:")
print(f"特征数:{len(protein)}")
print(f"特征:{protein.keys()}")
print(protein['extra_msa'].shape)
print(protein['aatype'].shape)
print(protein['msa_feat'].shape)
print("protein_0['msa_feat'].shape")
print(protein_0['msa_feat'].shape)