view docker/alphafold/alphafold/model/tf/input_pipeline.py @ 1:6c92e000d684 draft

"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"

# 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.

"""Feature pre-processing input pipeline for AlphaFold."""

from alphafold.model.tf import data_transforms
from alphafold.model.tf import shape_placeholders
import tensorflow.compat.v1 as tf
import tree

# Pylint gets confused by the curry1 decorator because it changes the number
#   of arguments to the function.
# pylint:disable=no-value-for-parameter


NUM_RES = shape_placeholders.NUM_RES
NUM_MSA_SEQ = shape_placeholders.NUM_MSA_SEQ
NUM_EXTRA_SEQ = shape_placeholders.NUM_EXTRA_SEQ
NUM_TEMPLATES = shape_placeholders.NUM_TEMPLATES


def nonensembled_map_fns(data_config):
  """Input pipeline functions which are not ensembled."""
  common_cfg = data_config.common

  map_fns = [
      data_transforms.correct_msa_restypes,
      data_transforms.add_distillation_flag(False),
      data_transforms.cast_64bit_ints,
      data_transforms.squeeze_features,
      # Keep to not disrupt RNG.
      data_transforms.randomly_replace_msa_with_unknown(0.0),
      data_transforms.make_seq_mask,
      data_transforms.make_msa_mask,
      # Compute the HHblits profile if it's not set. This has to be run before
      # sampling the MSA.
      data_transforms.make_hhblits_profile,
      data_transforms.make_random_crop_to_size_seed,
  ]
  if common_cfg.use_templates:
    map_fns.extend([
        data_transforms.fix_templates_aatype,
        data_transforms.make_template_mask,
        data_transforms.make_pseudo_beta('template_')
    ])
  map_fns.extend([
      data_transforms.make_atom14_masks,
  ])

  return map_fns


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(
      data_transforms.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(
        data_transforms.make_masked_msa(common_cfg.masked_msa,
                                        eval_cfg.masked_msa_replace_fraction))

  if common_cfg.msa_cluster_features:
    map_fns.append(data_transforms.nearest_neighbor_clusters())
    map_fns.append(data_transforms.summarize_clusters())

  # Crop after creating the cluster profiles.
  if max_extra_msa:
    map_fns.append(data_transforms.crop_extra_msa(max_extra_msa))
  else:
    map_fns.append(data_transforms.delete_extra_msa)

  map_fns.append(data_transforms.make_msa_feat())

  crop_feats = dict(eval_cfg.feat)

  if eval_cfg.fixed_size:
    map_fns.append(data_transforms.select_feat(list(crop_feats)))
    map_fns.append(data_transforms.random_crop_to_size(
        eval_cfg.crop_size,
        eval_cfg.max_templates,
        crop_feats,
        eval_cfg.subsample_templates))
    map_fns.append(data_transforms.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(data_transforms.crop_templates(eval_cfg.max_templates))

  return map_fns


def process_tensors_from_config(tensors, data_config):
  """Apply filters and maps to an existing dataset, based on the config."""

  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)

  eval_cfg = data_config.eval
  tensors = compose(
      nonensembled_map_fns(
          data_config))(
              tensors)

  tensors_0 = wrap_ensemble_fn(tensors, tf.constant(0))
  num_ensemble = eval_cfg.num_ensemble
  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, tensors_0)
    tensors = tf.map_fn(
        lambda x: wrap_ensemble_fn(tensors, x),
        tf.range(num_ensemble),
        parallel_iterations=1,
        fn_output_signature=fn_output_signature)
  else:
    tensors = tree.map_structure(lambda x: x[None],
                                 tensors_0)
  return tensors


@data_transforms.curry1
def compose(x, fs):
  for f in fs:
    x = f(x)
  return x