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Clarify and fix documentation.

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Addresses the following pull requests:
* https://github.com/google-deepmind/alphafold/pull/1083
* https://github.com/google-deepmind/alphafold/pull/1079
* https://github.com/google-deepmind/alphafold/pull/893

PiperOrigin-RevId: 798021344
Change-Id: I51bbc56998b99d53697b9d95e28cf1d55d562291
This commit is contained in:
Ryan Pachauri
2025-08-21 20:21:56 -07:00
committed by Copybara-Service
parent aba97651a6
commit e57fba02b1
2 changed files with 8 additions and 6 deletions
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9
alphafold/model/modules.py
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@@ -556,10 +556,11 @@ class Attention(hk.Module):
Arguments:
q_data: A tensor of queries, shape [batch_size, N_queries, q_channels].
m_data: A tensor of memories from which the keys and values are
projected, shape [batch_size, N_keys, m_channels].
mask: A mask for the attention, shape [batch_size, N_queries, N_keys].
nonbatched_bias: Shared bias, shape [N_queries, N_keys].
m_data: A tensor of memories from which the keys and values are projected,
shape [batch_size, N_keys, m_channels].
mask: A mask for the attention, shape [batch_size, N_heads, N_queries,
N_keys].
nonbatched_bias: Shared bias, shape [N_heads, N_queries, N_keys].
Returns:
A float32 tensor of shape [batch_size, N_queries, output_dim].

5
run_alphafold.py
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@@ -89,8 +89,9 @@ flags.DEFINE_string('uniprot_database_path', None, 'Path to the Uniprot '
'database for use by JackHMMer.')
flags.DEFINE_string('pdb70_database_path', None, 'Path to the PDB70 '
'database for use by HHsearch.')
flags.DEFINE_string('pdb_seqres_database_path', None, 'Path to the PDB '
'seqres database for use by hmmsearch.')
flags.DEFINE_string('pdb_seqres_database_path', None, 'Full filepath to the '
'PDB seqres database file (not just the directory) for use '
'by hmmsearch.')
flags.DEFINE_string('template_mmcif_dir', None, 'Path to a directory with '
'template mmCIF structures, each named <pdb_id>.cif')
flags.DEFINE_string('max_template_date', None, 'Maximum template release date '