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[codex] Update AlphaFold3 submodule to v3.0.3 #625

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Merged
DimaMolod merged 3 commits into from
Jun 15, 2026
Merged

[codex] Update AlphaFold3 submodule to v3.0.3 #625

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3568329
Update AlphaFold3 submodule to v3.0.3
DimaMolod Jun 15, 2026
e739dea
Update AF3 v3.0.3 fork pointers and fix smoke tests
DimaMolod Jun 15, 2026
52a147f
Set AF3 container version to 3.0.3
DimaMolod Jun 15, 2026
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2 changes: 1 addition & 1 deletion .gitmodules
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Original file line number Diff line number Diff line change
Expand Up @@ -17,4 +17,4 @@
[submodule "alphafold3"]
path = alphafold3
url = https://github.com/KosinskiLab/alphafold3.git
branch = ap-gapped-discontinuous-chains-v3.0.2
branch = main
2 changes: 1 addition & 1 deletion alphafold
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Submodule alphafold updated 1 files
+1 −1 alphafold/data/msa_pairing.py
2 changes: 1 addition & 1 deletion alphafold3
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Submodule alphafold3 updated 153 files
10 changes: 4 additions & 6 deletions alphapulldown/utils/mmseqs_species_identifiers.py
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Expand Up @@ -388,12 +388,12 @@ def _write_identifier_rows_to_cache(
def build_mmseq_identifier_features(
a3m_string: str,
*,
species_resolver: Callable[[Sequence[str]], dict[str, str]] = (
resolve_species_ids_by_accession
),
species_resolver: Callable[[Sequence[str]], dict[str, str]] | None = None,
cache_path: str | None = None,
expected_rows: int | None = None,
) -> dict[str, np.ndarray]:
if species_resolver is None:
species_resolver = resolve_species_ids_by_accession
stripped_a3m = strip_mmseq_comment_lines(a3m_string)
source_sha256 = _calculate_mmseq_source_sha256(stripped_a3m)

Expand Down Expand Up @@ -431,9 +431,7 @@ def enrich_mmseq_feature_dict_with_identifiers(
feature_dict: dict[str, np.ndarray],
a3m_string: str,
*,
species_resolver: Callable[[Sequence[str]], dict[str, str]] = (
resolve_species_ids_by_accession
),
species_resolver: Callable[[Sequence[str]], dict[str, str]] | None = None,
cache_path: str | None = None,
) -> None:
msa = feature_dict.get("msa")
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5 changes: 3 additions & 2 deletions docker/alphafold3.dockerfile
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Expand Up @@ -68,7 +68,7 @@ RUN cd /hmmer_build && \
COPY . /app/AlphaPulldown

# ---------------------------------------------------------------------
# Install AlphaFold3 from its locked v3.0.2/Tokamax environment
# Install AlphaFold3 from its locked v3.0.3/Tokamax environment
# ---------------------------------------------------------------------
WORKDIR /app/AlphaPulldown/alphafold3

Expand All @@ -77,7 +77,8 @@ ENV PIP_INDEX_URL=${PIP_INDEX_URL} \
PIP_DEFAULT_TIMEOUT=600 \
PIP_RETRIES=10 \
PIP_NO_CACHE_DIR=1 \
PIP_DISABLE_PIP_VERSION_CHECK=1
PIP_DISABLE_PIP_VERSION_CHECK=1 \
SETUPTOOLS_SCM_PRETEND_VERSION_FOR_ALPHAFOLD3=3.0.3

ENV CMAKE_BUILD_PARALLEL_LEVEL=1
ENV CFLAGS="-O2 -pipe"
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