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Openfold update #51

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Merged
hlasimpk merged 3 commits into from
Apr 15, 2026
Merged

Openfold update #51

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200b7c4
Updates to use newer version of OF3 with pae built in. Need to wait f…
Mar 31, 2026
2ccdb43
Update openfold version number
Apr 15, 2026
4594c0f
Fixed bug in changed test and updated of3 data
Apr 15, 2026
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2 changes: 1 addition & 1 deletion abcfold/data/config.ini
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ protenix_env = abcfold-protenix-py311
af3_version = 3.0.0
boltz_version = 2.2.1
chai_version = 0.6.1
openfold_version = 0.3.1
openfold_version = 0.4.1
protenix_version = 1.0.0

[Models]
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1 change: 0 additions & 1 deletion abcfold/openfold3/af3_to_openfold3.py
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Expand Up @@ -235,7 +235,6 @@ def write_yaml(self, out_file: Union[str, Path]):
"model_update:",
" presets:",
" - predict",
" - pae_enabled",
" - low_mem",
" custom:",
" settings:",
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6 changes: 3 additions & 3 deletions abcfold/openfold3/check_install.py
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Expand Up @@ -6,9 +6,9 @@

logger = logging.getLogger("logger")

OPENFOLD_BUCKET = "openfold"
CHECKPOINT_NAME = "of3_ft3_v1.pt"
S3_KEY = f"openfold3_params/{CHECKPOINT_NAME}"
OPENFOLD_BUCKET = "openfold3-data"
CHECKPOINT_NAME = "of3-p2-155k.pt"
S3_KEY = f"openfold3-parameters/{CHECKPOINT_NAME}"
HTTPS_URL = (
f"https://{OPENFOLD_BUCKET}.s3.amazonaws.com/{S3_KEY}"
)
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5 changes: 3 additions & 2 deletions abcfold/openfold3/run_openfold3.py
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Expand Up @@ -5,7 +5,8 @@
from typing import Optional, Union

from abcfold.openfold3.af3_to_openfold3 import OpenfoldJson
from abcfold.openfold3.check_install import (ensure_openfold_checkpoint,
from abcfold.openfold3.check_install import (CHECKPOINT_NAME,
ensure_openfold_checkpoint,
ensure_openfold_env)

logger = logging.getLogger("logger")
Expand Down Expand Up @@ -55,7 +56,7 @@ def run_openfold(
else:
cache_path = Path.home().joinpath(".openfold3")

default_ckpt = cache_path.joinpath("of3_ft3_v1.pt")
default_ckpt = cache_path.joinpath(CHECKPOINT_NAME)
if input_ckpt is None:
if not default_ckpt.exists():
logger.info(
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2 changes: 1 addition & 1 deletion abcfold/output/utils.py
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Expand Up @@ -328,7 +328,7 @@ def from_openfold3(cls, scores: dict, cif_file: CifFile):
]
)

pae_matrix = np.asarray(scores["pde"])
pae_matrix = np.asarray(scores["pae"])
af3_scores["pae"] = pae_matrix.tolist()
af3_scores["atom_chain_ids"] = atom_chain_ids
af3_scores["atom_plddts"] = atom_plddts
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