Skip to content

Added handling of cache in both cli.py and inference.py #15

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
wants to merge 3 commits into
base: main
Choose a base branch
from
+8 −6
Open

Added handling of cache in both cli.py and inference.py #15

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
74f8056
Added handling of
jimmymcheung Sep 29, 2025
51b1e18
Fix an issue causing file not found err when the model is ran outside…
jimmymcheung Sep 29, 2025
9179e99
Merge branch 'main' into dev-1
jimmymcheung Oct 27, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions src/simplefold/cli.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,7 @@ def main():
parser.add_argument("--plddt", action="store_true", help="Enable pLDDT prediction.")
parser.add_argument("--output_format", type=str, default="mmcif", choices=["pdb", "mmcif"], help="Output file format.")
parser.add_argument("--backend", type=str, default='torch', choices=['torch', 'mlx'], help="Backend to run inference either torch or mlx")
parser.add_argument("--cache", type=str, default=None, help="Specify the cache directory other than default.")
parser.add_argument("--seed", type=int, default=42, help="Random seed for reproducibility.")
parser.add_argument(
"--version",
Expand Down
8 changes: 4 additions & 4 deletions src/simplefold/inference.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -62,7 +62,7 @@ def initialize_folding_model(args):
if not os.path.exists(ckpt_path):
os.makedirs(ckpt_dir, exist_ok=True)
os.system(f"curl -L {ckpt_url_dict[simplefold_model]} -o {ckpt_path}")
cfg_path = os.path.join("configs/model/architecture", f"foldingdit_{simplefold_model[11:]}.yaml")
cfg_path = os.path.join(Path(__file__).parents[2], "configs/model/architecture", f"foldingdit_{simplefold_model[11:]}.yaml")

checkpoint = torch.load(ckpt_path, map_location="cpu", weights_only=False)

Expand Down Expand Up @@ -100,7 +100,7 @@ def initialize_plddt_module(args, device):
os.makedirs(args.ckpt_dir, exist_ok=True)
os.system(f"curl -L {plddt_ckpt_url} -o {plddt_ckpt_path}")

plddt_module_path = "configs/model/architecture/plddt_module.yaml"
plddt_module_path = os.path.join(Path(__file__).parents[2], "configs/model/architecture/plddt_module.yaml")
plddt_checkpoint = torch.load(plddt_ckpt_path, map_location="cpu", weights_only=False)

if args.backend == "torch":
Expand Down Expand Up @@ -128,7 +128,7 @@ def initialize_plddt_module(args, device):
os.makedirs(args.ckpt_dir, exist_ok=True)
os.system(f"curl -L {ckpt_url_dict['simplefold_1.6B']} -o {plddt_latent_ckpt_path}")

plddt_latent_config_path = "configs/model/architecture/foldingdit_1.6B.yaml"
plddt_latent_config_path = os.path.join(Path(__file__).parents[2], "configs/model/architecture/foldingdit_1.6B.yaml")
plddt_latent_checkpoint = torch.load(plddt_latent_ckpt_path, map_location="cpu", weights_only=False)

if args.backend == "torch":
Expand Down Expand Up @@ -257,7 +257,7 @@ def predict_structures_from_fastas(args):
output_dir.mkdir(parents=True, exist_ok=True)
prediction_dir = output_dir / f"predictions_{args.simplefold_model}"
prediction_dir.mkdir(parents=True, exist_ok=True)
cache = output_dir / "cache"
cache = output_dir / "cache" if not args.cache else Path(args.cache)
cache.mkdir(parents=True, exist_ok=True)

# set random seed for reproducibility
Expand Down
5 changes: 3 additions & 2 deletions src/simplefold/wrapper.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -88,6 +88,7 @@ def from_pretrained_folding_model(self):

# load model checkpoint
cfg_path = os.path.join(
Path(__file__).parents[2],
"configs/model/architecture", f"foldingdit_{simplefold_model[11:]}.yaml"
)
if self.backend == "torch":
Expand Down Expand Up @@ -126,7 +127,7 @@ def from_pretrained_plddt_model(self):
if not os.path.exists(plddt_ckpt_path):
os.system(f"curl -L -o {plddt_ckpt_path} {plddt_ckpt_url}")

plddt_module_path = "configs/model/architecture/plddt_module.yaml"
plddt_module_path = os.path.join(Path(__file__).parents[2], "configs/model/architecture/plddt_module.yaml")
plddt_checkpoint = torch.load(
plddt_ckpt_path, map_location="cpu", weights_only=False
)
Expand Down Expand Up @@ -162,7 +163,7 @@ def from_pretrained_plddt_model(self):
f"curl -L -o {plddt_latent_ckpt_path} {ckpt_url_dict['simplefold_1.6B']}"
)

plddt_latent_config_path = "configs/model/architecture/foldingdit_1.6B.yaml"
plddt_latent_config_path = os.path.join(Path(__file__).parents[2], "configs/model/architecture/foldingdit_1.6B.yaml")
plddt_latent_checkpoint = torch.load(
plddt_latent_ckpt_path, map_location="cpu", weights_only=False
)
Expand Down