rc-foundry 0.1.2__py3-none-any.whl → 0.1.3__py3-none-any.whl

foundry/version.py

@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
 commit_id: COMMIT_ID
 __commit_id__: COMMIT_ID
 
-__version__ = version = '0.1.2'
-__version_tuple__ = version_tuple = (0, 1, 2)
+__version__ = version = '0.1.3'
+__version_tuple__ = version_tuple = (0, 1, 3)
 
 __commit_id__ = commit_id = None

foundry_cli/download_checkpoints.py

@@ -5,6 +5,7 @@ from pathlib import Path
 from typing import Optional
 from urllib.request import urlopen
 
+import rootutils
 import typer
 from dotenv import find_dotenv, load_dotenv, set_key
 from rich.console import Console
@@ -96,7 +97,7 @@ def install_model(
         raise typer.Exit(1)
 
     checkpoint_info = REGISTERED_CHECKPOINTS[model_name]
-    dest_path = checkpoint_dir / checkpoint_info["filename"]
+    dest_path = checkpoint_dir / checkpoint_info.filename
 
     # Check if already exists
     if dest_path.exists() and not force:
@@ -107,12 +108,12 @@ def install_model(
         return
 
     console.print(
-        f"[cyan]Installing {model_name}:[/cyan] {checkpoint_info['description']}"
+        f"[cyan]Installing {model_name}:[/cyan] {checkpoint_info.description}"
     )
 
     try:
         download_file(
-            checkpoint_info["url"], dest_path, checkpoint_info.get("sha256")
+            checkpoint_info.url, dest_path, checkpoint_info.sha256
         )
         console.print(
             f"[green]✓[/green] Successfully installed {model_name} to {dest_path}"
@@ -184,7 +185,7 @@ def list_models():
     """List available model checkpoints."""
     console.print("[bold]Available models:[/bold]\n")
     for name, info in REGISTERED_CHECKPOINTS.items():
-        console.print(f"  [cyan]{name:8}[/cyan] - {info['description']}")
+        console.print(f"  [cyan]{name:8}[/cyan] - {info.description}")
 
 
 @app.command()

mpnn/utils/inference.py

@@ -362,7 +362,7 @@ def build_arg_parser() -> argparse.ArgumentParser:
         "--fixed_residues",
         type=str,
         help=(
-            'List of residue IDs to fix: e.g. \'["A35","B40","C52"]\' or "A35,B40,C52"',
+            'List of residue IDs to fix: e.g. \'["A35","B40","C52"]\' or "A35,B40,C52"'
         ),
         default=MPNN_PER_INPUT_INFERENCE_DEFAULTS["fixed_residues"],
     )
@@ -371,20 +371,20 @@ def build_arg_parser() -> argparse.ArgumentParser:
         type=str,
         help=(
             "List of residue IDs to design: "
-            'e.g. \'["A35","B40","C52"]\' or "A35,B40,C52"',
+            'e.g. \'["A35","B40","C52"]\' or "A35,B40,C52"'
         ),
         default=MPNN_PER_INPUT_INFERENCE_DEFAULTS["designed_residues"],
     )
     design_group.add_argument(
         "--fixed_chains",
         type=str,
-        help=('List of chain IDs to fix: e.g. \'["A","B"]\' or "A,B"',),
+        help=('List of chain IDs to fix: e.g. \'["A","B"]\' or "A,B"'),
         default=MPNN_PER_INPUT_INFERENCE_DEFAULTS["fixed_chains"],
     )
     design_group.add_argument(
         "--designed_chains",
         type=str,
-        help=('List of chain IDs to design: e.g. \'["A","B"]\' or "A,B"',),
+        help=('List of chain IDs to design: e.g. \'["A","B"]\' or "A,B"'),
         default=MPNN_PER_INPUT_INFERENCE_DEFAULTS["designed_chains"],
     )
 

{rc_foundry-0.1.2.dist-info → rc_foundry-0.1.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rc-foundry
-Version: 0.1.2
+Version: 0.1.3
 Summary: Shared utilities and training infrastructure for biomolecular structure prediction models.
 Author-email: Institute for Protein Design <contact@ipd.uw.edu>
 License: BSD 3-Clause License
@@ -95,6 +95,8 @@ Description-Content-Type: text/markdown
 
 Foundry provides tooling and infrastructure for using and training all classes of models for protein design, including design (RFD3), inverse folding (ProteinMPNN) and protein folding (RF3).
 
+All models within Foundry rely on [AtomWorks](https://github.com/RosettaCommons/atomworks) - a unified framework for manipulating and processing biomolecular structures - for both training and inference. 
+
 ## Getting Started
 ### Quickstart guide
 **Installation**
@@ -107,14 +109,14 @@ pip install rc-foundry[all]
 ```
 foundry install all --checkpoint_dir <path/to/ckpt/dir>
 ```
-This will download all the models supported (including multiple checkpoints of rf3) but as a beginner you can start with:
+This will download all the models supported (including multiple checkpoints of RF3) but as a beginner you can start with:
 ```
 foundry install rfd3 ligandmpnn rf3 --checkpoint_dir  <path/to/ckpt/dir>
 ```
 
 >*See `examples/all.ipynb` for how to run each model in a notebook.*
 
-### RFdiffusion3
+### RFdiffusion3 (RFD3)
 
 [RFdiffusion3](https://www.biorxiv.org/content/10.1101/2025.09.18.676967v2) is an all-atom generative model capable of designing protein structures under complex constraints. 
 
@@ -129,7 +131,8 @@ foundry install rfd3 ligandmpnn rf3 --checkpoint_dir  <path/to/ckpt/dir>
 
 > *See [models/mpnn/README.md](models/mpnn/README.md) for complete documentation.*
 
-### RosettaFold3
+
+### RosettaFold3 (RF3)
 
 [RF3](https://doi.org/10.1101/2025.08.14.670328) is a structure prediction neural network that narrows the gap between closed-source AF-3 and open-source alternatives.
 

{rc_foundry-0.1.2.dist-info → rc_foundry-0.1.3.dist-info}/RECORD

@@ -1,7 +1,7 @@
 foundry/__init__.py,sha256=H8S1nl5v6YeW8ggn1jKy4GdtH7c-FGS-j7CqUCAEnAU,1926
 foundry/common.py,sha256=Aur8mH-CNmcUqSsw7VgaCQSW5sH1Bqf8Da91jzxPV1Y,3035
 foundry/constants.py,sha256=0n1wBKCvNuw3QaQehSbmsHYkIdaGn3tLeRFItBrdeHY,913
-foundry/version.py,sha256=Ok5oAXdWgR9aghaFXTafTeDW6sYO3uVe6d2Nket57R4,704
+foundry/version.py,sha256=q5nF98G8SoVeJqaknL0xdyxtv0egsqb0fK06_84Izu8,704
 foundry/callbacks/__init__.py,sha256=VsRT1e4sqlJHPcTCsfupMEx82Iz-LoOAGPpwvf_OJeE,126
 foundry/callbacks/callback.py,sha256=xZBo_suP4bLrP6gl5uJPbaXm00DXigePa6dMeDxucgg,3890
 foundry/callbacks/health_logging.py,sha256=tEtkByOlaAA7nnelxb7PbM9_dcIgOsdbxCdQY3K5pMc,16664
@@ -34,7 +34,7 @@ foundry/utils/squashfs.py,sha256=QlcwuJyVe-QVfIOS7o1QfLhaCQPNzzox7ln4n8dcYEg,523
 foundry/utils/torch.py,sha256=OLsqoxw4CTXbGzWUHernLUT7uQjLu0tVPtD8h8747DI,11211
 foundry/utils/weights.py,sha256=btz4S02xff2vgiq4xMfiXuhK1ERafqQPtmimo1DmoWY,10381
 foundry_cli/__init__.py,sha256=0BxY2RUKJLaMXUGgypPCwlTskTEFdVnkhTR4C4ft2Kw,52
-foundry_cli/download_checkpoints.py,sha256=TLwflDCm9RBCOfpv0KEiQegEp6DjnUIi4fGHiIHLrgc,8382
+foundry_cli/download_checkpoints.py,sha256=CDMxm3otzpb_c46AE2OwQY7aG7K_vnCJLKjP4U3b0Oc,8380
 mpnn/__init__.py,sha256=hgQcXFaCbAxFrhydVAy0xj8yC7UJF-GCCFhqD0sZ7I4,57
 mpnn/inference.py,sha256=wPtGR325eVRVeesXoWtBK6b_-VcU8BZae5IfQN3-mvA,1669
 mpnn/train.py,sha256=9eQGBd3rdNF5Zr2w8oUgETbqxBavNBajtA6Vbc5zESE,10239
@@ -56,7 +56,7 @@ mpnn/transforms/feature_aggregation/mpnn.py,sha256=jkhyMCqJipKQ2PvjqPkvvClhoiXx_
 mpnn/transforms/feature_aggregation/polymer_ligand_interface.py,sha256=gDdt9RZd0PO0YJdouNr0qsHFZV1i-5ewU6XuJrwPY54,2870
 mpnn/transforms/feature_aggregation/token_encodings.py,sha256=qVlUky4HcDSU5drrZpZBnUvTSGdT6C7MN8f_owa81Bw,2227
 mpnn/transforms/feature_aggregation/user_settings.py,sha256=uKyIDXz-QG0-KWQO1kqPlMj6i7RoVM6yH4iGNXFStoU,15007
-mpnn/utils/inference.py,sha256=pVZuzEldHjxLHSUYH4PvdWIFRemAfi46424Ne3Rey4k,96543
+mpnn/utils/inference.py,sha256=QLeukqLpedMNmvjbYgvLwDS5k7Q__NWILDSEbETkoCI,96539
 mpnn/utils/probability.py,sha256=EYisliXNGXjuSPbzZwcIKjlhyINikGsqQndGBEbQoPI,990
 mpnn/utils/weights.py,sha256=VsaIcOWTv8G-WJ9denxLRm3FQ9l6L66AVQN08E9BMSg,16411
 rf3/__init__.py,sha256=XBb5hF2RqBPHODGRmjiRbfTXgOGfOzdY91GbS4Vex00,70
@@ -148,7 +148,7 @@ rfd3/model/layers/chunked_pairwise.py,sha256=de5Qc3P7GEfZlX-QLaKfJxr6Ky5vgLcWWog
 rfd3/model/layers/encoders.py,sha256=CqByjHNSbtMIaNP_h2iEJZdTbm-N8SGo1bZgvRNpMJ8,15207
 rfd3/model/layers/layer_utils.py,sha256=UPYo-DYa__93KONSEj2YZWLtBqvYNSA9_wHDDPhVrIc,5710
 rfd3/model/layers/pairformer_layers.py,sha256=uimskhN-Ec0apEXAU6JqomyKX5-6ormrEsCFJotkBtM,3991
-rfd3/testing/debug.py,sha256=JqpSKbSp1l9V_3trLNzpdt3gazqrSOSq7NrmcuGjpJQ,4059
+rfd3/testing/debug.py,sha256=EeuGCEKyp-caoiskjnyfi88TfnJr5lcnPT2z4gblqvY,3958
 rfd3/testing/debug_utils.py,sha256=i_GjrsRjeaREv6hlX2sEmeztpo9w9rg7Ne3VT5-YILA,2170
 rfd3/testing/testing_utils.py,sha256=CtpTDxePbCluzuvd6jBfJNI2a3_8Ry2Whbgcf-5upiM,12202
 rfd3/trainer/dump_validation_structures.py,sha256=qY8s2hPBflJTXPiIUnqFFE9g36y_7s39MEcMRrxZUmA,6027
@@ -172,9 +172,9 @@ rfd3/transforms/util_transforms.py,sha256=2AcLkzx-73ZFgcWD1cIHv7NyniRPI4_zThHK8a
 rfd3/transforms/virtual_atoms.py,sha256=UpmxzPPd5FaJigcRoxgLSHHrLLOqsCvZ5PPZfQSGqII,12547
 rfd3/utils/inference.py,sha256=RQp5CCy6Z6uHVZ2Mx0zmmGluYEOrASke4bABtfRjpy0,26448
 rfd3/utils/io.py,sha256=wbdjUTQkDc3RCSM7gdogA-XOKR68HeQ-cfvyN4pP90w,9849
-rfd3/utils/vizualize.py,sha256=cumsMtSFQ8lfVtJDDQ9mpfMf9GSyM55RYmKl9H61_TM,11147
-rc_foundry-0.1.2.dist-info/METADATA,sha256=41TPsF9MGq2ab237zdmSqI4a6BujF7hyq3fvW78tsEA,10358
-rc_foundry-0.1.2.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
-rc_foundry-0.1.2.dist-info/entry_points.txt,sha256=BmiWCbWGtrd_lSOFMuCLBXyo84B7Nco-alj7hB0Yw9A,130
-rc_foundry-0.1.2.dist-info/licenses/LICENSE.md,sha256=NKtPCJ7QMysFmzeDg56ZfUStvgzbq5sOvRQv7_ddZOs,1533
-rc_foundry-0.1.2.dist-info/RECORD,,
+rfd3/utils/vizualize.py,sha256=HPlczrA3zkOuxV5X05eOvy_Oga9e3cPnFUXOEP4RR_g,11046
+rc_foundry-0.1.3.dist-info/METADATA,sha256=gY8d46JTRTfot6O9MqW34E0D1O64xNhMeVdpJrQ-G18,10578
+rc_foundry-0.1.3.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
+rc_foundry-0.1.3.dist-info/entry_points.txt,sha256=BmiWCbWGtrd_lSOFMuCLBXyo84B7Nco-alj7hB0Yw9A,130
+rc_foundry-0.1.3.dist-info/licenses/LICENSE.md,sha256=NKtPCJ7QMysFmzeDg56ZfUStvgzbq5sOvRQv7_ddZOs,1533
+rc_foundry-0.1.3.dist-info/RECORD,,

rfd3/testing/debug.py

@@ -1,4 +1,3 @@
-#!/usr/bin/env -S /bin/sh -c '"$(dirname "$0")/../../../scripts/shebang/modelhub_exec.sh" "$0" "$@"'
 # JBs debugging file, please create your own and go crazy!
 import logging
 import os

rfd3/utils/vizualize.py

@@ -1,4 +1,3 @@
-#!/usr/bin/env -S /bin/sh -c '"$(dirname "$0")/../../../scripts/shebang/modelhub_exec.sh" "$0" "$@"'
 """
 If you add the `/path/to/visualize.py` to your .bashrc/.zshrc like this: