rc-foundry 0.1.6__py3-none-any.whl → 0.1.9__py3-none-any.whl

foundry/inference_engines/checkpoint_registry.py

@@ -3,20 +3,62 @@
 import os
 from dataclasses import dataclass
 from pathlib import Path
+from typing import Iterable, List
 
+import dotenv
 
-def get_default_checkpoint_dir() -> Path:
-    """Get the default checkpoint directory.
+DEFAULT_CHECKPOINT_DIR = Path.home() / ".foundry" / "checkpoints"
+
+
+def _normalize_paths(paths: Iterable[Path]) -> list[Path]:
+    """Return absolute, deduplicated paths in order."""
+    seen = set()
+    normalized: List[Path] = []
+    for path in paths:
+        resolved = path.expanduser().absolute()
+        if resolved not in seen:
+            normalized.append(resolved)
+            seen.add(resolved)
+    return normalized
 
-    Priority:
-    1. FOUNDRY_CHECKPOINTS_DIR environment variable
-    2. ~/.foundry/checkpoints
+
+def get_default_checkpoint_dirs() -> list[Path]:
+    """Return checkpoint search paths.
+
+    Always starts with the default ~/.foundry/checkpoints directory and then
+    appends any additional directories from the colon-separated
+    FOUNDRY_CHECKPOINT_DIRS environment variable.
     """
-    if "FOUNDRY_CHECKPOINTS_DIR" in os.environ and os.environ.get(
-        "FOUNDRY_CHECKPOINTS_DIR"
-    ):
-        return Path(os.environ["FOUNDRY_CHECKPOINTS_DIR"]).absolute()
-    return Path.home() / ".foundry" / "checkpoints"
+    env_dirs = os.environ.get("FOUNDRY_CHECKPOINT_DIRS", "")
+
+    # For backward compatibility, also check FOUNDRY_CHECKPOINTS_DIR
+    if not env_dirs:
+        env_dirs = os.environ.get("FOUNDRY_CHECKPOINTS_DIR", "")
+
+    extra_dirs: list[Path] = []
+    if env_dirs:
+        extra_dirs = [Path(p.strip()) for p in env_dirs.split(":") if p.strip()]
+    return _normalize_paths([*extra_dirs, DEFAULT_CHECKPOINT_DIR])
+
+
+def get_default_checkpoint_dir() -> Path:
+    """Backward-compatible helper returning the primary checkpoint directory."""
+    return get_default_checkpoint_dirs()[0]
+
+
+def append_checkpoint_to_env(checkpoint_dirs: list[Path]) -> bool:
+    dotenv_path = dotenv.find_dotenv()
+    if dotenv_path:
+        checkpoint_dirs = _normalize_paths(checkpoint_dirs)
+        dotenv.set_key(
+            dotenv_path=dotenv_path,
+            key_to_set="FOUNDRY_CHECKPOINT_DIRS",
+            value_to_set=":".join(str(path) for path in checkpoint_dirs),
+            export=False,
+        )
+        return True
+    else:
+        return False
 
 
 @dataclass
@@ -27,7 +69,12 @@ class RegisteredCheckpoint:
     sha256: None = None  # Optional: add checksum for verification
 
     def get_default_path(self):
-        return get_default_checkpoint_dir() / self.filename
+        checkpoint_dirs = get_default_checkpoint_dirs()
+        for checkpoint_dir in checkpoint_dirs:
+            candidate = checkpoint_dir / self.filename
+            if candidate.exists():
+                return candidate
+        return checkpoint_dirs[0] / self.filename
 
 
 REGISTERED_CHECKPOINTS = {

foundry/utils/alignment.py

@@ -18,14 +18,19 @@ def weighted_rigid_align(
     Returns:
       X_align_L: [B, L, 3]
     """
-    assert X_L.shape == X_gt_L.shape
-    assert X_L.shape[:-1] == w_L.shape
 
+    # Canonicalize dimensions
+    if X_L.ndim == 2:
+        X_L = X_L[None]
+    if X_gt_L.ndim == 2:
+        X_gt_L = X_gt_L[None]
     if X_exists_L is None:
         X_exists_L = torch.ones((X_L.shape[-2]), dtype=torch.bool)
     if w_L is None:
         w_L = torch.ones_like(X_L[..., 0])
     else:
+        if w_L.ndim == 1:
+            w_L = w_L[None]
         w_L = w_L.to(torch.float32)
 
     # Assert `X_exists_L` is a boolean mask
@@ -33,6 +38,9 @@ def weighted_rigid_align(
         X_exists_L.dtype == torch.bool
     ), "X_exists_L should be a boolean mask! Otherwise, the alignment will be incorrect (silent failure)!"
 
+    assert X_L.shape == X_gt_L.shape
+    assert X_L.shape[:-1] == w_L.shape
+
     X_resolved = X_L[:, X_exists_L]
     X_gt_resolved = X_gt_L[:, X_exists_L]
     w_resolved = w_L[:, X_exists_L]

foundry/utils/ddp.py

@@ -2,7 +2,7 @@ import logging
 
 import torch
 from beartype.typing import Any
-from lightning_fabric.utilities import rank_zero_only
+from lightning.fabric.utilities import rank_zero_only
 from lightning_utilities.core.rank_zero import rank_prefixed_message
 from omegaconf import DictConfig
 

foundry/utils/logging.py

@@ -4,7 +4,7 @@ from contextlib import contextmanager
 
 import pandas as pd
 from beartype.typing import Any
-from lightning_fabric.utilities import rank_zero_only
+from lightning.fabric.utilities import rank_zero_only
 from omegaconf import DictConfig, OmegaConf
 from rich.console import Console
 from rich.syntax import Syntax

foundry/version.py

@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
 commit_id: COMMIT_ID
 __commit_id__: COMMIT_ID
 
-__version__ = version = '0.1.6'
-__version_tuple__ = version_tuple = (0, 1, 6)
+__version__ = version = '0.1.9'
+__version_tuple__ = version_tuple = (0, 1, 9)
 
 __commit_id__ = commit_id = None

foundry_cli/download_checkpoints.py

@@ -6,7 +6,7 @@ from typing import Optional
 from urllib.request import urlopen
 
 import typer
-from dotenv import find_dotenv, load_dotenv, set_key
+from dotenv import load_dotenv
 from rich.console import Console
 from rich.progress import (
     BarColumn,
@@ -20,7 +20,8 @@ from rich.progress import (
 
 from foundry.inference_engines.checkpoint_registry import (
     REGISTERED_CHECKPOINTS,
-    get_default_checkpoint_dir,
+    append_checkpoint_to_env,
+    get_default_checkpoint_dirs,
 )
 
 load_dotenv(override=True)
@@ -29,6 +30,27 @@ app = typer.Typer(help="Foundry model checkpoint installation utilities")
 console = Console()
 
 
+def _resolve_checkpoint_dirs(checkpoint_dir: Optional[Path]) -> list[Path]:
+    """Return checkpoint search path with defaults first."""
+    checkpoint_dirs = get_default_checkpoint_dirs()
+    if checkpoint_dir is not None:
+        resolved = checkpoint_dir.expanduser().absolute()
+        if resolved not in checkpoint_dirs:
+            checkpoint_dirs.insert(0, resolved)
+        else:
+            # Move to front
+            checkpoint_dirs.remove(resolved)
+            checkpoint_dirs.insert(0, resolved)
+
+        # Try to persist checkpoint dir to .env (optional, may not exist in Colab etc.)
+        if append_checkpoint_to_env(checkpoint_dirs):
+            console.print(
+                f"Tracked checkpoint directories: {':'.join(str(path) for path in checkpoint_dirs)}"
+            )
+
+    return checkpoint_dirs
+
+
 def download_file(url: str, dest: Path, verify_hash: Optional[str] = None) -> None:
     """Download a file with progress bar and optional hash verification.
 
@@ -123,134 +145,112 @@ def install_model(model_name: str, checkpoint_dir: Path, force: bool = False) ->
 def install(
     models: list[str] = typer.Argument(
         ...,
-        help="Models to install: 'all', 'rfd3', 'rf3', 'mpnn', or combination",
+        help="Models to install: 'all', 'rfd3', 'rf3', 'mpnn', or a combination thereof",
     ),
     checkpoint_dir: Optional[Path] = typer.Option(
         None,
         "--checkpoint-dir",
         "-d",
-        help="Directory to save checkpoints (default: $FOUNDRY_CHECKPOINTS_DIR or ~/.foundry/checkpoints)",
+        help="Directory to save checkpoints (default search path: ~/.foundry/checkpoints plus any $FOUNDRY_CHECKPOINT_DIRS entries)",
     ),
     force: bool = typer.Option(
         False, "--force", "-f", help="Overwrite existing checkpoints"
     ),
 ):
     """Install model checkpoints for foundry.
-
     Examples:
-
         foundry install all
-
         foundry install rfd3 rf3
-
         foundry install proteinmpnn --checkpoint-dir ./checkpoints
     """
     # Determine checkpoint directory
-    if checkpoint_dir is None:
-        checkpoint_dir = get_default_checkpoint_dir()
+    checkpoint_dirs = _resolve_checkpoint_dirs(checkpoint_dir)
+    primary_checkpoint_dir = checkpoint_dirs[0]
 
-    console.print(f"[bold]Checkpoint directory:[/bold] {checkpoint_dir}")
-    console.print()
+    console.print(f"[bold]Install target:[/bold] {primary_checkpoint_dir}\n")
 
     # Expand 'all' to all available models
     if "all" in models:
+        models_to_install = list(REGISTERED_CHECKPOINTS.keys())
+    elif "base-models" in models:
         models_to_install = ["rfd3", "proteinmpnn", "ligandmpnn", "rf3"]
     else:
         models_to_install = models
 
     # Install each model
     for model_name in models_to_install:
-        install_model(model_name, checkpoint_dir, force)
+        install_model(model_name, primary_checkpoint_dir, force)
         console.print()
 
-    # Try to persist checkpoint dir to .env (optional, may not exist in Colab etc.)
-    dotenv_path = find_dotenv()
-    if dotenv_path:
-        set_key(
-            dotenv_path=dotenv_path,
-            key_to_set="FOUNDRY_CHECKPOINTS_DIR",
-            value_to_set=str(checkpoint_dir),
-            export=False,
-        )
-        console.print(f"Saved FOUNDRY_CHECKPOINTS_DIR to {dotenv_path}")
-
     console.print("[bold green]Installation complete![/bold green]")
 
 
-@app.command(name="list")
-def list_models():
+@app.command(name="list-available")
+def list_available():
     """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}")
 
 
-@app.command()
-def show(
-    checkpoint_dir: Optional[Path] = typer.Option(
-        None,
-        "--checkpoint-dir",
-        "-d",
-        help="Checkpoint directory to show",
-    ),
-):
-    """Show installed checkpoints."""
-    if checkpoint_dir is None:
-        checkpoint_dir = get_default_checkpoint_dir()
+@app.command(name="list-installed")
+def list_installed():
+    """List installed checkpoints and their sizes."""
+    checkpoint_dirs = _resolve_checkpoint_dirs(None)
 
-    if not checkpoint_dir.exists():
-        console.print(
-            f"[yellow]No checkpoints directory found at {checkpoint_dir}[/yellow]"
-        )
-        raise typer.Exit(0)
+    checkpoint_files: list[tuple[Path, float]] = []
+    for checkpoint_dir in checkpoint_dirs:
+        if not checkpoint_dir.exists():
+            continue
+        ckpts = list(checkpoint_dir.glob("*.ckpt")) + list(checkpoint_dir.glob("*.pt"))
+        for ckpt in ckpts:
+            size = ckpt.stat().st_size / (1024**3)  # GB
+            checkpoint_files.append((ckpt, size))
 
-    checkpoint_files = list(checkpoint_dir.glob("*.ckpt"))
     if not checkpoint_files:
-        console.print(f"[yellow]No checkpoint files found in {checkpoint_dir}[/yellow]")
+        console.print(
+            "[yellow]No checkpoint files found in any checkpoint directory[/yellow]"
+        )
         raise typer.Exit(0)
 
-    console.print(f"[bold]Installed checkpoints in {checkpoint_dir}:[/bold]\n")
+    console.print("[bold]Installed checkpoints:[/bold]\n")
     total_size = 0
-    for ckpt in sorted(checkpoint_files):
-        size = ckpt.stat().st_size / (1024**3)  # GB
+    for ckpt, size in sorted(checkpoint_files, key=lambda item: str(item[0])):
         total_size += size
-        console.print(f"  {ckpt.name:30} {size:8.2f} GB")
+        console.print(f"  {ckpt} {size:8.2f} GB")
 
     console.print(f"\n[bold]Total:[/bold] {total_size:.2f} GB")
 
 
-@app.command()
+@app.command(name="clean")
 def clean(
-    checkpoint_dir: Optional[Path] = typer.Option(
-        None,
-        "--checkpoint-dir",
-        "-d",
-        help="Checkpoint directory to clean",
-    ),
     confirm: bool = typer.Option(
         True, "--confirm/--no-confirm", help="Ask for confirmation before deleting"
     ),
 ):
     """Remove all downloaded checkpoints."""
-    if checkpoint_dir is None:
-        checkpoint_dir = get_default_checkpoint_dir()
-
-    if not checkpoint_dir.exists():
-        console.print(f"[yellow]No checkpoints found at {checkpoint_dir}[/yellow]")
-        raise typer.Exit(0)
+    checkpoint_dirs = _resolve_checkpoint_dirs(None)
 
     # List files to delete
-    checkpoint_files = list(checkpoint_dir.glob("*.ckpt"))
+    checkpoint_files: list[Path] = []
+    for checkpoint_dir in checkpoint_dirs:
+        if not checkpoint_dir.exists():
+            continue
+        checkpoint_files.extend(checkpoint_dir.glob("*.ckpt"))
+        checkpoint_files.extend(checkpoint_dir.glob("*.pt"))
+
     if not checkpoint_files:
-        console.print(f"[yellow]No checkpoint files found in {checkpoint_dir}[/yellow]")
+        console.print(
+            "[yellow]No checkpoint files found in any checkpoint directory[/yellow]"
+        )
         raise typer.Exit(0)
 
     console.print("[bold]Files to delete:[/bold]")
     total_size = 0
-    for ckpt in checkpoint_files:
+    for ckpt in sorted(checkpoint_files, key=str):
         size = ckpt.stat().st_size / (1024**3)  # GB
         total_size += size
-        console.print(f"  {ckpt.name} ({size:.2f} GB)")
+        console.print(f"  {ckpt} ({size:.2f} GB)")
 
     console.print(f"\n[bold]Total:[/bold] {total_size:.2f} GB")
 

{rc_foundry-0.1.6.dist-info → rc_foundry-0.1.9.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rc-foundry
-Version: 0.1.6
+Version: 0.1.9
 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
@@ -97,40 +97,45 @@ Foundry provides tooling and infrastructure for using and training all classes o
 
 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. 
 
+
+> [!NOTE]
+> We have a slack now! Join for updates and to get your questions answered [here](https://join.slack.com/t/proteinmodelfoundry/shared_invite/zt-3kpwru8c6-nrmTW6LNHnSE7h16GNnfLA).
+
 ## Getting Started
 ### Quickstart guide
 **Installation**
 ```bash
-pip install rc-foundry[all]
+pip install "rc-foundry[all]"
 ```
 
-**Downloading weights** All models can be downloaded to a target folder with:
-
+**Downloading weights** Models can be downloaded to a target folder with:
 ```
-foundry install all --checkpoint_dir <path/to/ckpt/dir>
+foundry install base-models --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:
+where `checkpoint-dir` will be `~/.foundry/checkpoints` by default. Foundry always searches `~/.foundry/checkpoints` plus any colon-separated entries in `$FOUNDRY_CHECKPOINT_DIRS` during inference or subsequent commands to find checkpoints. `base-models` installs the latest RFD3, RF3 and MPNN variants - you can also download all of the models supported (including multiple checkpoints of RF3) with `all`, or by listing the models sequentially (e.g. `foundry install rfd3 rf3 ...`).
+To list the registry of available checkpoints:
 ```
-foundry install rfd3 ligandmpnn rf3 --checkpoint_dir  <path/to/ckpt/dir>
+foundry list-available
 ```
+To check what you already have downloaded (searches `~/.foundry/checkpoints` plus `$FOUNDRY_CHECKPOINT_DIRS` if set):
+```
+foundry list-installed
+```
+
+>*See `examples/all.ipynb` for how to run each model and design proteins end-to-end in a notebook.*
 
->*See `examples/all.ipynb` for how to run each model in a notebook.*
+### Google Colab
+For an interactive Google Colab notebook walking through a basic design pipeline with RFD3, MPNN, and RF3, please see the [IPD Design Pipeline Tutorial](https://colab.research.google.com/drive/1ZwIMV3n9h0ZOnIXX0GyKUuoiahgifBxh?usp=sharing).
 
 ### 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. 
 
-> *See [models/rfd3/README.md](models/rfd3/README.md) for complete documentation.*
-
 <div align="center">
-  <img src="models/rfd3/docs/.assets/trajectory.png" alt="RFdiffusion3 generation trajectory." width="700">
+  <img src="docs/_static/cover.png" alt="RFdiffusion3 generation trajectory." width="700">
 </div>
 
-### ProteinMPNN
-[ProteinMPNN](https://www.science.org/doi/10.1126/science.add2187) and [LigandMPNN](https://www.nature.com/articles/s41592-025-02626-1) are lightweight inverse-folding models which can be use to design diverse sequences for backbones under constrained conditions.
-
-> *See [models/mpnn/README.md](models/mpnn/README.md) for complete documentation.*
-
+> *See [models/rfd3/README.md](models/rfd3/README.md) for complete documentation.*
 
 ### RosettaFold3 (RF3)
 
@@ -142,6 +147,11 @@ foundry install rfd3 ligandmpnn rf3 --checkpoint_dir  <path/to/ckpt/dir>
 
 > *See [models/rf3/README.md](models/rf3/README.md) for complete documentation.*
 
+### ProteinMPNN
+[ProteinMPNN](https://www.science.org/doi/10.1126/science.add2187) and [LigandMPNN](https://www.nature.com/articles/s41592-025-02626-1) are lightweight inverse-folding models which can be use to design diverse sequences for backbones under constrained conditions.
+
+> *See [models/mpnn/README.md](models/mpnn/README.md) for complete documentation.*
+
 ---
 
 ## Development
@@ -159,11 +169,7 @@ foundry install rfd3 ligandmpnn rf3 --checkpoint_dir  <path/to/ckpt/dir>
 Install both `foundry` and models in editable mode for development:
 
 ```bash
-# Install foundry and RF3 in editable mode
-uv pip install -e . -e ./models/rf3 -e ./models/rfd3 -e ./models/mpnn
-
-# Or install only foundry (no models)
-uv pip install -e .
+uv pip install -e '.[all,dev]'
 ```
 
 This approach allows you to:
@@ -171,6 +177,9 @@ This approach allows you to:
 - Work on specific models without installing all models
 - Add new models as independent packages in `models/`
 
+> [!NOTE]
+> Running tests is not currently supported, test files may be missing.
+
 ### Adding New Models
 
 To add a new model:

{rc_foundry-0.1.6.dist-info → rc_foundry-0.1.9.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=riGXiVTWXmtdoju9hVCWvTxpszEMAAIK0sZZWoLKlnU,704
+foundry/version.py,sha256=ib8ckvf-NNDfacXd8unW0p5cf-gl57XyQvjoEMc_pvc,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
@@ -10,7 +10,7 @@ foundry/callbacks/timing_logging.py,sha256=u-r0hKp7fWOY3mLk7CcuIwHgZbhte13m5M09x
 foundry/callbacks/train_logging.py,sha256=Xs3tmZA88qLxmdSOwt-x8YKN4NKb1kVm59uptNXl4Qo,10399
 foundry/hydra/resolvers.py,sha256=xyJzo6OeWAc_LOu8RiHhX7_CRNoLZ22626AvYHXYl4U,2186
 foundry/inference_engines/base.py,sha256=ZHdlmGUqH4-p3v4RdrLH-Ps8_zalr7j5mQ4x-S53N4M,8375
-foundry/inference_engines/checkpoint_registry.py,sha256=kt2Z1JhrAjoOiEpkIIQ0sLttie1ceL8OgXUBmmyA6iw,2544
+foundry/inference_engines/checkpoint_registry.py,sha256=c_me8Uz2NWXAaELhQ4bT1HMPfY8XrH67kvCKdDPrD8g,4149
 foundry/metrics/__init__.py,sha256=qL4wwaiQ7EtR30pmZ9MCknqx909BJcNvHVmNJUaz_WM,236
 foundry/metrics/losses.py,sha256=2CLUmf7oCdFUCvgJukdNkff0FVG3BlATI-NI60TtpVY,903
 foundry/metrics/metric.py,sha256=23pKh_Ra0EcHGo5cSzYQQrUGr5zWRxeufKSJ58tfXXo,12687
@@ -22,19 +22,19 @@ foundry/trainers/fabric.py,sha256=cjaTHbGuJEQwaGBvIAXD_il4bHtY-crsTY14Xn77uXA,40
 foundry/training/EMA.py,sha256=3OWA9Pz7XuDr-SRxbz24tZf55DmhSa2fKy9r5v2IXqA,2651
 foundry/training/checkpoint.py,sha256=mUiObg-qcF3tvMfVu77sD9m3yVRp71czv07ccliU7qQ,1791
 foundry/training/schedulers.py,sha256=StmXegPfIdLAv31FreCTrDh9dsOvNUfzG4YGa61Y4oE,3647
-foundry/utils/alignment.py,sha256=OAN7H2TqraGxP1uMXUpwLO7g0qS0cxUVjuV33pY16z0,2316
+foundry/utils/alignment.py,sha256=2anqy0mn9zeFEiVWS_EG7zHiyPk1C_gbUu-SRvQ5mAM,2502
 foundry/utils/components.py,sha256=Piw2TfQF26uuxC3hXG3iv_4rgud1lVO-cv6N-p05EDY,15200
 foundry/utils/datasets.py,sha256=pLBxVezm-TSrYuC5gFnJZdGnNWV7aPH2QiWIVE2hkdQ,16629
-foundry/utils/ddp.py,sha256=ydHrO6peGbRnWAwgH5rmpHuQd55g2gFzzoZJYypn7GU,3970
+foundry/utils/ddp.py,sha256=202_7qqm4ihPjpB5Q9NhUjDl4u22pu5JvY0ui0UkRUQ,3970
 foundry/utils/instantiators.py,sha256=oGCp6hrmY-QPPPEjxKxe5uVFL125fH1RaLxjMKWCD_8,2169
-foundry/utils/logging.py,sha256=jrDgiB_56q_hWDc0jkBFekvqnNWcowJBt4B-S-ipJmM,9312
+foundry/utils/logging.py,sha256=ywV75MBlQsothV0IBvqoAQTNg6pjo2-Cib7Uo080nzQ,9312
 foundry/utils/rigid.py,sha256=_Z1pmitb6xgxyguLj_TukKscUBJjQsU4bsBD24GVS84,44444
 foundry/utils/rotation_augmentation.py,sha256=7q1WEX2iJ0i7-2aV-M97nEaEdpqexDTaZn5JquYpkUk,1927
 foundry/utils/squashfs.py,sha256=QlcwuJyVe-QVfIOS7o1QfLhaCQPNzzox7ln4n8dcYEg,5234
 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=UCNdy4VZyJe1PH_lnVLqy-VSMuTu875mGGd99ma7fTQ,8426
+foundry_cli/download_checkpoints.py,sha256=CxU9dKBa1vAkVd450tfH5aZAlQIUTrHsDGTbmxzd_JQ,8922
 mpnn/__init__.py,sha256=hgQcXFaCbAxFrhydVAy0xj8yC7UJF-GCCFhqD0sZ7I4,57
 mpnn/inference.py,sha256=wPtGR325eVRVeesXoWtBK6b_-VcU8BZae5IfQN3-mvA,1669
 mpnn/train.py,sha256=9eQGBd3rdNF5Zr2w8oUgETbqxBavNBajtA6Vbc5zESE,10239
@@ -63,8 +63,8 @@ rf3/__init__.py,sha256=XBb5hF2RqBPHODGRmjiRbfTXgOGfOzdY91GbS4Vex00,70
 rf3/_version.py,sha256=fCfpbI5aeA6yHqjo3tK78-l2dPGxhp-AyKSoCXp34Nc,739
 rf3/alignment.py,sha256=BvvwMqQGCVxV20xIsTighD1kXMadXXL2SkckLjTerx0,2102
 rf3/chemical.py,sha256=VECnRPgVm-icXbZeUG4svcENzdUiIupP6dhka_8zCrg,26572
-rf3/cli.py,sha256=dPKJFRHYoV2XS6xc_ZmdLTz6frqa6HZg4qgZU5oJcXU,2356
-rf3/inference.py,sha256=_AAJ07AfSeU3xTM2_KH9n_H12EK4qZ23IJuyauOrMaQ,2466
+rf3/cli.py,sha256=jxjq8u77J8itIK4aNTfIpnMsNgg8brW1A3NfVjlgE0s,2743
+rf3/inference.py,sha256=yUjSqCjIqsGErUezq42-8K9570Opm_2eYa-bNnwltwA,2494
 rf3/kinematics.py,sha256=V3yjalPupu1X2FEp7l3XZR-qzLKrhWLZyECk6RgIkcs,10901
 rf3/scoring.py,sha256=dTllswE-6Fgli2eLiNzLFc2Rhz4ouDT4WL-sVbvLTGU,41541
 rf3/train.py,sha256=V4nqCC_1JKLI3WQ-nErNa8sqFpvb1mFhXSe6ZPpEheM,7945
@@ -119,18 +119,18 @@ rfd3/__init__.py,sha256=2Wto2IsUIj2lGag9m_gqgdCwBNl5p21-Xnr7W_RpU3c,348
 rfd3/callbacks.py,sha256=Zjt8RiaYWquoKOwRmC_wCUbRbov-V4zd2_73zjhgDHE,2783
 rfd3/cli.py,sha256=ka3K5H117fzDYIDXFpOpJV21w_XBrHYJZdFE0thsGBI,1644
 rfd3/constants.py,sha256=wLvDzrThpOrK8T3wGFNQeGrhAXOJQze8l3v_7pjIdMM,13141
-rfd3/engine.py,sha256=La_dB48Ewz0IdY1ocxvSWg-PXVAsySm0OGvwyz42lI8,20824
-rfd3/run_inference.py,sha256=ljzsCKEtrlfAvP0SDFPeQwTM3rV_X3ewHOhcRFVI37c,1258
+rfd3/engine.py,sha256=viXzVGYkHPyzv5d0Ifg8zFZ6Wqg-U4I8Y4ldQLPe9x4,21536
+rfd3/run_inference.py,sha256=HfRMQ30_SAHfc-VFzBV52F-aLaNdG6PW8VkdMyB__wE,1264
 rfd3/train.py,sha256=rHswffIUhOae3_iYyvAiQ3jALoFuzrcRUgMlbJLinlI,7947
-rfd3/inference/datasets.py,sha256=u-2U7deHXu-iOs7doiKKynewP-NEyJfdORSTDzUSaQI,6538
-rfd3/inference/input_parsing.py,sha256=mk3HBvo7MPTFEET7NagCo5TSjb47w-hxUDoeQxUW_h4,45449
-rfd3/inference/legacy_input_parsing.py,sha256=1wf_KF7qWnGLaVM8IXDl8fIsWCmxtOi2YlAiHEVELqw,28046
-rfd3/inference/parsing.py,sha256=Nq8CYmimnql4RM-5ZfPAvOFvCae4_CC2pYDzE6iCpWU,5290
-rfd3/inference/symmetry/atom_array.py,sha256=HH50Z07bTUnNUgCwAGslADbvMYHgsXn9s-fqwx6BvKw,11034
-rfd3/inference/symmetry/checks.py,sha256=wb7K327GnMwGG9bgOvvDAbaPsFj4nGZpEAolICUapNc,8908
+rfd3/inference/datasets.py,sha256=9VLbzl7dpG8mk_pjs0R5C2wFYUoRIgXXoZcS9IohSy0,6510
+rfd3/inference/input_parsing.py,sha256=pocqnnhE3-szeBbCL9gy9E3kZJSP_CGHXd6FFRxfv0c,46563
+rfd3/inference/legacy_input_parsing.py,sha256=G2XxkrjdIpL6i1YY7xEmkFitVv__Pc45ow6IKKPHw64,28855
+rfd3/inference/parsing.py,sha256=ktAMUuZE3Pe4bKAjjV3zjqcEDmGlMZ-cotIUhJsEQQA,5402
+rfd3/inference/symmetry/atom_array.py,sha256=j8yhtZAjRNm4d06KyS4gk2XCquHPCwR0k9WiNmxz7WA,12941
+rfd3/inference/symmetry/checks.py,sha256=ZWpC1JjrAjXY__xDt8EFYb5WUdSF0kobZyxxmacFU7U,10076
 rfd3/inference/symmetry/contigs.py,sha256=6OvbZ2dJg-a0mvvKAC0VkzUH5HpUDxOJvkByIst_roU,2127
-rfd3/inference/symmetry/frames.py,sha256=G55p-aOXqEYG4kCyKxrgWAsS-gW9-gOTlBME6nhbKyU,10716
-rfd3/inference/symmetry/symmetry_utils.py,sha256=KwgxrdfO766RCEwF3VElAE85oEKiopPGRQDhJbKZaUA,15810
+rfd3/inference/symmetry/frames.py,sha256=kwog5jU_wgv6ACcUER2iU5qz-mdfdOe0cpi2OTEDKMU,18894
+rfd3/inference/symmetry/symmetry_utils.py,sha256=CGUzMI5CKVIcNi5_l2-YRu-ExroZX54GndxLb5P7RtY,14680
 rfd3/metrics/design_metrics.py,sha256=O1RqZdjQPNlAWYRg6UJTERYg_gUI1_hVleKsm9xbWBY,16836
 rfd3/metrics/hbonds_hbplus_metrics.py,sha256=Sewy9KzmrA1OnfkasN-fmWrQ9IRx9G7Yyhe2ua0mk28,11518
 rfd3/metrics/hbonds_metrics.py,sha256=SIR4BnDhYdpVSqwXXRYpQ_tB-M0_fVyugGl08WivCmE,15257
@@ -140,11 +140,11 @@ rfd3/metrics/sidechain_metrics.py,sha256=EGZuFuWQ0cCe83EVPAf4eysN8vP9ifNjfnmE0o5
 rfd3/model/RFD3.py,sha256=95aKzye-XzuDyLGgost-Wsfu8eT635zHIRky-pNoHSA,3569
 rfd3/model/RFD3_diffusion_module.py,sha256=BPjKGyQpbnqdzii3gXMKLhhijNqV8Xh4bSosmfDBt8w,12094
 rfd3/model/cfg_utils.py,sha256=XPBLyoB_bQRLmdrJ1Z0hCjcVvgUMGIPuw4rxTlHjB_s,2575
-rfd3/model/inference_sampler.py,sha256=qge7BNJttW0NXgerg3msPY3izxQ-6FsvWSTAMhZ4GJs,24696
+rfd3/model/inference_sampler.py,sha256=5k_UIkJCL6QO4BEqAxkR9GKxNAOz-NRq5Jh51Wm5MU8,25152
 rfd3/model/layers/attention.py,sha256=XuNA7WyFlRfLnAgky1PtGvXFCnDGv7GeEcXz8hodTBo,19472
-rfd3/model/layers/block_utils.py,sha256=EZq2qYUeO6_VCLKDVC60cxfBE_EPwvp84FPmqLr28ZQ,21197
+rfd3/model/layers/block_utils.py,sha256=oN0aD-vZiH4JbIFs2CzDmb2B74GNPKzdFurmGd-dirE,21244
 rfd3/model/layers/blocks.py,sha256=MOjJ53THxM2MMM27Ap7xiIXRCdI_SHzqKzLLQVX6FEc,24888
-rfd3/model/layers/chunked_pairwise.py,sha256=de5Qc3P7GEfZlX-QLaKfJxr6Ky5vgLcWWogatCw2UnY,14582
+rfd3/model/layers/chunked_pairwise.py,sha256=B8oUxXbdm9akwdbrmjA-7HtcNQBTppMB_gAMAz9VbvY,14712
 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
@@ -166,11 +166,11 @@ rfd3/transforms/ncaa_transforms.py,sha256=Lz4L8OGuOOG53sKJHcLSdV7WPQ3YzOzwd5tJG4
 rfd3/transforms/pipelines.py,sha256=FGH-XH3taTWQ6k1zpDO_d-097EQdXmL6uqXZXw4HIMs,22086
 rfd3/transforms/ppi_transforms.py,sha256=7rXyf-tn2TLz6ybYR_YVDtSDG7hOgqhYY4shNviA_Sw,23493
 rfd3/transforms/rasa.py,sha256=a4IPFvVMMxldoGLyJQiSlGg7IyUkcBASbRZLWmguAKk,4156
-rfd3/transforms/symmetry.py,sha256=GSnMF7oAnUxPozfafsRuHEv0yKXW0BpLTI6wsKGZrbc,2658
+rfd3/transforms/symmetry.py,sha256=9I9gzAZkk5vMUJm7x8XCDSHtNPYYLAHt4meXxOczGT0,2970
 rfd3/transforms/training_conditions.py,sha256=UXiUPjDwrNKM95tRe0eXrMeRN8XlTPc_MXUvo6UpePo,19510
 rfd3/transforms/util_transforms.py,sha256=2AcLkzx-73ZFgcWD1cIHv7NyniRPI4_zThHK8azyQaY,18119
 rfd3/transforms/virtual_atoms.py,sha256=UpmxzPPd5FaJigcRoxgLSHHrLLOqsCvZ5PPZfQSGqII,12547
-rfd3/utils/inference.py,sha256=RQp5CCy6Z6uHVZ2Mx0zmmGluYEOrASke4bABtfRjpy0,26448
+rfd3/utils/inference.py,sha256=Yf3aAUk_YZi58uIJr5Y2wfVnQ-2bh3S5GHLBPzCRjUs,26448
 rfd3/utils/io.py,sha256=wbdjUTQkDc3RCSM7gdogA-XOKR68HeQ-cfvyN4pP90w,9849
 rfd3/utils/vizualize.py,sha256=HPlczrA3zkOuxV5X05eOvy_Oga9e3cPnFUXOEP4RR_g,11046
 rf3/configs/inference.yaml,sha256=JmEZdkAnbnOrX79lGS5xrYYho9aBFfVxfUp-8KjJV5I,309
@@ -248,7 +248,7 @@ rfd3/configs/datasets/conditions/sequence_design.yaml,sha256=D1K6WOysmSAQ4LogltU
 rfd3/configs/datasets/conditions/tipatom.yaml,sha256=0010o7UUL-l75qI8HCjC_tdBXFWysm2dgVXzE7bQyZ0,650
 rfd3/configs/datasets/conditions/unconditional.yaml,sha256=z1eVHylswLyludXWFs1AMt3mTMu3EbAUHrP8J3XBsRU,446
 rfd3/configs/datasets/train/rfd3_monomer_distillation.yaml,sha256=1f61uFeRB8OD6sifFuIKFov8D7PcHpqRT4Z-M5EzO4w,1207
-rfd3/configs/datasets/train/pdb/af3_train_interface.yaml,sha256=mwbdGJQ9SXc8WvO3qqSWzS--K4rvbFsM0MR371FUrr0,1552
+rfd3/configs/datasets/train/pdb/af3_train_interface.yaml,sha256=DSIpXW2SQ3drDp12490y0tFbjbugecyA7TI_x3WrKng,1546
 rfd3/configs/datasets/train/pdb/af3_train_pn_unit.yaml,sha256=DPoEhLlyBu0RdBkkJeWB8pkOV4z0DBc6XmclLgww9II,1324
 rfd3/configs/datasets/train/pdb/base.yaml,sha256=2VUEAKADyvjJmWP4FeOJwRat9r6F3_GXuyGYjvMvArw,291
 rfd3/configs/datasets/train/pdb/base_no_weights.yaml,sha256=8HchN7DqYESBK520vShdg7xidWBSogGRAxfaxa5pKdE,554
@@ -285,7 +285,7 @@ rfd3/configs/hydra/default.yaml,sha256=SYDTSU8bAw20QssrtTi7lptiBD5H3XNyzApsyy0br
 rfd3/configs/hydra/no_logging.yaml,sha256=MUXDFcw-QwaRPz9HcE-1tdZwbNha1mexTe31G-Zt9_w,120
 rfd3/configs/inference_engine/base.yaml,sha256=ekP5U7bAALpeJGpwyj1v0N5LiEtptl5loRCtM8FRzRM,246
 rfd3/configs/inference_engine/dev.yaml,sha256=-2snClOTwj5TQt7jnwSrI4pzAiI4nFulXKJflmgIyUw,304
-rfd3/configs/inference_engine/rfdiffusion3.yaml,sha256=h2e9U9RFCcvXjKAJ6U8puj-8O-U57ZxeZLA0HLB2txA,2161
+rfd3/configs/inference_engine/rfdiffusion3.yaml,sha256=3bHIAhzFhFDIag0xQWYxHBUMSc71fjClHXKbZ-tpHzA,2112
 rfd3/configs/logger/csv.yaml,sha256=DtcywAIS4OxLXP2QxSEvqdrjhMpT6xHiGspoYw5qkus,245
 rfd3/configs/logger/default.yaml,sha256=pSyHyxT-J_T-g4_6TtD2yzN3rzxgY6rOG_Vh4RjZeFY,17
 rfd3/configs/logger/wandb.yaml,sha256=RhCnFtO0hNc3R75ts417l5ICZeGm74lOj9Bfe7ZvRNA,652
@@ -294,7 +294,7 @@ rfd3/configs/model/components/ema.yaml,sha256=AIzf4RZLKP8AcfaxdvZBS1rFw3AlSo431r
 rfd3/configs/model/components/rfd3_net.yaml,sha256=95FF4U7aWmLCoHvyxsRoE74n-bxTPD6KlAhPKNemVH4,3275
 rfd3/configs/model/optimizers/adam.yaml,sha256=cTRNo4_4lNgLv0b329v-KiC_MCQtTVVTxeer5Au_FIM,145
 rfd3/configs/model/samplers/edm.yaml,sha256=QycHAIrfhRgx0mJygTOs56FT93tGCWTGxrQSKBOA7Mc,483
-rfd3/configs/model/samplers/symmetry.yaml,sha256=BZZOIhk2ndAvIntf-16nnqCuOW43iWTB7iDU-RsxOcc,214
+rfd3/configs/model/samplers/symmetry.yaml,sha256=pI0Ens6jmbpAIl8E4eYsJR1SqIppe5OsWh91KfpjNjs,214
 rfd3/configs/model/schedulers/af3.yaml,sha256=xEtRb--KPjg_5pW_IJvN9AHWVqCtOM4QOnXlMH2KrEg,149
 rfd3/configs/paths/default.yaml,sha256=bjB04SNu_5E6W_v4mRBjwce0xmdKwO5wsVf4gfaRl0Y,1045
 rfd3/configs/paths/data/default.yaml,sha256=jfs1dbbcOqHja4_6lXheyRg4t0YExqVn2w0rZEWL6XE,788
@@ -304,8 +304,8 @@ rfd3/configs/trainer/rfd3_base.yaml,sha256=R3lZxdyjUirjlLU31qWlnZgHaz4GcWTGGIz4f
 rfd3/configs/trainer/loss/losses/diffusion_loss.yaml,sha256=FE4FCEfurE0ekwZ4YfS6wCvPSNqxClwg_kc73cPql5Y,323
 rfd3/configs/trainer/loss/losses/sequence_loss.yaml,sha256=kezbQcqwAZ0VKQPUBr2MsNr9DcDL3ENIP1i-j7h-6Co,64
 rfd3/configs/trainer/metrics/design_metrics.yaml,sha256=xVDpClhHqSHvsf-8StL26z51Vn-iuWMDG9KMB-kqOI0,719
-rc_foundry-0.1.6.dist-info/METADATA,sha256=EEOkAi2nABzo70kEP-n9t5aXZ8a4Gqr5wYZ2mjIBqp4,10585
-rc_foundry-0.1.6.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
-rc_foundry-0.1.6.dist-info/entry_points.txt,sha256=BmiWCbWGtrd_lSOFMuCLBXyo84B7Nco-alj7hB0Yw9A,130
-rc_foundry-0.1.6.dist-info/licenses/LICENSE.md,sha256=NKtPCJ7QMysFmzeDg56ZfUStvgzbq5sOvRQv7_ddZOs,1533
-rc_foundry-0.1.6.dist-info/RECORD,,
+rc_foundry-0.1.9.dist-info/METADATA,sha256=SBHGrkr8RsLTCTOhJnbusBs8G7C8HxJUPajCbmU6OyE,11502
+rc_foundry-0.1.9.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
+rc_foundry-0.1.9.dist-info/entry_points.txt,sha256=BmiWCbWGtrd_lSOFMuCLBXyo84B7Nco-alj7hB0Yw9A,130
+rc_foundry-0.1.9.dist-info/licenses/LICENSE.md,sha256=NKtPCJ7QMysFmzeDg56ZfUStvgzbq5sOvRQv7_ddZOs,1533
+rc_foundry-0.1.9.dist-info/RECORD,,