rc-foundry 0.1.1__py3-none-any.whl

rc_foundry-0.1.1.dist-info/RECORD

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+rfd3/transforms/conditioning_base.py,sha256=A0Z2-v7ttvNa6xArpBdV8srH58gSaMI1J48ULXvQJTg,19517
+rfd3/transforms/conditioning_utils.py,sha256=9Pn9AFbih2FCzp5OOM9y7z6KH7HPxVibxTrfuXiitMs,7498
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+rfd3/transforms/hbonds.py,sha256=ijfJapFlhsh3JktpDoT3VFqKTTg6ynrqMlD7dU2xFsA,16415
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+rfd3/transforms/pipelines.py,sha256=FGH-XH3taTWQ6k1zpDO_d-097EQdXmL6uqXZXw4HIMs,22086
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+rfd3/transforms/rasa.py,sha256=a4IPFvVMMxldoGLyJQiSlGg7IyUkcBASbRZLWmguAKk,4156
+rfd3/transforms/symmetry.py,sha256=GSnMF7oAnUxPozfafsRuHEv0yKXW0BpLTI6wsKGZrbc,2658
+rfd3/transforms/training_conditions.py,sha256=UXiUPjDwrNKM95tRe0eXrMeRN8XlTPc_MXUvo6UpePo,19510
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+rfd3/utils/io.py,sha256=wbdjUTQkDc3RCSM7gdogA-XOKR68HeQ-cfvyN4pP90w,9849
+rfd3/utils/vizualize.py,sha256=cumsMtSFQ8lfVtJDDQ9mpfMf9GSyM55RYmKl9H61_TM,11147
+rc_foundry-0.1.1.dist-info/METADATA,sha256=Jblzbw1ZsPICTEN0JXCPRzbP83w76Ari5SQe4S3TlRE,10578
+rc_foundry-0.1.1.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
+rc_foundry-0.1.1.dist-info/entry_points.txt,sha256=BmiWCbWGtrd_lSOFMuCLBXyo84B7Nco-alj7hB0Yw9A,130
+rc_foundry-0.1.1.dist-info/licenses/LICENSE.md,sha256=NKtPCJ7QMysFmzeDg56ZfUStvgzbq5sOvRQv7_ddZOs,1533
+rc_foundry-0.1.1.dist-info/RECORD,,

rc_foundry-0.1.1.dist-info/WHEEL

@@ -0,0 +1,4 @@
+Wheel-Version: 1.0
+Generator: hatchling 1.28.0
+Root-Is-Purelib: true
+Tag: py3-none-any

rc_foundry-0.1.1.dist-info/entry_points.txt

@@ -0,0 +1,5 @@
+[console_scripts]
+foundry = foundry_cli.download_checkpoints:app
+mpnn = mpnn.inference:main
+rf3 = rf3.cli:app
+rfd3 = rfd3.cli:app

rc_foundry-0.1.1.dist-info/licenses/LICENSE.md

@@ -0,0 +1,28 @@
+BSD 3-Clause License
+
+Copyright (c) 2025, Institute for Protein Design, University of Washington
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* Neither the name of the copyright holder nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

rf3/__init__.py

@@ -0,0 +1,3 @@
+"""RF3 - RosettaFold3 model implementation."""
+
+__version__ = "0.1.0"

rf3/_version.py

@@ -0,0 +1,33 @@
+# file generated by setuptools-scm
+# don't change, don't track in version control
+
+__all__ = [
+    "__version__",
+    "__version_tuple__",
+    "version",
+    "version_tuple",
+    "__commit_id__",
+    "commit_id",
+]
+
+TYPE_CHECKING = False
+if TYPE_CHECKING:
+    from typing import Tuple, Union
+
+    VERSION_TUPLE = Tuple[Union[int, str], ...]
+    COMMIT_ID = Union[str, None]
+else:
+    VERSION_TUPLE = object
+    COMMIT_ID = object
+
+version: str
+__version__: str
+__version_tuple__: VERSION_TUPLE
+version_tuple: VERSION_TUPLE
+commit_id: COMMIT_ID
+__commit_id__: COMMIT_ID
+
+__version__ = version = "0.1.dev917+gcbbe4c6a6.d20251001"
+__version_tuple__ = version_tuple = (0, 1, "dev917", "gcbbe4c6a6.d20251001")
+
+__commit_id__ = commit_id = None

rf3/alignment.py

@@ -0,0 +1,79 @@
+import logging
+
+import torch
+
+logger = logging.getLogger(__name__)
+
+
+def weighted_rigid_align(
+    X_L,  # [B, L, 3]
+    X_gt_L,  # [B, L, 3]
+    X_exists_L,  # [L]
+    w_L,  # [B, L]
+):
+    """
+    Weighted rigid body alignment of X_gt_L onto X_L with weights w_L
+    Allows for "moving target" ground truth that is se3 invariant
+    Following algorithm 28 in AF3 paper
+    Returns:
+      X_align_L: [B, L, 3]
+    """
+    assert X_L.shape == X_gt_L.shape
+    assert X_L.shape[:-1] == w_L.shape
+
+    # Assert `X_exists_L` is a boolean mask
+    assert (
+        X_exists_L.dtype == torch.bool
+    ), "X_exists_L should be a boolean mask! Otherwise, the alignment will be incorrect (silent failure)!"
+
+    X_resolved = X_L[:, X_exists_L]
+    X_gt_resolved = X_gt_L[:, X_exists_L]
+    w_resolved = w_L[:, X_exists_L]
+    u_X = torch.sum(X_resolved * w_resolved.unsqueeze(-1), dim=-2) / torch.sum(
+        w_resolved, dim=-1, keepdim=True
+    )
+    u_X_gt = torch.sum(X_gt_resolved * w_resolved.unsqueeze(-1), dim=-2) / torch.sum(
+        w_resolved, dim=-1, keepdim=True
+    )
+
+    X_resolved = X_resolved - u_X.unsqueeze(-2)
+    X_gt_resolved = X_gt_resolved - u_X_gt.unsqueeze(-2)
+
+    # Computation of the covariance matrix
+    C = torch.einsum("bji,bjk->bik", w_resolved[..., None] * X_gt_resolved, X_resolved)
+
+    U, S, V = torch.linalg.svd(C)
+
+    R = U @ V
+    B, _, _ = X_L.shape
+    F = torch.eye(3, 3, device=X_L.device)[None].tile(
+        (
+            B,
+            1,
+            1,
+        )
+    )
+
+    F[..., -1, -1] = torch.sign(torch.linalg.det(R))
+    R = U @ F @ V
+
+    X_gt_L = X_gt_L - u_X_gt.unsqueeze(-2)
+    X_align_L = X_gt_L @ R + u_X.unsqueeze(-2)
+
+    return X_align_L.detach()
+
+
+def get_rmsd(xyz1, xyz2, eps=1e-4):
+    L = xyz1.shape[-2]
+    rmsd = torch.sqrt(torch.sum((xyz2 - xyz1) * (xyz2 - xyz1), axis=(-1, -2)) / L + eps)
+    return rmsd
+
+
+def superimpose(xyz1, xyz2, mask, eps=1e-4):
+    """
+    Superimpose xyz1 onto xyz2 using mask
+    """
+    L = xyz1.shape[-2]
+    assert mask.shape == (L,)
+    assert xyz1.shape == xyz2.shape
+    assert mask.dtype == torch.bool

rf3/callbacks/dump_validation_structures.py

@@ -0,0 +1,101 @@
+from os import PathLike
+from pathlib import Path
+
+from atomworks.ml.example_id import parse_example_id
+from beartype.typing import Any
+from rf3.utils.io import (
+    build_stack_from_atom_array_and_batched_coords,
+    dump_structures,
+    dump_trajectories,
+)
+
+from foundry.callbacks.callback import BaseCallback
+
+
+class DumpValidationStructuresCallback(BaseCallback):
+    """Dump predicted structures and/or diffusion trajectories during validation"""
+
+    def __init__(
+        self,
+        save_dir: PathLike,
+        dump_predictions: bool = False,
+        one_model_per_file: bool = False,
+        dump_trajectories: bool = False,
+        compress_outputs: bool = False,
+    ):
+        """
+        Args:
+            dump_predictions: Whether to dump structures (CIF files) after validation batches.
+            one_model_per_file: If True, write each structure within a diffusion batch to its own CIF files. If False,
+                include each structure within a diffusion batch as a separate model within one CIF file.
+            dump_trajectories: Whether to dump denoising trajectories after validation batches.
+            compress_outputs: Whether to gzip output files. Defaults to ``False``.
+        """
+        super().__init__()
+        self.save_dir = Path(save_dir)
+        self.dump_predictions = dump_predictions
+        self.dump_trajectories = dump_trajectories
+        self.one_model_per_file = one_model_per_file
+        self.compress_outputs = compress_outputs
+
+    def on_validation_batch_end(
+        self,
+        trainer,
+        outputs: dict,
+        batch: Any,
+        dataset_name: str | None,
+        **_,
+    ):
+        if (not self.dump_predictions) and (not self.dump_trajectories):
+            return  # Nothing to do
+
+        assert (
+            "network_output" in outputs
+        ), "Validation outputs must contain `network_output` to dump structures!"
+
+        network_output = outputs["network_output"]
+        example = batch[0]  # Assume batch size = 1
+
+        try:
+            # ... try to extract the PDB ID and assembly ID from the example ID
+            parsed_id = parse_example_id(example["example_id"])
+            identifier = f"{parsed_id['pdb_id']}_{parsed_id['assembly_id']}"
+        except (KeyError, ValueError):
+            # ... if parsing fails, fall back to the original example ID
+            identifier = example["example_id"]
+
+        def _build_path_from_example_id(dir: str, extra: str = "") -> Path:
+            """Helper function to build a path from a training or validation example_id."""
+            path = self.save_dir / dir / f"epoch_{trainer.state['current_epoch']}"
+
+            path = path / dataset_name
+
+            return path / f"{identifier}{extra}"
+
+        # Determine file type based on compression setting
+        file_type = "cif.gz" if self.compress_outputs else "cif"
+
+        if self.dump_predictions:
+            atom_array_stack = build_stack_from_atom_array_and_batched_coords(
+                network_output["X_L"], example["atom_array"]
+            )
+            dump_structures(
+                atom_arrays=atom_array_stack,
+                base_path=_build_path_from_example_id("predictions"),
+                one_model_per_file=self.one_model_per_file,
+                file_type=file_type,
+            )
+
+        if self.dump_trajectories:
+            dump_trajectories(
+                trajectory_list=network_output["X_denoised_L_traj"],
+                atom_array=example["atom_array"],
+                base_path=_build_path_from_example_id("trajectories", "_denoised"),
+                file_type=file_type,
+            )
+            dump_trajectories(
+                trajectory_list=network_output["X_noisy_L_traj"],
+                atom_array=example["atom_array"],
+                base_path=_build_path_from_example_id("trajectories", "_noisy"),
+                file_type=file_type,
+            )