rowan-python 3.1.0__tar.gz → 3.1.1__tar.gz

rowan_python-3.1.1/.github/workflows/publish-skill.yml

@@ -0,0 +1,28 @@
+name: Publish Skill Zip
+
+on:
+  push:
+    branches: [master]
+    paths:
+      - 'skills/computational-chemistry-and-biology/**'
+      - '.github/workflows/publish-skill.yml'
+  workflow_dispatch:
+
+permissions:
+  contents: write
+
+jobs:
+  publish:
+    if: github.repository == 'rowansci/rowan-python'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Zip skill
+        run: cd skills && zip -r ../computational-chemistry-and-biology-skill.zip computational-chemistry-and-biology
+      - name: Publish/refresh release
+        uses: softprops/action-gh-release@v2
+        with:
+          tag_name: skill-latest
+          name: "Computational Chemistry & Biology Skill (latest)"
+          prerelease: true
+          files: computational-chemistry-and-biology-skill.zip

{rowan_python-3.1.0 → rowan_python-3.1.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rowan-python
-Version: 3.1.0
+Version: 3.1.1
 Summary: Rowan Python Library
 Project-URL: Homepage, https://github.com/rowansci/rowan-client
 Project-URL: Bug Tracker, https://github.com/rowansci/rowan-client/issues
@@ -32,6 +32,8 @@ The documentation is available [here](https://docs.rowansci.com/python-api).
 
 Ships with a [skill](skills/computational-chemistry-and-biology/) that makes it easy for coding agents to use Rowan's tools to power chemistry and biology tasks. To use it, copy the directory into your agent's skills folder.
 
+Download the latest skill as a zip [here](https://github.com/rowansci/rowan-python/releases/download/skill-latest/computational-chemistry-and-biology-skill.zip), then unzip it into your agent's skills folder.
+
 ## Running examples
 
 To run the examples, you will need to set your ROWAN_API_KEY environment variable or set it directly in the script.

{rowan_python-3.1.0 → rowan_python-3.1.1}/README.md

@@ -16,6 +16,8 @@ The documentation is available [here](https://docs.rowansci.com/python-api).
 
 Ships with a [skill](skills/computational-chemistry-and-biology/) that makes it easy for coding agents to use Rowan's tools to power chemistry and biology tasks. To use it, copy the directory into your agent's skills folder.
 
+Download the latest skill as a zip [here](https://github.com/rowansci/rowan-python/releases/download/skill-latest/computational-chemistry-and-biology-skill.zip), then unzip it into your agent's skills folder.
+
 ## Running examples
 
 To run the examples, you will need to set your ROWAN_API_KEY environment variable or set it directly in the script.

{rowan_python-3.1.0 → rowan_python-3.1.1}/pixi.lock

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@@ -1071,6 +1071,18 @@ packages:
   - mkdocs-redirects>=1.2 ; extra == 'recommended'
   - mkdocs-rss-plugin>=1.6 ; extra == 'recommended'
   requires_python: '>=3.8'
+- pypi: https://files.pythonhosted.org/packages/2c/02/3623e6169bed617ed1e2d372f7c69f92ec28d54c4dfc997055c8578ec148/virtualenv-21.5.1-py3-none-any.whl
+  name: virtualenv
+  version: 21.5.1
+  sha256: 55aa670b67bbfb991b03fda39bd3276d92c419d702376e98c5df1c9989a26783
+  requires_dist:
+  - distlib>=0.3.7,<1
+  - filelock>=3.24.2,<4 ; python_full_version >= '3.10'
+  - filelock>=3.16.1,<=3.19.1 ; python_full_version < '3.10'
+  - platformdirs>=3.9.1,<5
+  - python-discovery>=1.4.2
+  - typing-extensions>=4.13.2 ; python_full_version < '3.11'
+  requires_python: '>=3.9'
 - pypi: https://files.pythonhosted.org/packages/2c/19/04f9b178c2d8a15b076c8b5140708fa6ffc5601fb6f1e975537072df5b2a/mergedeep-1.3.4-py3-none-any.whl
   name: mergedeep
   version: 1.3.4
@@ -1352,6 +1364,17 @@ packages:
   - platformdirs>=2.2.0
   - pyyaml>=5.1
   requires_python: '>=3.9'
+- pypi: https://files.pythonhosted.org/packages/88/4f/fc88eed7a404a88f14a9d9cf8f96126f0a7e6b8a7cf32dd93e58646d25b1/stjames-0.0.205-py3-none-any.whl
+  name: stjames
+  version: 0.0.205
+  sha256: bf39bd8b1d8eaa93ec88e754c4633fa8a238d05f84b4f1c4d37a229c513cd52b
+  requires_dist:
+  - pydantic>=2.4
+  - numpy
+  - requests
+  - more-itertools
+  - rdkit ; extra == 'rdkit'
+  requires_python: '>=3.11'
 - pypi: https://files.pythonhosted.org/packages/88/b2/d0896bdcdc8d28a7fc5717c305f1a861c26e18c05047949fb371034d98bd/nodeenv-1.10.0-py2.py3-none-any.whl
   name: nodeenv
   version: 1.10.0
@@ -1701,6 +1724,16 @@ packages:
   version: 1.17.0
   sha256: 4721f391ed90541fddacab5acf947aa0d3dc7d27b2e1e8eda2be8970586c3274
   requires_python: '>=2.7,!=3.0.*,!=3.1.*,!=3.2.*'
+- pypi: https://files.pythonhosted.org/packages/ba/16/9826f089383c593cdfc4a6e5aca94d9e91ae1692c57af82c3b2aa5e810f7/anyio-4.14.0-py3-none-any.whl
+  name: anyio
+  version: 4.14.0
+  sha256: dd9b7a2a9799ed6552fde617b2c5df02b7fdd7d88392fc48101e51bae46164d9
+  requires_dist:
+  - exceptiongroup>=1.0.2 ; python_full_version < '3.11'
+  - idna>=2.8
+  - typing-extensions>=4.5 ; python_full_version < '3.13'
+  - trio>=0.32.0 ; extra == 'trio'
+  requires_python: '>=3.10'
 - pypi: https://files.pythonhosted.org/packages/ba/8c/1a9e46228571de18f8e28f16fabdfc20212a5d019f3e3303452b3f0a580d/pillow-12.2.0-cp314-cp314-macosx_11_0_arm64.whl
   name: pillow
   version: 12.2.0
@@ -1743,17 +1776,6 @@ packages:
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   sha256: 34d5fcd24b8445fadc33f9cf348c1047101756fd760b4dacb5c3e99755703310
   requires_python: '>=3.8'
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-  name: stjames
-  version: 0.0.204
-  sha256: 51106909397fc0e8aebee2323b127137b8967c4193924a730b345d9f5a835ea0
-  requires_dist:
-  - pydantic>=2.4
-  - numpy
-  - requests
-  - more-itertools
-  - rdkit ; extra == 'rdkit'
-  requires_python: '>=3.11'
 - pypi: https://files.pythonhosted.org/packages/c1/ea/53f2148663b321f21b5a606bd5f191517cf40b7072c0497d3c92c4a13b1e/executing-2.2.1-py2.py3-none-any.whl
   name: executing
   version: 2.2.1
@@ -1802,16 +1824,6 @@ packages:
   requires_dist:
   - pygments
   requires_python: '>=3.8'
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-  name: anyio
-  version: 4.13.0
-  sha256: 08b310f9e24a9594186fd75b4f73f4a4152069e3853f1ed8bfbf58369f4ad708
-  requires_dist:
-  - exceptiongroup>=1.0.2 ; python_full_version < '3.11'
-  - idna>=2.8
-  - typing-extensions>=4.5 ; python_full_version < '3.13'
-  - trio>=0.32.0 ; extra == 'trio'
-  requires_python: '>=3.10'
 - pypi: https://files.pythonhosted.org/packages/db/3c/33bac158f8ab7f89b2e59426d5fe2e4f63f7ed25df84c036890172b412b5/cfgv-3.5.0-py2.py3-none-any.whl
   name: cfgv
   version: 3.5.0
@@ -1856,18 +1868,6 @@ packages:
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   requires_python: '>=3.10'
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-  requires_dist:
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-  - filelock>=3.24.2,<4 ; python_full_version >= '3.10'
-  - filelock>=3.16.1,<=3.19.1 ; python_full_version < '3.10'
-  - platformdirs>=3.9.1,<5
-  - python-discovery>=1.4.2
-  - typing-extensions>=4.13.2 ; python_full_version < '3.11'
-  requires_python: '>=3.9'
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   name: python-dateutil
   version: 2.9.0.post0

{rowan_python-3.1.0 → rowan_python-3.1.1}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "rowan-python"
-version = "3.1.0"
+version = "3.1.1"
 description = "Rowan Python Library"
 readme = "README.md"
 requires-python = ">=3.12"

{rowan_python-3.1.0 → rowan_python-3.1.1}/rowan/workflows/protein_cofolding.py

@@ -23,10 +23,10 @@ class CofoldingScores:
     """
     Confidence scores for a cofolding prediction.
 
-    :param ptm: Predicted TM-score (0-1, higher is better).
-    :param iptm: Interface predicted TM-score (0-1, higher is better).
-    :param avg_lddt: Average per-residue LDDT confidence (0-1).
-    :param confidence_score: Overall confidence score (0-1).
+    :param ptm: Predicted TM-score, overall structure confidence (0-1, higher is better).
+    :param iptm: Interface pTM, inter-chain packing confidence (0-1, higher is better).
+    :param avg_lddt: Mean per-residue pLDDT, local atomic accuracy (0-1, higher is better).
+    :param confidence_score: Overall aggregate confidence in the prediction (0-1, higher is better).
     """
 
     ptm: float | None = None
@@ -40,12 +40,26 @@ class AffinityScore:
     """
     Predicted binding affinity scores.
 
-    :param pred_value: Predicted binding affinity (ensemble average).
-    :param pred_value1: Predicted binding affinity (model 1).
-    :param pred_value2: Predicted binding affinity (model 2).
-    :param probability_binary: Probability of binding (ensemble average, 0-1).
-    :param probability_binary1: Probability of binding (model 1, 0-1).
-    :param probability_binary2: Probability of binding (model 2, 0-1).
+    Every field is optional; which ones a given run populates depends on the
+    cofolding model. In current runs Boltz-2 fills the pred_value and
+    probability_binary fields while Boltz-2.1 fills binding_confidence and
+    optimization_score, but the schema does not guarantee this split.
+
+    :param pred_value: Predicted pIC50, -log10(IC50 in M); higher means stronger
+        binding (ensemble average of the two affinity heads).
+    :param pred_value1: Predicted pIC50 from affinity head 1.
+    :param pred_value2: Predicted pIC50 from affinity head 2.
+    :param probability_binary: Predicted probability (0-1) that the ligand binds
+        its target; higher is better (ensemble average of the two affinity heads).
+    :param probability_binary1: Binding probability (0-1) from affinity head 1.
+    :param probability_binary2: Binding probability (0-1) from affinity head 2.
+    :param binding_confidence: Predicted probability (0-1, higher is better) that
+        the molecule or binder is a true binder rather than a decoy. Primary metric
+        for hit discovery (computed when binding is requested).
+    :param optimization_score: Binding-strength ranking derived from the model's
+        predicted log(IC50) affinity; higher means stronger predicted binding. Use
+        to rank-order likely binders during lead optimization (computed when binding
+        is requested).
     """
 
     pred_value: float | None = None
@@ -54,6 +68,8 @@ class AffinityScore:
     probability_binary: float | None = None
     probability_binary1: float | None = None
     probability_binary2: float | None = None
+    binding_confidence: float | None = None
+    optimization_score: float | None = None
 
 
 @dataclass(frozen=True, slots=True)
@@ -230,6 +246,8 @@ class ProteinCofoldingResult(WorkflowResult):
                 probability_binary=a.get("probability_binary"),
                 probability_binary1=a.get("probability_binary1"),
                 probability_binary2=a.get("probability_binary2"),
+                binding_confidence=a.get("binding_confidence"),
+                optimization_score=a.get("optimization_score"),
             )
         return AffinityScore(
             pred_value=a.pred_value,
@@ -238,6 +256,8 @@ class ProteinCofoldingResult(WorkflowResult):
             probability_binary=a.probability_binary,
             probability_binary1=a.probability_binary1,
             probability_binary2=a.probability_binary2,
+            binding_confidence=getattr(a, "binding_confidence", None),
+            optimization_score=getattr(a, "optimization_score", None),
         )
 
 
@@ -271,7 +291,7 @@ def submit_protein_cofolding_workflow(
 
     See `examples/protein_cofolding_with_constraints.py` for a worked example
     of using `ConstraintTarget`, `ContactConstraint`, and `PocketConstraint`
-    (Boltz-2 only).
+    (Boltz models only).
 
     :param initial_protein_sequences: Protein sequences to be cofolded.
     :param initial_dna_sequences: DNA sequences to be cofolded.
@@ -283,13 +303,15 @@ def submit_protein_cofolding_workflow(
     :param use_potentials: Whether to use potentials (inference-time steering) with Boltz.
     :param contact_constraints: Boltz contact constraints between two tokens.
     :param pocket_constraints: Boltz pocket constraints between a binder and contact tokens.
-    :param templates: Structural templates to guide prediction (Boltz-2 or OpenFold-3 only).
+    :param templates: Structural templates to guide prediction (Boltz-2/2.1 or OpenFold-3 only).
     :param num_samples: Number of diffusion samples to generate. If None, uses the model default.
     :param compute_strain: Whether to compute the strain of the pose. Requires do_pose_refinement.
         (if `pose_refinement` is enabled).
     :param do_pose_refinement: Whether to optimize non-rotatable bonds in output poses.
     :param name: Name of the workflow.
-    :param model: Model to use for the computation.
+    :param model: Model to use for the computation. Boltz-2.1 runs via Boltz's
+        hosted API (slower than the locally-run models) and reports a different
+        set of affinity metrics than Boltz-2 (see `AffinityScore`).
     :param folder_uuid: UUID of the folder to store the workflow in.
     :param folder: Folder object to store the workflow in.
     :param max_credits: Maximum number of credits to use for the workflow.

{rowan_python-3.1.0 → rowan_python-3.1.1}/skills/computational-chemistry-and-biology/reference/protein_cofolding.md

@@ -9,7 +9,7 @@ One or more biomolecule sequences, optionally with ligands, supplied directly as
 - `initial_smiles_list`: a list of ligand SMILES, all co-folded together with the biomolecules in a single complex. One workflow is one prediction of the whole complex, not one job per ligand; to screen several ligands separately, submit one workflow per ligand.
 - `ligand_binding_affinity_index`: index into `initial_smiles_list` of the ligand to predict a binding affinity for.
 
-This workflow predicts 3D structures of biomolecules and protein-ligand complexes using AlphaFold 3-style models (Boltz-2, Chai-1r, Boltz-1).
+This workflow predicts 3D structures of biomolecules and protein-ligand complexes using AlphaFold 3-style models (Boltz-2, Boltz-2.1, Chai-1r, Boltz-1, OpenFold-3).
 
 ## Example
 
@@ -39,14 +39,14 @@ print(result)   # e.g. <ProteinCofoldingResult predictions=5 iptm=0.87>
 
 ## Settings
 
-- `model` (default `boltz_2`): co-folding model, one of `boltz_2`, `chai_1r`, `boltz_1`.
+- `model` (default `boltz_2`): co-folding model, one of `boltz_2`, `boltz_2_1`, `chai_1r`, `boltz_1`, `openfold_3`. The model changes which `affinity_score` fields are returned (see Result fields). `boltz_2_1` runs via Boltz's hosted API and is noticeably slower than the locally-run models.
 - `use_msa_server` (default `True`): generate a multiple-sequence alignment, which improves co-folding accuracy. Queries run on a secure Rowan-hosted server.
 - `use_potentials` (default `False`): use physics-based potentials to steer predictions toward more physical poses (this is what distinguishes Boltz-2x from Boltz-2). Required when a constraint sets `force=True`.
 - `num_samples` (default model-dependent): number of predicted samples to generate.
 - `compute_strain` (default `False`): run an OpenConf conformer search to estimate the predicted ligand's strain energy. Adds a few minutes (more for large ligands) and requires `do_pose_refinement=True` (`compute_strain=True` with it off raises a `ValueError`).
 - `do_pose_refinement` (default `False`): run a constrained AIMNet2 optimization on the output structure to refine the predicted pose.
 - `ligand_binding_affinity_index` (default none): index into `initial_smiles_list` of the ligand to predict a binding affinity for.
-- `templates` (default none): structural templates that guide the prediction toward a reference protein structure, each a `rowan.CofoldingTemplate(protein=..., max_distance=...)` where `protein` is a PDB or an uploaded protein UUID. Set `max_distance` (in angstroms) to enforce a maximum deviation from the template via potentials (requires `use_potentials=True`). Boltz-2 only.
+- `templates` (default none): structural templates that guide the prediction toward a reference protein structure, each a `rowan.CofoldingTemplate(protein=..., max_distance=...)` where `protein` is a PDB or an uploaded protein UUID. Set `max_distance` (in angstroms) to enforce a maximum deviation from the template via potentials (requires `use_potentials=True`). Boltz-2, Boltz-2.1, or OpenFold-3 only.
 
 ## Constraints
 
@@ -91,5 +91,6 @@ wf = rowan.submit_protein_cofolding_workflow(
 - `predicted_structure_uuid` and `predicted_refined_structure_uuid`: UUIDs of the predicted structure and, when pose refinement ran, the refined one. Fetch with `rowan.retrieve_protein(uuid)`.
 - `lddt`: per-residue LDDT confidence for the primary prediction.
 - `scores`: confidence scores; `affinity_score`: predicted binding affinity for the primary prediction.
+- `affinity_score` fields are all optional and **which ones are filled depends on the model** (the schema does not enforce this): Boltz-2 fills `pred_value`/`pred_value1`/`pred_value2` (predicted pIC50, higher = stronger; IC50 is derived from it) and `probability_binary`/`probability_binary1`/`probability_binary2` (binding probability, 0-1); Boltz-2.1 instead fills `binding_confidence` (probability the ligand is a true binder vs decoy — use for hit discovery) and `optimization_score` (binding-strength ranking, higher = stronger — use for lead optimization). The two models report non-overlapping affinity metrics, so a Boltz-2 vs Boltz-2.1 comparison shares only the `scores`.
 - `posebusters_valid`: whether the primary pose passes PoseBusters.
 - `strain`: ligand strain energy for the primary prediction.