rowan-python 3.1.0__py3-none-any.whl → 3.1.2__py3-none-any.whl

rowan/__init__.py

@@ -24,6 +24,7 @@ from stjames import (
     SolventSettings,
     Task,
 )
+from stjames.workflows.relative_binding_free_energy_perturbation import RBFEGraph, RBFEGraphEdge
 from stjames.excited_state_settings import TDDFTSettings
 from stjames.pbc_dft_settings import PBCDFTSmearing
 from stjames.engine_compatibility import (

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/workflows/rbfe_graph.py

@@ -4,6 +4,7 @@ from dataclasses import dataclass
 from typing import Literal
 
 import stjames
+from stjames.workflows.relative_binding_free_energy_perturbation import RBFEGraph
 
 from ..folder import Folder
 from ..molecule import Molecule
@@ -57,13 +58,9 @@ class RelativeBindingFreeEnergyGraphResult(WorkflowResult):
         return {k: Molecule.from_stjames(v) for k, v in self._workflow.ligands.items()}
 
     @property
-    def graph(self) -> dict | None:
-        """
-        The constructed RBFE perturbation graph as a dict, or None if not yet computed.
-
-        Pass directly to ``submit_rbfe_perturbation_workflow(graph=...)``.
-        """
-        return g.model_dump(mode="json") if (g := self._workflow.graph) else None
+    def graph(self) -> RBFEGraph | None:
+        """The constructed RBFE graph, or None if not yet computed."""
+        return self._workflow.graph
 
     @property
     def edges(self) -> list[RelativeBindingFreeEnergyGraphEdge]:
@@ -99,6 +96,7 @@ def submit_relative_binding_free_energy_graph_workflow(
     greedy_scoring: Literal["best", "jaccard", "dummy_atoms"] = "best",
     greedy_k_min_cut: int = 3,
     refine_cutoff: float | None = None,
+    seed_graph: RBFEGraph | None = None,
     name: str = "RBFE Graph",
     folder_uuid: str | None = None,
     folder: Folder | None = None,
@@ -119,6 +117,9 @@ def submit_relative_binding_free_energy_graph_workflow(
         ``"best"``, ``"jaccard"``, or ``"dummy_atoms"``.
     :param greedy_k_min_cut: Target edge-connectivity for greedy augmentation. Must be > 0.
     :param refine_cutoff: Optional MCS similarity cutoff for graph refinement.
+    :param seed_graph: RBFE graph from a prior run to extend, as returned by a
+        completed result's ``graph``. Its existing edges (and any computed results)
+        are preserved, and only edges for newly added ligands are built.
     :param name: Name of the workflow.
     :param folder_uuid: UUID of the folder to place the workflow in.
     :param folder: Folder object to store the workflow in.
@@ -126,7 +127,8 @@ def submit_relative_binding_free_energy_graph_workflow(
     :param webhook_url: URL that Rowan will POST to when the workflow completes.
     :param is_draft: If True, submit the workflow as a draft without starting execution.
     :returns: Workflow object representing the submitted workflow.
-    :raises ValueError: If both folder and folder_uuid are provided.
+    :raises ValueError: If both folder and folder_uuid are provided, if any ligand has
+        no defined charge, or if the ligands do not all share the same formal charge.
     :raises requests.HTTPError: if the request to the API fails.
     """
     if folder and folder_uuid:
@@ -138,6 +140,27 @@ def submit_relative_binding_free_energy_graph_workflow(
         require_coordinates(ligand)
     ligands_dict = {k: molecule_to_dict(v) for k, v in ligands.items()}
 
+    charges = {name: mol.get("charge") for name, mol in ligands_dict.items()}
+    missing_charge = sorted(name for name, charge in charges.items() if charge is None)
+    if missing_charge:
+        raise ValueError(
+            "Cannot verify charge consistency: no charge found for ligand(s) "
+            f"{', '.join(missing_charge)}. Provide ligands with a defined formal charge."
+        )
+    distinct_charges = {charge for charge in charges.values() if charge is not None}
+    if len(distinct_charges) > 1:
+        groups = {
+            charge: sorted(name for name, c in charges.items() if c == charge)
+            for charge in sorted(distinct_charges)
+        }
+        summary = "; ".join(
+            f"charge {charge}: {', '.join(names)}" for charge, names in groups.items()
+        )
+        raise ValueError(
+            "All RBFE ligands must share the same formal charge - charge-changing "
+            f"perturbations are not supported. Found multiple charge states ({summary})."
+        )
+
     workflow = stjames.RBFEGraphWorkflow(
         ligands=ligands_dict,
         mode=mode,
@@ -145,6 +168,7 @@ def submit_relative_binding_free_energy_graph_workflow(
         greedy_scoring=greedy_scoring,
         greedy_k_min_cut=greedy_k_min_cut,
         refine_cutoff=refine_cutoff,
+        seed_graph=seed_graph,
     )
 
     data = {

rowan/workflows/relative_binding_free_energy_perturbation.py

@@ -5,7 +5,7 @@ from pathlib import Path
 from typing import Literal
 
 import stjames
-from stjames.workflows.relative_binding_free_energy_perturbation import TMDRBFESettings
+from stjames.workflows.relative_binding_free_energy_perturbation import RBFEGraph, TMDRBFESettings
 
 from ..folder import Folder
 from ..molecule import Molecule
@@ -86,6 +86,16 @@ class RelativeBindingFreeEnergyPerturbationResult(WorkflowResult):
         """Ligand molecules keyed by identifier."""
         return {k: Molecule.from_stjames(v) for k, v in self._workflow.ligands.items()}
 
+    @property
+    def protein(self) -> Protein:
+        """Prepared protein structure used as the simulation target."""
+        return Protein(uuid=str(self._workflow.protein))
+
+    @property
+    def graph(self) -> RBFEGraph | None:
+        """The RBFE graph with per-edge results, or None if not constructed."""
+        return self._workflow.graph
+
     @property
     def edges(self) -> list[RelativeBindingFreeEnergyGraphEdge]:
         """Graph edges with per-edge FEP results."""

{rowan_python-3.1.0.dist-info → rowan_python-3.1.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rowan-python
-Version: 3.1.0
+Version: 3.1.2
 Summary: Rowan Python Library
 Project-URL: Homepage, https://github.com/rowansci/rowan-client
 Project-URL: Bug Tracker, https://github.com/rowansci/rowan-client/issues
@@ -11,7 +11,7 @@ Requires-Dist: httpx
 Requires-Dist: nest-asyncio
 Requires-Dist: rdkit
 Requires-Dist: setuptools
-Requires-Dist: stjames>=0.0.204
+Requires-Dist: stjames>=0.0.208
 Description-Content-Type: text/markdown
 
 # Rowan Python Library
@@ -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.dist-info → rowan_python-3.1.2.dist-info}/RECORD

@@ -1,4 +1,4 @@
-rowan/__init__.py,sha256=tyL1rh1lEZ1u9-E5Li3z20ymEFzO032ALyrATc-6zMw,1234
+rowan/__init__.py,sha256=UhyjCkQh7YDTtemmetfelGD1d36WSJ6oaWct7CP2eyQ,1331
 rowan/api_keys.py,sha256=TvG5l5MmQ3Qt8Z3Y7jCA_lcrwEHuI7xHy-KLbIdQ8_A,4793
 rowan/calculation.py,sha256=lZZ52DxPsuJWCTzFZXjhauHK6dV0KCUwzoxtmoxSY48,3442
 rowan/config.py,sha256=TejQKSxnzNKKTNL9-2bCLq6RvAh54oVA5Ivl1p_ZT8Q,20899
@@ -38,18 +38,18 @@ rowan/workflows/pka.py,sha256=xQPaOHxPQqCY_zi97LW9brpXPn3xjyeF9RDE1Rz8HQk,8772
 rowan/workflows/pocket_detection.py,sha256=aGHY0puxekp4c4nsNYHcvKCe1fsetygL04BcSvNFvE8,3864
 rowan/workflows/pose_analysis_md.py,sha256=XJIfvn-H7GA6lVtw9uKjlgznVSSsr9bJiDt_PjKlPbA,11572
 rowan/workflows/protein_binder_design.py,sha256=pgywTQDuXHplZYka-61_S6CC4WTPDCwJrbupp825eC4,9281
-rowan/workflows/protein_cofolding.py,sha256=Hp0A7nP5svMak1jITXUydGWZRMazBF3xnkwal2I66As,14611
+rowan/workflows/protein_cofolding.py,sha256=CV13VUHC0NLDDaS1-GGTQ3RySkzEE30xzu1_4oPu6lo,16239
 rowan/workflows/protein_md.py,sha256=41S-GIHP91ahW5mIVxjAkpZbxept98IgausM5JoeckA,9276
-rowan/workflows/rbfe_graph.py,sha256=LcVu3nFGZ5NTSdeojb-DeRfwEDh3gBTRkVF_jOrzVtQ,5893
+rowan/workflows/rbfe_graph.py,sha256=7UJA3ZBbvtaB9l1KQi9279Pc89moVnBHO-XJpxEr5uQ,7238
 rowan/workflows/redox_potential.py,sha256=bBeT1K9XGVpjCFZeeuv7Vtr3EYHN2okJ4LqYc3gMV04,5427
-rowan/workflows/relative_binding_free_energy_perturbation.py,sha256=uxC3Rr63U6GjNa9u2Hurahu48l4rYEz5RQX4hV0D250,13456
+rowan/workflows/relative_binding_free_energy_perturbation.py,sha256=vi5Qj5aDAERtjcHDsgzI6vRV_BZJnJ8boOj5aG6GXzo,13817
 rowan/workflows/scan.py,sha256=R5Y6Md3ohPoFVJ4NYvx3_k3JNwMnVw1CDsNPD9S8sr4,7518
 rowan/workflows/solubility.py,sha256=ulZwdG8JRl0RCwWPatYUZGMhlAZeb6wqjVbvzQYFKmE,8555
 rowan/workflows/solvent_dependent_conformers.py,sha256=Z2xESmcM8WcTsR2TSTUa--RrhrQ-5ri_WagD9wJeVwc,6812
 rowan/workflows/spin_states.py,sha256=rjkgie2-XVNIN7O6P93yn6EPv9Ogjy8iTj3ufZIsUgY,9331
 rowan/workflows/strain.py,sha256=kCW_BlX__sdQG1JVbFZuB-57rkpnxa_JCw3h4uKdGDk,6425
 rowan/workflows/tautomer_search.py,sha256=mbRl0ZJ7wibueRF8c8_idhXJ1rtwg7LBt--5QwQ_Cck,5767
-rowan_python-3.1.0.dist-info/METADATA,sha256=IR_vmRm6QdxoIbOMiHZgl3SGtkS-VQR7vh6_AioBNX0,1842
-rowan_python-3.1.0.dist-info/WHEEL,sha256=mffPy8wBnZQn2VnJUU5jE99KsxaSfiyMHV9Yt0aLVxs,87
-rowan_python-3.1.0.dist-info/licenses/LICENSE,sha256=i05z7xEhyrg6f8j0lR3XYjShnF-MJGFQ-DnpsZ8yiVI,1084
-rowan_python-3.1.0.dist-info/RECORD,,
+rowan_python-3.1.2.dist-info/METADATA,sha256=poPK5z_485P_QgH_M-RVS8GkqGUhlojTCR5BlZW-iC0,2052
+rowan_python-3.1.2.dist-info/WHEEL,sha256=mffPy8wBnZQn2VnJUU5jE99KsxaSfiyMHV9Yt0aLVxs,87
+rowan_python-3.1.2.dist-info/licenses/LICENSE,sha256=i05z7xEhyrg6f8j0lR3XYjShnF-MJGFQ-DnpsZ8yiVI,1084
+rowan_python-3.1.2.dist-info/RECORD,,