rowan-python 3.1.9__tar.gz → 3.1.10__tar.gz

{rowan_python-3.1.9 → rowan_python-3.1.10}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rowan-python
-Version: 3.1.9
+Version: 3.1.10
 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>=0.0.236
+Requires-Dist: stjames<0.0.238,>=0.0.237
 Description-Content-Type: text/markdown
 
 # Rowan Python Library

{rowan_python-3.1.9 → rowan_python-3.1.10}/docs/index.md

@@ -209,6 +209,17 @@
       group_by_category: true
       filters: ["!^__"]
 
+## LogP
+::: rowan.workflows.logp
+    handler: python
+    options:
+      show_source: false
+      show_root_heading: false
+      show_root_toc_entry: false
+      members_order: source
+      group_by_category: true
+      filters: ["!^__"]
+
 ## MacropKa
 ::: rowan.workflows.macropka
     handler: python

{rowan_python-3.1.9 → rowan_python-3.1.10}/examples/covalent_inhibitor_scan.py

@@ -15,10 +15,13 @@ protein.prepare(remove_heterogens=False)
 protein_reactive_atom_index = 1571
 ligand_reactive_atom_index = 4492
 
+ligand_smiles = "CC(C)(C)C[C@@H](C#N)C(=O)N1CCC[C@H](C1)n2nc(c3ccc(Oc4ccccc4)cc3)c5c(N)ncnc25"
+
 workflow = rowan.submit_covalent_inhibitor_scan_workflow(
     protein=protein,
     protein_reactive_atom_index=protein_reactive_atom_index,
     ligand_reactive_atom_index=ligand_reactive_atom_index,
+    ligand_smiles=ligand_smiles,
     settings=rowan.CovalentInhibitorScanSettings(scan_num=4),
     name="BTK covalent inhibitor scan (Cys481, 4YHF)",
     folder=folder,

{rowan_python-3.1.9 → rowan_python-3.1.10}/examples/docking.py

@@ -35,5 +35,5 @@ for i, score in enumerate(result.scores):
 
 # Download the top-scoring protein–ligand complex as a PDB
 complex_protein = result.get_complex(0)
-complex_protein.download_pdb_file("dasatinib_2GQG_complex.pdb")
+complex_protein.download_pdb_file(name="dasatinib_2GQG_complex")
 print("Saved dasatinib_2GQG_complex.pdb")

rowan_python-3.1.10/examples/logp.py

@@ -0,0 +1,19 @@
+import rowan
+
+# Set your API key or use the ROWAN_API_KEY environment variable
+# rowan.api_key = "rowan-sk..."
+folder = rowan.get_folder("examples")
+
+oseltamivir_SMILES = "C1CCOC(=O)C1=C[C@@H](OC(CC)CC)[C@H](NC(C)=O)[C@@H]([NH3+])C1CCC1"
+
+workflow = rowan.submit_logp_workflow(
+    initial_smiles=oseltamivir_SMILES,
+    method="chemprop_sangster2026",
+    name="Oseltamivir logP",
+    folder=folder,
+)
+
+print(f"View workflow privately at: https://labs.rowansci.com/logp/{workflow.uuid}")
+result = workflow.result()
+print(result)
+# e.g. <LogPResult logp=2.541>

{rowan_python-3.1.9 → rowan_python-3.1.10}/examples/protein_md.py

@@ -5,7 +5,7 @@ import rowan
 folder = rowan.get_folder("examples")
 
 protein = rowan.create_protein_from_pdb_id(
-    "crambin", "1CRN", project_uuid=rowan.default_project().uuid
+    "1CRN", name="crambin", project_uuid=rowan.default_project().uuid
 )
 
 protein.prepare()

{rowan_python-3.1.9 → rowan_python-3.1.10}/pixi.lock

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@@ -820,7 +820,7 @@ packages:
   name: rowan-python
   requires_dist:
   - httpx
-  - stjames>=0.0.236
+  - stjames>=0.0.237,<0.0.238
   - setuptools
   - rdkit
   - nest-asyncio
@@ -1706,17 +1706,6 @@ packages:
   version: 2.3.0
   sha256: f631c04d2c48c52b84d0d0549c99ff3859c98df65b3101406327ecc7d53fbf12
   requires_python: '>=3.10'
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-  name: stjames
-  version: 0.0.236
-  sha256: ea1459a5d0e0ccd206e5a387b201beec5e60ad6bc4f15dbcf649e2d4667fc40c
-  requires_dist:
-  - pydantic>=2.4
-  - numpy
-  - requests
-  - more-itertools
-  - rdkit ; extra == 'rdkit'
-  requires_python: '>=3.11'
 - pypi: https://files.pythonhosted.org/packages/d1/d6/3965ed04c63042e047cb6a3e6ed1a63a35087b6a609aa3a15ed8ac56c221/colorama-0.4.6-py2.py3-none-any.whl
   name: colorama
   version: 0.4.6
@@ -1803,6 +1792,17 @@ packages:
   - mkdocs-section-index ; extra == 'docs'
   - mkdocs-literate-nav ; extra == 'docs'
   requires_python: '>=3.10'
+- pypi: https://files.pythonhosted.org/packages/df/95/bdd01bbd523a63b113407c34c99af8495daa4651757cc28f3fabc393d131/stjames-0.0.237-py3-none-any.whl
+  name: stjames
+  version: 0.0.237
+  sha256: 790c32bdc829efe52b7ccc442083d0d95fc01587d4063a08ea73cd9f686f6d21
+  requires_dist:
+  - pydantic>=2.4
+  - numpy
+  - requests
+  - more-itertools
+  - rdkit ; extra == 'rdkit'
+  requires_python: '>=3.11'
 - pypi: https://files.pythonhosted.org/packages/df/b2/87e62e8c3e2f4b32e5fe99e0b86d576da1312593b39f47d8ceef365e95ed/packaging-26.2-py3-none-any.whl
   name: packaging
   version: '26.2'

{rowan_python-3.1.9 → rowan_python-3.1.10}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "rowan-python"
-version = "3.1.9"
+version = "3.1.10"
 description = "Rowan Python Library"
 readme = "README.md"
 requires-python = ">=3.12"
@@ -9,7 +9,7 @@ authors = [
 ]
 dependencies = [
     "httpx",
-    "stjames>=0.0.236",
+    "stjames>=0.0.237,<0.0.238",
     "setuptools",
     "rdkit",
     "nest-asyncio",

{rowan_python-3.1.9 → rowan_python-3.1.10}/rowan/__init__.py

@@ -3,6 +3,7 @@ from . import constants
 from stjames import (
     Atom,
     BandStructure,
+    Binder,
     BindingPoseContact,
     HydrationBridgeResidue,
     HydrationSite,

{rowan_python-3.1.9 → rowan_python-3.1.10}/rowan/protein.py

@@ -4,7 +4,8 @@ from datetime import datetime
 from pathlib import Path
 from typing import Any, Self
 
-from pydantic import BaseModel
+from pydantic import BaseModel, PrivateAttr
+from stjames.pdb import PDB, pdb_object_to_pdb_filestring
 
 from .project import Project
 from .utils import api_client
@@ -37,6 +38,8 @@ class Protein(BaseModel):
     public: bool | None = None
     pocket: list[list[float]] | None = None
 
+    _workflow_uuid: str | None = PrivateAttr(default=None)
+
     def __repr__(self) -> str:
         return f"<Protein name='{self.name}' created_at='{self.created_at}' uuid='{self.uuid}'>"
 
@@ -119,18 +122,24 @@ class Protein(BaseModel):
             response.raise_for_status()
             return Protein(**response.json())
 
-    def refresh(self, in_place: bool = True) -> Self:
+    def refresh(self, in_place: bool = True, workflow_uuid: str | None = None) -> Self:
         """
         Loads protein data
 
+        :param workflow_uuid: UUID of a workflow referencing this protein, for proteins reachable
+            only through a workflow you can read. Not needed for proteins from a workflow result.
         :returns: protein with loaded data
         """
+        workflow_uuid = workflow_uuid or self._workflow_uuid
+        params = {"workflow_uuid": workflow_uuid} if workflow_uuid else None
         with api_client() as client:
-            response = client.get(f"/protein/{self.uuid}")
+            response = client.get(f"/protein/{self.uuid}", params=params)
             response.raise_for_status()
             protein_data = response.json()
             if not in_place:
-                return self.__class__.model_validate(protein_data)
+                refreshed = self.__class__.model_validate(protein_data)
+                refreshed._workflow_uuid = workflow_uuid
+                return refreshed
 
         self.name = protein_data.get("name")
         self.data = protein_data.get("data")
@@ -138,6 +147,7 @@ class Protein(BaseModel):
         self.pocket = protein_data.get("pocket")
         self.sanitized = protein_data.get("sanitized")
         self.used_in_workflow = protein_data.get("used_in_workflow")
+        self._workflow_uuid = workflow_uuid
         return self
 
     def update(
@@ -291,7 +301,7 @@ class Protein(BaseModel):
 
         raise RuntimeError(f"Protein preparation timed out after {timeout:.0f}s for {self.uuid}.")
 
-    def validate_protein_forcefield(self, exclude_residue_names: list[str] | None = None) -> None:
+    def validate_protein_forcefield(self, exclude_residues: list[str | int] | None = None) -> None:
         """
         Validate that this protein can be parameterized with the MD forcefield.
 
@@ -299,16 +309,24 @@ class Protein(BaseModel):
         recognized by OpenMM and that there are no clashing atoms. Call this
         before submitting any MD workflow to catch preparation issues early.
 
-        Ligand residues (``LIG``) are always excluded — they are parameterized
-        separately by the MD workflow from the provided SMILES.
+        Ligand residues (`LIG`) are always excluded — they are parameterized
+        separately by the MD workflow from the provided SMILES. Pass the keys of a
+        binder's `small_molecules` to exclude those as well.
+
+        A name is matched case-insensitively and excludes only the first residue
+        with that name, so further copies are still validated. Integer entries are
+        0-based indices into the protein's sorted non-polymer records, and reference
+        a record without naming it.
 
         If validation fails, try re-preparing with ``remove_invalid_hydrogens=True``:
         ``protein.prepare(remove_invalid_hydrogens=True)``
 
-        :param exclude_residue_names: Additional residue names to skip during validation.
+        :param exclude_residues: additional residue names and/or 0-based non-polymer indices to skip
         :raises requests.HTTPError: if validation fails or the API request fails.
         """
-        excluded = list({"LIG"} | {name.upper() for name in (exclude_residue_names or [])})
+        entries: list[str | int] = ["LIG"]
+        entries += [r.upper() if isinstance(r, str) else r for r in exclude_residues or []]
+        excluded = list(dict.fromkeys(entries))
         with api_client() as client:
             response = client.post(
                 f"/protein/{self.uuid}/validate_forcefield",
@@ -316,42 +334,66 @@ class Protein(BaseModel):
             )
             response.raise_for_status()
 
-    def download_pdb_file(self, path: Path | str | None = None, name: str | None = None) -> None:
+    def download_pdb_file(
+        self,
+        path: Path | str | None = None,
+        name: str | None = None,
+        workflow_uuid: str | None = None,
+    ) -> None:
         """
-        Downloads the PDB file for a protein
+        Downloads the PDB file for a protein.
+
+        Builds the file locally from this protein's data, calling `refresh()` if needed, so it
+        works anywhere `refresh()` does — including proteins reachable only through a workflow.
 
         :param path: Directory to save the file to (defaults to current directory)
         :param name: Optional custom name for the file (defaults to protein name)
+        :param workflow_uuid: UUID of a workflow referencing this protein, for proteins reachable
+            only through a workflow you can read. Not needed for proteins from a workflow result.
         :raises requests.HTTPError: if the request to the API fails
         """
         path = Path(path) if path is not None else Path.cwd()
 
         path.mkdir(parents=True, exist_ok=True)
 
-        with api_client() as client:
-            response = client.get(f"/protein/{self.uuid}/get_pdb_file")
-            response.raise_for_status()
+        if self.data is None:
+            self.refresh(workflow_uuid=workflow_uuid)
+
+        pdb_object = PDB.model_validate(self.data)
+        pdb_string = pdb_object_to_pdb_filestring(
+            pdb=pdb_object,
+            header=True,
+            source=True,
+            keyword=True,
+            crystallography=True,
+            remark=False,
+        )
 
-        file_path = path / f"{name or self.name}.pdb"
-        with open(file_path, "wb") as f:
-            f.write(response.content)
+        file_path = path / f"{name or self.name or self.uuid}.pdb"
+        with open(file_path, "w") as f:
+            f.write(pdb_string)
 
 
-def retrieve_protein(uuid: str) -> Protein:
+def retrieve_protein(uuid: str, workflow_uuid: str | None = None) -> Protein:
     """
     Retrieves a protein from the API using its UUID.
 
     :param uuid: UUID of the protein to retrieve.
+    :param workflow_uuid: UUID of a workflow referencing this protein, for proteins reachable
+        only through a workflow you can read. Not needed for proteins from a workflow result.
     :returns: Protein object representing the retrieved protein.
     :raises requests.HTTPError: if the request to the API fails.
     """
+    params = {"workflow_uuid": workflow_uuid} if workflow_uuid else None
 
     with api_client() as client:
-        response = client.get(f"/protein/{uuid}")
+        response = client.get(f"/protein/{uuid}", params=params)
         response.raise_for_status()
         protein_data = response.json()
 
-    return Protein(**protein_data)
+    protein = Protein(**protein_data)
+    protein._workflow_uuid = workflow_uuid
+    return protein
 
 
 def list_proteins(

{rowan_python-3.1.9 → rowan_python-3.1.10}/rowan/workflows/__init__.py

@@ -83,6 +83,7 @@ from .interaction_energy_decomposition import (
 )
 from .ion_mobility import IonMobilityResult, submit_ion_mobility_workflow
 from .irc import IRCResult, submit_irc_workflow
+from .logp import LogPResult, submit_logp_workflow
 from .macropka import (
     MacropKaMicrostate,
     MacropKaResult,

{rowan_python-3.1.9 → rowan_python-3.1.10}/rowan/workflows/analogue_docking.py

@@ -160,7 +160,7 @@ class AnalogueDockingResult(WorkflowResult):
 
         cache_key = f"complex_{smiles}_{index}"
         if cache_key not in self._cache:
-            self._cache[cache_key] = retrieve_protein(uuid)
+            self._cache[cache_key] = retrieve_protein(uuid, workflow_uuid=self.workflow_uuid)
         return self._cache[cache_key]
 
     def get_complexes(self, smiles: str) -> list[Protein]:

{rowan_python-3.1.9 → rowan_python-3.1.10}/rowan/workflows/base.py

@@ -144,10 +144,10 @@ the server (a field is missing, extra, or the wrong type). Underlying validation
 RESULT_REGISTRY: dict[str, type[WorkflowResult]] = {}
 
 
-def register_result(workflow_type: str) -> Callable[[type[WorkflowResult]], type[WorkflowResult]]:
+def register_result[R: WorkflowResult](workflow_type: str) -> Callable[[type[R]], type[R]]:
     """Decorator to register a result class for a workflow type."""
 
-    def decorator(cls: type[WorkflowResult]) -> type[WorkflowResult]:
+    def decorator(cls: type[R]) -> type[R]:
         RESULT_REGISTRY[workflow_type] = cls
         return cls
 

{rowan_python-3.1.9 → rowan_python-3.1.10}/rowan/workflows/docking.py

@@ -133,7 +133,7 @@ class DockingResult(WorkflowResult):
 
         cache_key = f"complex_{index}"
         if cache_key not in self._cache:
-            self._cache[cache_key] = retrieve_protein(uuid)
+            self._cache[cache_key] = retrieve_protein(uuid, workflow_uuid=self.workflow_uuid)
         return self._cache[cache_key]
 
     def get_complexes(self) -> list[Protein]:

rowan_python-3.1.10/rowan/workflows/logp.py

@@ -0,0 +1,80 @@
+"""logP workflow - predict the octanol/water partition coefficient."""
+
+from typing import Literal
+
+import stjames
+
+from ..folder import Folder
+from ..utils import api_client
+from .base import SMILES, Workflow, WorkflowResult, extract_smiles, register_result
+
+
+@register_result("logp")
+class LogPResult(WorkflowResult):
+    """Result from a logP workflow."""
+
+    _stjames_class = stjames.LogPWorkflow
+
+    def __repr__(self) -> str:
+        return f"<LogPResult logp={self.logp}>"
+
+    @property
+    def logp(self) -> float | None:
+        """Predicted octanol/water partition coefficient."""
+        return self._workflow.logp
+
+
+def submit_logp_workflow(
+    initial_smiles: SMILES,
+    method: Literal["chemprop_sangster2026", "crippen", "cosmors"] = "chemprop_sangster2026",
+    name: str = "LogP Workflow",
+    folder_uuid: str | None = None,
+    folder: Folder | None = None,
+    max_credits: int | None = None,
+    webhook_url: str | None = None,
+    is_draft: bool = False,
+) -> Workflow:
+    """
+    Submits a logP workflow to the API.
+
+    :param initial_smiles: Molecule to predict logP for. Accepts a SMILES string or any
+        molecule type (RowanMolecule, stjames.Molecule, RDKit Mol, or dict). The molecule
+        must have a SMILES string associated with it, as this workflow is SMILES-based and
+        does not use 3D coordinates.
+    :param method: logP prediction method:
+        - "chemprop_sangster2026": chemprop v2 D-MPNN trained on experimental octanol/water
+          logP from the Sangster dataset.
+        - "crippen": RDKit implementation of the Wildman-Crippen atom-contribution model.
+        - "cosmors": Boltzmann-weighted COSMO-RS logP over a conformer ensemble.
+    :param name: Name of the workflow.
+    :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.
+    :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 the molecule has no SMILES associated with it.
+    :raises requests.HTTPError: if the request to the API fails.
+    """
+    if folder and folder_uuid:
+        raise ValueError("Provide either `folder` or `folder_uuid`, not both.")
+    if folder:
+        folder_uuid = folder.uuid
+    initial_smiles = extract_smiles(initial_smiles)
+    workflow = stjames.LogPWorkflow(initial_smiles=initial_smiles, logp_method=method)
+
+    data = {
+        "workflow_type": "logp",
+        "workflow_data": workflow.model_dump(mode="json"),
+        "initial_smiles": initial_smiles,
+        "name": name,
+        "folder_uuid": folder_uuid,
+        "max_credits": max_credits,
+        "webhook_url": webhook_url,
+        "is_draft": is_draft,
+    }
+
+    with api_client() as client:
+        response = client.post("/workflow", json=data)
+        response.raise_for_status()
+        return Workflow(**response.json())

{rowan_python-3.1.9 → rowan_python-3.1.10}/rowan/workflows/pose_analysis_md.py

@@ -62,7 +62,7 @@ class PoseAnalysisMDResult(WorkflowResult):
         return [
             TrajectoryResult(
                 uuid=t.uuid,
-                ligand_rmsd=t.ligand_rmsd,
+                ligand_rmsd=t.binder_rmsd,
                 contacts=t.contacts,
                 sasa=t.sasa,
                 polar_sasa=t.polar_sasa,
@@ -104,7 +104,9 @@ class PoseAnalysisMDResult(WorkflowResult):
         if not (uuid := self.minimized_protein_uuid):
             return None
         if "minimized_protein" not in self._cache:
-            self._cache["minimized_protein"] = retrieve_protein(uuid)
+            self._cache["minimized_protein"] = retrieve_protein(
+                uuid, workflow_uuid=self.workflow_uuid
+            )
         return self._cache["minimized_protein"]
 
     @property

{rowan_python-3.1.9 → rowan_python-3.1.10}/rowan/workflows/protein_cofolding.py

@@ -165,7 +165,9 @@ class ProteinCofoldingResult(WorkflowResult):
         if not (uuid := self.predicted_structure_uuid):
             return None
         if "predicted_structure" not in self._cache:
-            self._cache["predicted_structure"] = retrieve_protein(uuid)
+            self._cache["predicted_structure"] = retrieve_protein(
+                uuid, workflow_uuid=self.workflow_uuid
+            )
         return self._cache["predicted_structure"]
 
     def get_refined_structure(self) -> Protein | None:
@@ -178,7 +180,9 @@ class ProteinCofoldingResult(WorkflowResult):
         if not (uuid := self.predicted_refined_structure_uuid):
             return None
         if "refined_structure" not in self._cache:
-            self._cache["refined_structure"] = retrieve_protein(uuid)
+            self._cache["refined_structure"] = retrieve_protein(
+                uuid, workflow_uuid=self.workflow_uuid
+            )
         return self._cache["refined_structure"]
 
     @property

{rowan_python-3.1.9 → rowan_python-3.1.10}/rowan/workflows/protein_md.py

@@ -4,7 +4,7 @@ from dataclasses import dataclass
 from pathlib import Path
 
 import stjames
-from stjames import GreedyClusteringSettings, KMeansClusteringSettings
+from stjames import Binder, GreedyClusteringSettings, KMeansClusteringSettings
 
 from ..folder import Folder
 from ..protein import Protein, retrieve_protein
@@ -87,7 +87,9 @@ class ProteinMDResult(WorkflowResult):
         if not (uuid := self.minimized_protein_uuid):
             return None
         if "minimized_protein" not in self._cache:
-            self._cache["minimized_protein"] = retrieve_protein(uuid)
+            self._cache["minimized_protein"] = retrieve_protein(
+                uuid, workflow_uuid=self.workflow_uuid
+            )
         return self._cache["minimized_protein"]
 
     @property
@@ -171,6 +173,10 @@ def submit_protein_md_workflow(
     ionic_strength_M: float = 0.0,
     water_buffer: float = 10.0,
     save_solvent: bool = False,
+    num_solvent_to_save: int | None = None,
+    binder: Binder | None = None,
+    protein_restraint_cutoff: float | None = None,
+    protein_restraint_constant: float = 100,
     analysis_interval_ps: float | None = None,
     clustering: KMeansClusteringSettings | GreedyClusteringSettings | None = None,
     validate_forcefield: bool = True,
@@ -198,13 +204,26 @@ def submit_protein_md_workflow(
     :param ionic_strength_M: ionic strength of the solution, in M (molar)
     :param water_buffer: amount of water to add around the protein, in A
     :param save_solvent: whether solvent should be saved
+    :param num_solvent_to_save: keep this many solvent molecules nearest the binder, or all if None;
+        only meaningful when save_solvent is True and a binder is present
+    :param binder: optional binder specification (protein chains and/or small molecules).
+        When set, per-frame MM/GBSA scores are computed against the whole binder.
+        Per-frame binder RMSD is populated only when the binder is a single component
+        (one small molecule → heavy-atom RMSD; one binder chain → backbone N/CA/C/O RMSD);
+        it is empty for multi-molecule, multi-chain, or combined chain+molecule binders.
+    :param protein_restraint_cutoff: cutoff distance from the binder past which Cα atoms are
+        harmonically restrained, in Å; None disables restraints
+    :param protein_restraint_constant: force constant for Cα backbone restraints, in kcal/mol/Ų
     :param analysis_interval_ps: Interval at which to compute per-frame SASA and polar SASA, in ps.
         None disables those analyses.
     :param clustering: How to cluster trajectory frames. None disables clustering; pass a
         KMeansClusteringSettings (num_clusters) or GreedyClusteringSettings (cutoff_angstrom).
     :param validate_forcefield: if True (default), validate the protein forcefield
         compatibility before submitting. Raises an error early if the protein cannot
-        be parameterized or has clashing residues.
+        be parameterized or has clashing residues. Binder small molecules are skipped,
+        whether given by residue name or by index, since they are parameterized from their
+        SMILES rather than the protein forcefield; cofactors, metals, and glycans outside
+        the binder are still validated.
     :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.
@@ -222,7 +241,10 @@ def submit_protein_md_workflow(
         protein = protein.uuid
 
     if validate_forcefield:
-        Protein(uuid=protein).validate_protein_forcefield()
+        exclude_residues = (
+            list(binder.small_molecules) if binder is not None and binder.small_molecules else None
+        )
+        Protein(uuid=protein).validate_protein_forcefield(exclude_residues=exclude_residues)
 
     workflow = stjames.ProteinMolecularDynamicsWorkflow(
         protein=protein,
@@ -238,6 +260,10 @@ def submit_protein_md_workflow(
         ionic_strength_M=ionic_strength_M,
         water_buffer=water_buffer,
         save_solvent=save_solvent,
+        num_solvent_to_save=num_solvent_to_save,
+        binder=binder,
+        protein_restraint_cutoff=protein_restraint_cutoff,
+        protein_restraint_constant=protein_restraint_constant,
         analysis_interval_ps=analysis_interval_ps,
         clustering=clustering,
     )

{rowan_python-3.1.9 → rowan_python-3.1.10}/rowan/workflows/relative_binding_free_energy_perturbation.py

@@ -90,7 +90,9 @@ class RelativeBindingFreeEnergyPerturbationResult(WorkflowResult):
     @property
     def protein(self) -> Protein:
         """Prepared protein structure used as the simulation target."""
-        return Protein(uuid=str(self._workflow.protein))
+        protein = Protein(uuid=str(self._workflow.protein))
+        protein._workflow_uuid = self.workflow_uuid
+        return protein
 
     @property
     def settings(self) -> TMDRBFESettings: