rowan-python 3.1.1__py3-none-any.whl → 3.1.3__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/molecule.py

@@ -280,7 +280,8 @@ def load_named_ligands(path: Path | str) -> dict[str, Molecule]:
     Molecule names are read from the title field of each record. Use this when
     ligand identity needs to be preserved - for example, building a ligand dict
     for an RBFE workflow where names are used as keys throughout submission and
-    results.
+    results. Every record must therefore have a unique name; duplicates raise
+    rather than silently collapsing into one ligand.
 
     Supported formats (all carry per-molecule name fields):
     - SDF / MOL (``.sdf``, ``.mol``) - name from the title line
@@ -288,7 +289,8 @@ def load_named_ligands(path: Path | str) -> dict[str, Molecule]:
 
     :param path: Path to an SDF, MOL, or MOL2 file.
     :returns: Dict mapping ligand name to Molecule, in file order.
-    :raises ValueError: If no valid molecules are found or the format is unsupported.
+    :raises ValueError: If no valid molecules are found, the format is
+        unsupported, or two records share a name.
     """
     path = Path(path)
     suffix = path.suffix.lower()
@@ -311,4 +313,13 @@ def load_named_ligands(path: Path | str) -> dict[str, Molecule]:
     if not pairs:
         raise ValueError(f"No valid molecules found in {path}")
 
+    # require every record to have a unique name rather than dropping data
+    names = [name for name, _ in pairs]
+    duplicates = sorted({name for name in names if names.count(name) > 1})
+    if duplicates:
+        raise ValueError(
+            f"Ligand names must be unique, but {path} repeats: {', '.join(duplicates)}. "
+            "Rename the duplicate records before loading."
+        )
+
     return {name: Molecule(_stjames=stjames.Molecule.from_rdkit(rdkm)) for name, rdkm in pairs}

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-3.1.1.dist-info → rowan_python-3.1.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rowan-python
-Version: 3.1.1
+Version: 3.1.3
 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

{rowan_python-3.1.1.dist-info → rowan_python-3.1.3.dist-info}/RECORD

@@ -1,10 +1,10 @@
-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
 rowan/constants.py,sha256=emCH4m9OL2Hm5E-6mJGM_FgzrK_JrZT-FiKJ6pMNQ4Y,84
 rowan/folder.py,sha256=eyKdZjHR-LsNK0yS8iedb0vPi3OB10gluuA1-Ee_JCg,9202
-rowan/molecule.py,sha256=AcH13oKxfysQ5y44bxucUVlUdV1BTT6vwjBANP-waVo,10296
+rowan/molecule.py,sha256=LyneBgSbNS7ByQ2sI8hcRLOXwljZMZQtALgAYcqX2tM,10844
 rowan/project.py,sha256=RtxYE9jv3Yz6fH5I56iDGRG5EbwlOHiSK-HF1uxc0d4,4582
 rowan/protein.py,sha256=hfDqk_LgU8o39Zg2kHHWf8EqPcQOnT3Mo43Ik1gAO68,14856
 rowan/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -40,16 +40,16 @@ rowan/workflows/pose_analysis_md.py,sha256=XJIfvn-H7GA6lVtw9uKjlgznVSSsr9bJiDt_P
 rowan/workflows/protein_binder_design.py,sha256=pgywTQDuXHplZYka-61_S6CC4WTPDCwJrbupp825eC4,9281
 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-3.1.1.dist-info/METADATA,sha256=BJ6RevJYUsM7A5ivp7ahR7S9CUG91fcVqRJXEFP89QM,2052
-rowan_python-3.1.1.dist-info/WHEEL,sha256=mffPy8wBnZQn2VnJUU5jE99KsxaSfiyMHV9Yt0aLVxs,87
-rowan_python-3.1.1.dist-info/licenses/LICENSE,sha256=i05z7xEhyrg6f8j0lR3XYjShnF-MJGFQ-DnpsZ8yiVI,1084
-rowan_python-3.1.1.dist-info/RECORD,,
+rowan_python-3.1.3.dist-info/METADATA,sha256=mv9y4fxN9Ds7WCnd2W-vZL-LdLCNkp_1XxWipE5Q2Yg,2052
+rowan_python-3.1.3.dist-info/WHEEL,sha256=mffPy8wBnZQn2VnJUU5jE99KsxaSfiyMHV9Yt0aLVxs,87
+rowan_python-3.1.3.dist-info/licenses/LICENSE,sha256=i05z7xEhyrg6f8j0lR3XYjShnF-MJGFQ-DnpsZ8yiVI,1084
+rowan_python-3.1.3.dist-info/RECORD,,