rowan-python 3.1.4__py3-none-any.whl → 3.1.5__py3-none-any.whl

rowan/__init__.py

@@ -2,7 +2,10 @@
 from . import constants
 from stjames import (
     Atom,
+    BandStructure,
     BindingPoseContact,
+    HydrationBridgeResidue,
+    HydrationSite,
     ConformerGenSettings,
     Constraint,
     ConstraintType,
@@ -27,6 +30,7 @@ from stjames import (
     Settings,
     Solvent,
     SolventSettings,
+    SinglePointEnergySettings,
     Task,
     VibrationalMode,
 )

rowan/molecule.py

@@ -237,6 +237,50 @@ class Molecule(BaseModel):
         """Nuclear gradient (Hartree/Bohr)."""
         return self._stjames.gradient
 
+    @property
+    def symmetry(self) -> str | int | None:
+        """Space group number (1–230) or point group symbol."""
+        return self._stjames.symmetry
+
+    @property
+    def xrd_peaks(self) -> list[tuple[int, int, int, float]] | None:
+        """XRD reflections as (h, k, l, intensity) tuples."""
+        return self._stjames.x_ray_diffraction_peaks
+
+    @property
+    def band_structure(self) -> "stjames.BandStructure | None":
+        """Electronic band structure and DOS (periodic systems only)."""
+        return self._stjames.band_structure
+
+    @property
+    def band_gap(self) -> float | None:
+        """Band gap (Hartree)."""
+        bs = self._stjames.band_structure
+        return bs.band_gap if bs is not None else None
+
+    @property
+    def density_of_states(self) -> list[tuple[float, float]] | None:
+        """Total DOS as (energy in Hartree, k-weighted count) pairs (Fermi level = 0)."""
+        bs = self._stjames.band_structure
+        return bs.total_density_of_states if bs is not None else None
+
+    @property
+    def elastic_tensor(
+        self,
+    ) -> (
+        tuple[
+            tuple[float, float, float, float, float, float],
+            tuple[float, float, float, float, float, float],
+            tuple[float, float, float, float, float, float],
+            tuple[float, float, float, float, float, float],
+            tuple[float, float, float, float, float, float],
+            tuple[float, float, float, float, float, float],
+        ]
+        | None
+    ):
+        """Elastic stiffness matrix in GPa (Voigt order: xx yy zz yz xz xy)."""
+        return self._stjames.elastic_tensor
+
     # -- Geometric utilities --
 
     def distance(self, i: int, j: int) -> float:

rowan/workflows/__init__.py

@@ -47,6 +47,11 @@ from .bde import (
     find_cx_bonds,
     submit_bde_workflow,
 )
+from .binding_affinity import (
+    BindingAffinityResult,
+    BindingAffinityScore,
+    submit_binding_affinity_workflow,
+)
 from .conformer_search import ConformerSearchResult, submit_conformer_search_workflow
 from .descriptors import DescriptorsResult, submit_descriptors_workflow
 from .docking import DockingResult, DockingScore, submit_docking_workflow

rowan/workflows/basic_calculation.py

@@ -136,6 +136,54 @@ class BasicCalculationResult(WorkflowResult):
         mol = self.molecule
         return mol.frequencies if mol else None
 
+    @property
+    def symmetry(self) -> str | int | None:
+        """Space group number (1–230) or point group symbol."""
+        mol = self.molecule
+        return mol.symmetry if mol else None
+
+    @property
+    def xrd_peaks(self) -> list[tuple[int, int, int, float]] | None:
+        """XRD reflections as (h, k, l, intensity) tuples."""
+        mol = self.molecule
+        return mol.xrd_peaks if mol else None
+
+    @property
+    def band_structure(self) -> stjames.BandStructure | None:
+        """Electronic band structure and DOS (periodic systems only)."""
+        mol = self.molecule
+        return mol.band_structure if mol else None
+
+    @property
+    def band_gap(self) -> float | None:
+        """Band gap (Hartree)."""
+        mol = self.molecule
+        return mol.band_gap if mol else None
+
+    @property
+    def density_of_states(self) -> list[tuple[float, float]] | None:
+        """Total DOS as (energy in Hartree, k-weighted count) pairs (Fermi level = 0)."""
+        mol = self.molecule
+        return mol.density_of_states if mol else None
+
+    @property
+    def elastic_tensor(
+        self,
+    ) -> (
+        tuple[
+            tuple[float, float, float, float, float, float],
+            tuple[float, float, float, float, float, float],
+            tuple[float, float, float, float, float, float],
+            tuple[float, float, float, float, float, float],
+            tuple[float, float, float, float, float, float],
+            tuple[float, float, float, float, float, float],
+        ]
+        | None
+    ):
+        """Elastic stiffness matrix in GPa (Voigt order: xx yy zz yz xz xy)."""
+        mol = self.molecule
+        return mol.elastic_tensor if mol else None
+
 
 def settings_from_preset(preset: PresetName, **overrides: Any) -> stjames.Settings:
     """

rowan/workflows/binding_affinity.py

@@ -0,0 +1,140 @@
+"""Binding affinity workflow — SQM-based scoring of protein–ligand complexes."""
+
+from dataclasses import dataclass
+
+import stjames
+from stjames import SinglePointEnergySettings
+
+from ..folder import Folder
+from ..protein import Protein
+from ..types import StructureInput
+from ..utils import api_client
+from .base import (
+    Message,
+    Workflow,
+    WorkflowResult,
+    molecule_to_dict,
+    parse_messages,
+    register_result,
+    require_coordinates,
+)
+
+
+@dataclass(frozen=True, slots=True)
+class BindingAffinityScore:
+    """
+    Binding affinity score for a single pose.
+
+    :param binding_affinity: binding affinity in kcal/mol
+    :param strain: strain energy in kcal/mol, or None if not computed
+    """
+
+    binding_affinity: float
+    strain: float | None
+
+
+@register_result("binding_affinity")
+class BindingAffinityResult(WorkflowResult):
+    """Result from a binding affinity workflow."""
+
+    _stjames_class = stjames.BindingAffinityWorkflow
+
+    def __repr__(self) -> str:
+        n = len(self.scores)
+        return f"<BindingAffinityResult scores={n}>"
+
+    @property
+    def scores(self) -> list[BindingAffinityScore]:
+        """Binding affinity scores for each scored pose."""
+        return [
+            BindingAffinityScore(
+                binding_affinity=r.binding_affinity,
+                strain=r.strain,
+            )
+            for r in (self._workflow.binding_affinity_results or [])
+        ]
+
+    @property
+    def messages(self) -> list[Message]:
+        """Any messages or warnings from the workflow."""
+        return parse_messages(self._workflow.messages)
+
+
+def submit_binding_affinity_workflow(
+    protein: str | Protein,
+    ligand_residue_name: str | None = None,
+    ligand_structures: list[StructureInput] | None = None,
+    binding_affinity_settings: SinglePointEnergySettings | None = None,
+    name: str = "Binding Affinity 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 binding affinity workflow to the API.
+
+    Scores ligand poses using SQM-based energies. Two submission modes:
+
+    **Mode 1 — holo protein:** protein already contains the bound ligand. Pass
+    ``ligand_residue_name`` to identify which residue is the ligand vs. the receptor.
+    Do not pass ``ligand_structures``.
+
+    **Mode 2 — apo protein + external poses:** protein has no bound ligand. Pass
+    ``ligand_structures`` with poses that are already in the protein's coordinate frame.
+    Do not pass ``ligand_residue_name``. When scoring multiple ligands, prefer this mode
+    over separate per-ligand workflows — all poses share the same pocket geometry.
+
+    :param protein: protein structure. Can be input as a UUID or a Protein object.
+    :param ligand_residue_name: residue name identifying the ligand in a holo protein PDB
+        (mode 1 only).
+    :param ligand_structures: external ligand poses to score, already in the protein's
+        coordinate frame. Must have 3D coordinates (mode 2 only).
+    :param binding_affinity_settings: SQM settings controlling geometry optimization and
+        energy evaluation. Defaults to PM6-D3H4X/COSMO optimization followed by
+        PM6-D3H4X/COSMO2 single-point in water.
+    :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.
+    :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 folder arguments conflict.
+    :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
+    if isinstance(protein, Protein):
+        protein = protein.uuid
+
+    mol_dicts: list[dict] = []
+    if ligand_structures:
+        for mol in ligand_structures:
+            require_coordinates(mol)
+            mol_dicts.append(molecule_to_dict(mol))
+
+    workflow = stjames.BindingAffinityWorkflow(
+        protein=protein,
+        ligand_residue_name=ligand_residue_name,
+        ligand_structures=mol_dicts or [],
+        binding_affinity_settings=binding_affinity_settings or SinglePointEnergySettings(),
+    )
+
+    data = {
+        "workflow_type": "binding_affinity",
+        "workflow_data": workflow.model_dump(serialize_as_any=True, mode="json"),
+        "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/workflows/pose_analysis_md.py

@@ -73,6 +73,11 @@ class PoseAnalysisMDResult(WorkflowResult):
             for t in raw
         ]
 
+    @property
+    def hydration_sites(self) -> list[stjames.HydrationSite]:
+        """Hydration sites identified across all trajectories."""
+        return self._workflow.hydration_sites or []
+
     @property
     def average_rmsds(self) -> list[float | None]:
         """Average ligand RMSD per trajectory (Angstrom)."""

rowan/workflows/rbfe_graph.py

@@ -97,6 +97,9 @@ def submit_relative_binding_free_energy_graph_workflow(
     greedy_k_min_cut: int = 3,
     refine_cutoff: float | None = None,
     seed_graph: RBFEGraph | None = None,
+    generate_intermediate_ligands: bool = False,
+    intermediate_max_dummy_atoms: int = 25,
+    intermediate_min_dummy_atom_improvement: int = 5,
     name: str = "RBFE Graph",
     folder_uuid: str | None = None,
     folder: Folder | None = None,
@@ -120,6 +123,12 @@ def submit_relative_binding_free_energy_graph_workflow(
     :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 generate_intermediate_ligands: Generate virtual intermediate ligands to make
+        difficult edges easier.
+    :param intermediate_max_dummy_atoms: An edge with more dummy atoms than this is split
+        when a generated intermediate brings both resulting legs back to at most this value.
+    :param intermediate_min_dummy_atom_improvement: Minimum reduction in the worst leg's
+        dummy-atom count required for a generated intermediate to be accepted.
     :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.
@@ -169,6 +178,9 @@ def submit_relative_binding_free_energy_graph_workflow(
         greedy_k_min_cut=greedy_k_min_cut,
         refine_cutoff=refine_cutoff,
         seed_graph=seed_graph,
+        generate_intermediate_ligands=generate_intermediate_ligands,
+        intermediate_max_dummy_atoms=intermediate_max_dummy_atoms,
+        intermediate_min_dummy_atom_improvement=intermediate_min_dummy_atom_improvement,
     )
 
     data = {

{rowan_python-3.1.4.dist-info → rowan_python-3.1.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rowan-python
-Version: 3.1.4
+Version: 3.1.5
 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>=0.0.208
+Requires-Dist: stjames>=0.0.217
 Description-Content-Type: text/markdown
 
 # Rowan Python Library

{rowan_python-3.1.4.dist-info → rowan_python-3.1.5.dist-info}/RECORD

@@ -1,23 +1,24 @@
-rowan/__init__.py,sha256=AfjV9IsjgykiU39Eh9vjUP_3at-OSqqhSgNhPxutma0,1456
+rowan/__init__.py,sha256=ui5-72WoXjhvvKU3XqOZAvaz-BXkDT13z1m62fISsvg,1553
 rowan/api_keys.py,sha256=TvG5l5MmQ3Qt8Z3Y7jCA_lcrwEHuI7xHy-KLbIdQ8_A,4793
 rowan/calculation.py,sha256=nuUtLTtn9D-FCM9TJl3h5euBgIYqa5fr5r_PSNBS7Xo,3809
 rowan/config.py,sha256=TejQKSxnzNKKTNL9-2bCLq6RvAh54oVA5Ivl1p_ZT8Q,20899
 rowan/constants.py,sha256=emCH4m9OL2Hm5E-6mJGM_FgzrK_JrZT-FiKJ6pMNQ4Y,84
 rowan/folder.py,sha256=RRg68dObluJ2RCTKX3rb7RxziOXOQUYxkfQSU2R5VMk,13708
-rowan/molecule.py,sha256=W6eBuIQAjZs5JiQFmyRnbcbj2Qy2XbZnm_J0WuMslG4,13881
+rowan/molecule.py,sha256=1l-3YCN_A75Uz_Q-dMWuhkeF8rhD1z2JQM7AENyjKYM,15512
 rowan/project.py,sha256=RtxYE9jv3Yz6fH5I56iDGRG5EbwlOHiSK-HF1uxc0d4,4582
 rowan/protein.py,sha256=T2JAqfncP80yV5gEWYA-TlpNY3WeWaNHPE0Xg5voU24,17968
 rowan/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 rowan/types.py,sha256=MvcYvEYr6N9RXLal44MqsnMxoWfcBa-VLD_rGsW4HOc,591
 rowan/user.py,sha256=rOCYVhSoRY71fCG_OCSD7cLAWWnAMANWGitF3ogfq30,6212
 rowan/utils.py,sha256=DBphY1he8Vl3RNf6CbLp5BSX9RG5EfHzhMs-9TmcE_g,4299
-rowan/workflows/__init__.py,sha256=ohl2q-Nqgs4E9cl5KIGigQgE2ifiTmY5dib5R_qNxO4,4510
+rowan/workflows/__init__.py,sha256=qQZrfkB0f8B82WyNP6a9YeP6I3Cmfans9HvqD2amw28,4635
 rowan/workflows/admet.py,sha256=jDx1Kkgmp0XaeojPzaCFY_yUwvqtSM7Cezps-93cqPw,2865
 rowan/workflows/analogue_docking.py,sha256=IxVaYD8ITsLFfvZ6N7v4KmvIS25DcUQkv-_tMhEfG_4,9707
 rowan/workflows/base.py,sha256=k858otXLuorw4MZ1hvqZI_m0n_38htC7Hy3OMCX1TOA,32961
-rowan/workflows/basic_calculation.py,sha256=CnAnbRYrnjbxgcPAZxPUARUjaqPCnAAjf-RFku8R1r0,11240
+rowan/workflows/basic_calculation.py,sha256=EovymT6fV6mxmt4G4kRtiskSPGB7w7KAHqBaGtgQI2Q,12941
 rowan/workflows/batch_docking.py,sha256=ePnb1hcsmnUfffl1-k9HNkOC09RjY9bZS9XcqAGNeFs,3621
 rowan/workflows/bde.py,sha256=1ieYUeu-5Lg637eSjhbRr_6qSIiIcjhsLOzaA4zbg3o,6681
+rowan/workflows/binding_affinity.py,sha256=Pengz5gmhYvRd3P6yTe1p7nLZnDENp_gwDJo2q5kiEg,5089
 rowan/workflows/conformer_search.py,sha256=9_DpRfmeNWIVm68Y95zcHCK5Q0yt9le6W70rMeIQndY,15467
 rowan/workflows/constants.py,sha256=el8jWE9gnGTLNWn5_n_V0H362vIRneOqgy7BOQ8CScg,575
 rowan/workflows/descriptors.py,sha256=QjjpzPDpAO_EhPOK--gle6sGpVHMpdAs_yrvC0oiseY,3092
@@ -36,11 +37,11 @@ rowan/workflows/multistage_optimization.py,sha256=04kZPC3SmVOxqEQOwyBrS3DlelM-b8
 rowan/workflows/nmr.py,sha256=68be_Xgiy1AykGdIL4fR1pqKllD1nLm3IidsStzKtz4,5521
 rowan/workflows/pka.py,sha256=NZ-3i-cH_b7YOHj2iq0roXEcZmC8SYapmzMOX6ObRqw,8546
 rowan/workflows/pocket_detection.py,sha256=aGHY0puxekp4c4nsNYHcvKCe1fsetygL04BcSvNFvE8,3864
-rowan/workflows/pose_analysis_md.py,sha256=XJIfvn-H7GA6lVtw9uKjlgznVSSsr9bJiDt_PjKlPbA,11572
+rowan/workflows/pose_analysis_md.py,sha256=5TRsCBFD0QObE5tpmCOxi137xsKMfQrRO6ef8TLrnkk,11767
 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=zqKEtL514uchgbxsyO4vhokzTU-X4lTFA1BM5O8HvTU,10117
-rowan/workflows/rbfe_graph.py,sha256=7UJA3ZBbvtaB9l1KQi9279Pc89moVnBHO-XJpxEr5uQ,7238
+rowan/workflows/rbfe_graph.py,sha256=0eMfvwtQhyajUC8T-bhdcYNKi6Pkja6x6dHjCnEwxPw,8081
 rowan/workflows/redox_potential.py,sha256=bBeT1K9XGVpjCFZeeuv7Vtr3EYHN2okJ4LqYc3gMV04,5427
 rowan/workflows/relative_binding_free_energy_perturbation.py,sha256=vi5Qj5aDAERtjcHDsgzI6vRV_BZJnJ8boOj5aG6GXzo,13817
 rowan/workflows/scan.py,sha256=R5Y6Md3ohPoFVJ4NYvx3_k3JNwMnVw1CDsNPD9S8sr4,7518
@@ -49,7 +50,7 @@ rowan/workflows/solvent_dependent_conformers.py,sha256=Z2xESmcM8WcTsR2TSTUa--Rrh
 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-3.1.4.dist-info/METADATA,sha256=qogpVoI_aoX_24Z2diW8JdOR2sphEYp-HuLtTFvvN-w,2052
-rowan_python-3.1.4.dist-info/WHEEL,sha256=mffPy8wBnZQn2VnJUU5jE99KsxaSfiyMHV9Yt0aLVxs,87
-rowan_python-3.1.4.dist-info/licenses/LICENSE,sha256=i05z7xEhyrg6f8j0lR3XYjShnF-MJGFQ-DnpsZ8yiVI,1084
-rowan_python-3.1.4.dist-info/RECORD,,
+rowan_python-3.1.5.dist-info/METADATA,sha256=g-Ttz5kgCuMcbHCBKoHlsBOJJLEvEdcTtornkx9eIQA,2052
+rowan_python-3.1.5.dist-info/WHEEL,sha256=mffPy8wBnZQn2VnJUU5jE99KsxaSfiyMHV9Yt0aLVxs,87
+rowan_python-3.1.5.dist-info/licenses/LICENSE,sha256=i05z7xEhyrg6f8j0lR3XYjShnF-MJGFQ-DnpsZ8yiVI,1084
+rowan_python-3.1.5.dist-info/RECORD,,