rowan-python 3.0.9__py3-none-any.whl → 3.0.11__py3-none-any.whl

rowan/__init__.py

@@ -12,6 +12,7 @@ from stjames import (
     Method,
     Mode,
     MultiStageOptSettings,
+    OpenConfSettings,
     OptimizationSettings,
     PBCDFTSettings,
     PeriodicCell,

rowan/workflows/batch_docking.py

@@ -52,7 +52,7 @@ def submit_batch_docking_workflow(
 
     :param smiles_list: SMILES strings to dock.
     :param protein: Protein to dock (UUID or Protein object).
-    :param pocket: Binding pocket coordinates [[x,y,z], [x,y,z]].
+    :param pocket: Binding pocket as ``[[cx, cy, cz], [sx, sy, sz]]`` — center (Å) and box size (Å).
     :param executable: Which docking implementation to use.
     :param scoring_function: Which docking scoring function to use.
     :param exhaustiveness: Docking exhaustiveness parameter.

rowan/workflows/docking.py

@@ -151,7 +151,7 @@ def submit_docking_workflow(
     Submits a docking workflow to the API.
 
     :param protein: Protein to dock. Can be input as a uuid or a Protein object.
-    :param pocket: Binding pocket coordinates [[x,y,z], [x,y,z]].
+    :param pocket: Binding pocket as ``[[cx, cy, cz], [sx, sy, sz]]`` — center (Å) and box size (Å).
     :param initial_molecule: Initial molecule to be docked.
     :param executable: Which docking implementation to use.
     :param scoring_function: Which docking scoring function to use.

rowan/workflows/protein_binder_design.py

@@ -101,7 +101,8 @@ class ProteinBinderDesignResult(WorkflowResult):
         """Generated protein binder designs, sorted by quality score."""
         binders: list[ProteinBinder] = []
         for b in self._workflow.generated_binders:
-            scores_dict = getattr(b, "scores", None) or {}
+            raw_scores = getattr(b, "scores", None)
+            scores_dict = raw_scores.model_dump() if raw_scores is not None else {}
             scores = BinderScores(
                 iptm=scores_dict.get("iptm"),
                 design_ptm=scores_dict.get("design_ptm"),

rowan/workflows/strain.py

@@ -129,8 +129,8 @@ def submit_strain_workflow(
     :param harmonic_constraint_spring_constant: Spring constant for harmonic
         constraints (kcal/mol/A). Default 5.0.
     :param constrain_hydrogens: Whether to constrain hydrogen positions. Default False.
-    :param conf_gen_settings: Conformer generation settings. Defaults to RDKit
-        ETKDG with max 200 conformers (no solvent).
+    :param conf_gen_settings: Conformer generation settings. Defaults to
+        OpenConf with max 200 conformers.
     :param multistage_opt_settings: Optimization settings for conformer ranking.
         Defaults to GFN2-xTB optimization in water (ALPB) with a g-xTB singlepoint
         in water (CPCMx).
@@ -153,7 +153,7 @@ def submit_strain_workflow(
         "initial_molecule": initial_molecule,
         "harmonic_constraint_spring_constant": harmonic_constraint_spring_constant,
         "constrain_hydrogens": constrain_hydrogens,
-        "conf_gen_settings": conf_gen_settings or stjames.ETKDGSettings(max_confs=200),
+        "conf_gen_settings": conf_gen_settings or stjames.OpenConfSettings(max_confs=200),
     }
     if multistage_opt_settings is not None:
         workflow_kwargs["multistage_opt_settings"] = multistage_opt_settings

rowan/workflows/tautomer_search.py

@@ -11,7 +11,6 @@ from ..molecule import Molecule
 from ..utils import api_client
 from .base import (
     Message,
-    Mode,
     MoleculeInput,
     Workflow,
     WorkflowResult,
@@ -105,7 +104,6 @@ class TautomerResult(WorkflowResult):
 
 def submit_tautomer_search_workflow(
     initial_molecule: MoleculeInput,
-    mode: Mode = Mode.CAREFUL,
     conf_gen_settings: stjames.ConformerGenSettingsUnion | None = None,
     multistage_opt_settings: stjames.MultiStageOptSettings | None = None,
     name: str = "Tautomer Search Workflow",
@@ -119,11 +117,11 @@ def submit_tautomer_search_workflow(
     Submits a tautomer-search workflow to the API.
 
     :param initial_molecule: Molecule to find tautomers for.
-    :param mode: *Deprecated.*
     :param conf_gen_settings: Conformer generation settings. Defaults to ETKDG with
         250 initial conformers, 20 max conformers, and 15 kcal/mol MMFF energy cutoff.
-    :param multistage_opt_settings: Optimization settings for tautomer ranking.
-        Defaults to AIMNet2/wB97M-D3 optimization with CPCMx singlepoint.
+    :param multistage_opt_settings: Optimization stages and singlepoint settings
+        describing the method stack. Defaults to AIMNet2/wB97M-D3 optimization with
+        CPCMx(water) singlepoint.
     :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.
@@ -139,7 +137,7 @@ def submit_tautomer_search_workflow(
         folder_uuid = folder.uuid
     initial_molecule = molecule_to_dict(initial_molecule)
 
-    workflow_kwargs: dict[str, Any] = {"initial_molecule": initial_molecule, "mode": mode}
+    workflow_kwargs: dict[str, Any] = {"initial_molecule": initial_molecule}
     if conf_gen_settings is not None:
         workflow_kwargs["conf_gen_settings"] = conf_gen_settings
     if multistage_opt_settings is not None:

{rowan_python-3.0.9.dist-info → rowan_python-3.0.11.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rowan-python
-Version: 3.0.9
+Version: 3.0.11
 Summary: Rowan Python Library
 Project-URL: Homepage, https://github.com/rowansci/rowan-client
 Project-URL: Bug Tracker, https://github.com/rowansci/rowan-client/issues

{rowan_python-3.0.9.dist-info → rowan_python-3.0.11.dist-info}/RECORD

@@ -1,4 +1,4 @@
-rowan/__init__.py,sha256=wiEroKH5I6VQ-tiseUcrNGJaS_0soFnYMX0EtpwyLIs,859
+rowan/__init__.py,sha256=TiZEbNQ3amq8QDhBS6JHsQjb19ueHkpy-AgNETZEQxI,881
 rowan/api_keys.py,sha256=TvG5l5MmQ3Qt8Z3Y7jCA_lcrwEHuI7xHy-KLbIdQ8_A,4793
 rowan/calculation.py,sha256=lZZ52DxPsuJWCTzFZXjhauHK6dV0KCUwzoxtmoxSY48,3442
 rowan/config.py,sha256=3cVKHUNzkIPnN2bvx7l5sia7Zc5poXS8lKOJlowXyLA,21088
@@ -18,12 +18,12 @@ rowan/workflows/admet.py,sha256=0_wIwXXLfHF-3kgGx_1EM1ljjaYHLeEijJ-GbMYxpL8,2904
 rowan/workflows/analogue_docking.py,sha256=LJpbbaug0tZ9Cg-m0b7EgGH5hJ5894fHOC16Wefx7mE,9206
 rowan/workflows/base.py,sha256=AyV4ZBta4vz0eiOCi9mcDPTbh-30x-11lfKKwcRJdQw,30330
 rowan/workflows/basic_calculation.py,sha256=FKYczKpYaGE-koaHKi2VARmV9Nhqr0lTOx0Jv1RzC7k,10835
-rowan/workflows/batch_docking.py,sha256=u_4hH7OeWkIbXqEm4uWTc3p0u9mpnR8EWqWCw7sVya4,3581
+rowan/workflows/batch_docking.py,sha256=IRsqbYzJ_WGET9Vu_U7ffNpMthhi9Z679zkUqMVKCGo,3620
 rowan/workflows/bde.py,sha256=JJUx2wFJ8yZu0sqIn7Jkm6B6O84WrrpAstCck8c7FLI,5621
 rowan/workflows/conformer_search.py,sha256=rzarx3PKRM2rf9x1F17Jg8ZCed7_3-yEBan4g0b2HK4,9868
 rowan/workflows/constants.py,sha256=el8jWE9gnGTLNWn5_n_V0H362vIRneOqgy7BOQ8CScg,575
 rowan/workflows/descriptors.py,sha256=rGrNca6kA4SzX5BAOjP6rE91MOLTvCWSYKF_LW2Z0y4,2963
-rowan/workflows/docking.py,sha256=wmE7QJu1uDHBDynTT1XesXXAZtpB6xLjZUKsHOQyCcU,7386
+rowan/workflows/docking.py,sha256=T-_wTyuxV0DFHLJn4JDy6zJoQETPqG6lM1A2cI4YXUY,7425
 rowan/workflows/double_ended_ts_search.py,sha256=abBblMkshhbzq5UTwIf-ovNFxY8Ltp2O-bGu_plkI58,7806
 rowan/workflows/electronic_properties.py,sha256=ia4mlmgnioEuLDrcgDuxAyyI6VqRkdxBqshjb9uiEI8,8385
 rowan/workflows/fukui.py,sha256=wLimH3QmorSpvkovRPlI91VuxHG4J91F2EcLYqg3eP0,5112
@@ -39,7 +39,7 @@ rowan/workflows/nmr.py,sha256=hergJdsiawKj7iV-jHxDOS03n_EnZcaCIt_ZTl34-JY,5183
 rowan/workflows/pka.py,sha256=TCFSE5HI5JLPslKdbUvJe4IxrVaLExrI_3PnDfXtxTw,8691
 rowan/workflows/pocket_detection.py,sha256=aGHY0puxekp4c4nsNYHcvKCe1fsetygL04BcSvNFvE8,3864
 rowan/workflows/pose_analysis_md.py,sha256=UvotLhWv0_VAkKteZboOutDry7l-Zt1K6_SBx3EXqgM,9530
-rowan/workflows/protein_binder_design.py,sha256=J-9NSbRLdHb6JQRhY_vq43HlHCDCiQqrkOZUCAF-2dk,8604
+rowan/workflows/protein_binder_design.py,sha256=OW4GG1cBWzPhM-2MomSsV99ZzMiivMGZdxim9SmFPw4,8681
 rowan/workflows/protein_cofolding.py,sha256=D2PVwL51H3traml1JDG-9jU3R0E29AdfR9Bk0tLX1Zw,14093
 rowan/workflows/protein_md.py,sha256=_n0IdmTQsunbP1geF-wUjXNMKNYV-ngmAPEMJlj0dkI,7021
 rowan/workflows/rbfe_graph.py,sha256=PLqzBRkxD7tPdBViYJZjgaCP8aA2UXKc9dD4odx5XUo,5788
@@ -49,9 +49,9 @@ rowan/workflows/scan.py,sha256=KQm58utOxs6qIpX1Jv3usoUpkVHeLw4mKCs8RTUkRhk,5696
 rowan/workflows/solubility.py,sha256=9-zHEHkf4AgGNDCE3x1S-6wTgwxVm4ihRmh0kwLvPFs,8594
 rowan/workflows/solvent_dependent_conformers.py,sha256=ovvnhCE4xlkpdhccLHEq7oBJRI2-rHmZ-7_ewGECerM,7020
 rowan/workflows/spin_states.py,sha256=c0y2cwO9NE8DmxmQ9ZouA5QoBhxgZiTYFIqhC-geVAo,7382
-rowan/workflows/strain.py,sha256=tb6PGng8B4wSDl4a_MWd0P-cdlSTRpT410VgOJAqXHQ,6393
-rowan/workflows/tautomer_search.py,sha256=aqwXoj0ffWsb5gbvzfz_bpx5ifIfR_K07fbdWhU62Ko,5820
-rowan_python-3.0.9.dist-info/METADATA,sha256=IdBYpQWGOhztIvdM5El7LpplQu9kzzF46ATGkgPIJMc,1600
-rowan_python-3.0.9.dist-info/WHEEL,sha256=QccIxa26bgl1E6uMy58deGWi-0aeIkkangHcxk2kWfw,87
-rowan_python-3.0.9.dist-info/licenses/LICENSE,sha256=i05z7xEhyrg6f8j0lR3XYjShnF-MJGFQ-DnpsZ8yiVI,1084
-rowan_python-3.0.9.dist-info/RECORD,,
+rowan/workflows/strain.py,sha256=N-CoOT-hjYzjYTMYR9Uzoy4EhnrLQEOeDNSNphsUIXQ,6380
+rowan/workflows/tautomer_search.py,sha256=GB96BjvVsJDgLCTH4S4nkAlBoCvKud_18Y3PTY9Q528,5779
+rowan_python-3.0.11.dist-info/METADATA,sha256=YvbKSL7wGaXuiFFHhnXUEvUvLj0G6Dx-HXOY5kw8X3I,1601
+rowan_python-3.0.11.dist-info/WHEEL,sha256=QccIxa26bgl1E6uMy58deGWi-0aeIkkangHcxk2kWfw,87
+rowan_python-3.0.11.dist-info/licenses/LICENSE,sha256=i05z7xEhyrg6f8j0lR3XYjShnF-MJGFQ-DnpsZ8yiVI,1084
+rowan_python-3.0.11.dist-info/RECORD,,