stjames 0.0.92__py3-none-any.whl → 0.0.93__py3-none-any.whl

stjames/pdb.py

@@ -448,6 +448,7 @@ def _format_atom_line(
         chg = "  "
 
     atom_name = atom.name if atom.name else atom.element
+
     occupancy = atom.occupancy if atom.occupancy else 1.0
 
     # Construct the line.
@@ -455,7 +456,7 @@ def _format_atom_line(
     line = (
         f"{record_type}"
         f"{serial:5d} "  # atom serial number (columns 7-11)
-        f"{atom_name:<4}"  # atom name (columns 13-16, left-justified in this snippet)
+        f"{(' ' + atom_name if len(atom_name) < 4 else atom_name):<4}"  # atom name (columns 13-16, left-justified in this snippet)
         f"{alt_loc_char}"  # altLoc (column 17)
         f"{residue_name:>3}"  # residue name (columns 18-20)
         f" {chain_char}"  # chain ID (column 22)

stjames/workflows/docking.py

@@ -7,6 +7,7 @@ from pydantic import AfterValidator, ConfigDict, field_validator, model_validato
 from ..base import Base, round_float
 from ..pdb import PDB
 from ..types import UUID, Vector3D
+from .conformer_search import ConformerGenSettings, ETKDGSettings
 from .workflow import MoleculeWorkflow
 
 
@@ -20,6 +21,28 @@ class Score(Base):
 
     pose: UUID | None  # for calculation
     score: Annotated[float, AfterValidator(round_float(3))]
+    posebusters_valid: bool
+
+
+class DockingSettings(Base):
+    """
+    Base class for controlling how docked poses are generated.
+
+    :param max_poses: the maximum number of poses generated per input molecule
+    """
+
+    max_poses: int = 4
+
+
+class VinaSettings(DockingSettings):
+    """
+    Controls how AutoDock Vina is run.
+
+    :param exhaustiveness: how many times Vina attempts to find a pose.
+        8 is typical, 32 is considered relatively careful.
+    """
+
+    exhaustiveness: int = 8
 
 
 class DockingWorkflow(MoleculeWorkflow):
@@ -35,31 +58,38 @@ class DockingWorkflow(MoleculeWorkflow):
     :param mode: Mode for workflow (currently unused)
 
     New:
-    :param molecules: Molecules to dock (optional)
-    :param smiles: SMILES strings of the ligands (optional)
+    :param docking_engine: which docking method to use
     :param do_csearch: whether to csearch starting structures
+    :param csearch_settings: settings for initial conformer search.
     :param do_optimization: whether to optimize starting structures
+    :param opt_settings: settings for conformer optimization.
     :param do_pose_refinement: whether to optimize non-rotatable bonds in output poses
-    :param conformers: UUIDs of optimized conformers
     :param target: PDB of the protein.
     :param target_uuid: UUID of the protein.
     :param pocket: center (x, y, z) and size (x, y, z) of the pocket
 
     Results:
+    :param conformers: UUIDs of optimized conformers
     :param scores: docked poses sorted by score
     """
 
     model_config = ConfigDict(arbitrary_types_allowed=True)
 
-    do_csearch: bool = True
-    do_optimization: bool = True
-    conformers: list[UUID] = []
-
     target: PDB | None = None
     target_uuid: UUID | None = None
     pocket: tuple[Vector3D, Vector3D]
 
+    do_csearch: bool = True
+    conformer_gen_settings: ConformerGenSettings = ETKDGSettings(mode="reckless")
+
+    do_optimization: bool = True
+    # optimization_settings - here in future once we have a cleaner mode sol'n, ccw 7.9.25
+
+    docking_settings: DockingSettings = VinaSettings()
+
     do_pose_refinement: bool = True
+
+    conformers: list[UUID] = []
     scores: list[Score] = []
 
     def __str__(self) -> str:
@@ -80,7 +110,7 @@ class DockingWorkflow(MoleculeWorkflow):
     def check_protein(self) -> Self:
         """Check if protein is provided."""
         if not self.target and not self.target_uuid:
-            raise ValueError("Must provide either molecules or smiles")
+            raise ValueError("Must provide either target or target_uuid")
         return self
 
     @field_validator("pocket", mode="after")

{stjames-0.0.92.dist-info → stjames-0.0.93.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: stjames
-Version: 0.0.92
+Version: 0.0.93
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames

{stjames-0.0.92.dist-info → stjames-0.0.93.dist-info}/RECORD

@@ -16,7 +16,7 @@ stjames/method.py,sha256=8Cj0JYGMEaS_Cetfz8Wcu6-BZAv1SejRSagMgkKaXs0,4469
 stjames/mode.py,sha256=xw46Cc7f3eTS8i35qECi-8DocAlANhayK3w4akD4HBU,496
 stjames/molecule.py,sha256=l4S6prH1xflnZtbwidSF2THsiHaSJtRiy1rmUbH366Q,20631
 stjames/opt_settings.py,sha256=LEwGXUEKq5TfU5rr60Z4QQBhCqiw1Ch5w0M_lXawWo8,642
-stjames/pdb.py,sha256=NtNB3M_OXq8raQA5ivjFKcIxOGemBvpGDIlCeb-s80E,26461
+stjames/pdb.py,sha256=6ayVUUdTufkXs_nfpRQuT1yGvymuyICB4L5Wh55OsaA,26507
 stjames/periodic_cell.py,sha256=eV_mArsY_MPEFSrFEsTC-CyCc6V8ITAXdk7yhjjNI7M,1080
 stjames/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 stjames/scf_settings.py,sha256=WotVgVrayQ_8PUHP39zVtG7iLT9PV41lpzruttFACP8,2356
@@ -45,7 +45,7 @@ stjames/workflows/bde.py,sha256=g_In-caftXiimrhfdptHjpfrYQUs3vF58qYmRnaTN8g,1082
 stjames/workflows/conformer.py,sha256=18aO6ngMBeGAmQkBdLGCCHr398RIYr1v2hD2IT1u4cc,3005
 stjames/workflows/conformer_search.py,sha256=4yPEKIIedeaVvaAwgjwC1FxiHqM6n2zOF6c9Yk_q1oA,13513
 stjames/workflows/descriptors.py,sha256=T4tc7xdtBdxESGO86KR323jPQ2pgwxBqgV0khA6MEgQ,584
-stjames/workflows/docking.py,sha256=GCW_-JeEZcMXKZ9EQFOxWUYRo0jsbzwIv10aSz8KuaQ,3027
+stjames/workflows/docking.py,sha256=CgpLjMfpPka1fcg0VJPeyJCOnZjnJTrgfNeMAKiX4zM,3897
 stjames/workflows/electronic_properties.py,sha256=GT3-NC7w-dbcOJ-3AzJ7LgzH6frTbiH2Iyb9BCa-SvY,4112
 stjames/workflows/fukui.py,sha256=T6TDg-lcE-sfTDVpa3KFBenLe7PGUO2QrQ2jNuw_iiU,1756
 stjames/workflows/hydrogen_bond_basicity.py,sha256=q9eXty68ZyCmrB6G_8bfeOT8Ui_IQquRPu6z-3rNreQ,1589
@@ -63,8 +63,8 @@ stjames/workflows/solubility.py,sha256=kGfVyPPGDLRpf2j6dSY7woCkfsoXSbUzdSImA4mcM
 stjames/workflows/spin_states.py,sha256=0degmE-frovgoXweshZyjfjqL7nkbaFoO9YoJhvQnaI,4748
 stjames/workflows/tautomer.py,sha256=7eYKziGPg8Km6lfowTzSkgJfJ4SHUPrAmnTf8Bi-SB0,1164
 stjames/workflows/workflow.py,sha256=OE05pt2ZOd8TzTOlBngXCVg9wv_553ZR60VNRPlq0f8,1953
-stjames-0.0.92.dist-info/licenses/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
-stjames-0.0.92.dist-info/METADATA,sha256=QQ4yZAEcRFwv4KCTOBZxuCrOzmNb_kBv2G3Jd4-2hR4,1724
-stjames-0.0.92.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-stjames-0.0.92.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
-stjames-0.0.92.dist-info/RECORD,,
+stjames-0.0.93.dist-info/licenses/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
+stjames-0.0.93.dist-info/METADATA,sha256=45Vdq_ji_cnZN3uRObImOTBgOsc9lcVCJOTWVms8xjY,1724
+stjames-0.0.93.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+stjames-0.0.93.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
+stjames-0.0.93.dist-info/RECORD,,