stjames 0.0.58__tar.gz → 0.0.61__tar.gz

{stjames-0.0.58/stjames.egg-info → stjames-0.0.61}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: stjames
-Version: 0.0.58
+Version: 0.0.61
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames

{stjames-0.0.58 → stjames-0.0.61}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "stjames"
-version = "0.0.58"
+version = "0.0.61"
 description = "standardized JSON atom/molecule encoding scheme"
 readme = "README.md"
 requires-python = ">=3.11"

{stjames-0.0.58 → stjames-0.0.61}/stjames/atomium_stjames/mmcif.py

@@ -606,6 +606,16 @@ def atom_dict_to_atom_dict(d: dict[str, Any], aniso_dict: dict[int, Any]) -> dic
     for key in ["x", "y", "z", "charge", "bvalue", "occupancy"]:
         if atom[key] is not None:
             atom[key] = float(atom[key])
+    if atom["charge"] == 0:
+        atom["charge"] = None
+    if not atom["is_hetatm"]:
+        atom["is_hetatm"] = None
+    if not atom["alt_loc"]:
+        atom["alt_loc"] = None
+    if atom["occupancy"] == 1:
+        atom["occupancy"] = None
+    if atom["name"] == atom["element"]:
+        atom["name"] = None
     return atom
 
 

{stjames-0.0.58 → stjames-0.0.61}/stjames/atomium_stjames/pdb.py

@@ -557,6 +557,10 @@ def atom_line_to_dict(line: str, aniso_dict: dict[Any, Any]) -> dict[str, Any]:
         a["is_hetatm"] = None
     if not a["alt_loc"]:
         a["alt_loc"] = None
+    if a["occupancy"] == 1:
+        a["occupancy"] = None
+    if a["name"] == a["element"]:
+        a["name"] = None
     return a
 
 

{stjames-0.0.58 → stjames-0.0.61}/stjames/pdb.py

@@ -22,7 +22,7 @@ class PDBAtom(BaseModel):
     y: float
     z: float
     element: str
-    name: str
+    name: str | None = None
     charge: float | None = None
     occupancy: float | None = None
     alt_loc: str | None = None
@@ -413,12 +413,15 @@ def _format_atom_line(
     else:
         chg = "  "
 
+    atom_name = atom.name if atom.name else atom.element
+    occupancy = atom.occupancy if atom.occupancy else 1.0
+
     # Construct the line.
     # Use exact spacing & field widths to match PDB guidelines.
     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:<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)
@@ -427,7 +430,7 @@ def _format_atom_line(
         f"{atom.x:8.3f}"  # x (columns 31-38)
         f"{atom.y:8.3f}"  # y (columns 39-46)
         f"{atom.z:8.3f}"  # z (columns 47-54)
-        f"{atom.occupancy:6.2f}"  # occupancy (columns 55-60)
+        f"{occupancy:6.2f}"  # occupancy (columns 55-60)
         f"{atom.bvalue:6.2f}"  # temp factor (columns 61-66)
         f"          "  # columns 67-76 (padding)
         f"{atom.element:>2}"  # element (columns 77-78)
@@ -468,6 +471,8 @@ def _format_anisou_line(
     else:
         chg = "  "
 
+    atom_name = atom.name if atom.name else atom.element
+
     if atom.anisotropy:
         aniso_lines = (
             f"{_float_to_pdb_string(atom.anisotropy[0]):>7}"  # x (columns 29-35)
@@ -493,7 +498,7 @@ def _format_anisou_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:<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-0.0.58 → stjames-0.0.61}/stjames/workflows/docking.py

@@ -1,8 +1,8 @@
 """Docking workflow."""
 
-from typing import Annotated
+from typing import Annotated, Self
 
-from pydantic import AfterValidator, ConfigDict, field_validator
+from pydantic import AfterValidator, ConfigDict, field_validator, model_validator
 
 from ..base import Base, round_float
 from ..pdb import PDB
@@ -26,6 +26,10 @@ class DockingWorkflow(Workflow):
     """
     Docking workflow.
 
+    Note that the protein can be supplied either by UUID or raw PDB object.
+    We anticipate that the former will dominate deployed usage, but the latter is handy for isolated testing.
+    If, for whatever reason, the workflow is initialized with both a `target_uuid` and a `target`, the UUID will be ignored.
+
     Inherited:
     :param initial_molecule: Molecule of interest
     :param mode: Mode for workflow (currently unused)
@@ -36,7 +40,8 @@ class DockingWorkflow(Workflow):
     :param do_csearch: whether to csearch starting structures
     :param do_optimization: whether to optimize starting structures
     :param conformers: UUIDs of optimized conformers
-    :param target: PDB of the protein
+    :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:
@@ -49,7 +54,8 @@ class DockingWorkflow(Workflow):
     do_optimization: bool = True
     conformers: list[UUID] = []
 
-    target: PDB
+    target: PDB | None = None
+    target_uuid: UUID | None = None
     pocket: tuple[Vector3D, Vector3D]
 
     do_pose_hydrogen_refinement: bool = True
@@ -60,16 +66,25 @@ class DockingWorkflow(Workflow):
 
     def __repr__(self) -> str:
         """Return a string representation of the Docking workflow."""
-        desc = self.target.description
-        target = desc.code or desc.title
-        ligand = "".join(atom.atomic_symbol for atom in self.initial_molecule.atoms)
+        if self.target is not None:
+            desc = self.target.description
+            target = desc.code or desc.title
+        else:
+            target = ""
 
+        ligand = "".join(atom.atomic_symbol for atom in self.initial_molecule.atoms)
         return f"<{type(self).__name__} {target} {ligand}>"
 
+    @model_validator(mode="after")
+    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")
+        return self
+
     @field_validator("pocket", mode="after")
     def validate_pocket(cls, pocket: tuple[Vector3D, Vector3D]) -> tuple[Vector3D, Vector3D]:
         center, size = pocket
         if any(q <= 0 for q in size):
             raise ValueError(f"Pocket size must be positive, got: {size}")
-
         return pocket

{stjames-0.0.58 → stjames-0.0.61/stjames.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: stjames
-Version: 0.0.58
+Version: 0.0.61
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames