stjames 0.0.62__py3-none-any.whl → 0.0.64__py3-none-any.whl

stjames/molecule.py

@@ -68,6 +68,7 @@ class Molecule(Base):
     thermal_free_energy_corr: Annotated[Optional[float], AfterValidator(round_optional_float(6))] = None
 
     smiles: Optional[str] = None
+    calculation_index: int | None = None
 
     def __len__(self) -> int:
         return len(self.atoms)
@@ -273,7 +274,7 @@ class Molecule(Base):
             rdkm = _embed_rdkit_mol(rdkm)
 
         atoms = []
-        atomic_numbers = [atom.GetAtomicNum() for atom in rdkm.GetAtoms()]  # type: ignore [no-untyped-call]
+        atomic_numbers = [atom.GetAtomicNum() for atom in rdkm.GetAtoms()]  # type: ignore [no-untyped-call, unused-ignore]
         geom = rdkm.GetConformers()[cid].GetPositions()
 
         for i in range(len(atomic_numbers)):
@@ -286,25 +287,27 @@ class Molecule(Base):
 
     @classmethod
     def from_smiles(cls: type[Self], smiles: str) -> Self:
-        return cls.from_rdkit(Chem.MolFromSmiles(smiles))
+        rdkm = Chem.MolFromSmiles(smiles)
+        assert rdkm is not None
+        return cls.from_rdkit(rdkm)
 
 
 def _embed_rdkit_mol(rdkm: RdkitMol) -> RdkitMol:
     try:
-        AllChem.SanitizeMol(rdkm)  # type: ignore [attr-defined]
+        AllChem.SanitizeMol(rdkm)  # type: ignore [attr-defined, unused-ignore]
     except Exception as e:
         raise ValueError("Molecule could not be generated -- invalid chemistry!\n") from e
 
-    rdkm = AllChem.AddHs(rdkm)  # type: ignore [attr-defined]
+    rdkm = AllChem.AddHs(rdkm)  # type: ignore [attr-defined, unused-ignore]
     try:
-        status1 = AllChem.EmbedMolecule(rdkm, maxAttempts=200)  # type: ignore [attr-defined]
+        status1 = AllChem.EmbedMolecule(rdkm, maxAttempts=200)  # type: ignore [attr-defined, unused-ignore]
         assert status1 >= 0
     except Exception as e:
-        status1 = AllChem.EmbedMolecule(rdkm, maxAttempts=200, useRandomCoords=True)  # type: ignore [attr-defined]
+        status1 = AllChem.EmbedMolecule(rdkm, maxAttempts=200, useRandomCoords=True)  # type: ignore [attr-defined, unused-ignore]
         if status1 < 0:
             raise ValueError(f"Cannot embed molecule! Error: {e}")
 
-    AllChem.MMFFOptimizeMolecule(rdkm, maxIters=200)  # type: ignore [attr-defined]
+    AllChem.MMFFOptimizeMolecule(rdkm, maxIters=200)  # type: ignore [attr-defined, call-arg, unused-ignore]
 
     return rdkm
 

stjames/pdb.py

@@ -214,23 +214,42 @@ def pdb_from_mmcif_filestring(pdb: str) -> PDB:
     return PDB.model_validate(mmcif_dict_to_data_dict(mmcif_string_to_mmcif_dict(pdb)))
 
 
-def pdb_object_to_pdb_filestring(pdb: PDB) -> str:
+def pdb_object_to_pdb_filestring(
+    pdb: PDB,
+    header: bool = False,
+    source: bool = False,
+    keyword: bool = False,
+    seqres: bool = True,
+    hetnam: bool = True,
+    remark: bool = True,
+    crystallography: bool = False,
+) -> str:
     pdb_lines: list[str] = []
     chains: list[str] = []
-    # Header
-    pdb_lines.extend(_build_header_section(pdb))
-    pdb_lines.extend(_build_source_section(pdb))
-    pdb_lines.extend(_build_keyword_section(pdb))
+
+    if header:
+        pdb_lines.extend(_build_header_section(pdb))
+
+    if source:
+        pdb_lines.extend(_build_source_section(pdb))
+
+    if keyword:
+        pdb_lines.extend(_build_keyword_section(pdb))
 
     full_name_dict: dict[str, str] = {}
     seqres_lines, chains = _build_secondary_structure_and_seqres(pdb, full_name_dict)
 
-    pdb_lines.extend(seqres_lines)
-    pdb_lines.extend(_build_hetname_section(full_name_dict))
+    if seqres:
+        pdb_lines.extend(seqres_lines)
+
+    if hetnam:
+        pdb_lines.extend(_build_hetname_section(full_name_dict))
 
-    pdb_lines.extend(_build_remark_section(pdb, chains))
+    if remark:
+        pdb_lines.extend(_build_remark_section(pdb, chains))
 
-    pdb_lines.extend(_build_crystallography_section(pdb))
+    if crystallography:
+        pdb_lines.extend(_build_crystallography_section(pdb))
 
     for model_index, model in enumerate(pdb.models, start=1):
         # If more than one model, add MODEL line
@@ -633,11 +652,11 @@ def _build_hetname_section(full_name_dict: dict[str, str]) -> list[str]:
 def _build_remark_section(pdb: PDB, chains: list[str]) -> list[str]:
     """Builds REMARK lines (resolution, R factors, biomolecule and missing residues)."""
     lines = []
-    lines.append(f"REMARK   2 RESOLUTION. {pdb.quality.resolution:>7} ANGSTROMS.")
+    lines.append(f"REMARK   2 RESOLUTION. {pdb.quality.resolution or '':>7} ANGSTROMS.")
     if pdb.quality.rfree:
-        lines.append(f"REMARK   3   FREE R VALUE                     : {pdb.quality.rfree}")
+        lines.append(f"REMARK   3   FREE R VALUE                     : {pdb.quality.rfree or ''}")
     if pdb.quality.rvalue:
-        lines.append(f"REMARK   3   R VALUE            (WORKING SET) : {pdb.quality.rvalue}")
+        lines.append(f"REMARK   3   R VALUE            (WORKING SET) : {pdb.quality.rvalue or ''}")
 
     # REMARK 350: Biomolecule details
     lines.append("REMARK 350")

stjames/workflows/docking.py

@@ -39,6 +39,7 @@ class DockingWorkflow(MoleculeWorkflow):
     :param smiles: SMILES strings of the ligands (optional)
     :param do_csearch: whether to csearch starting structures
     :param do_optimization: whether to optimize starting structures
+    :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.
@@ -58,7 +59,7 @@ class DockingWorkflow(MoleculeWorkflow):
     target_uuid: UUID | None = None
     pocket: tuple[Vector3D, Vector3D]
 
-    do_pose_hydrogen_refinement: bool = True
+    do_pose_refinement: bool = True
     scores: list[Score] = []
 
     def __str__(self) -> str:

{stjames-0.0.62.dist-info → stjames-0.0.64.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: stjames
-Version: 0.0.62
+Version: 0.0.64
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames

{stjames-0.0.62.dist-info → stjames-0.0.64.dist-info}/RECORD

@@ -13,9 +13,9 @@ stjames/int_settings.py,sha256=5HXp8opt5ZyY1UpmfaK7NVloWVLM5jkG0elEEqpVLUo,896
 stjames/message.py,sha256=Rq6QqmHZKecWxYH8fVyXmuoCCPZv8YinvgykSeorXSU,216
 stjames/method.py,sha256=5hBHk2xQLpxZ52LwJ9FHWaqQMdFKnsbQEOxaVe6O4Go,2321
 stjames/mode.py,sha256=xw46Cc7f3eTS8i35qECi-8DocAlANhayK3w4akD4HBU,496
-stjames/molecule.py,sha256=GLOWgXPiIsy3cjqRUNAMR0YLQVlzYilGESsGdNIhxww,14075
+stjames/molecule.py,sha256=2BRXYKtkm5ztYiywyC2S__Zu4a-QoDEgb7LR7F4xHvs,14268
 stjames/opt_settings.py,sha256=gxXGtjy9l-Q5Wen9eO6T6HHRCuS8rfOofdVQIJj0JcI,550
-stjames/pdb.py,sha256=UxbgtIbc28L9O74AESYQiLBeiWZhdEbrBUT3mlyqRt8,25411
+stjames/pdb.py,sha256=-i0H029NEX-pcyCqdVyq7D62ZDvmUPWK7l83WdoDmpk,25759
 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
@@ -44,7 +44,7 @@ stjames/workflows/bde.py,sha256=hdTjwma5L9SrU5F5r6dB1ruB_B6buBUtZHf2sanNW2k,9802
 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=p-L1s3NxLcliwDs8uLaohcz1Lap01Nuogq9Xe1eOT2k,2949
+stjames/workflows/docking.py,sha256=GCW_-JeEZcMXKZ9EQFOxWUYRo0jsbzwIv10aSz8KuaQ,3027
 stjames/workflows/electronic_properties.py,sha256=GT3-NC7w-dbcOJ-3AzJ7LgzH6frTbiH2Iyb9BCa-SvY,4112
 stjames/workflows/fukui.py,sha256=e7CF7Mp2Dt1JTipQx-Sz_37W1urL-iRpjXY-9ItSvhM,1268
 stjames/workflows/hydrogen_bond_basicity.py,sha256=XDpHEluw6DQ9Zk5g2Je2a81HqIkqPglZ-6f2YZnd4Bc,1159
@@ -58,8 +58,8 @@ 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=sk2BUz59wdIkT_EyKOnMt5woNrjo3aHVK38cU8x8I7Q,1423
-stjames-0.0.62.dist-info/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
-stjames-0.0.62.dist-info/METADATA,sha256=Vni7VUt_d2w-dqOUh4pUhK6ldBtd8PxJHl0hBtkK1cU,1672
-stjames-0.0.62.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
-stjames-0.0.62.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
-stjames-0.0.62.dist-info/RECORD,,
+stjames-0.0.64.dist-info/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
+stjames-0.0.64.dist-info/METADATA,sha256=33n-Ix3Rfcue2dKm4SUqmWow8MeXv1_SF6UcpfOPYiQ,1672
+stjames-0.0.64.dist-info/WHEEL,sha256=jB7zZ3N9hIM9adW7qlTAyycLYW9npaWKLRzaoVcLKcM,91
+stjames-0.0.64.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
+stjames-0.0.64.dist-info/RECORD,,

{stjames-0.0.62.dist-info → stjames-0.0.64.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.8.0)
+Generator: setuptools (75.8.2)
 Root-Is-Purelib: true
 Tag: py3-none-any