pyjess 0.6.0__pp38-pypy38_pp73-macosx_11_0_arm64.whl → 0.7.0__pp38-pypy38_pp73-macosx_11_0_arm64.whl

pyjess/__main__.py

@@ -0,0 +1,4 @@
+import sys
+from .cli import main
+
+sys.exit(main())

pyjess/_jess.pyi

@@ -1,12 +1,29 @@
 import os
 import typing
-from typing import Any, Generic, Union, Optional, Sequence, Iterator, Iterable, List, TextIO, Sized, TypeVar, Tuple
+from typing import Any, Dict, Generic, Union, Optional, Sequence, Iterator, Iterable, List, TextIO, Sized, TypeVar, Tuple
 
 try:
     from typing import Literal
 except ImportError:
     from typing_extensions import Literal  # type: ignore
 
+try:
+    from Bio.PDB.Model import Model
+    from Bio.PDB.Structure import Structure
+except ImportError:
+    Model = Structure = Any  # type: ignore
+
+try:
+    import gemmi
+except ImportError:
+    gemmi = Any    # type: ignore
+
+try:
+    import biotite.structure
+except ImportError:
+    biotite = Any    # type: ignore
+
+
 MATCH_MODE = Literal[
     -1, 0, 1, 2, 3, 4, 5, 6, 7, 8, 100, 101, 102, 103, 104, 105, 106, 107
 ]
@@ -17,9 +34,33 @@ __version__: str
 
 class Molecule(Sequence[Atom]):
     @classmethod
-    def load(cls, file: Union[TextIO, str, os.PathLike[str]], id: Optional[str] = None, ignore_endmdl: bool = False) -> Molecule: ...
+    def from_biopython(cls, structure: Union[Structure, Model]) -> Molecule: ...
+    @classmethod
+    def from_gemmi(cls, structure: gemmi.Structure) -> Molecule: ...
+    @classmethod
+    def from_biotite(cls, atom_array: biotite.structure.AtomArray, id: Optional[str] = None) -> Molecule: ...
     @classmethod
-    def loads(cls, text: str, id: Optional[str] = None, ignore_endmdl: bool = False) -> Molecule: ...
+    def load(
+        cls,
+        file: Union[TextIO, str, os.PathLike[str]],
+        format: Literal["pdb", "cif", "detect"] = "detect",
+        *,
+        id: Optional[str] = None,
+        ignore_endmdl: bool = False,
+        use_author: bool = False,
+        skip_hetatm: bool = False,
+    ) -> Molecule: ...
+    @classmethod
+    def loads(
+        cls,
+        text: str,
+        format: Literal["pdb", "cif", "detect"] = "detect",
+        *,
+        id: Optional[str] = None,
+        ignore_endmdl: bool = False,
+        use_author: bool = False,
+        skip_hetatm: bool = False,
+    ) -> Molecule: ...
     def __init__(self, atoms: Sequence[Atom] = (), id: Optional[str] = None): ...
     def __len__(self) -> int: ...
     @typing.overload
@@ -47,16 +88,16 @@ class Atom:
         *,
         serial: int,
         name: str,
-        altloc: str,
         residue_name: str,
         chain_id: str,
         residue_number: int,
-        insertion_code: str,
         x: float,
         y: float,
         z: float,
         occupancy: float = 0.0,
         temperature_factor: float = 0.0,
+        altloc: str = " ",
+        insertion_code: str = " ",
         segment: str = "",
         element: str = "",
         charge: int = 0,
@@ -172,11 +213,11 @@ class Query(Generic[_T], Iterator[Hit[_T]]):
     @property
     def molecule(self) -> Molecule: ...
     @property
-    def ignore_chain(self) -> bool: ...
+    def ignore_chain(self) -> Literal[None, "atoms", "residues"]: ...
     @property
     def rmsd_threshold(self) -> float: ...
     @property
-    def max_candidates(self) -> int: ...
+    def max_candidates(self) -> Optional[int]: ...
     @property
     def best_match(self) -> bool: ...
     def __iter__(self) -> Query[_T]: ...
@@ -197,6 +238,8 @@ class Hit(Generic[_T]):
     def evalue(self) -> float: ...
     def atoms(self, transform: bool = True) -> List[Atom]: ...
     def molecule(self, transform: bool = False) -> Molecule: ...
+    def dump(self, file: TextIO, format: Literal["pdb"] = "pdb", transform: bool = True) -> None: ...
+    def dumps(self, format: Literal["pdb"] = "pdb", transform: bool = True) -> str: ...
 
 class Jess(Generic[_T], Sequence[_T]):
     def __init__(self, templates: Iterable[_T] = ()): ...
@@ -218,8 +261,8 @@ class Jess(Generic[_T], Sequence[_T]):
         distance_cutoff: float,
         max_dynamic_distance: float,
         *,
-        max_candidates: int = 1000,
-        ignore_chain: bool = False,
+        max_candidates: Optional[int] = None,
+        ignore_chain: Literal[None, "atoms", "residues"] = None,
         best_match: bool = False,
         reorder: bool = True,
     ) -> Query[_T]: ...