pyjess 0.7.0__cp38-abi3-macosx_11_0_arm64.whl

pyjess/.gitignore

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+_jess.c
+_jess.html

pyjess/CMakeLists.txt

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+cython_extension(_jess LINKS jess)

pyjess/__init__.py

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+# noqa: D104
+from . import _jess
+from ._jess import Atom, Hit, Jess, Query, Molecule, Template, TemplateAtom
+
+__author__ = "Martin Larralde <martin.larralde@embl.de>"
+__all__ = ["Atom", "Hit", "Jess", "Query", "Molecule", "Template", "TemplateAtom"]
+__doc__ = _jess.__doc__
+__version__ = _jess.__version__
+
+# Small addition to the docstring: we want to show a link redirecting to the
+# rendered version of the documentation, but this can only work when Python
+# is running with docstrings enabled
+if __doc__ is not None:
+    __doc__ += """See Also:
+    An online rendered version of the documentation for this version
+    of the library on
+    `Read The Docs <https://pyjess.readthedocs.io/en/v{}/>`_.
+
+    """.format(
+        __version__
+    )

pyjess/__main__.py

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+import sys
+from .cli import main
+
+sys.exit(main())

pyjess/_jess.pyi

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+import os
+import typing
+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
+]
+
+_SELF = TypeVar("_SELF")
+
+__version__: str
+
+class Molecule(Sequence[Atom]):
+    @classmethod
+    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 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
+    def __getitem__(self, index: int) -> Atom: ...
+    @typing.overload
+    def __getitem__(self: _SELF, index: slice) -> _SELF: ...
+    @typing.overload
+    def __getitem__(self: _SELF, index: Union[int, slice]) -> Union[Atom, _SELF]: ...
+    def __copy__(self) -> Molecule: ...
+    def __eq__(self, other: object) -> bool: ...
+    def __hash__(self) -> int: ...
+    def __reduce__(self) -> Tuple[Any, ...]: ...
+    @property
+    def id(self) -> Optional[str]: ...
+    def conserved(self: _SELF, cutoff: float = 0.0) -> _SELF: ...
+    def copy(self) -> Molecule: ...
+
+class Atom:
+    @classmethod
+    def load(cls, file: Union[TextIO, str, os.PathLike[str]]) -> Atom: ...
+    @classmethod
+    def loads(cls, text: str) -> Atom: ...
+    def __init__(
+        self,
+        *,
+        serial: int,
+        name: str,
+        residue_name: str,
+        chain_id: str,
+        residue_number: int,
+        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,
+    ): ...
+    def __eq__(self, other: object) -> bool: ...
+    def __hash__(self) -> int: ...
+    def __reduce__(self) -> Tuple[Any, ...]: ...
+    def __repr__(self) -> str: ...
+    def __copy__(self) -> Atom: ...
+    @property
+    def serial(self) -> int: ...
+    @property
+    def altloc(self) -> str: ...
+    @property
+    def name(self) -> str: ...
+    @property
+    def residue_name(self) -> str: ...
+    @property
+    def residue_number(self) -> int: ...
+    @property
+    def segment(self) -> str: ...
+    @property
+    def element(self) -> str: ...
+    @property
+    def insertion_code(self) -> str: ...
+    @property
+    def chain_id(self) -> str: ...
+    @property
+    def occupancy(self) -> float: ...
+    @property
+    def temperature_factor(self) -> float: ...
+    @property
+    def charge(self) -> int: ...
+    @property
+    def x(self) -> float: ...
+    @property
+    def y(self) -> float: ...
+    @property
+    def z(self) -> float: ...
+    def copy(self) -> Atom: ...
+
+class TemplateAtom:
+    @classmethod
+    def load(cls, file: Union[TextIO, str, os.PathLike[str]]) -> Atom: ...
+    @classmethod
+    def loads(cls, text: str) -> TemplateAtom: ...
+    def __init__(
+        self,
+        *,
+        chain_id: str,
+        residue_number: int,
+        x: float,
+        y: float,
+        z: float,
+        residue_names: Sequence[str],
+        atom_names: Sequence[str],
+        distance_weight: float = 0.0,
+        match_mode: MATCH_MODE = 0,
+    ): ...
+    def __repr__(self) -> str: ...
+    def __eq__(self, other: object) -> bool: ...
+    def __hash__(self) -> int: ...
+    def __reduce__(self) -> Tuple[Any, ...]: ...
+    def __copy__(self: _SELF) -> _SELF: ...
+    @property
+    def match_mode(self) -> MATCH_MODE: ...
+    @property
+    def residue_number(self) -> int: ...
+    @property
+    def chain_id(self) -> str: ...
+    @property
+    def x(self) -> float: ...
+    @property
+    def y(self) -> float: ...
+    @property
+    def z(self) -> float: ...
+    @property
+    def atom_names(self) -> Tuple[str, ...]: ...
+    @property
+    def residue_names(self) -> Tuple[str, ...]: ...
+    @property
+    def distance_weight(self) -> float: ...
+    def copy(self: _SELF) -> _SELF: ...
+
+class Template(Sequence[TemplateAtom]):
+    @classmethod
+    def load(cls, file: Union[TextIO, str, os.PathLike[str]], id: Optional[str] = None) -> Template: ...
+    @classmethod
+    def loads(cls, text: str, id: Optional[str] = None) -> Template: ...
+    def __init__(self, atoms: Sequence[TemplateAtom] = (), id: Optional[str] = None): ...
+    def __len__(self) -> int: ...
+    @typing.overload
+    def __getitem__(self, index: int) -> TemplateAtom: ...
+    @typing.overload
+    def __getitem__(self: _SELF, index: slice) -> _SELF: ...
+    @typing.overload
+    def __getitem__(self: _SELF, index: Union[int, slice]) -> Union[TemplateAtom, _SELF]: ...
+    def __eq__(self, other: object) -> bool: ...
+    def __hash__(self) -> int: ...
+    def __reduce__(self) -> Tuple[Any, ...]: ...
+    def __copy__(self) -> Template: ...
+    @property
+    def id(self) -> str: ...
+    @property
+    def dimension(self) -> int: ...
+    def copy(self) -> Template: ...
+
+_T = TypeVar("_T", bound=Template)
+
+class Query(Generic[_T], Iterator[Hit[_T]]):
+    @property
+    def jess(self) -> Jess[_T]: ...
+    @property
+    def molecule(self) -> Molecule: ...
+    @property
+    def ignore_chain(self) -> Literal[None, "atoms", "residues"]: ...
+    @property
+    def rmsd_threshold(self) -> float: ...
+    @property
+    def max_candidates(self) -> Optional[int]: ...
+    @property
+    def best_match(self) -> bool: ...
+    def __iter__(self) -> Query[_T]: ...
+    def __next__(self) -> Hit[_T]: ...
+
+class Hit(Generic[_T]):
+    def __getstate__(self) -> Dict[str, object]: ...
+    def __setstate__(self, state: Dict[str, object]) -> None: ...
+    @property
+    def rmsd(self) -> float: ...
+    @property
+    def template(self) -> _T: ...
+    @property
+    def determinant(self) -> float: ...
+    @property
+    def log_evalue(self) -> float: ...
+    @property
+    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] = ()): ...
+    def __len__(self) -> int: ...
+    @typing.overload
+    def __getitem__(self, index: int) -> _T: ...
+    @typing.overload
+    def __getitem__(self, index: slice) -> Jess[_T]: ...
+    @typing.overload
+    def __getitem__(self, index: Union[int, slice]) -> Union[_T, Jess[_T]]: ...
+    def __eq__(self, other: object) -> bool: ...
+    def __hash__(self) -> int: ...
+    def __copy__(self: _SELF) -> _SELF: ...
+    def __reduce__(self) -> Tuple[Any, ...]: ...
+    def query(
+        self,
+        molecule: Molecule,
+        rmsd_threshold: float,
+        distance_cutoff: float,
+        max_dynamic_distance: float,
+        *,
+        max_candidates: Optional[int] = None,
+        ignore_chain: Literal[None, "atoms", "residues"] = None,
+        best_match: bool = False,
+        reorder: bool = True,
+    ) -> Query[_T]: ...