from __future__ import annotations
import builtins
import datetime
import typing
class Atom:
name: builtins.str
resname: builtins.str
resid: builtins.int
atomic_number: builtins.int
mass: builtins.float
charge: builtins.float
type_name: builtins.str
type_id: builtins.int
chain: builtins.str
bfactor: builtins.float
occupancy: builtins.float
def __new__(cls) -> Atom: ...
class Particle:
id: builtins.int
pos: typing.Any
x: builtins.float
y: builtins.float
z: builtins.float
atom: typing.Any
name: builtins.str
resname: builtins.str
resid: builtins.int
resindex: builtins.int
atomic_number: builtins.int
mass: builtins.float
charge: builtins.float
type_name: builtins.str
type_id: builtins.int
chain: builtins.str
bfactor: builtins.float
occupancy: builtins.float
class Topology:
def __len__(self) -> builtins.int: ...
class State:
box: PeriodicBox
time: builtins.float
def __len__(self) -> builtins.int: ...
def set_box_from(self, arg: System | Sel) -> None: ...
class PeriodicBox:
@typing.overload
def __new__(cls, matrix: typing.Any) -> PeriodicBox: ...
@typing.overload
def __new__(cls, vectors: typing.Any, angles: typing.Any) -> PeriodicBox: ...
def to_vectors_angles(self) -> tuple[typing.Any, typing.Any]: ...
def shortest_vector(self, arr: typing.Any, dims: list[builtins.bool] = [True, True, True]) -> typing.Any: ...
def closest_image(self, point: typing.Any, target: typing.Any, dims: list[builtins.bool] = [True, True, True]) -> typing.Any: ...
def get_matrix(self) -> typing.Any: ...
def to_box_coords(self, point: typing.Any) -> typing.Any: ...
def to_lab_coords(self, point: typing.Any) -> typing.Any: ...
def get_box_extents(self) -> typing.Any: ...
def get_lab_extents(self) -> typing.Any: ...
def is_triclinic(self) -> builtins.bool: ...
def distance_squared(self, p1: typing.Any, p2: typing.Any, dims: list[builtins.bool]) -> builtins.float: ...
def distance(self, p1: typing.Any, p2: typing.Any, dims: list[builtins.bool]) -> builtins.float: ...
def wrap_point(self, p: typing.Any) -> typing.Any: ...
class FileStats:
elapsed_time: datetime.timedelta
frames_processed: builtins.int
cur_t: builtins.float
def __repr__(self) -> builtins.str: ...
def __str__(self) -> builtins.str: ...
class FileHandler:
stats: FileStats
file_name: builtins.str
def __new__(cls, fname: builtins.str, mode: builtins.str) -> FileHandler: ...
def read(self) -> tuple[Topology, State]: ...
def read_topology(self) -> Topology: ...
def read_state(self) -> State: ...
def write(self, data: typing.Any) -> None: ...
def write_topology(self, data: typing.Any) -> None: ...
def write_state(self, data: typing.Any) -> None: ...
def __iter__(self) -> FileHandler: ...
def __next__(self) -> typing.Optional[State]: ...
def skip_to_frame(self, fr: builtins.int) -> None: ...
def skip_to_time(self, t: builtins.float) -> None: ...
class System:
state: State
topology: Topology
time: builtins.float
box: PeriodicBox
@typing.overload
def __new__(cls) -> System: ...
@typing.overload
def __new__(cls, fname: builtins.str) -> System: ...
@typing.overload
def __new__(cls, topology: Topology, state: State) -> System: ...
def __len__(self) -> builtins.int: ...
def __call__(self, arg: builtins.str | tuple[builtins.int, builtins.int] | list[builtins.int] | None = None) -> Sel: ...
def replace_state_deep(self, st: State) -> None: ...
def save(self, fname: builtins.str) -> None: ...
def remove(self, arg: Sel | builtins.str | tuple[builtins.int, builtins.int] | list[builtins.int]) -> None: ...
@typing.overload
def append(self, arg: Sel | builtins.str | tuple[builtins.int, builtins.int] | list[builtins.int]) -> None: ...
@typing.overload
def append(self, atom: Atom, pos: typing.Any) -> None: ...
def set_box_from(self, src: System | Sel) -> None: ...
def iter_pos(self) -> SysPosIterator: ...
def iter_atoms(self) -> SysAtomIterator: ...
class Sel:
index: typing.Any
coords: typing.Any
system: System
state: State
topology: Topology
time: builtins.float
box: PeriodicBox
def __len__(self) -> builtins.int: ...
def __call__(self, arg: builtins.str | tuple[builtins.int, builtins.int] | list[builtins.int]) -> Sel: ...
def __getitem__(self, i: builtins.int) -> Particle: ...
def __iter__(self) -> typing.Iterator[Particle]: ...
def replace_state_deep(self, st: State) -> None: ...
def set_same_chain(self, val: builtins.str) -> None: ...
def set_same_resname(self, val: builtins.str) -> None: ...
def set_same_resid(self, val: builtins.int) -> None: ...
def set_same_name(self, val: builtins.str) -> None: ...
def set_same_mass(self, val: builtins.float) -> None: ...
def set_same_bfactor(self, val: builtins.float) -> None: ...
def set_box_from(self, sys: System) -> None: ...
def com(self, dims: list[builtins.bool] = [False, False, False]) -> typing.Any: ...
def cog(self, dims: list[builtins.bool] = [False, False, False]) -> typing.Any: ...
def principal_transform(self) -> typing.Any: ...
def principal_transform_pbc(self) -> typing.Any: ...
def apply_transform(self, tr: typing.Any) -> None: ...
def gyration(self) -> builtins.float: ...
def gyration_pbc(self) -> builtins.float: ...
def min_max(self) -> tuple[typing.Any, typing.Any]: ...
def inertia(self) -> tuple[typing.Any, typing.Any]: ...
def inertia_pbc(self) -> tuple[typing.Any, typing.Any]: ...
def save(self, fname: builtins.str) -> None: ...
def translate(self, arg: typing.Any) -> None: ...
def split_resindex(self) -> list[Sel]: ...
def split_chain(self) -> list[Sel]: ...
def split_molecule(self) -> list[Sel]: ...
def to_gromacs_ndx(self, name: builtins.str) -> builtins.str: ...
def iter_pos(self) -> SelPosIterator: ...
def iter_atoms(self) -> SelAtomIterator: ...
class SasaResults:
areas: typing.Any
volumes: typing.Any
total_area: builtins.float
total_volume: builtins.float
class NdxFile:
def __new__(cls, fname: builtins.str) -> NdxFile: ...
def get_group_as_sel(self, gr_name: builtins.str, sys: System) -> Sel: ...
class SysPosIterator:
def __iter__(self) -> SysPosIterator: ...
def __next__(self) -> typing.Any: ...
class SysAtomIterator:
def __iter__(self) -> SysAtomIterator: ...
def __next__(self) -> typing.Any: ...
class SelPosIterator:
def __iter__(self) -> SelPosIterator: ...
def __next__(self) -> typing.Any: ...
class SelAtomIterator:
def __iter__(self) -> SelAtomIterator: ...
def __next__(self) -> typing.Any: ...
def greeting() -> None: ...
def fit_transform(sel1: Sel, sel2: Sel) -> typing.Any: ...
def fit_transform_matching(sel1: Sel, sel2: Sel) -> typing.Any: ...
def rmsd_py(sel1: Sel, sel2: Sel) -> builtins.float: ...
def rmsd_mw(sel1: Sel, sel2: Sel) -> builtins.float: ...
def distance_search(
cutoff: builtins.float | builtins.str,
data1: Sel,
data2: Sel | None = None,
dims: list[builtins.bool] = [False, False, False],
) -> tuple[typing.Any, typing.Any]: ...