Extract

`extract_atoms(path_topo, select=None, frames=None, path_output=None, path_coords=None, kwargs_universe=dict(), kwargs_writer=dict(), overwrite=False)` ¶

Extract atoms or frames from molecular structure(s) using MDAnalysis.

PARAMETER	DESCRIPTION
`path_topo`	Path to topology file. TYPE: `str`
`select`	MDAnalysis selection string. TYPE: `str \| None` DEFAULT: `None`
`frames`	Extract frames from a trajectory. If `None`, the whole trajectory will be included. This is only relevant when `path_output` is specified. TYPE: `Sequence[int] \| None` DEFAULT: `None`
`path_output`	Path to save new coordinate file. If `None`, then no file is written. TYPE: `str \| None` DEFAULT: `None`
`path_coords`	Paths to coordinate file(s) to load. TYPE: `str \| list[str] \| None` DEFAULT: `None`
`kwargs_universe`	Keyword arguments for initializing the MDAnalysis Universe. TYPE: `dict[str, Any]` DEFAULT: `dict()`
`kwargs_writer`	Keyword arguments for MDAnalysis writers. TYPE: `dict[str, Any]` DEFAULT: `dict()`
`overwrite`	Overwrites coordinate file located at `path_output`. This will error out if `False` and the file exists. TYPE: `bool` DEFAULT: `False`

RETURNS	DESCRIPTION
`AtomGroup`	Atomic positions after atom selection.

Example

Suppose we want to extract just protein atoms from an Amber simulation.

run_select_atoms(
    path_topo="mol.prmtop",
    select="protein",
    frames=[0, -1],
    path_output="protein.nc",
    path_coords="traj.nc",
)