api

A module including the API for the topology subpackage.

Summary

Functions:

generate_shake_topology_file	Wrapper function to generate a shake topology file for a given trajectory.
select_from_restart_file	Selects atoms from a restart file and writes them to a new file.
selection_from_restart_file_as_list	Selects atoms from a restart file and writes them to a new file.

Reference

generate_shake_topology_file(

trajectory: Trajectory,

selection: SelectionCompatible = None,

output: str | None = None,

mode: FileWritingMode | str = 'w',

use_full_atom_info: bool = False,

) → None

Wrapper function to generate a shake topology file for a given trajectory.

Parameters:

• trajectory (Trajectory) – The trajectory to generate the shake topology for.

• selection (SelectionCompatible, optional) – Selection is either a selection object or any object that can be initialized via ‘Selection(selection)’. default None (all atoms)

• output (str | None, optional) – The output file. If not specified, the output is printed to stdout.

• mode (FileWritingMode | str, optional) – The writing mode, by default “w”. The following modes are available: - “w”: write - “a”: append - “o”: overwrite

• use_full_atom_info (bool, optional) – If True, the full atom information (name, index, mass) is used for the selection, by default False Is always ignored if atoms is not a list of atom objects.

select_from_restart_file(

selection: SelectionCompatible,

restart_file: str,

moldescriptor_file: str | None = None,

use_full_atom_info: bool = False,

) → Np1DIntArray

Selects atoms from a restart file and writes them to a new file.

Parameters:

• selection (SelectionCompatible) – Selection is either a selection object or any object that can be initialized via ‘Selection(selection)’.

• restart_file (str) – The restart file to read the atoms from.

• moldescriptor_file (str | None, optional) – The moldescriptor file to read the atom types from, by default None

• use_full_atom_info (bool, optional) – If True, the full atom information (name, index, mass) is used for the selection, by default False Is always ignored if atoms is not a list of atom objects.

selection_from_restart_file_as_list(

selection: SelectionCompatible,

restart_file: str,

moldescriptor_file: str | None = None,

use_full_atom_info: bool = False,

) → list[int]

Selects atoms from a restart file and writes them to a new file.

Parameters:

• selection (SelectionCompatible) – Selection is either a selection object or any object that can be initialized via ‘Selection(selection)’.

• restart_file (str) – The restart file to read the atoms from.

• moldescriptor_file (str | None, optional) – The moldescriptor file to read the atom types from, by default None

• use_full_atom_info (bool, optional) – If True, the full atom information (name, index, mass) is used for the selection, by default False Is always ignored if atoms is not a list of atom objects.