pyqmmm.qm.traj_atom_filter

Generate a new trajectory with only selected atoms.

Module Contents

Functions

get_selection()	Request the atoms to remove.
remove_atoms(→ List[List[str]])	Removes an atom and creates a new xyz.
get_pdb_ensemble()	Takes an xyz trajectory and a PDB template file.
traj_atom_filter()

pyqmmm.qm.traj_atom_filter.get_selection()

Request the atoms to remove.

Returns:

selection – A list of atoms.

Return type:

list[int]

pyqmmm.qm.traj_atom_filter.remove_atoms(selection: List[int]) → List[List[str]]

Removes an atom and creates a new xyz.

Takes an atom selection as input. Generates a new trajectory with those atoms removed. The final format is the .xyz format.

Parameters:

selection (list[int]) – A list of atoms.

pyqmmm.qm.traj_atom_filter.get_pdb_ensemble()

Takes an xyz trajectory and a PDB template file. Creates a PDB ensemble file.

pyqmmm.qm.traj_atom_filter.traj_atom_filter()