peppr.standardize#

peppr.standardize(system: AtomArray | AtomArrayStack, remove_monoatomic_ions: bool = True) → AtomArray | AtomArrayStack[source]#

Standardize the given system.

This function

  • removes hydrogen atoms

  • removes solvent atoms

  • removes monoatomic ions, if specified

  • checks if an associated biotite.structure.BondList is present

Parameters:
systemstruc.AtomArray or struc.AtomArrayStack

The system to standardize.

remove_monoatomic_ionsbool, optional

If set to True, monoatomic ions will be removed from system.

Returns:
struc.AtomArray or struc.AtomArrayStack

The standardized system.