mmtbx.ions.halides module

Functions specific to identifying halide ions. Very preliminary - needs much more sophisticated analysis.

mmtbx.ions.halides.is_favorable_halide_environment(i_seq, contacts, pdb_atoms, sites_frac, connectivity, unit_cell, params, assume_hydrogens_all_missing=<libtbx.AutoType object>)

Detects if an atom’s site exists in a favorable environment for a halide ion. This includes coordinating by a positively charged sidechain or backbone as well as an absense of negatively charged coordinating groups.

Parameters:
Return type:

bool

mmtbx.ions.halides.is_negatively_charged_oxygen(atom_name, resname)

Determine whether the oxygen atom of interest is either negatively charged (usually a carboxyl group or sulfate/phosphate), or has a lone pair (and no hydrogen atom) that would similarly repel anions.

Parameters:
  • atom_name (str)

  • resname (str)

Return type:

bool