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:
i_seq (int)
contacts (list of mmtbx.ions.environment.atom_contact)
pdb_atoms (iotbx.pdb.hierarchy.af_shared_atom)
connectivity (scitbx.array_family.shared.stl_set_unsigned)
unit_cell (uctbx.unit_cell)
params (libtbx.phil.scope_extract)
assume_hydrogens_all_missing (bool, optional)
- Return type:
- 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.