aim2dat.strct.ext_analysis.h_bonds

Module implementing hydrogen analysis functions.

Functions

calc_hydrogen_bonds(structure[, host_elements, ...])

Search for hydrogen bonds.

Module Contents

aim2dat.strct.ext_analysis.h_bonds.calc_hydrogen_bonds(structure: aim2dat.strct.Structure, host_elements='O', bond_threshold=1.25, index_constraint=None, scheme: str = 'baker_hubbard')[source]

Search for hydrogen bonds.

Parameters:

  • structure (aim2dat.strct.Structure) – Structure object.

  • host_elements (list or str) – Elements considered as host atoms for hydrogen atoms and hydrogen bonds.

  • bond_threshold (float) – Upper threshold to consider the hydrogen atom chemically bonded to the donor.

  • index_constraint (list or None) – List of site indices to constrain the search.

  • scheme (str) – The applied scheme. Supported options are ‘baker_hubbard’ (doi:10.1016/0079-6107(84)90007-5).

Returns:

tuple – Tuple of triples: site of the hydrogen acceptor, hydrogen site, and site of the hydrogen donor.