mbuild_polybuild.aa_functional_groups.ammonium.Ammonium.from_pybel¶

Ammonium.from_pybel(pybel_mol, use_element=True, coords_only=False, infer_hierarchy=True, ignore_box_warn=False)¶

Create a Compound from a Pybel.Molecule.

Parameters:

pybel_mol (pybel.Molecule)
use_element (bool, default True) – If True, construct mb Particles based on the pybel Atom’s element. If False, construcs mb Particles based on the pybel Atom’s type
coords_only (bool, default False) – Set preexisting atoms in compound to coordinates given by structure. Note: Not yet implemented, included only for parity with other conversion functions
infer_hierarchy (bool, optional, default=True) – If True, infer hierarchy from residues
ignore_box_warn (bool, optional, default=False) – If True, ignore warning if no box is present.