mbuild_polybuild.aa_functional_groups.amide.Amide.from_parmed

Amide.from_parmed(structure, coords_only=False, infer_hierarchy=True)

Extract atoms and bonds from a pmd.Structure.

Will create sub-compounds for every chain if there is more than one and sub-sub-compounds for every residue.

Parameters:

• structure (pmd.Structure) – The structure to load.

• coords_only (bool) – Set preexisting atoms in compound to coordinates given by structure.

• infer_hierarchy (bool, optional, default=True) – If true, infer compound hierarchy from chains and residues