mbuild_polybuild.aa_functional_groups.tftp.TFTP.from_parmed

TFTP.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