mbuild_polybuild.aa_functional_groups.ester.Ester.to_parmed¶

Ester.to_parmed(box=None, title='', residues=None, include_ports=False, infer_residues=False, infer_residues_kwargs={})¶

Create a ParmEd Structure from a Compound.

Parameters:

box (mb.Box, optional, default=self.boundingbox (with buffer)) – Box information to be used when converting to a Structure. If ‘None’, self.box is used. If self.box is None, a bounding box is used with 0.5 nm buffer in each dimension to avoid overlapping atoms.
title (str, optional, default=self.name) – Title/name of the ParmEd Structure
residues (str of list of str, optional, default=None) – Labels of residues in the Compound. Residues are assigned by checking against Compound.name.
include_ports (boolean, optional, default=False) – Include all port atoms when converting to a Structure.
infer_residues (bool, optional, default=True) – Attempt to assign residues based on the number of bonds and particles in an object. This option is not used if residues == None
infer_residues_kwargs (dict, optional, default={}) – Keyword arguments for mbuild.conversion.pull_residues()

Returns:

ParmEd Structure object converted from self

Return type:

parmed.structure.Structure