mbuild_polybuild.aa_functional_groups.ester.Ester.to_trajectory¶

Ester.to_trajectory(include_ports=False, chains=None, residues=None, box=None)¶

Convert to an md.Trajectory and flatten the compound.

Parameters:

include_ports (bool, optional, default=False) – Include all port atoms when converting to trajectory.
chains (mb.Compound or list of mb.Compound) – Chain types to add to the topology
residues (str of list of str) – Labels of residues in the Compound. Residues are assigned by checking against Compound.name.
box (mb.Box, optional, default=self.boundingbox (with buffer)) – Box information to be used when converting to a Trajectory. If ‘None’, self.box is used. If self.box is None, a bounding box is used with a 0.5 nm buffer in each dimension to avoid overlapping atoms.

Returns:

trajectory

Return type:

md.Trajectory