polymerist.polymers.building.linear

For generating linear polymer structure from monomer, sequence, and chain length information

Attributes

LOGGER

Functions

build_linear_polymer(→ mbuild.lib.recipes.polymer.Polymer)

Builds a linear polymer structure from a specified pool of monomers, sequence, target chain length, and other parameters

Module Contents

polymerist.polymers.building.linear.LOGGER
polymerist.polymers.building.linear.build_linear_polymer(monomers: polymerist.polymers.monomers.repr.MonomerGroup, n_monomers: int, sequence: str = 'A', minimize_sequence: bool = True, allow_partial_sequences: bool = False, add_Hs: bool = False, energy_minimize: bool = False) → mbuild.lib.recipes.polymer.Polymer[source]

Builds a linear polymer structure from a specified pool of monomers, sequence, target chain length, and other parameters

Parameters:

  • monomers (MonomerGroup) – A group of fragments containing at least the distinct repeat units which occur in the target polymer

    IMPORTANT: if the “term_orient” field of the MonomerGroup is not set (with “head” and “tail” monomer designations), the first two terminal (1-valent) monomers in the group will be auto-assigned and taken as the head and tail, respectively, or, if there is only one terminal monomer present, it will be used as both the head and tail.

  • n_monomers (int) – The number of monomer units in the target polymer chain This includes the terminal monomers in the count, e.g. n_monomers=10 with a head and tail group specified will induce 8 middle monomers

  • sequence (str, default=’A’) – A string of characters representing the sequence of monomers as they should occur within the polymer chain Each unique character in the string will be associated with a unique monomer in the provided MonomerGroup, in the order that they appear, e.g. “BACA” will take the second, first, third, and first monomers defined in the group

    IMPORTANT: the sequence string only specifies the MIDDLE monomers in the chain, i.e. terminal monomers are not given by the sequence string, but either by the “term_orient” field of the MonomerGroup or the auto-determined end groups if that is unset

    If the sequence is shorter than n_monomers, the sequence will be repeated until the target chain length is reached.

  • minimize_sequence (bool, default=True) – Whether to attempt to reduce the sequence provided into a minimal, repeating subsequence E.g. “ABABAB” will be reduced to 3*”AB” if this is set to True

    Note carefully that this has NOTHING TO DO WITH energy minimization; that is controlled by the energy_minimize flag

  • allow_partial_sequences (bool, default=False) – Whether to allow fractional repetitions of the sequence kernel to fill the target chain length

    For example, given a monomer group with head/tail specified and parameters n_monomers=10 and sequence=”BAC” (inducing 10 - 2 = 8 middle monomers): allow_partial_sequences=True will repeat the sequence 2 + 2/3 times, yielding the equivalent middle monomer sequence “BACBACBA”, while allow_partial_sequences=False would raise Exception, since the sequence “BAC” cannot be repeated to fill 8 middle monomers exactly.

  • add_Hs (bool, default=False) – Whether to instruct the mbuild Polymer recipe to cap uncapped terminal groups with hydrogens, in cases where the user has failed to provide ANY terminal monomers in the MonomerGroup

  • energy_minimize (bool, default=False) – Whether to perform a brief UFF energy minimization after build to relax the resulting polymer structure Tends to give less-unphysical conformers for larger polymers, but is significantly slower, especially for longer chains

Returns:

chain – An mbuild Polymer (Compound) object representing the assembled linear polymer chain

Return type:

mbuild.Compound