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Polymers vs Molecules

AutoPoly has two model classes. Picking the right one is the first decision in any script.

Feature Polymer Molecule
Use for Polymer chains of any length Solvents, additives, any small molecule
SMILES Complement SMILES with [*] wildcards Regular SMILES — no wildcards
Defined by chain_num, sequence, topology, tacticity Count, Smiles, Name
Chain bonds Bonds created between sequence neighbors Independent molecules, no inter-molecule bonds
Example Polymer(chain_num=10, sequence=["CC[*]"]+["[*]CC[*]"]*48+["[*]CC"]) Molecule(Count=100, Smiles="O", Name="water")

Wildcard rule

[*] wildcards belong to Polymer sequences only. A Molecule SMILES containing [*] is rejected — this is the most common mix-up between the two classes.

When to use Polymer

Anything with a backbone built from repeated units — homopolymers, block copolymers, alternating copolymers, ring polymers:

from AutoPoly import Polymer

polymer = Polymer(
    chain_num=10,                    # chains in the box
    sequence=["CC[*]"] + ["[*]CC[*]"] * 48 + ["[*]CC"],
    topology="linear",               # or "ring"
    tacticity="atactic",             # or "isotactic", "syndiotactic"
)

Key points:

  • DOP is implicit — len(sequence), never a separate parameter
  • Sequence order is chain order — mix monomers for copolymers
  • Ring topology uses only middle variants — see Complement SMILES

When to use Molecule

Anything that stays a single, unbonded molecule in the box:

from AutoPoly import Molecule

water   = Molecule(Count=100, Smiles="O",   Name="water")
ethanol = Molecule(Count=20,  Smiles="CCO", Name="ethanol")

Note the capitalized parameter names (Count, Smiles, Name) — Molecule keeps this older calling convention, unlike the snake_case Polymer.

Mixed systems

Pass both classes together in the models list to build polymer solutions, melts with additives, or multi-solvent mixtures:

from AutoPoly import System, Polymer, Molecule, generate

system = System(out="solution")

polymer = Polymer(
    chain_num=5,
    sequence=["COC[*]"] + ["[*]COC[*]"] * 48 + ["[*]COC"],   # PEO
)
water = Molecule(Count=200, Smiles="O", Name="water")

generate(
    system,
    "peo_solution",
    [polymer, water],     # polymers and molecules mix freely
    force_field="gaff",
)

For force field choice in mixed systems, see the Force Fields guide — GAFF/GAFF2 usually handle both polymers and small organic solvents well. A full worked example is the Polymer Solution tutorial.