Guides

Each guide in this section addresses a concrete modeling task, from input specification to simulation-ready output. The notebooks and worked examples are self-contained and emphasize workflows in polymer construction, reactive topology editing, force-field assignment, and file generation. Readers are assumed to be familiar with MolPy's core data model, as described in Concepts.

Foundational Subsystems

• Chemistry Notation Parsing — conversion of SMILES, SMARTS, BigSMILES, and CGSmiles strings into Atomistic structures

Polymer Construction Workflows

• Stepwise Chain Construction — explicit reaction-based monomer coupling, the PolymerBuilder interface, and high-level facade functions
• Topology-Driven Assembly — specification of linear, cyclic, and branched polymer architectures via CGSmiles expressions
• Crosslinked Network Generation — template-based network formation and pre/post topology generation for LAMMPS fix bond/react
• Polydisperse System Construction — molecular-weight distribution sampling, atomistic chain construction, and box packing

Parameterization and External Tool Integration

• Force Field Typification — SMARTS-based atom type assignment and force field parameter resolution
• PEO–LiTFSI Electrolyte via AmberTools — a complete polymer electrolyte system preparation workflow using the AmberTools integration

Related Concept Pages

• Tool Layer — how MolPy packages common multi-step workflows behind Tool interfaces
• I/O — how Frame and ForceField objects are serialized to files and trajectories
• Engine — how generated structures and scripts are handed off to LAMMPS, CP2K, and OpenMM