Guides¶

Each guide takes one concrete modeling task from input to simulation-ready output — the how-to layer of the manual. The Example Gallery holds copy-paste short forms of several of these; the guides are the full story. When a term is unfamiliar, the data-model tutorials are where it is defined.

Several guides use polymers as the working example — a demonstration domain, not a statement of scope. Chain growth, crosslinking, and polydispersity exercise every part of MolPy's editing machinery; the same operations apply to any complex molecular system.

Foundations¶

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

Chain & Network Construction¶

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

Parameterization¶

• Force Field Typification — SMARTS-based atom type assignment and force field parameter resolution

Geometry & Packing¶

• 3D Conformer Generation — embedding chemically valid 3D coordinates for a parsed or constructed structure
• Geometry Optimization — force-field-driven structure minimization and how to read the optimization report
• Packing Systems — filling a simulation cell with molecules under geometric constraints via the Packmol backend
• Polarizable & Virtual-Site Models — Drude shells and TIP4P M-sites through the virtual-site builder protocol

Export & Engines¶

• File I/O — reading and writing molecular data, trajectories, log files, and force-field formats
• Simulation Engines — generating input decks for LAMMPS, CP2K, and OpenMM, and running them from Python

Tools & Ecosystem¶

• AmberTools Integration — a complete electrolyte preparation workflow driving antechamber, parmchk2, and tleap
• Moltemplate CLI — converting moltemplate .lt files to MolPy systems and back
• MCP Suite — exposing MolPy symbols and docs to Model Context Protocol agents