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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 and SMARTS strings into Atomistic structures (BigSMILES is no longer parsed; CGsmiles is covered in Assembly)

Chain & Network Construction

  • Assembly — units with ports joined along a site graph by Assembler: grown from a CGsmiles topology, or backmapped onto a coarse-grained model
  • Polydisperse Systems — molecular-weight distribution sampling, atomistic chain construction, and box packing

Polymer Topologies

From one ethylene-oxide kit to every architecture the site-graph assembler supports. Each page pairs with examples/topology/<same-name>.py.

Parameterization

Geometry & Packing

  • Nanostructures — zigzag, armchair, and chiral carbon nanotubes with open or periodic axial topology
  • 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 restraints via molpack
  • 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