Skip to content

API Reference

Auto-generated reference for every public symbol, with typed signatures throughout. Start from the tables below: find your task, get the symbol and its package.

Index of Operations and Symbols

Operation Primary symbols Package
Construct a molecule from atoms and bonds Atomistic, def_atom, def_bond Core
Store tabular molecular data Block, Frame Core
Define a periodic simulation cell Box Core
Represent a time-ordered frame sequence Trajectory Core
Query bond-graph relations (angles, paths, rings) get_topo, get_topo_neighbors, get_topo_distances Core
Define and query force field parameters AtomisticForcefield, Style, Type Core
Parse SMILES / BigSMILES / SMARTS / CGSmiles parse_molecule, parse_monomer, parse_smarts, parse_cgsmiles Parser
Execute a chemical reaction (bond formation / removal) Reacter, find_port, select_neighbor Reacter
Generate fix bond/react pre/post topology templates TemplateReacter Reacter
Assemble polymer chains from CGSmiles PolymerBuilder, Connector, Placer Builder
Pack molecules into a periodic simulation box Molpack, InsideBoxConstraint Pack
Generate 3D conformers from a molecular graph Conformer Conformer
Assign force field atom types via SMARTS matching OplsTypifier, ClpTypifier, MMFFTypifier Typifier
Evaluate bond, angle, and pair potentials BondHarmonicStyle, LJ126Style, Potentials Potential
Read and write molecular files (PDB, LAMMPS, GRO, …) read_pdb, write_lammps_data, read_xml_forcefield I/O
Convert between MolPy and RDKit / OpenBabel objects RDKitAdapter, OpenBabelAdapter Adapter
Invoke external CLI tools (antechamber, tleap) Wrapper, AntechamberWrapper Wrapper
Execute packaged multi-step preparation workflows prepare_monomer, polymer, generate_3d Builder
Compute mean-squared displacement, correlations, RDF, clustering MSD, MCDCompute, RDF Compute
Locate bundled data files and built-in force fields get_forcefield_path, get_path Data
Generate LAMMPS, CP2K, or OpenMM input decks LAMMPSEngine, CP2KEngine, OpenMMEngine Engine

Package Responsibilities

Package Responsibility
Core Foundational data structures: Atomistic, Frame, Block, Box, Trajectory, Entity/Link, Region, UnitSystem, ForceField
Parser Grammar-based notation parsing: SMILES, SMARTS, BigSMILES, CGSmiles, G-BigSMILES
Reacter Chemical reaction framework: site and leaving-group selectors, bond formers, reactive MD templates
Builder Polymer system construction: builders, port connectors, geometric placers
Pack Spatial packing of molecular ensembles via the Packmol executable
Conformer 3D conformer generation from molecular graphs (molrs backend)
Typifier SMARTS-based atom typing for OPLS-AA, CL&P, and MMFF force fields (GAFF atom types come from the AmberTools wrappers)
Potential Numerical potential kernels for bonds, angles, dihedrals, and non-bonded interactions
I/O Format-specific readers and writers for molecular data, force fields, and trajectories
Adapter In-memory representation bridges to RDKit and OpenBabel
Wrapper Subprocess interfaces for AmberTools command-line executables
Engine Simulation engine abstractions for LAMMPS and CP2K
Optimization Potential wrappers for geometry optimization workflows
Compute Trajectory analysis: MSD, displacement correlation, RDF, clustering, and custom compute operators
Data Locators for bundled data files and built-in force fields