API Reference¶
All public symbols are documented on the package pages listed below. Docstrings are auto-generated from source annotations; signatures include type hints throughout. The tables on this page provide a task-oriented index for locating the appropriate symbol and package without prior knowledge of MolPy's internal organization.
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) | Topology |
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 |
| Assign force field atom types via SMARTS matching | OplsAtomisticTypifier, GaffTypifier |
Typifier |
| Evaluate bond, angle, and pair potentials | BondHarmonic, LJ126 |
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 | PrepareMonomer, polymer, generate_3d |
Tool |
| Compute mean-squared displacement and correlations | MSD, DisplacementCorrelation |
Tool |
| Generate LAMMPS or CP2K input decks | LAMMPSEngine, CP2KEngine |
Engine |
Package Responsibilities¶
| Package | Responsibility |
|---|---|
| Core | Foundational data structures: Atomistic, Frame, Block, Box, Trajectory, Topology, 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 |
| Typifier | SMARTS-based atom typing for OPLS-AA and GAFF force fields |
| 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 |
| Tool | High-level multi-step preparation workflows and analysis operators |
| Engine | Simulation engine abstractions for LAMMPS and CP2K |
| Optimization | Potential wrappers for geometry optimization workflows |