| 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 |
| Perceive angles/dihedrals in place; k-hop bond-graph queries |
get_topo, get_topo_neighbors, get_topo_distances |
Core |
| Define and query force field parameters |
ForceField, Style, Type |
Core |
| Parse SMILES / SMARTS |
mp.io.read_smiles, SmilesIR, SmartsPattern |
Parser |
| Perceive hydrogens / aromaticity / rings |
Perceive, RingInfo |
Core |
| Execute a chemical reaction (bond formation / removal) |
Reaction, GraphAssembler, Selector |
Builder |
Generate fix bond/react pre/post topology templates |
BondReactTemplate, write_bond_react_map |
IO |
| Assemble polymer chains |
MonomerLibrary, PolymerBuilder, Selector, Placer |
Builder |
| Pack molecules into a simulation box |
molpack.Molpack, Target, restraints |
Pack |
| Generate 3D conformers from a molecular graph |
Conformer |
Conformer |
| Assign force field atom types via SMARTS matching |
OPLSAATypifier, 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 |
| Bridge to a third-party library (in-memory) |
Adapter, RDKitAdapter (optional example) |
Adapter |
| Invoke external CLI tools (antechamber, tleap) |
Wrapper, AntechamberWrapper |
Wrapper |
| Build polymer chains and crosslinked networks |
PolymerBuilder, GraphAssembler, Conformer |
Builder |
| Compute mean-squared displacement, correlations, RDF, clustering |
MSD, Onsager, 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 |