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.
Public surface: one path per name¶
Write import molpy as mp and reach every name through mp. Each name has exactly
one public path — there is no molpy.core.Atomistic, molpy.parser or
molpy.optimize spelling. Two layers own the names:
| Layer | What it means | Names |
|---|---|---|
| Re-exported from the native core (molrs) | Identity re-export: mp.Atomistic is molrs.Atomistic. Behaviour and docs come from the native core; molpy adds nothing. |
Graphs and views: Atomistic, CoarseGrain, Atom, Bond, Angle, Dihedral, Improper, VirtualSite, DrudeParticle, MasslessSite, Bead, CGBond, NodeRef, RelationRef, Refs, Port, Graph, Topology, Trace, ExtractedSubgraph · Data: Frame, Block, FrameMeta, MetaDocument, MetaValue, Element, keys, schema · Force field: ForceField, Style / Type and their Atom/Bond/Angle/Dihedral/Improper/Pair subclasses, PotentialCompiler, Potentials, FragmentScaling, BccModel, GasteigerModel, MullikenModel · Notation and perception: SmilesIR, CGSmilesIR, SmilesError, SmartsPattern, SmartsMatch, Perceive, RingInfo, Reaction, Coarsener, SubgraphMatcher · Assembly: Assembler, GrowthPlacer, SitePlacer, AxisOrienter · Shapes: Cuboid, Sphere, Parallelepiped, HalfSpace · Units: Unit, Quantity, UnitRegistry, UnitPreset, UnitsError · Neighbours: NeighborQuery, NeighborList, Neighbors, VerletSkin · Optimisation and conformer reports: LBFGS, OptReport, ConformerReport, ConformerStageReport · Namespaces mp.md, mp.op |
| molpy's own | Defined in molpy; sub marks a subclass of a native type that adds molpy behaviour. | Box (sub), Trajectory (sub), TrajectorySplitter and its strategies, Region, BoxRegion / SphereRegion / Cube / AndRegion / OrRegion / NotRegion (sub), the selectors, UnitSystem (sub), Conformer (sub), Config, Script, fields, FrameCollection |
| Subpackage namespaces | molpy code plus the native names that belong to that subsystem, exported there and nowhere else. | mp.io (readers / writers), mp.builder (planning, crystals, nanostructures, PackingTemplate), mp.compute (every analysis, e.g. mp.compute.RDF, mp.compute.signal), mp.typifier (e.g. mp.typifier.OPLSAATypifier), mp.engine, mp.adapter, mp.data, and molpy.wrapper (imported explicitly) |
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 |
| Perceive angles/dihedrals in place; bond-graph distances; molecule ids of a frame | generate_topology, topo_distances, Topology.from_frame |
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 |
| Apply a reaction SMARTS to a graph (bond formation / removal) | Reaction |
Parser |
Generate fix bond/react pre/post topology templates |
BondReactTemplate, write_bond_react_map |
IO |
| Assemble units along a site graph (chains, rings, stars, combs, backmapping) | Assembler, GrowthPlacer, SitePlacer, AxisOrienter, CGSmilesIR |
Builder |
| Pack molecules into a simulation box | molpack.GenCanPack, Target, molrs regions as restraints |
Pack |
| Generate 3D conformers from a molecular graph | Conformer |
Conformer |
| Assign force field types (OPLS-AA, MMFF94, GAFF via AmberTools) | OPLSAATypifier, MMFF94Typifier, AtdTypifier, AntechamberTypifier, TLeapTypifier |
Typifier |
| Evaluate bond, angle, and pair potentials | PotentialCompiler, Potentials |
Potential |
| Read and write molecular files (PDB, LAMMPS, GRO, …) | read_pdb, write_lammps_data, read_xml_forcefield |
I/O |
Store a frame, trajectory or force field as a *.mrec record |
write_mrec, read_mrec_trajectory, read_mrec_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 |
| Plan polydisperse polymer systems | SystemPlanner, PolydisperseChainGenerator, SchulzZimmPolydisperse |
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 |
Package Responsibilities¶
| Package | Responsibility |
|---|---|
| Core | Foundational data structures: Atomistic, Frame, Block, Box, Trajectory, NodeRef/RelationRef, Region, UnitSystem, ForceField |
| Parser | SMILES / SMARTS / CGsmiles types at the root (mp.SmilesIR, mp.SmartsPattern, mp.CGSmilesIR) |
| Builder | System construction: site-graph assembly and placers, polydisperse planning, nanostructures, crystals, virtual sites |
| Pack | Spatial packing via molpack (molcrafts-molpack) |
| Conformer | 3D conformer generation from molecular graphs |
| Typifier | Force-field typing: OPLS-AA and MMFF94 (native), GAFF / GAFF2 through AmberTools |
| 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 | Optional in-memory bridge to RDKit (worked example) |
| Wrapper | Subprocess interfaces for AmberTools command-line executables |
| Engine | Simulation engine abstractions for LAMMPS, CP2K, OpenMM |
| Optimization | Native L-BFGS minimizer at the root (mp.LBFGS, mp.OptReport) |
| Compute | Trajectory analysis: MSD, Onsager, transport, dielectric, RDF, clustering, … |
| Data | Locators for bundled data files and built-in force fields |