Glossary

Glossary¶

Quick definitions for MolPy's core terminology. Each entry links to the page that covers the concept in depth.

Data structures¶

Atomistic: An editable molecular graph where atoms are nodes and bonds are edges. Use it when the structure is still under construction — adding atoms, removing leaving groups, querying neighbors. See Atomistic and Topology.
Entity: Base class for atoms and beads. Dictionary-like: read and write properties with bracket notation. Uses identity-based hashing (id(self)), not value-based equality.
Atom: An Entity subclass representing one atom. Carries arbitrary key-value properties (element, charge, type, etc.).
Bead: An Entity subclass representing one coarse-grained site.
Link: Base class for topology connections. Holds an ordered tuple of Entity endpoints. Subclasses: Bond, Angle, Dihedral, Improper.
Struct: Base class that aggregates entities and links into a container. Subclasses: Atomistic, CoarseGrain.
Topology: The derived view of an Atomistic's bond graph, computed by the molrs Rust kernels. get_topo() returns a new Atomistic with angles/dihedrals perceived from the bonds; get_topo_neighbors() / get_topo_distances() answer k-hop graph queries. There is no standalone topology class. See Atomistic and Topology.
Block: A columnar table mapping string keys to NumPy arrays. All columns share the same row count. Used inside Frame to store atoms, bonds, angles, etc. See Block and Frame.
Frame: A named collection of Block objects plus free-form metadata. Represents one complete system snapshot. The universal exchange object for I/O. See Block and Frame.
Box: A simulation cell defined by a 3x3 lattice matrix and periodic boundary conditions. Provides wrapping, minimum-image distances, and coordinate conversion. See Box and Periodicity.
Trajectory: An ordered sequence of Frame objects. Supports lazy access via generators and map transforms. See Trajectory.

Force field¶

ForceField: A container that holds all styles, types, and parameters for a molecular system. Created manually or loaded from XML/LAMMPS/AMBER files.
Style: An interaction family within a force field — for example, "harmonic" bonds or "lj126/cut" pairs. Defines which parameters are expected. Subclasses: BondStyle, AngleStyle, DihedralStyle, PairStyle.
Type: One concrete parameter record within a style. For example, a bond type "CT-OH" with k=320.0 and r0=1.41. Subclasses: AtomType, BondType, AngleType, DihedralType, PairType.
Potential: The numerical realization of a force field's styles and types, ready for energy/force computation. Produced by ff.to_potentials() (a deferred Potentials) and evaluated against a typed Frame via pots.calc_energy(frame) / pots.calc_forces(frame); the kernels run in the molrs Rust extension. See Force Field.

Modules¶

Parser: Converts string notations (SMILES, SMARTS, BigSMILES, CGSmiles) into MolPy structures. See Parsing Chemistry.
Reacter: Executes a chemical reaction by connecting two Atomistic objects at designated port atoms, removing leaving groups, and forming new bonds. See Stepwise Polymer Construction.
Port: A marker on an atom (<, >, or $) indicating that it is a reactive connection point for polymerization.
Typifier: Assigns force field types to atoms, bonds, angles, and dihedrals via SMARTS pattern matching. Subclasses: OplsTypifier, ClpTypifier, MMFFTypifier, PairTypifier. (GAFF atom types are not a Typifier — they come from AmberTools/antechamber; see AmberTools Integration.) See Force Field Typification.
Selector: A composable predicate that filters atoms in a Block by element, type, coordinate range, or distance. Combinable with &, |, ~. See Selector.
Wrapper: Runs an external executable (antechamber, tleap, Packmol) as a subprocess and captures its results. Crosses an execution boundary. See Wrapper and Adapter.
Adapter: Translates between MolPy objects and another library's in-memory objects (RDKit, OpenBabel). Crosses a representation boundary. See Wrapper and Adapter.

Naming conventions¶

atomi / atomj / atomk / atoml: Integer atom indices used in Frame and Block (the data-interchange layer). Always 0-based. Never store object references.
itom / jtom / ktom / ltom: Atom object references used in Entity-level topology (Bond, Angle, Dihedral). Never store integers. See Naming Conventions.

Compute terminology¶

Acronyms used across the Compute analyses.

RDF — radial distribution function g(r): Probability of finding a neighbour at distance r relative to an ideal gas. See Structural Analysis.
MSD — mean-squared displacement: ⟨|r(t) − r(0)|²⟩; its slope gives the self-diffusion coefficient. See Diffusion & Ionic Transport.
VACF — velocity autocorrelation function: ⟨v(0)·v(t)⟩; its integral (Green–Kubo) gives diffusion, its FFT gives the VDOS. See Velocity Autocorrelation & VDOS.
VDOS — vibrational density of states: Spectral density of atomic motion, ∝ FFT[VACF]. See Velocity Autocorrelation & VDOS.
MCD — mean-displacement correlation (distinct diffusion): Cross-correlated displacements between different species — the distinct part of diffusion, beyond the single-particle MSD. See Diffusion & Ionic Transport.
PMSD — polarization mean-squared displacement: MSD of the collective charge dipole; the Einstein route to ionic conductivity. See Dielectric Spectroscopy.
SDF — spatial distribution function: Three-dimensional density of neighbours around a reference frame (angular structure, not just radial). See Distribution Functions.
CDF — combined distribution function: A joint histogram over two geometric observables (e.g. distance × angle). See Distribution Functions.
PMFT — potential of mean force and torque: Free energy −k_BT ln g over relative position/orientation coordinates. See Distribution Functions.
ROA / VCD — Raman optical activity / vibrational circular dichroism: Chiroptical vibrational spectra derived from correlation functions of the polarizability / magnetic-dipole responses. See Vibrational Spectra.