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 (symbol, 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: A thin wrapper around an igraph graph, derived from the bond list of an Atomistic. Provides graph algorithms (shortest paths, connected components, ring detection). 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 k0=320.0 and r0=1.41. Subclasses: AtomType, BondType, AngleType, DihedralType, PairType.
Potential: The numerical realization of a style's types — arrays of parameters ready for energy/force computation. Produced by style.to_potential(). 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: OplsAtomisticTypifier, GaffTypifier. 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.
Tool: A packaged recipe that wires multiple MolPy modules into a single callable — for example, PrepareMonomer, polymer(). See Tool Layer.
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.