Crate molrs 

molrs

Unified façade for the molrs molecular simulation toolkit.

This crate re-exports the molrs workspace crates under a single namespace. Downstream users add one dependency and opt into sub-systems via features:

molcrafts-molrs = { version = "0.0.11", features = ["io", "smiles"] }

Then:

use molrs::Frame;              // from molrs-core
use molrs::io::read_xyz;       // feature = "io"
use molrs::smiles::parse;      // feature = "smiles"

Features

• io — file I/O (PDB, XYZ, LAMMPS, CHGCAR, Cube, Zarr)
• compute — trajectory analysis (RDF, MSD, clustering, tensors)
• smiles — SMILES parser
• ff — force fields (MMFF94, PME, typifier)
• embed — 3D coordinate generation
• full — everything above

Core flags forwarded to molrs-core: rayon, zarr, filesystem, blas.

Molecular packing

The Packmol port lives in the standalone molcrafts-molpack crate (https://github.com/MolCrafts/molpack); add it as a separate dependency when needed.

Modules

atomistic

All-atom molecular graph with element-level semantics.

block

Block: dict-like keyed arrays with consistent axis-0 length and heterogeneous types.

coarsegrain

Coarse-grained molecular graph.

data

Embedded data files shipped with molrs-core.

element

Element data and basic lookup utilities.

error

Unified error types for the molrs library.

field

Field observables for MolRec-style continuous physical quantities.

frame

Frame: a dictionary mapping string keys to heterogeneous Blocks.

frame_access

Unified access trait for owned and borrowed frame types.

frame_view

Zero-copy borrowed view of a Frame.

gasteiger

Gasteiger-Marsili (1980) iterative electronegativity equalization.

grid

Uniform spatial grid storing multiple named scalar arrays.

hydrogens

Hydrogen addition for molecular graphs.

mapping

AA ↔ CG mapping: coarsen and backmap between Atomistic and CoarseGrain molecular graphs.

math

Small linear algebra helpers with optional BLAS-backed implementation.

molgraph

Dynamic molecular graph for editing-oriented CRUD operations.

molrec

Backend-agnostic MolRec logical model.

neighbors

Neighbor-list algorithms for pairwise distance queries.

region

Region module exports

rings

Ring detection for molecular graphs.

rotatable

Rotatable bond detection and downstream atom BFS.

stereo

Stereochemistry support for molecular graphs.

topology

Graph-based molecular topology using petgraph.

types

Common numeric and geometry type aliases used across the crate.

Structs

Atom

A dynamic property bag representing an atom (or bead).

AtomId

Stable handle to an atom in a MolGraph.

Atomistic

All-atom molecular graph.

Block

A dictionary from string keys to ndarray arrays with a consistent axis-0 length.

Bond

A bond between two atoms.

BondId

Stable handle to a bond in a MolGraph.

CGMapping

AA ↔ CG mapping definition.

CoarseGrain

Coarse-grained molecular graph.

Frame

A dictionary from string keys to Blocks.

FrameView

A borrowed, read-only view of a Frame.

GasteigerCharges

Computed Gasteiger partial charges for one heavy atom.

Grid

A collection of named scalar arrays on a shared uniform spatial grid.

MolGraph

A dynamic molecular graph supporting ergonomic CRUD for atoms, bonds, angles, and dihedrals.

MolRec

Single logical MolRec object.

ObservableRecord

Named observable with semantic metadata.

RingInfo

All ring information for a MolGraph, produced by find_rings.

Topology

Graph-based molecular topology.

TopologyRingInfo

Ring information from SSSR detection on a Topology graph.

Trajectory

Trajectory-like list of frame states plus shared indexing arrays.

UniformGridField

Uniform real-space grid samples of a scalar field.

Enums

BondStereo

Double-bond stereochemistry.

Element

Chemical element with complete periodic table (elements 1-118)

MolRsError

Main error type for the molrs library.

ObservableData

Raw observable payload.

ObservableKind

Observable kind aligned with the MolRec metadata contract.

PropValue

Heterogeneous property value stored in an Atom.

TetrahedralStereo

Tetrahedral stereochemistry at an atom.

WeightScheme

How bead positions are computed from constituent atoms.

Traits

FrameAccess

Unified read-only access for Frame and FrameView.

Functions

add_hydrogens

Return a new MolGraph with explicit hydrogen atoms added to every heavy atom that has unfilled valence.

assign_bond_stereo_from_3d

Infer E/Z stereochemistry for every double bond from 3-D coordinates.

assign_stereo_from_3d

Infer tetrahedral chirality for every potential stereocentre from 3-D coordinates.

chiral_volume

Compute the signed scalar triple product (chiral volume) at center.

compute_gasteiger_charges

Compute Gasteiger-Marsili (1980) partial charges for every heavy atom in mol.

find_chiral_centers

Return the atom IDs that are potential tetrahedral stereocentres: atoms with exactly 4 distinct neighbour atom IDs.

find_rings

Compute the ring information (SSSR / minimum cycle basis) for mol.

implicit_h_count

Compute the number of hydrogens to add to atom_id.

remove_hydrogens

Return a new MolGraph with all terminal explicit hydrogen atoms removed.

Type Aliases

Bead

Alias for coarse-grained usage — same type, different prop keys by convention.

SchemaValue

Hierarchical schema node used by meta, method, and parameters.