Crate dreid_forge 

A high-performance, pure Rust library for automated DREIDING force field parameterization. It orchestrates structure repair, topology perception, and partial atomic charge calculation to produce simulation-ready inputs for both biological macromolecules and arbitrary chemical systems.

Features

• Atom typing — Automatic assignment of DREIDING atom types based on element, hybridization, and local bonding environment
• Flexible charge calculation — Global QEq, hybrid (classical + QEq), or embedded QEq with environment polarization for ligands in protein complexes
• Parameter generation — Bond, angle, dihedral, improper, van der Waals, and hydrogen bond potentials with multiple functional forms
• Flexible I/O — Read/write PDB, mmCIF, MOL2, SDF formats; export to BGF and LAMMPS simulation input files

Quick Start

The main entry point is the forge function, which takes a System and ForgeConfig and produces a fully parameterized ForgedSystem:

use dreid_forge::{System, Atom, Bond, Element, BondOrder};
use dreid_forge::{forge, ForgeConfig, ForgeError};

// Build an ethanol molecule (C₂H₅OH)
let mut system = System::new();

// Atoms: C1 (methyl), C2 (methylene), O, and hydrogens
system.atoms.push(Atom::new(Element::C, [-1.270,  0.248,  0.000])); // C1
system.atoms.push(Atom::new(Element::C, [ 0.139, -0.308,  0.000])); // C2
system.atoms.push(Atom::new(Element::O, [ 1.036,  0.789,  0.000])); // O
system.atoms.push(Atom::new(Element::H, [-1.317,  0.885,  0.883])); // H on C1
system.atoms.push(Atom::new(Element::H, [-1.317,  0.885, -0.883])); // H on C1
system.atoms.push(Atom::new(Element::H, [-2.030, -0.533,  0.000])); // H on C1
system.atoms.push(Atom::new(Element::H, [ 0.358, -0.920,  0.876])); // H on C2
system.atoms.push(Atom::new(Element::H, [ 0.358, -0.920, -0.876])); // H on C2
system.atoms.push(Atom::new(Element::H, [ 1.939,  0.473,  0.000])); // H on O

// Bonds
system.bonds.push(Bond::new(0, 1, BondOrder::Single)); // C1-C2
system.bonds.push(Bond::new(1, 2, BondOrder::Single)); // C2-O
system.bonds.push(Bond::new(0, 3, BondOrder::Single)); // C1-H
system.bonds.push(Bond::new(0, 4, BondOrder::Single)); // C1-H
system.bonds.push(Bond::new(0, 5, BondOrder::Single)); // C1-H
system.bonds.push(Bond::new(1, 6, BondOrder::Single)); // C2-H
system.bonds.push(Bond::new(1, 7, BondOrder::Single)); // C2-H
system.bonds.push(Bond::new(2, 8, BondOrder::Single)); // O-H

// Parameterize with default settings
let forged = forge(&system, &ForgeConfig::default())?;

// Atom types: C_3 (sp³ carbon), O_3 (sp³ oxygen), H_, H_HB (H-bond donor)
assert_eq!(forged.atom_types.len(), 4);
assert!(forged.atom_types.contains(&"C_3".to_string()));
assert!(forged.atom_types.contains(&"O_3".to_string()));
assert!(forged.atom_types.contains(&"H_HB".to_string()));

// Per-atom properties: charge, mass, type index
assert_eq!(forged.atom_properties.len(), 9);

// Bond potentials: C-C, C-O, C-H, O-H
assert_eq!(forged.potentials.bonds.len(), 8);

// Angle potentials: all angles around sp³ centers
assert_eq!(forged.potentials.angles.len(), 13);

// Dihedral potentials: H-C-C-H, H-C-C-O, C-C-O-H, H-C-O-H
assert_eq!(forged.potentials.dihedrals.len(), 12);

// Improper potentials: none for all-sp³ molecule
assert!(forged.potentials.impropers.is_empty());

// VdW pair potentials: n(n+1)/2 = 4×5/2 = 10 pairs
assert_eq!(forged.potentials.vdw_pairs.len(), 10);

// H-bond potential: O_3 as donor/acceptor with H_HB
assert_eq!(forged.potentials.h_bonds.len(), 1);

Module Organization

• io — File I/O for molecular structures (PDB, mmCIF, MOL2, SDF, BGF, LAMMPS)
• forge — Main parameterization function
• ForgeConfig — Configuration for potential types and charge methods

Data Types

Input Structures

• System — Molecular system with atoms, bonds, and optional metadata
• Atom — Single atom with element and Cartesian coordinates
• Bond — Bond between two atoms with bond order
• Element — Chemical element (H through Og)
• BondOrder — Bond order (Single, Double, Triple, Aromatic)

Output Structures

• ForgedSystem — Fully parameterized system ready for simulation
• AtomParam — Per-atom charge, mass, and type index
• Potentials — Collection of all potential energy functions
• BondPotential — Harmonic or Morse bond stretching
• AnglePotential — Cosine-harmonic or theta-harmonic bending
• DihedralPotential — Periodic torsion potentials
• ImproperPotential — Planar or umbrella out-of-plane terms
• VdwPairPotential — Lennard-Jones or Exponential-6 dispersion
• HBondPotential — Directional hydrogen bond terms

Configuration

• ChargeMethod — None, QEq, or Hybrid charge equilibration
• QeqConfig — QEq solver settings (total charge, convergence)
• HybridConfig — Hybrid biological/QEq charge assignment settings
• BondPotentialType — Harmonic vs Morse selection
• AnglePotentialType — Cosine-harmonic vs theta-harmonic
• VdwPotentialType — Lennard-Jones vs Exponential-6

Biological Metadata

• BioMetadata — Per-atom PDB/mmCIF annotations
• AtomResidueInfo — Residue name, chain, sequence number
• StandardResidue — Standard amino acids and nucleotides
• ResidueCategory — Standard, hetero, or ion classification
• ResiduePosition — Terminal position (N/C-terminal, 5’/3’-end)

Modules

io

Molecular structure file I/O operations.

Structs

Atom

A single atom with element type and 3D position.

AtomParam

Per-atom force field parameters.

AtomResidueBuilder

Builder for constructing AtomResidueInfo instances.

AtomResidueInfo

Biological annotation for a single atom.

BioMetadata

Collection of biological metadata for all atoms in a system.

Bond

A chemical bond between two atoms.

DihedralPotential

Proper dihedral (torsion) potential.

EmbeddedQeqConfig

Configuration for embedded QEq calculations.

ForgeConfig

Main configuration for DREIDING force field parameterization.

ForgedSystem

A fully parameterized molecular system.

HBondPotential

Hydrogen bond directional potential.

HybridConfig

Configuration for hybrid biological/QEq charge assignment.

LigandChargeConfig

Charge configuration for a specific ligand residue.

ParseBondOrderError

Error returned when parsing an invalid bond order string.

ParseElementError

Error returned when parsing an invalid or unsupported element symbol.

Potentials

Collection of all potential energy functions for a system.

QeqConfig

Configuration for QEq charge equilibration.

ResidueSelector

Residue selector for identifying specific residues.

SolverOptions

Configuration parameters for the charge equilibration solver.

System

A complete molecular system.

Enums

AnglePotential

Angle bending potential functions.

AnglePotentialType

Angle bending potential function type.

BasisType

Specifies the type of basis functions used for Coulomb integrals.

BondOrder

Bond order classification for chemical bonds.

BondPotential

Bond stretching potential functions.

BondPotentialType

Bond stretching potential function type.

ChargeMethod

Method for calculating partial atomic charges.

DampingStrategy

Strategy for damping charge updates during SCF iterations.

Element

Chemical element from the periodic table (Z = 1 through 118).

ForgeError

Errors that can occur during DREIDING parameterization.

ImproperPotential

Improper dihedral (out-of-plane) potential functions.

LigandQeqMethod

QEq method variant for ligand charge assignment.

NucleicScheme

Nucleic acid charge scheme.

ProteinScheme

Protein charge scheme.

ResidueCategory

Classification of a residue’s chemical nature.

ResiduePosition

Position of a residue within its polymer chain.

StandardResidue

Standard residue types from PDB/mmCIF nomenclature.

VdwPairPotential

Van der Waals non-bonded pair potential functions.

VdwPotentialType

Van der Waals non-bonded potential function type.

WaterScheme

Water charge scheme.

Functions

forge

Parameterizes a molecular system with DREIDING force field parameters.