feat(forge): Implement Core Force Field Parameterization Engine by TKanX · Pull Request #6 · caltechmsc/dreid-forge

TKanX · 2025-12-11T09:04:35Z

Summary:

Implemented the central "Forge" engine responsible for transforming a raw molecular system into a parameterized, simulation-ready topology. This engine orchestrates atom typing (via dreid-typer), charge assignment (via cheq's QEq solver), and the rigorous mapping of DREIDING force field parameters to bonds, angles, dihedrals, impropers, and non-bonded interactions. Establishes the core computational pipeline for molecular mechanics preparation.

Changes:

Implemented Forge Pipeline:
- Created src/forge/mod.rs as the main entry point, exposing the forge() function that drives the parameterization workflow.
- Developed ForgeConfig to control simulation settings, including potential types (Harmonic/Morse, Cosine/Theta), charge methods, and custom parameters.
Integrated Atom Typing:
- Implemented src/forge/typer.rs to bridge IntermediateSystem with the dreid-typer library.
- Added support for both automatic topological analysis and custom SMARTS-based typing rules.
- Mapped chemical hybridization states and bond orders to force field atom types.
Implemented Charge Assignment:
- Created src/forge/charge.rs to integrate the cheq library for electronegativity equalization (QEq).
- Configured charge equilibration solvers with support for total system charge constraints and hydrogen SCF options.
Developed Parameter Generator:
- Implemented src/forge/paramgen.rs to systematically assign physics parameters based on atom types.
- Bonds: Calculates equilibrium lengths and force constants based on atomic radii and bond orders.
- Angles: Generates angle potentials using type-specific equilibrium angles.
- Dihedrals: Implemented complex logic for torsion barriers based on hybridization states (SP3/SP2/Resonant) and special cases (e.g., oxygen columns).
- Impropers: Added inversion potentials for planar centers.
- Non-bonded: Generates Lennard-Jones or Exponential-6 (Buckingham) pair potentials using geometric mean mixing rules.
- Hydrogen Bonds: Identifies donor-acceptor pairs and assigns explicit hydrogen bond potentials.
Defined Force Field Parameters:
- Added src/forge/params.rs and resources/default.params.toml containing the official DREIDING force field specification (masses, radii, angles, vdW parameters).
- Implemented a parameter loader that supports both embedded defaults and user-provided TOML overrides.
Created Intermediate Representation:
- Defined IntermediateSystem to hold transient data required during the forging process (e.g., neighbors, partial charges, graph connectivity) without polluting the core System model.
- Implemented conversion logic to initialize this intermediate state from a raw System.
Updated BGF Writer:
- Refined src/io/bgf/writer.rs to include atomic mass in the output and ensure strict fixed-width formatting, fixing column alignment issues and ensuring compatibility with legacy tools.

…t function

…riter

…argo.toml

…zation

…iateBond, and IntermediateSystem

…om functionality

… force field parameterization

…in ForgeConfig

…alities

…d molecular graph construction

…pology generation

…ameter generation

…ameterization

…arameterization

…dral parameterization

…oper parameterization

…aals parameterization

…n bond parameterization

…ameterization

Copilot

Pull request overview

This PR implements the core "Forge" engine for DREIDING force field parameterization, establishing a complete pipeline that transforms raw molecular systems into simulation-ready topologies with assigned atom types, charges, and force field parameters. The implementation integrates external libraries for atom typing (dreid-typer) and charge calculation (cheq), and includes comprehensive test coverage across all modules.

Key Changes:

Implemented complete force field parameterization pipeline with configurable potential types (Harmonic/Morse bonds, ThetaHarmonic/CosineHarmonic angles, LennardJones/Exponential6 VdW)
Integrated atom typing via dreid-typer and charge assignment via cheq's QEq solver
Generated systematic parameter assignment for bonds, angles, dihedrals, impropers, VdW pairs, and hydrogen bonds
Updated BGF writer with fixed-width formatting and atomic mass output
Added comprehensive unit tests for all forge modules

Reviewed changes

Copilot reviewed 12 out of 12 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
src/lib.rs	Exports new `forge` module to public API
src/io/bgf/writer.rs	Updates FORMAT_ATOM to include mass field (f10.5), changes residue_name alignment to left, adds atomic mass output, improves test assertions with column-based validation
src/forge/mod.rs	Main forge module exposing `forge()` function and configuration types; orchestrates typing, charge assignment, and parameter generation
src/forge/typer.rs	Bridges IntermediateSystem with dreid-typer library for atom typing and topology analysis
src/forge/params.rs	Defines force field parameter structures, loads from embedded TOML or custom overrides, provides torsion parameter lookup
src/forge/paramgen.rs	Generates all force field potentials (bonds, angles, dihedrals, impropers, VdW, H-bonds) based on atom types and configuration
src/forge/intermediate.rs	Defines IntermediateSystem holding transient data during parameterization (neighbors, charges, hybridization)
src/forge/error.rs	Defines forge-specific error types with conversions from external libraries (dreid-typer, cheq)
src/forge/config.rs	Defines ForgeConfig with charge methods and potential type selections
src/forge/charge.rs	Integrates cheq library for QEq charge assignment with configurable solver options
resources/default.params.toml	Official DREIDING force field parameters including atom types, global constants, and H-bond settings
Cargo.toml	Updates dependency versions for bio-forge (0.2.1), dreid-typer (0.4.0), and cheq (0.3.0)

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…assertions

…dices

…ices

…cos^4 -> cos^2)

…ta_file

…a_file

…accuracy

…stency

…f static references, preventing memory leaks and simplifying ownership for callers

Copilot

Pull request overview

Copilot reviewed 14 out of 14 changed files in this pull request and generated no new comments.

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TKanX added 28 commits December 9, 2025 21:38

fix(io): Correct formatting in atom output and remove unused fit_righ…

d7cc54b

…t function

test(io): Add tests for fixed-width formatting of atom lines in BGF w…

de3625b

…riter

chore(package): Update bio-forge, dreid-typer, and cheq versions in C…

e24f3b6

…argo.toml

test(io): Enhance atom line formatting tests for BGF writer

d7c52bf

feat(forge): Implement core error handling for force field parameteri…

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…zation

feat(params): Add official DREIDING force field parameters configuration

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feat(forge): Implement core structures for IntermediateAtom, Intermed…

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…iateBond, and IntermediateSystem

test(forge): Add unit tests for IntermediateSystem and IntermediateAt…

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…om functionality

feat(forge): Implement ForgeConfig and associated potential types for…

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… force field parameterization

test(forge): Add unit tests for default values and Qeq configuration …

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…in ForgeConfig

feat(forge): Add force field parameter management module

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test(forge): Add unit tests for ForceFieldParams and related function…

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…alities

feat(forge): Implement core functionality for atom type assignment an…

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…d molecular graph construction

test(forge): Add unit tests for atom type assignment and molecular to…

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…pology generation

feat(forge): Implement charge assignment functionality with QEq method

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test(forge): Add unit tests for charge assignment methods

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feat(forge): Implement atom type collection functionality in paramgen

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feat(forge): Implement generate_atom_properties function for atom par…

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…ameter generation

feat(forge): Implement generate_bond_potentials function for bond par…

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…ameterization

feat(forge): Implement generate_angle_potentials function for angle p…

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…arameterization

feat(forge): Implement generate_dihedral_potentials function for dihe…

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…dral parameterization

feat(forge): Implement generate_improper_potentials function for impr…

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…oper parameterization

feat(forge): Implement generate_vdw_potentials function for van der W…

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…aals parameterization

feat(forge): Implement generate_hbond_potentials function for hydroge…

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…n bond parameterization

feat(forge): Add centralized parameter generation pipeline

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test(forge): Add comprehensive tests for parameter generation functions

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feat(forge): Implement core forge engine for Dreiding force field par…

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…ameterization

test(forge): Add unit tests for water, ethane, and benzene forging

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TKanX self-assigned this Dec 11, 2025

Copilot AI review requested due to automatic review settings December 11, 2025 09:04

TKanX added the enhancement ✨ New feature or request label Dec 11, 2025

TKanX linked an issue Dec 11, 2025 that may be closed by this pull request

Implement the Core Forge Engine for DREIDING Force Field Parameterization #5

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Copilot started reviewing on behalf of TKanX December 11, 2025 09:05 View session

Copilot AI reviewed Dec 11, 2025

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Comment thread src/forge/params.rs Outdated

Comment thread src/forge/paramgen.rs Outdated

Comment thread src/forge/paramgen.rs

Comment thread src/forge/paramgen.rs

Comment thread src/forge/paramgen.rs

TKanX added 13 commits December 11, 2025 17:08

fix(forge): Rename fields in HBondPotential for consistency

c93ccc5

test(forge): Rename fields in HBondPotential for consistency in test …

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…assertions

fix(forge): Updates hydrogen bond potential generation to use type in…

96ec109

…dices

test(forge): Update hydrogen bond potential tests to include type ind…

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…ices

test(model): Update HBondPotential parameters in tests for accuracy

cc6fa68

fix(io): Update hydrogen bond potential parameters in settings file (…

efa7332

…cos^4 -> cos^2)

refactor(io): Remove write_hbonds function and its call from write_da…

64dfbab

…ta_file

fix(io): Update improper coefficient output format for consistency

70e3290

refactor(io): Remove unused write_pair_coeffs function from write_dat…

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…a_file

fix(io): Update hydrogen bond coefficient output format for improved …

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…accuracy

fix(io): Simplify improper styles collection by merging match arms

095b04f

test(io): Update hydrogen bond parameters and output format for consi…

3c02a5b

…stency

fix(forge): Update parameter loading to return owned values instead o…

a65af62

…f static references, preventing memory leaks and simplifying ownership for callers

TKanX requested a review from Copilot December 12, 2025 03:19

Copilot started reviewing on behalf of TKanX December 12, 2025 03:19 View session

Copilot AI reviewed Dec 12, 2025

View reviewed changes

TKanX merged commit c09fcfa into main Dec 12, 2025
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TKanX deleted the feature/5-implement-the-core-forge-engine-for-dreiding-force-field-parameterization branch December 12, 2025 03:26

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feat(forge): Implement Core Force Field Parameterization Engine#6

feat(forge): Implement Core Force Field Parameterization Engine#6
TKanX merged 41 commits intomainfrom
feature/5-implement-the-core-forge-engine-for-dreiding-force-field-parameterization

TKanX commented Dec 11, 2025

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TKanX commented Dec 11, 2025

Summary:

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