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feat(io): Implement Modular I/O Subsystem and Bio-Forge Integration#4

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TKanX merged 56 commits intomainfrom
feature/3-implement-modular-io-subsystem-with-encapsulated-bio-forge-pipeline
Dec 8, 2025
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feat(io): Implement Modular I/O Subsystem and Bio-Forge Integration#4
TKanX merged 56 commits intomainfrom
feature/3-implement-modular-io-subsystem-with-encapsulated-bio-forge-pipeline

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@TKanX TKanX commented Dec 8, 2025

Summary:

Implemented a comprehensive Input/Output subsystem that serves as the interface between external file formats and the internal System model. Introduces a unified API for handling both macromolecular data (via an encapsulated bio-forge pipeline) and small molecule informatics. It includes native parsers for chemical formats and robust writers for simulation engines, establishing the project's capability to ingest raw structure data and export simulation-ready configurations.

Changes:

  • Designed Unified I/O Architecture:

    • Established ChemReader/ChemWriter for small molecule formats and BioReader/BioWriter for macromolecular structures.
    • Implemented a centralized Error handling system covering I/O, parsing, and conversion failures.
    • created src/io/mod.rs as the public facade, exporting configuration structs for topology, cleaning, protonation, and solvation.

  • Integrated bio-forge Pipeline:

    • Implemented src/io/util.rs to adapt bio-forge models (Structure, Topology) to local System models.
    • Added support for PDB and mmCIF formats (Read/Write) with automated structure preparation steps (repair, hydrogen addition, solvation).
    • Mapped biological configuration options (pH, salt concentration, histidine strategies) to the underlying engine.

  • Refactored Metadata System:

    • Updated AtomResidueInfo in src/model/metadata.rs to use a Builder Pattern, improving ergonomics for complex residue data.
    • Added StandardResidue, ResidueCategory, and ResiduePosition enums to richer biological context preservation.

  • Implemented Native Chemical Format Support:

    • SDF: Developed a V2000-compliant reader and writer, including coordinate parsing and bond order inference.
    • Mol2: Implemented a parser for TRIPOS Mol2 files, handling @<TRIPOS>ATOM, BOND, and MOLECULE sections.

  • Developed Simulation Output Formats:

    • BGF: Created a writer for the BioDesign/Dreiding BGF format, featuring atom sorting by chain/residue and CONECT record generation.
    • LAMMPS: Implemented a sophisticated writer capable of generating both Data files and Settings files.
      • Supports periodic and non-periodic boundary conditions.
      • Handles complex forcefield parameter mapping for Bonds, Angles, Dihedrals, Impropers, and Non-bonded interactions (LJ/Buckingham).

TKanX added 30 commits December 7, 2025 13:59
@TKanX
feat(io): Implement modular I/O error handling with detailed error types
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feat(io): Implement Format enum with Display implementation for I/O f…
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…ormats
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feat(io): Add Conversion error variant and implement From for Convers…
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…ionError
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feat(model): Introduce StandardResidue, ResidueCategory, and ResidueP…
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…osition enums with AtomResidueInfo updates
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test(model): Enhance AtomResidueInfo tests with all fields and defaul…
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…t cases
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test(model): Add test for AtomResidueInfo to validate input acceptanc…
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…e and field correctness
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feat(io): Implement modular I/O subsystem with encapsulated bio-forge…
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… pipeline utilities
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test(io): Add tests for bio topology conversion and error handling
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refactor(io): Simplify element and residue conversion functions for c…
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…larity and efficiency
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refactor(model): Refactor AtomResidueInfo to use builder pattern for …
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…improved flexibility
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test(model): Update AtomResidueInfo tests to use builder pattern for …
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…improved readability
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refactor(io): Refactor AtomResidueInfo instantiation to use builder p…
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…attern for improved clarity
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test(io): Update AtomResidueInfo instantiation to use builder pattern…
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… for improved clarity
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feat(io): Implement modular IO subsystem with encapsulated configurat…
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…ions for Clean, Protonation, Solvate, and Topology
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feat(io): Add conversion functions for Clean, Hydro, Solvate configur…
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…ations and topology building
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test(io): Add unit tests for CleanConfig, ProtonationConfig, and Solv…
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…ateConfig conversions
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refactor(io): Remove unused peptide_bond_cutoff and nucleic_bond_cuto…
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…ff from TopologyConfig
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feat(io): Add BioReader struct for modular reading with configurable …
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…settings
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feat(io): Implement PDB reader functionality for modular IO subsystem
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test(io): Add unit tests for PDB reader functionality and input valid…
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…ation
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feat(io): Implement mmCIF reader functionality for modular IO subsystem
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test(io): Add unit tests for mmCIF reader functionality and input val…
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…idation
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feat(io): Implement PDB writer functionality for modular IO subsystem
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test(io): Add unit tests for PDB writer functionality and system equi…
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…valence checks
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feat(io): Implement writer module for mmCIF format in modular IO subs…
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…ystem
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test(io): Add comprehensive tests for mmCIF writer functionality and …
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…system equivalence
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feat(io): Add mmCIF reader support in BioReader for modular IO subsystem
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feat(io): Implement BioWriter for modular IO subsystem with format su…
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…pport
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feat(io): Add metadata validation in PDB writer to ensure required da…
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…ta is present
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feat(io): Add metadata validation in mmCIF writer to handle missing b…
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…io metadata
TKanX added 21 commits December 7, 2025 20:23
@TKanX
feat(io): Implement SDF reader module for modular IO subsystem
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test(io): Add unit tests for SDF reader functionality
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feat(io): Implement writer module for SDF format in modular IO subsystem
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test(io): Add roundtrip tests for SDF writer functionality
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feat(io): Implement guess_element_symbol function for element symbol …
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…inference
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feat(io): Add bond order conversion functions for CTfile and MOL2 for…
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…mats
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test(io): Add unit tests for element symbol guessing and bond order c…
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…onversions for CTfile and MOL2 formats
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feat(io): Implement ChemReader for reading chemical formats with supp…
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…ort for Mol2 and SDF
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feat(io): Implement ChemWriter for writing chemical formats with supp…
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…ort for Mol2 and SDF
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feat(io): Implement BGF module with writer functionality for BGF file…
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… format
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test(io): Add unit tests for BGF writer functionality and error handling
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refactor(io): Simplify element symbol guessing logic by using array i…
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…n split method
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fix(io): Remove unnecessary empty line in SDF writer output
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feat(io): Enhance atom parsing logic to handle both padded and unpadd…
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…ed formats
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fix(io): Improve error handling for missing residue id map in writer …
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…function
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refactor(io): Simplify logic in guess_element_symbol function for bet…
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…ter readability
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fix(io): Optimize residue ID assignment logic in BGF writer function
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feat(io): Implement LAMMPS module for enhanced simulation support
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test(io): Add unit tests for LAMMPS writer functionality
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refactor(io): Adjust module visibility for better encapsulation
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refactor(io): Move error module visibility to improve structure
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@TKanX TKanX self-assigned this Dec 8, 2025
Copilot AI review requested due to automatic review settings December 8, 2025 10:50
@TKanX TKanX added the enhancement ✨ New feature or request label Dec 8, 2025
@TKanX TKanX linked an issue Dec 8, 2025 that may be closed by this pull request
Implement Modular I/O Subsystem with Encapsulated bio-forge Pipeline #3
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Pull request overview

This PR implements a comprehensive I/O subsystem that establishes the project's capability to read and write molecular structure data across multiple file formats. The implementation introduces a clean separation between chemical formats (small molecules) and biological formats (macromolecules), with a unified error handling system and robust bio-forge integration for structure preparation workflows.

Key Changes:

  • Introduced builder pattern for AtomResidueInfo with new biological metadata fields (StandardResidue, ResidueCategory, ResiduePosition enums)
  • Implemented ChemReader/ChemWriter for SDF and Mol2 formats with native parsers
  • Implemented BioReader/BioWriter for PDB and mmCIF with configurable preparation pipelines (cleaning, protonation, solvation)
  • Created sophisticated LAMMPS and BGF writers supporting complex forcefield parameters and system topologies

Reviewed changes

Copilot reviewed 21 out of 21 changed files in this pull request and generated 1 comment.

Show a summary per file
File Description
src/lib.rs Exports new io module
src/model/metadata.rs Refactored to builder pattern, added biological metadata enums
src/io/mod.rs Public API facade with reader/writer structs and configuration types
src/io/util.rs Bio-forge integration with bidirectional model conversions
src/io/error.rs Centralized error handling with thiserror and contextual information
src/io/sdf/* V2000-compliant SDF reader/writer with element inference
src/io/mol2/* TRIPOS Mol2 parser with section-based parsing
src/io/pdb/* PDB reader/writer with structure preparation pipeline
src/io/mmcif/* mmCIF reader/writer mirroring PDB functionality
src/io/bgf/* BGF writer with chain/residue sorting and CONECT generation
src/io/lammps/* LAMMPS Data/Settings file writer with hybrid style support

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Comment thread src/io/lammps/writer.rs Outdated
@TKanX TKanX merged commit 6ebf34e into main Dec 8, 2025
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@TKanX TKanX deleted the feature/3-implement-modular-io-subsystem-with-encapsulated-bio-forge-pipeline branch December 8, 2025 19:39
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Implement Modular I/O Subsystem with Encapsulated bio-forge Pipeline

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