Crate bio_forge 

BioForge

BioForge is a pure-Rust molecular preparation engine that ingests experimental macromolecular files, reconciles them with curated residue templates, and emits topology-aware structures ready for simulation or analysis. The crate favors deterministic workflows, strong typing, and clean error surfaces so pipelines remain auditable from parsing to solvation.

Features

• High-fidelity templates – Embedded TOML templates for proteins, nucleic acids, and solvent ensure reproducible coordinates, elements, and bonding across runs.
• Ergonomic structure model – Lightweight Atom, Residue, Chain, and Structure types backed by nalgebra power geometric manipulation and metadata-aware queries.
• Versatile I/O – Buffered readers and writers for PDB, mmCIF, and MOL2 share a common context that normalizes residue aliases and captures precise diagnostics.
• Compositional operations – Cleaning, repairing, hydrogenation, solvation, topology building, and transforms live under ops, producing interoperable results with a unified error type.
• Topology reconstruction – Topology and Bond exports allow downstream force-field assignment or connectivity validation without re-parsing raw coordinates.

Modules

io

IO front-end exposing structure parsing and export utilities for common biomolecular formats.

ops

High-level operations that clean, repair, solvate, and otherwise prepare structures.

templates

Read-only access to residue templates.

Structs

Atom

Labeled atom with immutable element identity and mutable position.

Bond

Undirected bond connecting two atoms within a structure.

Chain

Polymer chain containing an ordered list of residues.

Residue

A residue within a biomolecular structure.

Structure

High-level biomolecular assembly composed of zero or more chains.

Template

Describes the atom inventory and connectivity for a residue or ligand template.

Topology

Bond graph overlay for a Structure.

Enums

BondOrder

Bond multiplicity definitions used when describing topology edges.

Element

Periodic table entries supported by bio-forge.

ResidueCategory

High-level classification for residues appearing in a structure.

ResiduePosition

Topological context of a residue within a polymer chain.

StandardResidue

Canonical polymer residue names recognized by bio-forge.

Type Aliases

Point

Cartesian coordinate storing atomic positions in ångströms.