Crate cgkitten 

Convert mmCIF protein structures to coarse-grained xyzq representation.

Each amino acid residue is represented as a single bead at its center of mass. Titratable side-chains (ASP, GLU, HIS, CYS, TYR, LYS, ARG) generate an additional bead at the charge center. Charges are computed via ChargeCalc, which supports Henderson-Hasselbalch and Monte Carlo titration.

let cif_data = std::fs::read("structure.cif").unwrap();
let beads = cgkitten::coarse_grain(cif_data.as_slice());
let result = cgkitten::ChargeCalc::new()
    .ph(7.0)
    .mc(10000)
    .run(&beads);
let charged = result.apply(&beads);

Modules

forcefield

Force field model definitions. Force field models for coarse-grained beads.

residue

Amino acid residue definitions and constants. Amino acid definitions and titratable side-chain groups.

topology

Topology type assignment for coarse-grained beads. Topology type assignment for coarse-grained beads.

Structs

Bead

A coarse-grained bead with position and charge.

ChargeCalc

Charge calculation builder.

ChargeResult

Result of a charge calculation.

MultiBead

Multi-bead coarse-graining: one backbone bead + optional sidechain bead per titratable residue.

Multipole

Multipole moments: net charge and dipole with their squares.

ResidueKey

Unique residue key for grouping atoms, used in the CoarseGrain trait.

SingleBead

Single-bead coarse-graining: one bead per residue. Titratable residues get BeadType::Titratable.

Enums

BeadType

Classification of a coarse-grained bead.

Traits

CoarseGrain

Convert one amino acid residue into beads (backbone/sidechain only, not terminals).

Functions

coarse_grain

Convert mmCIF data to coarse-grained beads using the default multi-bead policy.

coarse_grain_pdb_with

Convert PDB data to coarse-grained beads using the given policy.

coarse_grain_to_files

Run the full coarse-graining pipeline and write XYZ and topology YAML files.

coarse_grain_with

Convert mmCIF data to coarse-grained beads using the given policy.

filter_chains

Filter beads to keep only the requested chains.

format_topology

Format topology as YAML with unique atom types and optional force field parameters.

format_xyz

Format beads as plain XYZ string (name x y z).