pdbrust 0.2.0

A comprehensive Rust library for parsing and analyzing Protein Data Bank (PDB) files
Documentation 
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[![Crates.io](https://img.shields.io/crates/v/pdbrust.svg)](https://crates.io/crates/pdbrust)
[![Documentation](https://docs.rs/pdbrust/badge.svg)](https://docs.rs/pdbrust)
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[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)

# PDBRust

A fast Rust library for parsing and analyzing PDB and mmCIF protein structure files.

## Installation

```toml
[dependencies]
pdbrust = "0.2"
```

With optional features:

```toml
[dependencies]
pdbrust = { version = "0.2", features = ["filter", "descriptors", "rcsb"] }
```

## Quick Start

```rust
use pdbrust::{parse_pdb_file, PdbStructure};

fn main() -> Result<(), Box<dyn std::error::Error>> {
    let structure = parse_pdb_file("protein.pdb")?;

    println!("Atoms: {}", structure.atoms.len());
    println!("Chains: {:?}", structure.get_chain_ids());

    Ok(())
}
```

## Features

| Feature | Description |
|---------|-------------|
| `filter` | Filter atoms, extract chains, remove ligands, clean structures |
| `descriptors` | Radius of gyration, amino acid composition, geometric metrics |
| `quality` | Structure quality assessment (altlocs, missing residues, etc.) |
| `summary` | Combined quality + descriptors in one call |
| `rcsb` | Search and download structures from RCSB PDB |

## Examples

### Filter and Clean Structures

```rust
use pdbrust::parse_pdb_file;

let structure = parse_pdb_file("protein.pdb")?;

// Extract CA coordinates
let ca_coords = structure.get_ca_coords(None);

// Chain operations with fluent API
let chain_a = structure
    .remove_ligands()
    .keep_only_chain("A")
    .keep_only_ca();
```

### Compute Structural Descriptors

```rust
let structure = parse_pdb_file("protein.pdb")?;

let rg = structure.radius_of_gyration();
let max_dist = structure.max_ca_distance();
let composition = structure.aa_composition();

// Or get everything at once
let descriptors = structure.structure_descriptors();
```

### Download from RCSB PDB

```rust
use pdbrust::rcsb::{download_structure, rcsb_search, SearchQuery, FileFormat};

// Download a structure
let structure = download_structure("1UBQ", FileFormat::Pdb)?;

// Search RCSB
let query = SearchQuery::new()
    .with_text("kinase")
    .with_organism("Homo sapiens")
    .with_resolution_max(2.0);

let results = rcsb_search(&query, 10)?;
```

## Performance

Benchmarks against equivalent Python code show **40-260x speedups** for in-memory operations:

| Operation | Speedup |
|-----------|---------|
| Parsing | 2-3x |
| get_ca_coords | 240x |
| max_ca_distance | 260x |
| radius_of_gyration | 100x |

## Documentation

- [API Documentation](https://docs.rs/pdbrust)
- [Examples](examples/)

## License

MIT