rivet-rs 0.1.0

Rivet - Structural Alignment of Multiple Proteins

Rivet

A fast, modern implementation of the STAMP (Structural Alignment of Multiple Proteins) algorithm in Rust with Python bindings.

Features

• Full PDB Output: Aligns and transforms complete structures (all atoms), not just C-alpha
• Simple API: One function call to align multiple PDB files and write output
• Fast: Written in Rust for maximum performance
• Safe: Memory-safe by design, zero unsafe code
• Cross-platform: Linux, macOS, and Windows

Installation

pip install rivet-rs

Quick Start

Align Multiple Structures (Simplest)

import rivet

# Align PDB files and write full structures to output directory
result = rivet.align_pdbs(
    ["protein1.pdb", "protein2.pdb", "protein3.pdb"],
    output_dir="aligned/",
    chain="A"
)

print(f"Average RMSD: {result.avg_rmsd:.2f} Å")
print(f"Core positions: {result.n_core}")
# Output files written to aligned/aligned_protein1.pdb, etc.

Pairwise Alignment

import rivet

# Load structures
d1 = rivet.Domain.from_pdb("reference.pdb", chain="A")
d2 = rivet.Domain.from_pdb("mobile.pdb", chain="A")

# Align (use scan_mode=True for structures in different coordinate frames)
result = rivet.pairwise_align(d1, d2, scan_mode=True)

print(f"RMSD: {result.rmsd:.2f} Å")
print(f"Score: {result.score:.4f}")
print(f"Aligned: {result.n_aligned} residues")

# Write aligned structure (full PDB with all atoms by default)
d2.to_pdb("mobile_aligned.pdb", transform=result.transform)

Parameters for Remote Homologs

When comparing distantly related structures, use tolerant parameters:

params = rivet.Parameters()
params.e1 = 5.0   # Distance tolerance (default: 2.0)
params.e2 = 10.0  # Conformational tolerance (default: 5.0)

result = rivet.pairwise_align(d1, d2, params, scan_mode=True)

Output Options

By default, to_pdb() writes the full structure (all atoms: backbone, side chains, waters, ligands):

# Default: full structure with all atoms
d2.to_pdb("output.pdb", transform=result.transform)

# Explicit: C-alpha only (smaller file, faster)
d2.to_pdb("output_ca.pdb", transform=result.transform, full=False)

Multiple Alignment with Manual Control

For more control over the alignment process:

import rivet

# Load domains
domains = [
    rivet.Domain.from_pdb("protein1.pdb", chain="A"),
    rivet.Domain.from_pdb("protein2.pdb", chain="A"),
    rivet.Domain.from_pdb("protein3.pdb", chain="A"),
]

params = rivet.Parameters()
params.e1 = 5.0
params.e2 = 10.0

# Step 1: Pre-align to reference
aligned_domains = [domains[0]]
pre_transforms = [rivet.Transform()]

for i in range(1, len(domains)):
    result = rivet.pairwise_align(domains[0], domains[i], params, scan_mode=True)
    pre_transforms.append(result.transform)

    # Create pre-aligned domain
    coords = result.get_transformed_coordinates(domains[i])
    aligned = rivet.Domain.from_arrays(
        domains[i].id, coords, domains[i].sequence, chain=domains[i].chain
    )
    aligned_domains.append(aligned)

# Step 2: Run multiple alignment
result = rivet.multiple_align(aligned_domains, params, pre_transforms=pre_transforms)

# Step 3: Write output using composed transforms
original_files = ["protein1.pdb", "protein2.pdb", "protein3.pdb"]
for pdb_file, full_transform in zip(original_files, result.full_transforms):
    rivet.transform_pdb_file(pdb_file, f"aligned_{pdb_file}", full_transform)

Database Scanning

query = rivet.Domain.from_pdb("query.pdb", chain="A")
targets = [rivet.Domain.from_pdb(f, chain="A") for f in target_files]

hits = rivet.scan_database(query, targets, score_cutoff=0.3)

for hit in hits:
    print(f"{hit.target_id}: Score={hit.score:.4f}, RMSD={hit.rmsd:.2f} Å")

Rust API

Add to your Cargo.toml:

[dependencies]
stamp-core = "0.1"

use stamp_core::{io::{parse_pdb, transform_pdb}, pairwise::align_pair, types::Parameters};

fn main() -> Result<(), Box<dyn std::error::Error>> {
    let d1 = parse_pdb("reference.pdb", Some('A'))?;
    let d2 = parse_pdb("mobile.pdb", Some('A'))?;

    let params = Parameters::default();
    let result = align_pair(&d1, &d2, &params)?;

    println!("RMSD: {:.2} Å, Score: {:.4}", result.rmsd, result.score);

    // Transform full PDB (all atoms)
    transform_pdb("mobile.pdb", "mobile_aligned.pdb", &result.transform, None)?;

    Ok(())
}

API Reference

Functions

Function	Description
align_pdbs(files, output_dir, ...)	High-level: align PDB files and write output
pairwise_align(d1, d2, params, scan_mode)	Align two structures
multiple_align(domains, params, pre_transforms)	Multiple structure alignment
transform_pdb_file(input, output, transform)	Transform full PDB file
scan_database(query, targets, ...)	Scan query against database
compute_rmsd(coords1, coords2)	Compute RMSD
superpose(fixed, mobile)	Optimal superposition

Classes

Class	Description
Domain	Protein domain with coordinates
Parameters	Alignment parameters
Transform	3D rigid body transformation
AlignmentResult	Pairwise alignment result
MultipleAlignmentResult	Multiple alignment result with full_transforms

Key Parameters

Parameter	Default	Description
e1	2.0	Distance tolerance (Å) - increase for remote homologs
e2	5.0	Conformational tolerance (Å) - increase for flexible regions
n_passes	2	Number of refinement passes
scan_mode	False	Enable sliding window scan for different coordinate frames

Algorithm

STAMP uses the Rossmann-Argos probability measure for structural equivalence:

1. Calculate probability matrix based on inter-residue distances
2. Smith-Waterman dynamic programming to find optimal alignment
3. Extract equivalent residue pairs above threshold
4. Compute optimal superposition (Kabsch algorithm)
5. Iterate until convergence

References:

• Russell & Barton, Proteins 14:309-323 (1992)
• Rossmann & Argos, J. Mol. Biol. 105:75-95 (1976)

License

MIT License - see LICENSE for details.

Citation

@article{russell1992multiple,
  title={Multiple protein sequence alignment from tertiary structure comparison},
  author={Russell, Robert B and Barton, Geoffrey J},
  journal={Proteins: Structure, Function, and Bioinformatics},
  volume={14},
  number={2},
  pages={309--323},
  year={1992}
}