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minitpr: Library for Reading Gromacs TPR Files

minitpr is a pure Rust library designed for parsing Gromacs tpr files, focusing on extracting system topology and structure.

Capabilities and Limitations

  • Supports parsing of tpr files from version 103 onwards (Gromacs 5.1 and later).
  • Extracts system topology and structure: atoms, their basic properties (including positions, velocities, and forces), and bonds between atoms (including intermolecular bonds).
  • Does not support parsing of force-field and simulation parameters, nor does it offer capabilities to write tpr files.

Usage

To include minitpr in your project, add it as a dependency using Cargo:

cargo add minitpr

Parsing a tpr file

Example usage to parse a tpr file and handle potential errors:

use minitpr::TprFile;

fn main() {
    let tpr = match TprFile::parse("topol.tpr") {
        Ok(file) => file,
        Err(error) => {
            eprintln!("{}", error);
            return;
        },
    };

    // now you can work with the `tpr` object, accessing its properties and data
    // for instance, to iterate through the atoms of the molecular system, use:
    for atom in tpr.topology.atoms.iter() {
        // perform some operation with the atom
    }
}

Data Structures

The TprFile structure encapsulates the following information:

  • Header: Metadata about the tpr file (see TprHeader structure).
  • Molecular System Name: The name of the simulated system.
  • Simulation Box Dimensions: Available within the SimBox structure if present.
  • System Topology: Topology of the molecular system containing atoms and bonds (see TprTopology structure).

Each atom (see Atom) represented in the system topology includes:

  • Atom name.
  • Sequential atom number, starting from 1.
  • Residue name.
  • Sequential residue number, starting from 1.
  • Mass.
  • Charge.
  • Element (None if unidentifiable).
  • Position (None if not present).
  • Velocity (None if not present).
  • Force (None if not present).

Features

Serialization/Deserialization

Enable (de)serialization support for TprFile with serde by adding the feature flag during installation:

cargo add minitpr --features serde

License

minitpr is open-sourced under either the Apache License 2.0 or the MIT License at your option.

Disclaimer

Due to the huge number of various force field and simulation parameters and Gromacs options, it is very difficult to comprehensively test the minitpr library.Your contributions in the form of tests, tpr files with unusual parameters, or new functionality are very welcome.

If the library is unable to parse your tpr file, but you believe it should be able to, please open a GitHub issue and upload your tpr file.