molar 1.0.1

Molar is a rust library for analysis of MD trajectories and molecular modeling
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MolAR - a Molecular Analysis and modeling library for Rust.

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Table of contents

What is molar?

MolAR is a library for molecular modeling and analysis written in Rust with an emphasis on memory safety and performance.

Molar is designed to simplify the analysis of molecular dynamics trajectories and to implement new analysis algorithms. Molar is intended to provide facilities, which are routinely used in all molecular analysis programs, namely input/output of popular file formats, powerful and flexible atom selections, geometry transformations, RMSD fitting and alignment, etc.

MolAR is a logical successor of Pteros molecular modeling library, which is written in C++ and become hard to develop and maintain due to all C++ idiosyncrasies.

Features

  • Reading and writing PDB, GRO, XYZ, XTC, TPR files
    • Reading and writing Gromacs XTC format with random access.
    • Reading Gromacs TPR files (if Gromacs is installed).
    • Recognizes any VMD molfile plugins.
  • Selections using the syntax similar to VMD and Pteros.
    • Memory-safe selections for serial and parallel analysis tasks.
    • Powerful subselections and selection splitting.
  • SASA calculations with the fastest PowerSasa method.
  • RMSD fitting and alignment.
  • Basic algorithm (center of mass, center of geometry, etc.).
  • Seamless PBC treatment.
  • Trajectory processing with powerful built-in features.
  • Python bindings.

Design and Performance

Initial design is described in the MolAR paper. However, this concept appeared to be too complex in practice and didn't cover all the real world scenarios properly. Starting from version 1.0 it was changed completely. Now selections are just indices of selected atoms, which have to "bound" to [System] (that is an actual container for atoms and coordinates) to do useful work. The API becomes more noisy but you get proper compile-time borrow checking, soundness and all Rust memory safety guarantees. The "binding" of selections is very cheap (one integer comparison), so it should not affect the performance reported in the paper.

Current status

Molar is usable in real-life projects and is close to be feature complete. Documentation is still rudimentary.

Installation

Molar requires Rust 1.83 or above and a C/C++ compiler for compiling third-party libraries. Any sufficiently modern gcc or clang compiler should work.

To add MolAR to your Rust project just use cargo add molar.

For installation of the Python bindings look here.

Linking to Gromacs

In order to be able to read Gromacs TPR files MolAR should link to locally installed Gromacs. Unfortunately, modern versions of Gromacs do not expose all needed functionality in the public API, so MolAR has to hack into the internals and thus requires an access to the whole Gromacs source and build directories. This means that you have to compile Gromacs on your local machine from source.

In order to link with Gromacs create a .cargo/config.toml file in the root directory of your project with the following content:

[env]
# Location of Gromacs source tree
GROMACS_SOURCE_DIR = "<path-to-gromacs-source>/gromacs"
# Location of Gromacs *build* directory (for generated headers)
GROMACS_BUILD_DIR = "<path-to-gromacs-source>/gromacs/build"
# Location of installed gromacs libraries (where libgromacs.so is located)
GROMACS_LIB_DIR = "<path-to-installed-gromacs>/lib64"

You may use a template: mv config.toml.template config.toml.

Tutorial

We will write an example program that reads a file of some molecular system containing TIP3P water molecules, convert all water to TIP4P and saves this as a new file. TIP3P water has 3 particles (oxygen and two hydrogens), while TIP4P has 4 (oxygen, two hydrogens and a dummy particle). Our goal is to add these dummy particles to each water molecule.

Preparing the stage

First, let's create a new Rust project called tip3to4:

cargo new tip3to4

Then, let's add dependencies: the MolAR itself and anyhow crate for easy error reporting:

cargo add molar anyhow

In src/main.rs add needed boilerplate:

// For processing command line arguments
use std::env;
// Import all basic things from molar
use molar::prelude::*;
// For error handling
use anyhow::Result;

fn main() -> Result<()> {
    // Get the command line arguments
    let args: Vec<String> = env::args().collect();

    // Here our program is going to be written

    // Report successful completion of the program
    Ok(())
}

Now we can start writing our program.

Reading an input file

The simples way of loading the molecular system in MolAR is to use a Source - an object that holds a Topology and State of the system and is used to create atom selections for manipulating this data:

// Load the source file from the first command line argument
let src = System::from_file(&args[0])?;

The file type (PDB, GRO, etc) is automatically recognized by its extention. If reading the file fails for whatever reason the ? operator will return an error, which will be nicely printed by anyhow crate.

Making selections

Now we need to select all waters that are going to be converted to TIP4. We also need to select all non-water part of the system to keep it as is.

In MolAR selection (Sel) is just a list of atom indexes, which has to be "bound" to the System to do useful work using system.bind(&sel) for read-only acces or system.bind_mut(&sel) for read-write access. There are also convenience methods that produce bound selection right away. This is useful if you know that you won't re-bind the same System for different type of access often.

let water = sys.select_bound("resname TIP3")?;
let non_water = sys.select_bound("not resname TIP3")?;

Selections are created with the syntax that is very similar to one used in VMD Pteros and Gromacs. Here we select water and non-water by residue name.

In MolAR empty selections are not permitted, so if no atoms are selected (or if anything else goes wrong) the error will be reported.

Looping over indiviudual water molecules

We selected all water molecules as a single selection but we need to loop over individual water molecules to add an additional dummy particle to each of them. In order to do this we are splitting a selection to fragments by the residue index:

// Go over water molecules one by one                   
for mol in water.split_resindex_bound() {
    // Do something with mol
}

The method split_resindex_bound() returns a Rust iterator, which produces contigous bound selections containig distinct residue index each. There are many other ways of splitting selections into parts using arbitrary logic in MolAR, but this simplest one is what we need now.

Working with coordinates

Now we need to get the coordinates of atoms for current water molecules and compute a position of the dummy atom.

// Go over water molecules one by one                   
for mol in water.split_resindex_bound() {
    // TIP3 is arranged as O->H->H
    // so atom 0 is O, atoms 1 and 2 are H
    // Get cooridnates
    let o_pos = mol.get_pos(0).unwrap();
    let h1_pos = mol.get_pos(1).unwrap();
    let h2_pos = mol.get_pos(2).unwrap();
    // Get center of masses of H
    let hc = 0.5*(h1_pos.coords + h2_pos.coords);
    // Unit vector from o to hc
    let v = (hc-o_pos.coords).normalize();	
    // Position of the M dummy particle in TIP4
    let m_pos = o_pos + v*0.01546;
    // Dummy atom M
    let m_at = Atom {
        resname: "TIP4".into(),
        name: "M".into(),
        ..mol.first_particle().atom.clone()
    };
    println!("{:?} {:?}",m_at,m_pos);
}

First, we are getting the coordinates of oxigen and two hydrogens. get_pos(n) returns the position of n-th atom in selection. Since n may potentially be out of range, it returns an Option<&Pos>. We are sure that there are just 3 atoms in water molecule, so we just unwrapping an option.

Then we are computing the position of the dummy atom, which is on the bissection of H-O-H angle at the distance of 0.01546 from the oxygen.

Finally, we are constructing a new Atom with name 'M', residue name 'TIP4' and all other fields (resid,resindex, etc) the same as in our water molecule.

We are printing our new dummy atom and its position just to be sure that everything works as intended.

Constructing output system

All this is fine, but we still have no system to write our converted water molecules to. Let's fix this and modify the beginning of our main funtion like this:

// Load the source file from the first command line argument
let src = Source::serial_from_file(&args[0])?;

// Make empty output system
let out = Source::empty_builder();

Here we are creating new empty Source of kind builder. This means that we will be able to add and delete the atoms to this source. Conventional serial source can access and alter existing atoms, but can't add or delete them. Such a distinction is dictated by performance and memory safety reasons - builder sources and selections require additional range checks, which make them a tiny bit slower, so it only makes sense to use them when you actually need to add or delete the atoms.

The first thing that we add to out new empty system is all non-water atoms:

// Add non-water atoms to the output
out.append(&non_water);

Now, at the end of our loop over water molecules, we can add new dummy atoms properly to the new system:

// Add new converted water molecule
// We assume that the dummy is the last atom.
let added = out.append_coords(
    mol.iter_atoms().cloned().chain(std::iter::once(m_at)),
    mol.iter_pos().cloned().chain(std::iter::once(m_pos)),
)?;

This code snippet may look a bit puzzling for non-rustaceans, so let's go through it.

  • append_atoms() method accepts two iterators: the first yielding atoms and the second yielding their corresponding coordinates.
  • Our selected water molecule mol has methods iter_atoms() and iter_pos() for getting these iterators.
  • cloned() adaptor is used to get copies of existing atoms and coordinates instead of references to them.
  • We add our new dummy atom at the end of water molecule by "chaining" another iterator at the end of the current one. std::iter::once(value) returns an iterator yielding a single value and allows us to add newly constructed m_at and m_pos to the corrsponding iterators.

We also need to chnage the resname of the old atoms of water molecule from TIP3 to TIP4. As you noticed, append_atoms_coords() returns a selection with added atoms, so we can bind it mutably to the output system and set new residue name:

// Change resname for added atoms
// Note the use of bind_mut()!
out.bind_mut(&added).set_same_resname("TIP4");

Writing the output file

Out output system is now fully constructed but it still lacks an important element - the periodic box description. Most molecular systems originating from MD are periodic and the information about the periodic box has to be copied to our newly constructed system:

// Transfer the box from original file
out.set_box_from(&src);

Here we provide a reference to the input system, so the box is cloned from it to the output system.

Finally we are ready to write the output file:

// Write out new system
out.save(&args[1])?;

Again, file format will be determined by extension. The file name is provided by the second command line argument.

The final result

The complete program looks like this:

// For processing command line arguments
use std::env;
// Import all baic things from molar
use molar::prelude::*;
// For error handling
use anyhow::Result;

fn main() -> Result<()> {
    // Get the command line arguments
    let args: Vec<String> = env::args().collect();

    // Load the source file from the first command line argument
    let sys = System::from_file(&args[0])?;

    // Make empty output system
    let mut out = System::default();

    // Select water and non-water. 
    // Normally selections are just indexes of atoms, which have to be
    // "bound" to system to do useful work using 
    // `sys.bind(&sel)` for read-only acces or 
    // `sys.bind_mut(&sel)` for read-write access. 
    // In this particular case we use `select_bound()` to get 
    // bound selections. This works here because we know in advance
    // that `sys` is used read-only and we'll never re-bind it for mut access.
    let water = sys.select_bound("resname TIP3")?;
    let non_water = sys.select_bound("not resname TIP3")?;

    // Add non-water atoms to the output
    out.append(&non_water);

    // Go over water molecules one by one                   
    for mol in water.split_resindex_bound() {
        // TIP3 is arranged as O->H->H
        // so atom 0 is O, atoms 1 and 2 are H
	    // Get cooridnates
        let o_pos = mol.get_pos(0).unwrap();
        let h1_pos = mol.get_pos(1).unwrap();
        let h2_pos = mol.get_pos(2).unwrap();
	    // Get center of masses of H
	    let hc = 0.5*(h1_pos.coords + h2_pos.coords);
	    // Unit vector from o to hc
	    let v = (hc-o_pos.coords).normalize();	
	    // Position of the M dummy particle in TIP4
	    let m_pos = o_pos + v*0.01546;
        // Dummy atom M
        let m_at = Atom {
            resname: "TIP4".into(),
            name: "M".into(),
            ..mol.first_particle().atom.clone()
        };

        // Add new converted water molecule
        // We assume that the dummy is the last atom.
        let added = out.append_atoms_coords(
            mol.iter_atoms().chain(std::iter::once(&m_at)),
            mol.iter_pos().chain(std::iter::once(&m_pos)),
        )?;

        // Change resname for added atoms
        // Note the use of bind_mut()!
        out.bind_mut(&added).set_same_resname("TIP4");
    }

    // Transfer the box
    out.set_box_from(&sys);

    // Write out new system
    out.save(&args[1])?;

    // Report successful completion of the program
    Ok(())
}

Parallel splits

MolAR allows performing operations on non-overlapping selections in parallel, which typically gives a huge speed up in such tasks as removing periodicity for individual molecules, which are rather heavy computationally.

Here is how you can do this:

// Import all baic things from molar
use molar::prelude::*;
// For error handling
use anyhow::Result;

fn main() -> Result<()> {
    // Load lipid membrane
    let mut sys = System::from_file("tests/membr.gro")?;

    // Make a parallel split: distinct selection for each POPG lipid.
    let par = sys.split_par(|p| {
        if p.atom.resname == "POPG" {
            // Whenever distinct result is returned form this closure
            // new selection is created, so each distinct POPG residue
            // becomes a separate selection.
            Some(p.atom.resindex)
        } else {
            // All other atoms are ignored
            None
        }
    })?;

    // Bind split to a system
    sys.bind_par_mut(&par)? 
        // Get rayon parallel iterator over selections
        .par_iter_mut() 
        // Run unwrap on each selection in parallel
        .try_for_each(|mut sel| sel.unwrap_simple())?; 
    Ok(())
}

Analysis tasks

Motivation

The vast majority of molecular dynamics trajectory analysis tasks follows the same pattern:

  1. Do initialization and pre-processing (read and process the parameters, allocate and initialize data structures, create atom selections, etc.)
  2. On each trajectory frame call an analysis function, which computes needed properties.
  3. Do post-processing (compute averages, write results to file).

Reading trajectories themselves also requires some standard options:

  1. Ability to start from given frame or time stamp.
  2. Ability to stop at given frame or time stamp.
  3. Ability to read each N-th frame (decimation).
  4. Ability to report the progress with given periodicity.

These patterns are so common that it very quickly become annoynig and repetitive to implement them from scratch for each analysis task. That is why MolAR provides [AnalysisTask] trait, which automates all the common steps and takes care of all the boilerplate.

Implementing analysis tasks

Here is an example of implementing custom analysis task, which prints a center of mass for a user provided selection on each frame and also computes an average center of mass over the trajectory:

// Import all basic things from molar
use molar::prelude::*;
// For error handling
use anyhow::Result;
// For processing custom command line arguments
use clap::Args;

// User-defined command line arguments
#[derive(Args, Debug, Default)]
struct UserArgs {
    // Selection string
    #[arg(long, default_value = "all")]
    sel: String,
}

// Our analysis task type
struct ComTask {
    // Selection to use
    sel: Sel,
    // COM vector
    com_aver: nalgebra::Vector3<f32>,
}

// Implement AnalysisTask trait
// The type with custom parameters is provided as generic parameter
impl AnalysisTask<UserArgs> for ComTask {
    // Name of the analysis task
    fn task_name() -> String {
        "Center of mass computation".to_owned()
    }

    // Constructor of our analysis type
    // It is called on the first valid trajectory frame.
    // Context contains all needed data such as topology, 
    // state and parsed command line arguments
    fn new(context: &mut AnalysisContext<UserArgs>) -> anyhow::Result<Self> {
        // Create our selection from the user-supplied string.
        // Arguments are stored in context.args.
        let sel = context.sys.select(&context.args.sel)?;
        // Create our analysis type instance
        Ok(Self {
            sel,
            com_aver: nalgebra::Vector3::zeros(),
        })
    }

    // Function to be called at each frame.
    fn process_frame(&mut self, context: &mut AnalysisContext<UserArgs>) -> anyhow::Result<()> {
        // Compute the center of mass
        let com = context.sys.bind(&self.sel).center_of_mass()?;
        // Print current center of mass. We get current time stamp from the context
        println!("time={}, com={}", context.sys.get_time(), com);
        // Add to average
        self.com_aver += com.coords;
        Ok(())
    }

    // Post-processing
    fn post_process(&mut self, context: &mut AnalysisContext<UserArgs>) -> anyhow::Result<()> {
        // Compute average
        self.com_aver /= context.consumed_frames as f32;
        println!("average com={}", self.com_aver);
        Ok(())
    }
}

// Run our task
fn main() -> anyhow::Result<()> {
    ComTask::run()?;
    Ok(())
}

Trajectory processing aguments

All analysis tasks accept a number of common command line arguments (see [TrajAnalysisArgs]) allowing to select which frames to process and which files to read.

For example, the following command line will run our analysis task sequencially for two trajectories starting from frame 150 and ending when reaching 100 ns, while reporting progress each 100 frames. Custom selection is provided in the --sel argument, which is declared and recognised by ComTask

analysis_task -f structure.pdb traj_1.xtc traj_2.xtc -b 150 -e 100ns -log 100 --sel "resid 10:20"

Python bindings

MolAR provides convenient Python bindings, creatively named pymolar, which has its own "Pythonic" API. The bindings are made as performant as possible, but they are not as fast as the Rust functions.

Installation

It is highly recommended to use a Python virtual environment. It is assumed that pip is used for installation, but you can use any Python package manager.

#1. Install maturin in the current virtual environment
pip install maturin
#2. Go to molar_python subfolder of molar source tree
cd <path_to_molar>/molar_python
#3. Compile the bindings
maturin build -r
#4. Install the bindings in the current virtual environment
python -m pip install .

Usage

Pymolar bindings could be used in two modes: manual and as analysis tasks. In the first case you have a full fine-grained control on how you read your input files, but this may involve a lot of boilerplate. In contrast, "analysis tasks" hide most of the input handling from the user providing a very simple command-line interface to load structure and trajectory files, skip frames, begin and end reading at particular frame or time stamp, etc. The user only needs to implement three methods: pre_process, process_frame and post_process, which are called during the analysis.

As an example we will write a script that prints center of mass of CA protein atoms on each trajectory frame and then computes the average center of masses for the whole trajectory:

#file: average.py

# Import pymolar
from pymolar import *
import numpy as np

# Create an analysis task
class MyTask(AnalysisTask):
    # Register a custom command line argument for selection
    def register_args(self,parser):
        parser.add_argument('--sel',default="protein")
        
    # This method is called before starting trajectory processing
    def pre_process(self):
        # Create a selection using selection string from the command line
        # self.src contains a Source with the first state read
        self.sel = self.src(self.args.sel)
        # Average center of masses
        self.com_ave = np.array([0.0,0.0,0.0])


    # This method is called on each trajectory frame
    def process_frame(self):
        cm = self.sel.com()
        print(f"time: {self.state.time}, com: {cm}")
        self.com_ave += cm


    # This method is called after trajectory processing is finished
    def post_process(self):
        self.com_ave /= self.consumed_frames
        print(f"Average com: {self.com_ave}")


if __name__ == "__main__":
    # Run the analysis task.
    MyTask()

This script can be run as following:

python3 average.py -f struct.gro traj.xtc -e 100 --sel "resid 1:10"