molar 1.3.1

Molar is a rust library for analysis of MD trajectories and molecular modeling
Documentation 
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use std::{collections::HashMap, num::ParseIntError, path::Path};
use itertools::Itertools;
use thiserror::Error;
use crate::prelude::*;

/// Representation of Gromacs index files
pub struct NdxFile {
    groups: HashMap<String, SVec>,
}

impl NdxFile {
    /// Creates a new NdxFile by parsing a Gromacs index file
    pub fn new(path: impl AsRef<Path>) -> Result<Self, SelectionError> {
        let path = path.as_ref();
        let ndx_str = std::fs::read_to_string(path)
            .map_err(|e| NdxError::NdxIo(path.to_owned(), e))?;
        
        let mut groups = HashMap::new();
        let mut current_group = None;
        let mut current_numbers = Vec::new();

        for line in ndx_str.lines() {
            let line = line.trim();
            if line.is_empty() {
                continue;
            }

            if line.starts_with('[') && line.ends_with(']') {
                // Store previous group if exists
                if let Some(group_name) = current_group.take() {
                    if !current_numbers.is_empty() {
                        groups.insert(group_name, current_numbers.into());
                    }
                }
                // Start new group
                let group_name = line[1..line.len()-1].trim().to_string();
                current_group = Some(group_name);
                current_numbers = Vec::new();
            } else if let Some(group_name) = &current_group {
                // Parse numbers for current group
                current_numbers.extend(
                    line.split_whitespace()
                        .map(|s| s.parse::<usize>())
                        .map_ok(|i| i - 1) // Convert to zero-based
                        .collect::<Result<Vec<_>, _>>()
                        .map_err(|e| NdxError::Parse(group_name.clone(), e))?,
                );
            } else {
                return Err(NdxError::MalformedNdxFile(path.to_owned()))?;
            }
        }

        // Store last group if exists
        if let Some(group_name) = current_group {
            if !current_numbers.is_empty() {
                groups.insert(group_name, current_numbers.into());
            }
        }

        Ok(Self { groups })
    }

    /// Get an index group by name
    pub fn get_group(&self, name: impl AsRef<str>) -> Result<&SVec, SelectionError> {
        let gr = name.as_ref();
        Ok(self.groups.get(gr).ok_or_else(|| NdxError::NoGroup(gr.to_owned()))?)
    }

    pub fn get_group_as_sel(&self, name: impl AsRef<str>, src: &System) -> Result<Sel, SelectionError> {
        let gr = name.as_ref();
        let ind = self.groups.get(gr).ok_or_else(|| NdxError::NoGroup(gr.to_owned()))?;
        Ok(src.select(ind)?)
    }
}

/// Errors related to reading and manipulating Gromacs index files
#[derive(Debug, Error)]
pub enum NdxError {
    #[error("group {0} not found")]
    NoGroup(String),

    #[error("group {0} is empty")]
    EmptyGroup(String),

    #[error("index parse error in group {0}")]
    Parse(String, #[source] ParseIntError),

    #[error("error reading ndx file {0}")]
    NdxIo(std::path::PathBuf, #[source] std::io::Error),

    #[error("malformed ndx file {0}")]
    MalformedNdxFile(std::path::PathBuf),
}