molar 1.3.1

Molar is a rust library for analysis of MD trajectories and molecular modeling
Documentation 
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use crate::{atom::{Atom, AtomStr, ATOM_NAME_EXPECT, ATOM_RESNAME_EXPECT, ATOM_TYPE_NAME_EXPECT}, io::FileFormatHandler};
use std::{
    fs::File,
    io::{BufRead, BufReader},
    num::{ParseFloatError, ParseIntError},
    path::Path,
};
use thiserror::Error;

use super::Topology;
use regex;

pub struct ItpFileHandler {
    file: File,
    already_read: bool,
}

impl FileFormatHandler for ItpFileHandler {
    fn open(fname: impl AsRef<Path>) -> Result<Self, super::FileFormatError>
    where
        Self: Sized,
    {
        Ok(Self {
            file: File::open(fname).map_err(|e| ItpHandlerError::OpenRead(e))?,
            already_read: false,
        })
    }

    fn read_topology(&mut self) -> Result<Topology, super::FileFormatError> {
        if self.already_read {
            return Err(super::FileFormatError::Eof);
        }
        
        let mut top = Topology::default();

        let mut reader = BufReader::new(&self.file);
        let mut line = String::new();

        // Loop over lines until we encounted moleculetype
        let moltype_re = regex::Regex::new(r"\[\s+moleculetype\s+\]").unwrap();
        loop {
            line.clear();
            let nread = reader.read_line(&mut line).unwrap();
            if nread == 0 {
                return Err(ItpHandlerError::NoMoleculetype)?;
            }
            if moltype_re.is_match(&line) {
                break;
            }
        }

        // We are now in moleculetype
        // Skip until we get atoms
        let atoms_re = regex::Regex::new(r"\[\s+atoms\s+\]").unwrap();
        loop {
            line.clear();
            let nread = reader.read_line(&mut line).unwrap();
            if nread == 0 {
                return Err(ItpHandlerError::NoAtoms)?;
            }
            if atoms_re.is_match(&line) {
                break;
            }
        }

        // We are in atoms. Read them
        loop {
            line.clear();
            let nread = reader.read_line(&mut line).unwrap();
            let l = line.trim();
            if nread == 0 {
                break;
            }
            // Skip comments and empty lines
            if l.trim_start().starts_with(";") || l.len() == 0 {
                continue;
            }

            let fields = l.split_ascii_whitespace().collect::<Vec<_>>();
            if fields.len() < 8 {
                break;
            }
            let mut at = Atom {
                name: AtomStr::try_from_str(fields[4]).expect(ATOM_NAME_EXPECT),
                resname: AtomStr::try_from_str(fields[3]).expect(ATOM_RESNAME_EXPECT),
                type_name: AtomStr::try_from_str(fields[1]).expect(ATOM_TYPE_NAME_EXPECT),
                resid: fields[2].parse().map_err(ItpHandlerError::ParseInt)?,
                charge: fields[6].parse().map_err(ItpHandlerError::ParseFloat)?,
                mass: fields[7].parse().map_err(ItpHandlerError::ParseFloat)?,
                ..Default::default()
            };
            // We don't have element number, guess it
            at.guess_element_from_name();
            // Add atom to topology
            top.atoms.push(at);
        }

        Ok(top.into())
    }
}

#[derive(Debug, Error)]
pub enum ItpHandlerError {
    #[error("can't open itp file for reading")]
    OpenRead(#[source] std::io::Error),

    #[error("no moleculetype found")]
    NoMoleculetype,

    #[error("no atoms found")]
    NoAtoms,

    #[error(transparent)]
    Regex(#[from] regex::Error),

    #[error(transparent)]
    ParseInt(#[from] ParseIntError),

    #[error(transparent)]
    ParseFloat(#[from] ParseFloatError),
}