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use std::{num::NonZeroU16, ops::Range};
use context_error::*;
use crate::{
chemistry::{Element, MolecularFormula, Molecule},
glycan::MonoSaccharide,
helper_functions::{RangeExtension, explain_number_error},
};
enum Brick {
Element(Element),
Formula(MolecularFormula),
}
/// # Errors
/// Errors if the provided text is not a Unimod composition brick.
fn parse_unimod_composition_brick(
text: &str,
range: Range<usize>,
) -> Result<Brick, BoxedError<'_, BasicKind>> {
match text[range.clone()].to_lowercase().as_str() {
"ac" => Ok(Brick::Formula(molecular_formula!(C 2 H 2 O 1))),
"me" => Ok(Brick::Formula(molecular_formula!(C 1 H 2))),
"kdn" => Ok(Brick::Formula(molecular_formula!(C 9 H 14 O 8))),
"kdo" => Ok(Brick::Formula(molecular_formula!(C 8 H 12 O 7))),
"sulf" => Ok(Brick::Formula(molecular_formula!(S 1 O 3))),
"phos" => Ok(Brick::Formula(molecular_formula!(P 1 O 3))),
"water" => Ok(Brick::Formula(molecular_formula!(H 2 O 1))),
_ => Element::try_from(text[range.clone()].to_lowercase().as_str()).map_or_else(
|()| {
if let Ok((ms, _)) = MonoSaccharide::from_short_iupac(text, range.start_index(), 0) {
Ok(Brick::Formula(ms.formula()))
} else {
Err(BoxedError::new(
BasicKind::Error,
"Invalid Unimod chemical formula",
"Unknown Unimod composition brick, use an element or one of the unimod shorthands. Eg: 'H(13) C(12) N O(3)'.",
Context::default().lines(0, text).add_highlight((0, range)),
))
}
},
|el| Ok(Brick::Element(el)),
),
}
}
impl MolecularFormula {
/// Parse a molecular formula from a Unimod formula.
/// # Errors
/// If the formula is not valid according to the Unimod molecular formula format, with some help
/// on what is going wrong.
/// ```rust
/// use mzcore::prelude::*;
/// assert!(MolecularFormula::unimod("H(25) C(8) 13C(7) N 15N(2) O(3)").is_ok());
/// assert!(MolecularFormula::unimod("H(6) C(4) N(2) dHex").is_ok());
/// assert_eq!(MolecularFormula::unimod("C(1) 13C(1) H(6)"), Ok(molecular_formula!(C 1 [13 C 1] H 6)));
/// assert_eq!(MolecularFormula::unimod("Water"), Ok(molecular_formula!(H 2 O 1)));
/// ```
pub fn unimod(value: &str) -> Result<Self, BoxedError<'_, BasicKind>> {
Self::unimod_inner(&Context::default().lines(0, value), value, 0..value.len())
}
/// This parses a substring of the given string as a Unimod molecular formula definition.
/// Additionally, this allows passing a base context to allow to set the line index and source
/// and other properties. Note that the base context is assumed to contain the full line at
/// line index 0.
///
/// # Errors
/// It fails when the string is not a valid Unimod molecular formula string.
pub fn unimod_inner<'a>(
base_context: &Context<'a>,
value: &'a str,
range: Range<usize>,
) -> Result<Self, BoxedError<'a, BasicKind>> {
let (mut index, end) = range.bounds(value.len());
let mut formula = Self::default();
let mut isotope = None;
let mut last_name: Option<(usize, String)> = None;
while index <= end {
match (value.as_bytes()[index], last_name.as_ref()) {
(b'(', Some((last_name_i, last_name_s))) => {
let length = value
.chars()
.skip(index + 1)
.take_while(|c| *c == '-' || *c == '+' || c.is_ascii_digit())
.count();
let num =
value[index + 1..index + 1 + length].parse::<i32>().map_err(|err| {
BoxedError::new(
BasicKind::Error,
"Invalid Unimod chemical formula",
format!("The element amount {}", explain_number_error(&err)),
base_context.clone().add_highlight((0, index + 1, length)),
)
})?;
match parse_unimod_composition_brick(
value,
*last_name_i..last_name_i + last_name_s.len(),
)? {
Brick::Element(el) => {
if let Err(err) = formula.add((el, isotope.take(), num)) {
return Err(BoxedError::new(
BasicKind::Error,
"Invalid Unimod chemical formula",
err.reason(),
base_context.clone().add_highlight((
0,
*last_name_i..last_name_i + last_name_s.len(),
)),
));
}
}
Brick::Formula(f) => formula += f * num,
}
last_name = None;
index += length + 2;
if value.as_bytes()[index - 1] != b')' {
return Err(BoxedError::new(
BasicKind::Error,
"Invalid Unimod chemical formula",
"The amount of an element should be closed by ')'",
base_context.clone().add_highlight((0, index - 1, 1)),
));
}
}
(b' ', Some((last_name_i, last_name_s))) => {
match parse_unimod_composition_brick(
value,
*last_name_i..last_name_i + last_name_s.len(),
)? {
Brick::Element(el) => {
if let Err(err) = formula.add((el, isotope.take(), 1)) {
return Err(BoxedError::new(
BasicKind::Error,
"Invalid Unimod chemical formula",
err.reason(),
base_context.clone().add_highlight((
0,
*last_name_i..last_name_i + last_name_s.len(),
)),
));
}
}
Brick::Formula(f) => formula += f,
}
last_name = None;
index += 1;
}
(b' ', None) => {
index += 1;
}
(n, _) if n.is_ascii_digit() => {
let length = value.chars().skip(index).take_while(char::is_ascii_digit).count();
isotope = Some(value[index..index + length].parse::<NonZeroU16>().map_err(
|err| {
BoxedError::new(
BasicKind::Error,
"Invalid Unimod chemical formula",
format!("The isotope {}", explain_number_error(&err)),
base_context.clone().add_highlight((0, index, length)),
)
},
)?);
index += length;
}
(n, _) if n.is_ascii_alphabetic() => {
if let Some((_, name)) = last_name.as_mut() {
name.push(n as char);
} else {
last_name = Some((index, (n as char).to_string()));
}
index += 1;
}
_ => {
return Err(BoxedError::new(
BasicKind::Error,
"Invalid Unimod chemical formula",
"Unexpected character, use an element or one of the unimod shorthands. Eg: 'H(13) C(12) N O(3)'.",
base_context.clone().add_highlight((0, index, 1)),
));
}
}
}
if let Some((last_name_i, last_name_s)) = last_name {
match parse_unimod_composition_brick(
value,
last_name_i..last_name_i + last_name_s.len(),
)? {
Brick::Element(el) => {
if let Err(err) = formula.add((el, isotope.take(), 1)) {
return Err(BoxedError::new(
BasicKind::Error,
"Invalid Unimod chemical formula",
err.reason(),
base_context
.clone()
.add_highlight((0, last_name_i..last_name_i + last_name_s.len())),
));
}
}
Brick::Formula(f) => formula += f,
}
}
Ok(formula)
}
}