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use std::{num::NonZeroU16, ops::RangeBounds};
use context_error::*;
use crate::{
chemistry::{ELEMENT_PARSE_LIST, Element, MolecularFormula},
helper_functions::{self, RangeExtension, explain_number_error},
};
impl MolecularFormula {
/// XLMOD: `C7 D10 H2 N4`
/// `-C1 -H2 O1` `C7 D10 H2 N4` `13C6 H6 O2`
/// # Errors
/// If the formula is not valid according to the above specification, with some help on what is going wrong.
/// # Panics
/// It can panic if the string contains not UTF8 symbols.
pub fn from_xlmod(
value: &str,
range: impl RangeBounds<usize>,
) -> Result<Self, BoxedError<'_, BasicKind>> {
let (start, end) = range.bounds(value.len());
let mut formula = Self::default();
for (offset, block) in helper_functions::split_ascii_whitespace(&value[start..end]) {
let negative = block.starts_with('-');
let isotope_len = block
.chars()
.skip(usize::from(negative))
.take_while(char::is_ascii_digit)
.count();
let number = block.chars().rev().take_while(char::is_ascii_digit).count();
if number + isotope_len + usize::from(negative) >= block.len() {
return Err(BoxedError::new(
BasicKind::Error,
"Invalid Xlmod molecular formula",
"No element is defined",
Context::line(None, value, offset, block.len()),
));
}
let element_len = block.len() - number - isotope_len - usize::from(negative);
let element = &block[isotope_len + usize::from(negative)..block.len() - number];
let (mut isotope, element) = if element == "D" {
if isotope_len == 0 {
(Some(NonZeroU16::new(2).unwrap()), Element::H)
} else {
return Err(BoxedError::new(
BasicKind::Error,
"Invalid Xlmod molecular formula",
"A deuterium cannot have a defined isotope as deuterium is by definition always isotope 2 of hydrogen",
Context::line(None, value, offset + usize::from(negative), isotope_len),
));
}
} else {
let mut found = None;
for possible in ELEMENT_PARSE_LIST {
if element == possible.0 {
found = Some(possible.1);
break;
}
}
if let Some(element) = found {
(None, element)
} else {
return Err(BoxedError::new(
BasicKind::Error,
"Invalid Xlmod molecular formula",
"Not a valid character in formula",
Context::line(
None,
value,
offset + usize::from(negative) + isotope_len,
element_len,
),
));
}
};
if isotope.is_none() && isotope_len > 0 {
isotope = Some(
block[usize::from(negative)..usize::from(negative) + isotope_len]
.parse::<NonZeroU16>()
.map_err(|err| {
BoxedError::new(
BasicKind::Error,
"Invalid Xlmod molecular formula",
format!("The isotope number {}", explain_number_error(&err)),
Context::line(
None,
value,
offset + usize::from(negative),
isotope_len,
),
)
})?,
);
}
let number = if negative { -1 } else { 1 }
* if number == 0 {
1
} else {
block[block.len() - number..block.len()]
.parse::<i32>()
.map_err(|err| {
BoxedError::new(
BasicKind::Error,
"Invalid Xlmod molecular formula",
format!("The element count {}", explain_number_error(&err)),
Context::line(
None,
value,
offset + usize::from(negative) + isotope_len + element_len,
number,
),
)
})?
};
if !Self::add(&mut formula, (element, isotope, number)) {
return Err(BoxedError::new(
BasicKind::Error,
"Invalid Xlmod molecular formula",
format!(
"An element without a defined mass ({}{element}) was used",
isotope.map_or_else(String::default, |i| i.to_string())
),
Context::line(
None,
value,
offset + usize::from(negative),
isotope_len + element_len,
),
));
}
}
Ok(formula)
}
}