Function acetylene_parser::tokenize

pub fn tokenize(input: &str, kind: &str) -> Substance

Tokenizes a string describing a chemical, yielding a Substance with (optional) functional groups corresponding to (more) fundamental components.

"kind" can be one of two strings: "formula" or "smiles". "formula" expects a simple molecular formula notation. "smiles" expects an OpenSMILES-specified string. See the tutorial at Daylight for info.

Examples

Molecular formula parsing

Here are a couple examples of what molecular formula parsing can do.

Parsing H2SO4 (sulfuric acid) without any structural annotations:

 
use acetylene_parser::tokenize;
use acetylene_parser::types::Substance;

assert_eq!(
  tokenize("H2SO4", "formula"),
  Substance {
    symbol: String::from("H2SO4"),
    quantity: 1,
    charge: None,
    groups: Some(Box::new(vec![
      Substance { symbol: String::from("H"), quantity: 2, charge: None, groups: None },
      Substance { symbol: String::from("S"), quantity: 1, charge: None, groups: None },
      Substance { symbol: String::from("O"), quantity: 4, charge: None, groups: None }
    ]))
  }
);

In this case, the parser just pulls out the individual elements and tallies them up.

If we annotate the structure with parentheses (denoting groups), we'll get something slightly different:

 
use acetylene_parser::tokenize;
use acetylene_parser::types::Substance;

assert_eq!(
  tokenize("H2(SO4)", "formula"),
  Substance {
    symbol: String::from("H2(SO4)"),
    quantity: 1,
    charge: None,
    groups: Some(Box::new(vec![
      Substance { symbol: String::from("H"), quantity: 2, charge: None, groups: None },
      Substance { symbol: String::from("(SO4)"), quantity: 1, charge: None, groups: None },
      Substance { symbol: String::from("S"), quantity: 1, charge: None, groups: None },
      Substance { symbol: String::from("O"), quantity: 4, charge: None, groups: None },
    ]))
  }
);

This time we can explicitly parse out both dihydrogen (H2) and sulfate (SO4). Note that charges are not inferred.

There's not much error checking going on in either case--only regex for now.

SMILES parsing

SMILES parsing has access to much more elaborate structural information. For example, ring closures are annotations that allow a ring of molecules to be unrolled into a 1-dimensional string, by marking the two breaks with a number following the atoms that need to reconnect.

For example, benzene looks like this:

 
use acetylene_parser::tokenize;
use acetylene_parser::types::Substance;

let test_str = r"c1ccccc1";
let res = tokenize(test_str, "smiles");
 
let sub = Substance {
  symbol: String::from("c1ccccc1"),
  quantity: 1,
  charge: None,
  groups: Some(Box::new(vec![
    Substance {
      symbol: String::from("c1ccccc1"),
      quantity: 1,
      charge: None,
      groups: None
    },
    Substance { symbol: String::from("c"), quantity: 1, charge: None, groups: None },
    Substance { symbol: String::from("c"), quantity: 1, charge: None, groups: None },
    Substance { symbol: String::from("c"), quantity: 1, charge: None, groups: None },
    Substance { symbol: String::from("c"), quantity: 1, charge: None, groups: None },
    Substance { symbol: String::from("c"), quantity: 1, charge: None, groups: None },
    Substance { symbol: String::from("c"), quantity: 1, charge: None, groups: None }      
  ]))
};

assert_eq!(res, sub);

The first functional group listed is identical to the "whole substance" described with the input string, which makes sense--the whole string is composed of one big ring closure, and so the parser detects that and rolls it all up.

Note that the individual atoms in the ring aren't collected up into a single molecular formula. I'm still working out how I want to go about it.

Here's one last example with hydronium. Hydronium is an ion, so it's required to be in brackets.

 
use acetylene_parser::tokenize;
use acetylene_parser::types::Substance;

let test_str = r"[OH3+]";
let res = tokenize(test_str, "smiles");

let sub = Substance {
  symbol: String::from("[OH3+]"),
  quantity: 1,
  charge: Some(1),
  groups: Some(Box::new(vec![
    Substance {
      symbol: String::from("[OH3+]"),
      quantity: 1,
      charge: Some(1),
      groups: None
    }
  ]))
};

assert_eq!(res, sub);