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//! A string parser for different chemical nomenclature. Focused on SMILES. extern crate regex; #[macro_use] extern crate lazy_static; mod formula; mod smiles; pub mod types; use formula::tokenize_formula; use smiles::tokenize_smiles; use types::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][ref] for info. /// /// [ref]: http://www.daylight.com/dayhtml_tutorials/languages/smiles/index.html /// /// # 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); /// ``` /// pub fn tokenize(input: &str, kind: &str) -> Substance { match kind { "formula" => tokenize_formula(input), "smiles" => tokenize_smiles(input), // "iupac" => tokenize_iupac(input), _ => tokenize_formula(input) } }