KiThe 0.3.0

//! # Stoichiometry Analyzer Module
//!
//! ## Purpose
//! This module analyzes chemical reaction equations and generates comprehensive stoichiometric data.
//! It parses reaction strings, extracts substances, and creates matrices for kinetic modeling.
//! Handles database parsing artifacts and supports empirical reactions with custom power coefficients.
//!
//! ## Main Data Structures
//! - `StoichAnalyzer`: Core structure containing all stoichiometric analysis results
//!   - `reactions`: Vector of reaction equation strings
//!   - `substances`: Vector of unique substance names found in reactions
//!   - `stecheo_matrx`: Stoichiometric coefficient matrix (reactions × substances)
//!   - `stecheo_reags`/`stecheo_prods`: Separate matrices for reactants and products
//!   - `G_matrix_reag`/`G_matrix_prod`: Power coefficient matrices for kinetic equations
//!   - `matrix_of_elements`: Elemental composition matrix
//!   - `vec_of_molmasses`: Molecular masses of substances
//!
//! ## Key Logic Implementation
//! 1. **Artifact Cleaning**: Removes database parsing artifacts like '_DUP', 'M)', phase markers
//! 2. **Regex Parsing**: Uses complex regex patterns to handle various reaction arrow formats (=, ->, =>, <=>)
//! 3. **Substance Extraction**: Parses stoichiometric coefficients and power coefficients (A**0.3)
//! 4. **Matrix Construction**: Builds multiple matrices for different aspects of kinetic modeling
//! 5. **Third Body Handling**: Recognizes and filters out collision partners marked as 'M'
//!
//! ## Usage Pattern
//! ```rust
//! use KiThe::Kinetics::stoichiometry_analyzer::StoichAnalyzer;
//! let mut analyzer = StoichAnalyzer::new();
//! analyzer.reactions = vec!["A=2B".to_string(), "B->A + 3C".to_string()];
//! analyzer.search_substances();  // Find all unique substances
//! analyzer.analyse_reactions();  // Generate stoichiometric matrices
//! analyzer.create_matrix_of_elements();  // Generate elemental composition
//! ```
//!
//! ## Interesting Features
//! - **Empirical Reaction Support**: Handles power coefficients different from stoichiometric (A**0.5)
//! - **Database Artifact Cleaning**: Removes '_DUP', '_dup' suffixes and collision partner markers
//! - **Flexible Arrow Recognition**: Supports =, ->, =>, <=>, and variations with spaces
//! - **Third Body Recognition**: Automatically filters out 'M' and '(M)' collision partners
//! - **Dual Matrix System**: Separate tracking of stoichiometric vs kinetic power coefficients
//! - **Integrated Molecular Data**: Combines with molmass module for complete substance characterization

use crate::Kinetics::molmass::{
    calculate_molar_mass_of_vector_of_subs, create_elem_composition_matrix,
};
use nalgebra::DMatrix;
use regex::Regex;
/// ru
/// Модуль берет на вход  вектор уравнений реации, заданных в виде String и выдает следующие данные:
/// 1) стехиометрическую матрицу заданную в виде вектора векторов
/// 2) вектор веществ
/// 3) вектор векторов стехиометрических коэффициентов реагентов в каждой реакции
/// 4) то же для продуктов
/// В процессе производится избавление от артефактов парсинга уравнений из баз данных
/// Примечание:
/// 1) уравнения реакции содержат последние символы '_dup' или '_DUP' (то есть дублирующие) - эти
/// символы удаляются как артефакты парсинга
/// 2) для работы с эмпирическими реакциями у которых
///  код возвращает следующие структуры данных: матрица стехеометрических коэффициентов,
///  матрица коэффициентов прямых реакций и матрица коэффициентов обратных реакций, матрица степеней концентраций для кинетической функции, G_matrix,
/// как правило степени концентраций в кинетической функции совпадают со стехеометрическими коэффициентами веществ в реакциии, однако,
/// для эмпирических реакций они могут и отличаться от стехеометрических коэффициентов.
///  Предусмотрена вохможность прямого указания этих коэффициентов в уравнениях реакции в виде "степени"
/// после формулы вещества (например A**0.3 ) такие степени записываются в  G_matrix вместо стехеометрических коэффициентов
/// в противном случае записывается стехеометрический коэффициент
/// ----------------------------------------------------------------
/// eng
/// The module takes as input a vector of reaction equations specified as a vector of String and produces the following data:
/// 1) a stoichiometric matrix specified as a vector of vectors
/// 2) a vector of substances
/// 3) a vector of vectors of stoichiometric coefficients of reactants in each reaction
/// 4) the same for products
/// The process involves getting rid of artifacts of parsing equations from databases
///
/// Note:
/// 1) reaction equations contain the last characters '_dup' or '_DUP' (that is, duplicate ones) - these
/// characters are removed as parsing artifacts
/// 2) for working with empirical reactions in which  the code returns the following data structures: matrix of stoicheometric coefficients,
/// matrix of coefficients of direct reactions and matrix of coefficients of reverse reactions, matrix of degrees of concentration for the
/// kinetic function, G_matrix. As a rule, the degrees of concentration in the kinetic function coincide with the stoicheometric coefficients of
/// the substances in the reaction; however, for empirical reactions they may differ from the stoicheometric coefficients.
/// It is possible to directly indicate these coefficients in the reaction equations in the form of a “degree” after the formula of a substance
/// (for example A**0.3), such degrees are written in G_matrix instead of stoicheometric coefficients otherwise, the stoicheometric coefficient is written
/// # Examples
/// reaction data with  artifacts of parsing equations from databases
/// ```
/// use KiThe::Kinetics::stoichiometry_analyzer::StoichAnalyzer  ;
/// let mut ReactionAnalyzer_instance = StoichAnalyzer  ::new();
/// let reactions_: Vec<&str> = vec!["A=2BM)", "B->A + 3C_DUP", "2B+A=D"];
/// let reaction = reactions_.iter().map(|s| s.to_string()).collect();
/// ReactionAnalyzer_instance.reactions = reaction;
/// ReactionAnalyzer_instance.search_substances();
/// println!("substances: {:?}", ReactionAnalyzer_instance.substances);
/// let substancses_ = vec!["A", "B", "C", "D"];
/// let substancses = substancses_.iter().map(|s| s.to_string()).collect();
/// ReactionAnalyzer_instance.substances = substancses ;
/// ReactionAnalyzer_instance.analyse_reactions();
/// println!("{:?}", ReactionAnalyzer_instance);
/// ```
use std::collections::HashMap;

/*
        #  строковая переменная на которые разделяет по знаку "+" половину уравнения относящююся к
        # реагентам/продуктам может содержать '(', ')', а также 'M' - символ третьей частицы которая не относится к
        # продуктам и реагентам
*/
fn clean_off_artifacts(item: &mut String) -> &mut String {
    #[allow(unused_variables)]
    let items_to_clean = [" (", "(", "M)", "M)", ">", "S)", "s)"];
    if item.contains("M)")
        || item.contains("M)")
        || item.contains(" (")
        || item.contains("(")
        || item.contains(">")
        || item.contains("S)")
        || item.contains("s)")
    {
        *item = item
            .replace("M)", "")
            .replace("M)", "")
            .replace(" (", "")
            .replace("(", "")
            .replace(">", "")
            .replace("S)", "")
            .replace("s)", "");

        return item;
    } else {
        item
    }
}
///   half_reaction` - A string representing a half-reaction.
pub fn analyse_substances(half_reaction: &str) -> (Vec<String>, Vec<f64>, Vec<f64>) {
    let mut s_list = Vec::new();
    let mut g_list = Vec::new();
    let mut subs: Vec<String> = Vec::new();

    let re_coeff = Regex::new(r"(\d+(\.\d*)?)\*?").unwrap();
    //let re_power = Regex::new(r"\^\ *(\d+(\.\d*)?)").unwrap();
    let re_power = Regex::new(r"\^(\d+(\.\d*)?)").unwrap();

    for s in half_reaction.split('+') {
        let mut s = s.trim();
        print!("half reaction is:  {:#?}   ", s);
        let mut stec_coeff = 1.0;
        let mut power_coeff = 1.0;
        let _end_of_stoichiometric: usize = 0;
        //  captures.get(1) is used to access the first capture group in the regular expression match.
        if let Some(captures) = re_coeff.captures(s) {
            // refers to the first capture group in the regular expression match, example: Match { start: 0, end: 1, string: "2" }
            let regmatch = captures.get(0).unwrap();
            print!(" regmatch stoichiometric:  {:?}   ", regmatch);
            let start_of_stoichiometric = regmatch.start();
            let end_of_stoichiometric = regmatch.end();
            // стехиометрический коэффициент должен быть перед формулой вещества, т.е. номер его позиции должен начинаться с нуля
            if start_of_stoichiometric == 0 {
                s = &s[end_of_stoichiometric..];
                stec_coeff = captures.get(1).unwrap().as_str().parse().unwrap();
                print!(" stoichioemtric coeff:  {}   ", &stec_coeff);
            }
        }

        if let Some(captures) = re_power.captures(s) {
            let regmatch = captures.get(0).unwrap();
            print!(" regmatch power:  {:?}   ", regmatch);
            power_coeff = captures.get(1).unwrap().as_str().parse().unwrap();
            print!(" power coeff:  {}   ", &power_coeff);
            let start = captures.get(0).unwrap().start();
            #[allow(unused_variables)]
            let end = captures.get(0).unwrap().end();
            // println!("start: {} end: {}", start, end);
            s = &s[..start];
        } else {
            power_coeff == stec_coeff;
        }

        s = s.trim();
        if (s == "M") | (s == "(M)") {
            continue;
        } // "M" means "third body" it is not a real substance
        let s_to_filter: &mut String = &mut s.to_string();
        let s_filtered = clean_off_artifacts(s_to_filter);
        let s: String = s_filtered.to_string();
        s_list.push(stec_coeff);
        g_list.push(power_coeff);
        subs.push(s);
    }

    (subs, s_list, g_list)
}

// #  некоторые записи уравнения реакции содержат последние символы '_dup' или '_DUP' (то есть дублирующие)
// избавляемся от них
pub fn clean_off_DUP(item: &mut String) -> &String {
    if item.ends_with("_dup") || item.ends_with("_DUP") {
        *item = item.replace("_dup", "").replace("_DUP", "");
        return item;
    } else {
        item
    }
}

/// This struct is used to represent a reaction.
#[derive(Debug, Clone)]
pub struct StoichAnalyzer {
    pub reactions: Vec<String>, // вектор реакций/ a vector of reactions
    pub groups: Option<HashMap<String, HashMap<String, usize>>>, // Chemical formulae may contain spectial names for chemical groupls i.e. groups of atoms, e.g. Me (methyl) group, which is converted into {"C":1, "H":3}
    pub substances: Vec<String>, // вектор веществ/ a vector of substances
    pub stecheo_matrx: Vec<Vec<f64>>, // вектор векторов стехиометрических коэффициентов в каждой реакции/ a vector of vectors of stoichiometric coefficients in each reaction
    pub stecheo_reags: Vec<Vec<f64>>, // вектор векторов стехиометрических коэффициентов реагентов в каждой реакции/ a vector of vectors of stoichiometric coefficients of reactants in each reaction
    pub stecheo_prods: Vec<Vec<f64>>, // вектор векторов стехиометрических коэффициентов продуктов в каждой реакции/ a vector of vectors of stoichiometric coefficients of products in each reaction
    pub G_matrix_reag: Vec<Vec<f64>>, // matrix of powers of concentrations for constructng kinetic equation for forward reaction
    pub G_matrix_prod: Vec<Vec<f64>>, // matrix of powers of concentrations for constructng kinetic equation for reverse reaction
    pub matrix_of_elements: Option<DMatrix<f64>>, // matrix of elemental composition
    pub vec_of_molmasses: Option<Vec<f64>>, // vector of molecular masses
    pub unique_vec_of_elems: Option<Vec<String>>,
}

impl StoichAnalyzer {
    pub fn new() -> Self {
        StoichAnalyzer {
            reactions: Vec::new(),
            groups: None,
            substances: Vec::new(),
            stecheo_matrx: Vec::new(),
            stecheo_reags: Vec::new(),
            stecheo_prods: Vec::new(),
            G_matrix_reag: Vec::new(),
            G_matrix_prod: Vec::new(),
            matrix_of_elements: None,
            vec_of_molmasses: None,
            unique_vec_of_elems: None,
        }
    }

    pub fn analyse_reactions(&mut self) {
        println!(
            "\n______________ANALYSING REACTIONS________________________________________________________ \n"
        );
        let reactions_trimmed = self
            .reactions
            .iter()
            .map(|s| s.replace("**", "^").trim().to_string())
            .collect();
        self.reactions = reactions_trimmed;
        // allocate memory for matrices
        self.stecheo_matrx
            .resize(self.reactions.len(), vec![0.0; self.substances.len()]);
        self.stecheo_reags
            .resize(self.reactions.len(), vec![0.0; self.substances.len()]);
        self.stecheo_prods
            .resize(self.reactions.len(), vec![0.0; self.substances.len()]);
        self.G_matrix_reag
            .resize(self.reactions.len(), vec![0.0; self.substances.len()]);
        self.G_matrix_prod
            .resize(self.reactions.len(), vec![0.0; self.substances.len()]);
        for mut reaction in &self.reactions {
            // номер реакции
            if let Some(i) = self.reactions.iter().position(|s| s == reaction) {
                let reaction_: &mut String = &mut reaction.to_string();
                println!("\n \n \n parsing reaction number: {}, {}", i, reaction_);
                reaction = clean_off_DUP(reaction_);
                println!("Reaction after dup: {}", &reaction);
                // разделяем уравнение реакции на половины относящиеся к реагентам и продуктам по соответствующему знаку = или -> или =>
                let re = Regex::new(r"<= >|< =>|<=>|=>|->|=").unwrap();
                let sides: Vec<String> = re // divide reaction ino products and reagents
                    .split(reaction) // reaction.split(|s| s == '=' )
                    .map(|s| s.trim())
                    .map(|s| s.to_string())
                    .collect();
                let mut subs = Vec::new();
                let mut subs_r = Vec::new();
                let mut s_list = Vec::new();
                let mut g_list = Vec::new();
                let mut s_list_r = Vec::new();
                let mut g_list_r: Vec<f64> = Vec::new();
                // left side of reaction equation
                println!("direct reaction  {:?}", &sides[0]);
                let (left_subs, mut left_s_list, mut left_g_list) = analyse_substances(&sides[0]);
                println!(
                    "\n back to the reaction analyzer: \n s_list: {:?},\n g_list: {:?}",
                    left_s_list, left_g_list
                );
                let mut left_subs = left_subs.iter().map(|s| s.as_str()).collect();
                subs.append(&mut left_subs);
                s_list.append(&mut left_s_list);
                g_list.append(&mut left_g_list);
                println!(
                    "direct reaction substances: {:?} of lengh {}",
                    subs,
                    &subs.len()
                );
                println!("iterating over substances in direct reaction");

                for j in 0..subs.len() {
                    let subs_j = subs[j];
                    if let Some(k) = self.substances.iter().position(|s| s == subs_j) {
                        println!("Index of substance '{}' in list of substances of this react is: {}, in general list is {},
                     lengh of gen. list is {}", subs_j, j, k,  &self.substances.len());
                        self.stecheo_matrx[i][k] -= s_list[j];
                        self.stecheo_reags[i][k] = s_list[j];
                        self.G_matrix_reag[i][k] = g_list[j];
                    } else {
                        println!("'{}' not found in the vector", subs_j);
                    }
                }

                println!("reverse reaction {:?}", &sides[1]);
                let (right_subs, mut right_s_list, mut right_g_list) =
                    analyse_substances(&sides[1]);
                let mut right_subs = right_subs.iter().map(|s| s.as_str()).collect();
                subs_r.append(&mut right_subs);
                s_list_r.append(&mut right_s_list);
                g_list_r.append(&mut right_g_list);
                println!("reverse reaction substances: {:?}", subs_r);
                println!("iterating over substances in reverse reaction");
                println!("lengh of substance list found in reaction {}", &subs.len());
                for j in 0..subs_r.len() {
                    let subs_j = subs_r[j];
                    // индекс реагента в векторе реагентов
                    if let Some(k) = self.substances.iter().position(|s| s == subs_j) {
                        println!("Index of substance '{}' in list of substanced of this react is: {}, in general list is {},
                    lengh of gen. list is {}", subs_j, j, k,  &self.substances.len());
                        self.stecheo_matrx[i][k] += s_list_r[j];
                        self.stecheo_prods[i][k] = s_list_r[j];
                        self.G_matrix_prod[i][k] = g_list_r[j];
                    } else {
                        println!("'{}' not found in the vector", subs_j);
                    }
                }
                // Add code to populate self.stecheo_matrx, self.G_matrix_reag, self.G_matrix_prod,
                // self.stecheo_reags, and self.stecheo_prods with the appropriate values.
            }
        } // end of for reaction in &self.reactions {
        println!(
            "\n______________ANALYSING REACTIONS: END________________________________________________________ \n"
        );
    }

    pub fn search_substances(&mut self) {
        println!(
            "\n______________SEARCH SUBSTANCES________________________________________________________ \n"
        );
        let reactions_trimmed = self
            .reactions
            .iter()
            .map(|s| s.replace("**", "^").trim().to_string())
            .collect();
        self.reactions = reactions_trimmed;
        let mut found_substances: Vec<String> = Vec::new();
        for mut reaction in &self.reactions {
            // номер реакции
            if let Some(i) = self.reactions.iter().position(|s| s == reaction) {
                println!("reaction number: {}", i);
                let reaction_: &mut String = &mut reaction.to_string();
                reaction = clean_off_DUP(reaction_);
                println!("Reaction after dup: {}", &reaction);
                // разделяем уравнение реакции на половины относящиеся к реагентам и продуктам по соответствующему знаку = или -> или =>
                // let re = Regex::new(r"=|->|=>").unwrap();
                let re = Regex::new(r"<= >|< =>|<=>|=>|->|=").unwrap();
                let sides: Vec<String> = re
                    .split(reaction) // reaction.split(|s| s == '=' )
                    .map(|s| s.trim())
                    .map(|s| s.to_string())
                    .collect();
                let mut subs = Vec::new();
                println!("direct reaction  {:?}", &sides[0]);
                let (left_subs, _, _) = analyse_substances(&sides[0]);
                let mut left_subs = left_subs.iter().map(|s| s.as_str()).collect();
                subs.append(&mut left_subs);
                println!("direct reaction substances: {:?}", &left_subs);

                println!("reverse reaction {:?}", &sides[1]);
                let (right_subs, _, _) = analyse_substances(&sides[1]);
                let mut right_subs = right_subs.iter().map(|s| s.as_str()).collect();
                subs.append(&mut right_subs);
                println!("reverse  reaction substances: {:?}", &left_subs);
                let subs_mut = &mut subs.clone();
                subs_mut.retain(|s| !found_substances.contains(&s.to_string())); // remove duplicates
                found_substances.extend(subs_mut.iter().map(|s| s.to_string()).collect::<Vec<_>>());
            } // end of if let
        } // end of for reaction in &self.reactions {
        println!(
            "\n______________SEARCH SUBSTANCES ENDED________________________________________________________ \n"
        );
        self.substances = found_substances;
    }
    pub fn create_matrix_of_elements(&mut self) {
        // Only calculate molar masses if they haven't been set manually
        if self.vec_of_molmasses.is_none() {
            self.vec_of_molmasses = Some(calculate_molar_mass_of_vector_of_subs(
                self.substances.iter().map(|s| s.as_str()).collect(),
                self.groups.clone(),
            ));
        }
        let (matrix, vec_of_elems) = create_elem_composition_matrix(
            self.substances.iter().map(|s| s.as_str()).collect(),
            self.groups.clone(),
        );
        self.matrix_of_elements = Some(matrix);
        self.unique_vec_of_elems = Some(vec_of_elems);
    }
} // end of impl ReactionAnalyzer
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
// TESTS
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
#[cfg(test)]
mod tests {
    use super::*;

    #[test]
    fn test_analyse_substances() {
        let half_reaction = "5H2O + 10O2";
        let (subs, s_list, g_list) = analyse_substances(half_reaction);
        assert_eq!(subs, vec!["H2O".to_string(), "O2".to_string()]);
        assert_eq!(s_list, vec![5.0, 10.0]);
        assert_eq!(g_list, vec![1.0, 1.0]);
    }

    #[test]
    fn test_analyse_substances_with_exotic_names() {
        let mut ReactionAnalyzer_instance = StoichAnalyzer::new();
        let reactions_: Vec<&str> = vec!["HMX=>7HMXprod"];
        let reaction = reactions_.iter().map(|s| s.to_string()).collect();
        ReactionAnalyzer_instance.reactions = reaction;
        // ReactionAnalyzer_instance.search_substances();
        // assert_eq!(ReactionAnalyzer_instance.substances, vec!["A".to_string(), "B".to_string(), "C".to_string()]);
        let substancses_ = vec!["HMX", "HMXprod"];
        let substancses = substancses_.iter().map(|s| s.to_string()).collect();
        ReactionAnalyzer_instance.substances = substancses;
        ReactionAnalyzer_instance.analyse_reactions();
        let stecheo_matrx = ReactionAnalyzer_instance.stecheo_matrx;
        let result = [[-1.0, 7.0]];
        let result: Vec<Vec<f64>> = result.iter().map(|row| row.to_vec()).collect();
        assert_eq!(stecheo_matrx, result);
    }
    #[test]
    fn test_clean_off_artifacts_and_DUP() {
        let mut item = "A=2BM)".to_string();
        let cleaned_item = clean_off_artifacts(&mut item);
        assert_eq!(cleaned_item, "A=2B");

        let mut item = "B->A + 3C_DUP".to_string();
        let cleaned_item = clean_off_DUP(&mut item);
        assert_eq!(cleaned_item, "B->A + 3C");
    }

    #[test]
    fn test_search_substances() {
        let mut ReactionAnalyzer_instance = StoichAnalyzer::new();
        let reactions_: Vec<&str> = vec!["A=2BM)", "B->A + 3C_DUP"];
        let reaction = reactions_.iter().map(|s| s.to_string()).collect();
        ReactionAnalyzer_instance.reactions = reaction;
        ReactionAnalyzer_instance.search_substances();
        assert_eq!(
            ReactionAnalyzer_instance.substances,
            vec!["A".to_string(), "B".to_string(), "C".to_string()]
        );
    }
    #[test]
    fn test_reaction_analyzer() {
        let mut ReactionAnalyzer_instance = StoichAnalyzer::new();
        let reactions_: Vec<&str> = vec!["A=2BM)", "B=>A + 3C_DUP", "2B+A=D**0.5"];
        let reaction = reactions_.iter().map(|s| s.to_string()).collect();
        ReactionAnalyzer_instance.reactions = reaction;
        // ReactionAnalyzer_instance.search_substances();
        // assert_eq!(ReactionAnalyzer_instance.substances, vec!["A".to_string(), "B".to_string(), "C".to_string()]);
        let substancses_ = vec!["A", "B", "C", "D"];
        let substancses = substancses_.iter().map(|s| s.to_string()).collect();
        ReactionAnalyzer_instance.substances = substancses;
        ReactionAnalyzer_instance.analyse_reactions();
        let stecheo_matrx = ReactionAnalyzer_instance.stecheo_matrx;
        let result = [
            [-1.0, 2.0, 0.0, 0.0],
            [1.0, -1.0, 3.0, 0.0],
            [-1.0, -2.0, 0.0, 1.0],
        ];
        let result: Vec<Vec<f64>> = result.iter().map(|row| row.to_vec()).collect();
        assert_eq!(stecheo_matrx, result);
    }
}