File reaction_parser.hxx

Defines

REACTION_PARSER_H

Enums

enum class species_filter

An enum class with which to identify various useful species subsets.

Values:

enumerator consumed

enumerator electron

enumerator ion

enumerator neutral

enumerator reactants

enumerator produced

enumerator products

enumerator heavy

Functions

static inline std::map<std::string, int> count_species(std::string expr)

template<typename T>
static inline std::vector<std::string> get_str_keys(const std::map<std::string, T> &map)

Util function to get the keys of a std::string => T map.

Template Parameters:

T – the type of the map values

Parameters:

map – the map

Returns:

std::vector<std::string> vector of keys

class ReactionParser

#include <reaction_parser.hxx>

A class to parse reaction strings and extract the stoichiometric vector (net population changes for each species). Also used to retrieve the names of species in various useful subsets (reactants, products, non-electron species, etc.)

Public Functions

ReactionParser(const std::string &reaction_str)

inline const std::string get_reaction_str() const

Public getter for underlying reaction string.

inline const std::map<std::string, int> &get_stoich()

Get the stoichiometric vector for this reaction (as a species_name=>pop_change map)

std::vector<std::string> get_species() const

Get the names of all species identified by the parser.

Returns:

std::vector<std::string> the list of species names

std::vector<std::string> get_species(species_filter filter) const

Apply a filter to the list of species identified by the parser.

Parameters:

filter – the filter to apply

Returns:

std::vector<std::string> the filterered list of species names

std::vector<std::string> get_species(std::vector<std::string> species_names, species_filter filter) const

Apply a filter to a list of species names.

Parameters:

• species_names – the list of species names to filter

• filter – the filter to apply

Returns:

std::vector<std::string> the filtered list of names

template<typename ...FilterTypes>
inline std::vector<std::string> get_species(std::vector<std::string> species_names, species_filter first_filter, FilterTypes... other_filters) const

Apply multiple filters to a list of species names.

Variadic so that it can be applied recursively.

Template Parameters:

FilterTypes –

Parameters:

• species_names – the list of species names to filter

• first_filter – the first filter

• other_filters – other filters

Returns:

std::vector<std::string> the filtered list of names

template<typename ...FilterTypes>
inline std::vector<std::string> get_species(FilterTypes... filters) const

Apply multiple filters to the list of species identified by the parser.

Variadic so that it can be applied recursively.

Template Parameters:

FilterTypes –

Parameters:

• species_names – the list of species names to filter

• first_filter – the first filter

• other_filters – other filters

Returns:

std::vector<std::string> the filtered list of names

Private Functions

inline void diff_reactants_products(const std::map<std::string, int> &R, const std::map<std::string, int> &P)

Util function to compute the stoichiometric ‘vector’ (map) by taking the difference between the reactant and product population changes.

Parameters:

• R – the reactant population changes

• P – the product population changes

Private Members

const std::string reaction_str

The reaction string.

std::map<std::string, int> reactants

Map of species name => population change for reactants.

std::map<std::string, int> products

Map of species name => population change for products.

std::map<std::string, int> stoich

Stoichiometric ‘vector’ (map of species name => population change)