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Class ChemData

    Data about all the chemicals and (if applicable) reactions,
    including:
        - names
        - diffusion rates
        - macro-molecules Binding Site Affinities (for Transcription Factors)
        - reaction data (see also class "Reaction", in "reaction_data.py")


    Notes:  - for now, the temperature is assumed constant everywhere, and unvarying (or very slowly varying)

name	arguments	returns
__init__	self, names=None, diffusion_rates=None
If chemical names and their diffusion rates are both provided, they must have the same count, and appear in the same order. It's ok not to pass any data, and later add it. Reactions can be added later by means of calls to add_reaction() :param names: [OPTIONAL] A list with the names of the chemicals :param diffusion_rates: [OPTIONAL] A list or tuple with the diffusion rates of the chemicals

name

arguments

returns

__init__

self, names=None, diffusion_rates=None

        If chemical names and their diffusion rates are both provided, they must have the same count,
        and appear in the same order.
        It's ok not to pass any data, and later add it.
        Reactions can be added later by means of calls to add_reaction()

        :param names:           [OPTIONAL] A list with the names of the chemicals
        :param diffusion_rates: [OPTIONAL] A list or tuple with the diffusion rates of the chemicals

name	arguments	returns
number_of_chemicals	self	int

name	arguments	returns
number_of_reactions	self	int

name	arguments	returns
assert_valid_species_index	self, species_index: int	None
Raise an Exception if the specified species_index isn't valid :param species_index: An integer that indexes the chemical of interest (numbering starts at 0) :return: None

name	arguments	returns
assert_valid_rxn_index	self, index	None
Raise an Exception if the specified reaction index isn't valid :param index: An integer that indexes the reaction of interest (numbering starts at 0) :return: None

name	arguments	returns
assert_valid_diffusion	self, diff	None
Raise an Exception if the specified diffusion value isn't valid :param diff: Diffusion rate :return: None

name	arguments	returns
get_index	self, name: str	int
Return the index of the chemical species with the given name. If not found, an Exception is raised :param name: Name of the chemical species of interest :return: The index of the species with the given name

name

arguments

returns

get_index

self, name: str

int

        Return the index of the chemical species with the given name.
        If not found, an Exception is raised

        :param name:    Name of the chemical species of interest
        :return:        The index of the species with the given name

name	arguments	returns
get_name	self, species_index: int	Union[str, None]
Return the name of the species with the given index. If no name was assigned, return None. :param species_index: An integer (starting with zero) corresponding to the original order with which the chemical species were first added :return: The name of the species with the given index if present, or None if not

name

arguments

returns

get_name

self, species_index: int

Union[str, None]

        Return the name of the species with the given index.
        If no name was assigned, return None.

        :param species_index:   An integer (starting with zero) corresponding to the
                                    original order with which the chemical species were first added
        :return:                The name of the species with the given index if present,
                                    or None if not

name	arguments	returns
get_all_names	self	[Union[str, None]]
Return a list with the names of all the chemical species, in their index order. If any is missing, None is used :return: A list of strings

name	arguments	returns
get_diffusion_rate	self, species_index: int	Union[str, None]
Return the diffusion rate of the species with the given index. If no name was assigned, return None. :param species_index: An integer (starting with zero) corresponding to the original order with which the chemical species were first added :return: The value of the diffusion rate for the species with the given index if present, or None if not

name

arguments

returns

get_diffusion_rate

self, species_index: int

Union[str, None]

        Return the diffusion rate of the species with the given index.
        If no name was assigned, return None.

        :param species_index:   An integer (starting with zero) corresponding to the
                                    original order with which the chemical species were first added
        :return:                The value of the diffusion rate for the species with the given index if present,
                                    or None if not

name	arguments	returns
get_all_diffusion_rates	self	list
Return a list of the diffusion rates of all the chemicals, in the order of their indexes. If any value is missing, None is used for it :return: A list of numbers with the diffusion rates

name	arguments	returns
missing_diffusion_rate	self	bool
Return True if any of the diffusion rates is missing; False otherwise :return:

name	arguments	returns
get_reaction	self, i: int	dict
Return the data structure of the i-th reaction, in the order in which reactions were added (numbering starts at 0) :param i: An integer that indexes the reaction of interest (numbering starts at 0) :return: A dictionary with 4 keys ("reactants", "products", "kF", "kR"), where "kF" is the forward reaction rate constant, and "kR" the back reaction rate constant

name

arguments

returns

get_reaction

self, i: int

dict

        Return the data structure of the i-th reaction,
        in the order in which reactions were added (numbering starts at 0)

        :param i:   An integer that indexes the reaction of interest (numbering starts at 0)
        :return:    A dictionary with 4 keys ("reactants", "products", "kF", "kR"),
                    where "kF" is the forward reaction rate constant, and "kR" the back reaction rate constant

name	arguments	returns
get_reactants	self, i: int	[(int, int, int)]
Return a list of triplets with details of the reactants of the i-th reaction :param i: The index (0-based) to identify the reaction of interest :return: A list of triplets of the form (stoichiometry, species index, reaction order)

name

arguments

returns

get_reactants

self, i: int

[(int, int, int)]

        Return a list of triplets with details of the reactants of the i-th reaction

        :param i:   The index (0-based) to identify the reaction of interest
        :return:    A list of triplets of the form (stoichiometry, species index, reaction order)

name	arguments	returns
get_reactants_formula	self, i	str
Return a string with a user-friendly form of the left (reactants) side of the reaction formula :param i: The index (0-based) to identify the reaction of interest :return:

name	arguments	returns
get_products	self, i: int	[(int, int, int)]
Return a list of triplets with details of the products of the i-th reaction :param i: The index (0-based) to identify the reaction of interest :return: A list of triplets of the form (stoichiometry, species index, reaction order)

name

arguments

returns

get_products

self, i: int

[(int, int, int)]

        Return a list of triplets with details of the products of the i-th reaction

        :param i:   The index (0-based) to identify the reaction of interest
        :return:    A list of triplets of the form (stoichiometry, species index, reaction order)

name	arguments	returns
get_products_formula	self, i	str
Return a string with a user-friendly form of the right (products) side of the reaction formula :param i: The index (0-based) to identify the reaction of interest :return:

name	arguments	returns
get_forward_rate	self, i: int	float
:param i: The integer index (0-based) to identify the reaction of interest :return: The value of the forward rate constant for the above reaction

name	arguments	returns
get_reverse_rate	self, i: int	float
:param i: The integer index (0-based) to identify the reaction of interest :return: he value of the reverse (back) rate constant for the above reaction

name	arguments	returns
get_chemicals_in_reaction	self, rxn_index: int	{int}
Return a SET of indices (being a set, it's NOT in any particular order) of all the chemicals in the specified reaction :param rxn_index: An integer with the (zero-based) index to identify the reaction of interest :return: A SET of indices of the chemicals involved in the above reaction Note: being a set, it's NOT in any particular order

name

arguments

returns

get_chemicals_in_reaction

self, rxn_index: int

{int}

        Return a SET of indices (being a set, it's NOT in any particular order)
        of all the chemicals in the specified reaction

        :param rxn_index:   An integer with the (zero-based) index to identify the reaction of interest
        :return:            A SET of indices of the chemicals involved in the above reaction
                                Note: being a set, it's NOT in any particular order

name	arguments	returns
get_reactions_participating_in	self, species_index: int	[int]
Return a list of all the reactions that the given chemical species is involved in :param species_index: :return:

name	arguments	returns
init_chemical_data	self, names=None, diffusion_rates=None	None
Initialize the names (if provided) and diffusion rates (if provided) of all the chemical species, in the given order. If no names are provided, the strings "Chemical 1", "Chemical 2", ..., are used IMPORTANT: this function can be invoked only once, before any chemical data is set. To add new chemicals later, use add_chemical() :param names: [OPTIONAL] List or tuple of the names of the chemical species :param diffusion_rates: [OPTIONAL] A list or tuple with the diffusion rates of the chemicals, in the same order as the names :return: None

name

arguments

returns

init_chemical_data

self, names=None, diffusion_rates=None

None

        Initialize the names (if provided) and diffusion rates (if provided)
        of all the chemical species, in the given order.
        If no names are provided, the strings "Chemical 1", "Chemical 2", ..., are used

        IMPORTANT: this function can be invoked only once, before any chemical data is set.
                   To add new chemicals later, use add_chemical()

        :param names:           [OPTIONAL] List or tuple of the names of the chemical species
        :param diffusion_rates: [OPTIONAL] A list or tuple with the diffusion rates of the chemicals,
                                           in the same order as the names
        :return:                None

name	arguments	returns
add_chemical	self, name: str, diffusion_rate=None, note=None	None
Register a new chemical species, with a name and (optionally) a diffusion rate. :param name: Name of the chemical species to add :param diffusion_rate: [OPTIONAL] Floating-point number with the diffusion rate (in water) of this chemical :param note: [OPTIONAL] Note to attach to the chemical :return: None

name

arguments

returns

add_chemical

self, name: str, diffusion_rate=None, note=None

None

        Register a new chemical species, with a name and (optionally) a diffusion rate.

        :param name:            Name of the chemical species to add
        :param diffusion_rate:  [OPTIONAL] Floating-point number with the diffusion rate (in water) of this chemical
        :param note:            [OPTIONAL] Note to attach to the chemical
        :return:                None

name	arguments	returns
set_diffusion_rate	self, name, diff_rate
Set the diffusion rate of the given chemical species :param name: :param diff_rate: :return:

name	arguments	returns
set_temp	self, temp, units="K"
:param temp: Temperature, in Kelvins, or None :param units: Not yet implemented :return:

name	arguments	returns
add_reaction	self, reactants: Union[int, str, tuple, list], products: Union[int, str, tuple, list], forward_rate=None, reverse_rate=None, Delta_H=None, Delta_S=None, Delta_G=None	None
Add the parameters of a SINGLE reaction, optionally including kinetic and/or thermodynamic data. The involved chemicals must be already registered - use add_chemical() if needed. NOTE: in the reactants and products, if the stoichiometry and/or reaction order aren't specified, they're assumed to be 1. Their full structure is the triplet (stoichiometry coefficient, name, reaction order) EXAMPLES of formats for reactants and products (assuming that the chemical species with index 5 is called "F"): "F" gets turned into: (1, 5, 1) (3, "F") (3, 5, 1) (3, "F", 2) (3, 5, 2) It's equally acceptable to use LISTS in lieu of tuples :param reactants: A list of triplets (stoichiometry, species name or index, reaction order), or simplified terms in various formats; for details, see above :param products: A list of triplets (stoichiometry, species name or index, reaction order of REVERSE reaction), or simplified terms in various formats; for details, see above :param forward_rate: [OPTIONAL] Forward reaction rate constant :param reverse_rate: [OPTIONAL] Reverse reaction rate constant :param Delta_H: [OPTIONAL] Change in Enthalpy (from reactants to products) :param Delta_S: [OPTIONAL] Change in Entropy (from reactants to products) :param Delta_G: [OPTIONAL] Change in Free Energy (from reactants to products) :return: None

name

arguments

returns

add_reaction

self, reactants: Union[int, str, tuple, list], products: Union[int, str, tuple, list], forward_rate=None, reverse_rate=None, Delta_H=None, Delta_S=None, Delta_G=None

None

        Add the parameters of a SINGLE reaction, optionally including kinetic and/or thermodynamic data.
        The involved chemicals must be already registered - use add_chemical() if needed.

        NOTE: in the reactants and products, if the stoichiometry and/or reaction order aren't specified,
              they're assumed to be 1.
              Their full structure is the triplet (stoichiometry coefficient, name, reaction order)

        EXAMPLES of formats for reactants and products (*assuming* that the chemical species with index 5 is called "F"):
                    "F"         gets turned into:   (1, 5, 1)
                    (3, "F")                        (3, 5, 1)
                    (3, "F", 2)                     (3, 5, 2)
                    It's equally acceptable to use LISTS in lieu of tuples

        :param reactants:       A list of triplets (stoichiometry, species name or index, reaction order),
                                    or simplified terms in various formats; for details, see above
        :param products:        A list of triplets (stoichiometry, species name or index, reaction order of REVERSE reaction),
                                    or simplified terms in various formats; for details, see above
        :param forward_rate:    [OPTIONAL] Forward reaction rate constant
        :param reverse_rate:    [OPTIONAL] Reverse reaction rate constant
        :param Delta_H:         [OPTIONAL] Change in Enthalpy (from reactants to products)
        :param Delta_S:         [OPTIONAL] Change in Entropy (from reactants to products)
        :param Delta_G:         [OPTIONAL] Change in Free Energy (from reactants to products)
        :return:                None

name	arguments	returns
clear_reactions_data	self	None
Get rid of all reactions; start again with "an empty slate" (but still with reference to the same data object about the chemicals) :return: None

name	arguments	returns
describe_reactions	self, concise=False	None
Print out a user-friendly plain-text form of all the reactions. If wanting to describe just 1 reaction, use single_reaction_describe() EXAMPLE (not concise): Number of reactions: 2 (at temp. 25 C) (0) CH4 + 2 O2 <-> CO2 + 2 H2O (kF = 3.0 / kR = 2.0 / Delta_G = -1,005.13 / K = 1.5) \| 1st order in all reactants & products" (1) A + B <-> C (kF = 5.0 / kR = 1.0 / Delta_G = / K = 5.0) \| 1st order in all reactants & products" :param concise: If True, less detail is shown :return: None

name

arguments

returns

describe_reactions

self, concise=False

None

        Print out a user-friendly plain-text form of all the reactions.
        If wanting to describe just 1 reaction, use single_reaction_describe()

        EXAMPLE (not concise):
            Number of reactions: 2 (at temp. 25 C)
            (0) CH4 + 2 O2 <-> CO2 + 2 H2O  (kF = 3.0 / kR = 2.0 / Delta_G = -1,005.13 / K = 1.5) | 1st order in all reactants & products"
            (1) A + B <-> C  (kF = 5.0 / kR = 1.0 / Delta_G =  / K = 5.0) | 1st order in all reactants & products"

        :param concise:     If True, less detail is shown
        :return:            None

name	arguments	returns
multiple_reactions_describe	self, rxn_list=None, concise=False	[str]
The counterpart of single_reaction_describe() for many reactions :param rxn_list: Either a list of integers, to identify the reactions of interest, or None, meaning ALL reactions :param concise: If True, less detail is shown :return: A list of strings

name

arguments

returns

multiple_reactions_describe

self, rxn_list=None, concise=False

[str]

        The counterpart of single_reaction_describe() for many reactions

        :param rxn_list:    Either a list of integers, to identify the reactions of interest,
                                or None, meaning ALL reactions
        :param concise:     If True, less detail is shown
        :return:            A list of strings

name	arguments	returns
single_reaction_describe	self, rxn_index: int, concise=False	str
Return as a string, a user-friendly plain-text form of the given reaction EXAMPLE (concise): "CH4 + 2 O2 <-> CO2 + 2 H2O" EXAMPLE (not concise): "(0) CH4 + 2 O2 <-> CO2 + 2 H2O (kF = 3.0 / kR = 2.0 / Delta_G = -1,005.13 / K = 1.5) \| 1st order in all reactants & products" :param rxn_index: Integer to identify the reaction of interest :param concise: If True, less detail is shown :return: A string with a description of the specified reaction

name

arguments

returns

single_reaction_describe

self, rxn_index: int, concise=False

str

        Return as a string, a user-friendly plain-text form of the given reaction
        EXAMPLE (concise):      "CH4 + 2 O2 <-> CO2 + 2 H2O"
        EXAMPLE (not concise):  "(0) CH4 + 2 O2 <-> CO2 + 2 H2O  (kF = 3.0 / kR = 2.0 / Delta_G = -1,005.13 / K = 1.5) | 1st order in all reactants & products"

        :param rxn_index:   Integer to identify the reaction of interest
        :param concise:     If True, less detail is shown
        :return:            A string with a description of the specified reaction

name	arguments	returns
prepare_graph_network	self	dict
:return: A dictionary with 2 keys: 'graph' and 'color_mapping'

name	arguments	returns
create_graph_network_data	self	[{}]
Encode the reaction data in a form suitable for visualization with the graph module "vue_cytoscape" :return: A list of dictionaries. Each dictionary must have an 'id' key with a unique value. EXAMPLE, for an A <-> B reaction: [{'id': 0, 'label': 'Chemical', 'name': 'A', 'diff_rate': None, 'stoich': 1, 'rxn_order': 1}, {'id': 1, 'label': 'Chemical', 'name': 'B', 'diff_rate': None, 'stoich': 1, 'rxn_order': 1}, {'id': 2, 'label': 'Reaction', 'name': 'RXN', 'kF': 3.0, 'kR': 2.0, 'K': 1.5, 'Delta_G': -1005.13}, {'id': 3, 'name': 'produces', 'source': 2, 'target': 1}, {'id': 4, 'name': 'reacts', 'source': 0, 'target': 2} ]

name

arguments

returns

create_graph_network_data

self

[{}]

        Encode the reaction data in a form suitable for visualization
        with the graph module "vue_cytoscape"

        :return:    A list of dictionaries.  Each dictionary must have an 'id' key with a unique value.
                    EXAMPLE, for an  A <-> B reaction:
                       [{'id': 0, 'label': 'Chemical', 'name': 'A', 'diff_rate': None, 'stoich': 1, 'rxn_order': 1},
                        {'id': 1, 'label': 'Chemical', 'name': 'B', 'diff_rate': None, 'stoich': 1, 'rxn_order': 1},

                        {'id': 2, 'label': 'Reaction', 'name': 'RXN', 'kF': 3.0, 'kR': 2.0, 'K': 1.5, 'Delta_G': -1005.13},

                        {'id': 3, 'name': 'produces', 'source': 2, 'target': 1},
                        {'id': 4, 'name': 'reacts', 'source': 0, 'target': 2}
                       ]

name	arguments	returns
assign_color_mapping	self