psctb.analyse package¶
Subpackages¶
Submodules¶
psctb.analyse._ratechar module¶
- class psctb.analyse._ratechar.RateChar(mod, min_concrange_factor=100, max_concrange_factor=100, scan_points=256, auto_load=False)[source]¶
Bases:
objectMethods
do_ratechar
load_session
save_results
save_session
psctb.analyse._thermokin module¶
psctb.analyse._thermokin_file_tools module¶
- psctb.analyse._thermokin_file_tools.check_for_negatives(terms)[source]¶
Returns True for a list of sympy expressions contains any expressions that are negative.
- Parameters
- termslist of sympy expressions
A list where expressions may be either positive or negative.
- Returns
- bool
True if any negative terms in expression. Otherwise False
- psctb.analyse._thermokin_file_tools.check_term_format(lines, term_type)[source]¶
Inspects a list of string for the correct ThermoKin syntax. Returns True in case of correct format. Throws exception otherwise.
Correct format is a str matching the pattern “X{w*}{w*} .*” . Where “X” is either “!G” or “!T” as specified by term_type.
- Parameters
- lineslist of str
Clean list of lines from a ‘.reqn’ file.
- term_typestr
This string specifies the type of term.
- Returns
- bool
- psctb.analyse._thermokin_file_tools.construct_dict(lines)[source]¶
Constructs a dictionary of dictionaries for each reaction.
Here keys of the outer dictionary is reaction name strings while the inner dictionary keys are the term names. The inner dictionary values are the term expressions
- Parameters
- lineslist of str
- Returns
- dict of str:{str:str}
- psctb.analyse._thermokin_file_tools.get_binding_vc_terms(sympy_formulas, ma_terms)[source]¶
Returns dictionary with a combined “rate capacity” and “binding” term as values.
Uses the symbolic rate equations dictionary and mass action term dictionaries to construct a new dictionary with “rate capacity- binding” terms. The symbolic rate equations are divided by their mass action terms. The results are the “rate capacity-binding” terms. This use case requires reaction names as they appear in pysces as keys for both dictionaries.
- Parameters
- sympy_formulasdict of str:sympy expression
Full rate equations for all reactions in model. Keys are reaction names and correspond to this in ma_terms.
- ma_termsdict of str:sympy expression
Mass action terms for all reactions in model. Keys are reaction names and correspond to this in sympy_formulas.
- Returns
- dict of str:sympy expression
A dictionary with reaction names as keys and sympy expressions representing “rate capacity-binding” terms as values.
- psctb.analyse._thermokin_file_tools.get_ma_terms(mod, sympy_terms)[source]¶
Returns dict with reaction names as keys and mass action terms as values from a dict with reaction names as keys and lists of sympy expressions as values.
Only reversible reactions are handled. Any list in the
sympy_termsdict that does not have a length of 2 will be ignored.- Parameters
- modPysMod
The model from which the sympy_terms dict was originally constructed.
- sympy_terms: dict of str:list of sympy expressions
This dictionary should be created by get_sympy_terms.
- Returns
- dict of str:sympy expression
Each value will be a mass action term for each reaction key with a form depending on reversibility as described above.
See also
- psctb.analyse._thermokin_file_tools.get_reqn_path(mod)[source]¶
Gets the default path and filename of`.reqn` files belonging to a model
The .reqn files which contain rate equations split into different (arbitrary) components should be saved in the same directory as the model file itself by default. It should have the same filename (sans extension) as the model file.
- Parameters
- modPysMod
A pysces model which has corresponding .reqn file saved in the same directory with the same file name as the model file.
- Returns
- str
A sting with the path and filename of the .reqn file.
- psctb.analyse._thermokin_file_tools.get_st_pt_keq(expression, substrates, products)[source]¶
Takes an expression representing “substrates/products * Keq_expression” and returns substrates, products and keq_expression separately.
- Parameters
- expressionsympy expression
The expression containing “substrates/products * Keq_expression”
- substrateslist of sympy symbols
List with symbolic representations for each substrate involved in the reaction which expression represents.
- productslist of sympy symbols
List with symbolic representations for each product involved in the reaction which expression represents. Returns
- ——-
- tuple of sympy expressions and int
This tuple contains sympy expressions for the substrates, products and keq_expression in that order. The final value will be an int which indicates the strategy followed.
See also
- psctb.analyse._thermokin_file_tools.get_str_formulas(mod)[source]¶
Returns a dictionary with reaction_name:string_formula as key:value pairs.
Goes through mod.reactions and constructs a dictionary where reaction_name is the key and mod.reaction_name.formula is the value.
- Parameters
- modPysMod
The model which will be used to construct the dictionary
- Returns
- dict of str:str
A dictionary with reaction_name:string_formula as key:value pairs
- psctb.analyse._thermokin_file_tools.get_subs_dict(expression, mod)[source]¶
Builds a substitution dictionary of an expression based of the values of these symbols in a model.
- Parameters
- expressionsympy expression
- modPysMod
- Returns
- dict of sympy.Symbol:float
- psctb.analyse._thermokin_file_tools.get_sympy_formulas(str_formulas)[source]¶
Converts dict with str values to sympy expression values.
Used to convert key:string_formula to key:sympy_formula. Intended use case is for automatic separation of rate equation terms into mass action and binding terms. This use case requires reaction names as they appear in pysces as keys.
- Parameters
- str_formulasdict of str:str
Dictionary with str values that represent reaction expressions. This dictionary needs to have already passed through all sanitising functions/methods (e.g. replace_pow).
- Returns
- dict with sympy_expression values and original keys
Dictionary where values are symbolic sympy expressions
- psctb.analyse._thermokin_file_tools.get_sympy_terms(sympy_formulas)[source]¶
Converts a dict with sympy expressions as values to a new dict with list values containing either the original expression or a negative and a positive expressions.
This is used to separate reversible and irreversible reactions. Reversible reactions will have two terms, one negative and one positive. Here expressions are expanded and split into terms and tested for the above criteria: If met the dict value will be a list of two expressions, each representing a term of the rate equation. Otherwise the dict value will be a list with a single item - the original expression. This use case requires reaction names as they appear in pysces as keys.
- Parameters
- sympy_formulasdict of str:sympy expression values
Dictionary with values representing rate equations as sympy expressions. Keys are reaction names
- Returns
- dict of str:list sympy expression
Each list will have either have one item, the original dict value OR two items -the original dict value split into a negative and positive expression.
See also
- psctb.analyse._thermokin_file_tools.get_term_dict(raw_lines, term_type)[source]¶
Returns the term dictionary from a list of raw lines from a file.
The contents of a ‘.reqn’ file is read and passed to this function. Here the contents is parsed and ‘main terms’ are extracted and returned as a dict of str:{str:str}.
- Parameters
- raw_lineslist of str
List of lines from a ‘.reqn’ file.
- Returns
- dict of str:{str:str}
- psctb.analyse._thermokin_file_tools.get_term_types_from_raw_data(raw_data_dict)[source]¶
Determines the types of terms defined for ThermoKin based on the file contents. This allows for generation of latex expressions based on these terms.
- Parameters
- raw_data_dictdict of str:{str:str}
- Returns
- set of str
- psctb.analyse._thermokin_file_tools.get_terms(raw_lines, term_type)[source]¶
Takes a list of strings and returns a new list containing only lines starting with term_type and strips line endings.
Term can be either of the “main” (or !T) type or additional (or !G) type
- Parameters
- raw_lineslist of str
List of lines from a ‘.reqn’ file.
- term_typestr
This string specifies the type of term.
- Returns
- list of str
- psctb.analyse._thermokin_file_tools.read_reqn_file(path_to_file)[source]¶
Reads the contents of a file and returns it as a list of lines.
- Parameters
- path_to_filestr
Path to file that is to read in
- Returns
- list of str
The file contents as separate strings in a list
- psctb.analyse._thermokin_file_tools.replace_pow(str_formulas)[source]¶
Creates new dict from an existing dict with “pow(x,y)” in values replaced with “x**y”.
Goes through the values of an dictionary and uses regex to convert the pysces internal syntax for powers with standard python syntax. This is needed before conversion to sympy expressions. This use case requires reaction names as they appear in pysces as keys.
- Parameters
- str_formulasdict of str:str
A dictionary where the values as contain pysces format strings representing rate equation expressions with powers in the syntax “pow(x,y)”
- Returns
- dict of str:str
A new dictionary with str rate equations where powers are represented by standard python syntax e.g. x**y
- psctb.analyse._thermokin_file_tools.sort_terms(terms)[source]¶
Returns a list of two sympy expressions where the expression is positive and the second expression is negative.
- Parameters
- termslist of sympy expressions
A list with length of 2 where one element is positive and the other is negative (starts with a minus symbol)
- Returns
- tuple of sympy expressions
A tuple where the first element is positive and the second is negative.
- psctb.analyse._thermokin_file_tools.st_pt_keq_from_expression(expression, substrates, products, failure_threshold=10)[source]¶
Take an expression representing “substrates/products * Keq_expression” and returns substrates, products and keq_expression separately.
In this strategy there is no inspection of the stoichiometry as provided by the model map. Here the expressions is divided/multiplied by each substrate/product until it no longer appears in the expression. If the substrates or products are not removed after a defined number of attempts a total failure occurs and the function returns None
This is a fallback for cases where defined stoichiometry does not correspond to the actual rate equation.
Here cases where the substrate/product do not appear in the rate equation at all throws an assertion error.
- Parameters
- expressionsympy expression
The expression containing “substrates/products * Keq_expression”
- substrateslist of sympy symbols
List with symbolic representations for each substrate involved in the reaction which expression represents.
- productslist of sympy symbols
List with symbolic representations for each product involved in the reaction which expression represents.
- failure_thresholdint, optional (Default: 10)
A threshold value the defines the number of times the metabolite removal strategy should be tried before failure.
- Returns
- tuple of sympy_expressions or None
This tuple contains sympy expressions for the substrates, products and keq_expression in that order. None is returned if this strategy fails.