rebuild docs

docs/docs/api_reference/CatalyticEvent.md

@@ -13,8 +13,9 @@ It contains multiple functions which enable easy mapping and handling of one Eve
 class CatalyticEvent(Object)
 ```
 
-CatalyticEvent is a class for holding information regarding the catalysis of a Reaction in a cobra.Model object.
-It serves as an interface between the metabolic reaction and the associated enzyme constraints and variables.
+CatalyticEvent is a class for holding information regarding the
+catalysis of a Reaction in a cobra.Model object. It serves as an interface
+between the metabolic reaction and the associated enzyme constraints and variables.
 
 **Notes**:
 
@@ -142,13 +143,14 @@ constraint expressions related to the enzyme.
 def change_kcat_values(enzyme_kcat_dict: dict)
 ```
 
-Change kcat values for the enzyme variable.
+changes kcat values for the enzyme variable
 
 **Arguments**:
 
-- `enzyme_kcat_dict` - Dict[str, Dict[str, float]]
-  A nested dictionary with enzyme identifiers as keys and kcat dictionaries as values.
-  The kcat dictionary should have `f` and `b` keys for the forward and backward reactions, respectively.
+- `enzyme_kcat_dict` - nested Dict
+  A Dict with enzyme_id, kcat key, value pairs to connect the
+  enzyme with the associated reaction the kcat is another dict with 'f' and 'b'
+  for the forward and backward reactions respectively.
 
 #### \_\_copy\_\_
 

docs/docs/api_reference/Enzyme.md

@@ -89,6 +89,34 @@ Adds a catalytic event associated with a reaction to an enzyme.
 
 - `NoneType` - None
 
+#### add\_genes
+
+```python
+def add_genes(gene_list: list,
+              gene_length: list,
+              relation: str = 'OR') -> None
+```
+
+Add genes to the enzyme and the model related to the enzyme if applicable
+
+**Arguments**:
+
+- `gene_list` _list_ - A list of gene identifiers to be added.
+- `gene_length` _list_ - A list of lengths corresponding to each gene.
+- `relation` _str, optional_ - The relationship between genes in gene_list.
+  Defaults to 'OR'. Possible values: 'OR' or 'AND'.
+
+
+**Raises**:
+
+- `ValueError` - If an invalid relation is provided.
+
+
+**Notes**:
+
+  If relation is 'OR', each gene in gene_list will be treated as coding for an individual isozyme
+  If relation is 'AND', all genes in gene_list will be treated as coding for peptides in an enzyme complex
+
 #### create\_catalytic\_event
 
 ```python
@@ -311,13 +339,107 @@ The enzyme concentration equals the flux value.
 
 - `float` - Enzyme concentration in mmol/gDW.
 
+#### concentration
+
+```python
+@concentration.setter
+def concentration(conc: Union[float, int]) -> None
+```
+
+Sets the concentration of the enzyme by creating or updating a constraint
+that enforces the concentration to be equal to the sum of the forward and reverse
+variable primals.
+
+**Arguments**:
+
+  conc : float, int
+  The concentration value to be set for the enzyme. This value will be used
+  as both the lower and upper bound for the constraint, effectively fixing the
+  concentration to this value.
+
+  Notes
+  -----
+  - If a concentration constraint for the enzyme does not already exist in the model,
+  this function creates a new constraint named '<enzyme_id>_conc'.
+  - The concentration constraint is defined as:
+  concentration = forward_variable.primal + reverse_variable.primal
+  - If the constraint already exists, the linear coefficients for the forward and reverse
+  variables are updated to ensure the constraint remains valid.
+
+  Raises
+  ------
+  ValueError
+  If `conc` is not a valid numerical value.
+
+#### set\_forward\_concentration
+
+```python
+def set_forward_concentration(conc: Union[float, int]) -> None
+```
+
+Sets the concentration of the enzyme by creating or updating a constraint
+that enforces the concentration to be equal to the sum of only the forward
+variable primals. This forces a reaction to be active in the forward direction.
+It used the concentration setter functionality and subsequently sets the
+coefficient for the reverse variable in the constraint to 0.
+
+**Arguments**:
+
+  conc : float, int
+  The concentration value to be set for the enzyme. This value will be used
+  as both the lower and upper bound for the constraint, effectively fixing the
+  concentration to this value.
+
+  Notes
+  -----
+  - If a concentration constraint for the enzyme does not already exist in the model,
+  this function creates a new constraint named '<enzyme_id>_conc'.
+  - The concentration constraint is defined as:
+  concentration = forward_variable.primal
+
+  Raises
+  ------
+  ValueError
+  If `conc` is not a valid numerical value.
+
+#### set\_reverse\_concentration
+
+```python
+def set_reverse_concentration(conc: Union[float, int]) -> None
+```
+
+Sets the concentration of the enzyme by creating or updating a constraint
+that enforces the concentration to be equal to the sum of only the reverse
+variable primals. This forces a reaction to be active in the reverse direction.
+It used the concentration setter functionality and subsequently sets the
+coefficient for the forward variable in the constraint to 0.
+
+**Arguments**:
+
+  conc : float, int
+  The concentration value to be set for the enzyme. This value will be used
+  as both the lower and upper bound for the constraint, effectively fixing the
+  concentration to this value.
+
+  Notes
+  -----
+  - If a concentration constraint for the enzyme does not already exist in the model,
+  this function creates a new constraint named '<enzyme_id>_conc'.
+  - The concentration constraint is defined as:
+  concentration = reverse_variable.primal
+
+  Raises
+  ------
+  ValueError
+  If `conc` is not a valid numerical value.
+
 #### add\_catalytic\_events
 
 ```python
 def add_catalytic_events(catalytic_events: list, kcats: list)
 ```
 
-Adding catalytic events to an enzyme variable.
+Adding a catalytic event to an enzyme variable
 
 **Arguments**:
 

docs/docs/api_reference/EnzymeSectors.md

@@ -61,7 +61,9 @@ mean enzymes mass E.coli [g/mol]
 #### \_\_init\_\_
 
 ```python
-def __init__(rxn2protein: dict, configuration: Config = Config)
+def __init__(rxn2protein: dict,
+             protein2gene: dict = {},
+             configuration: Config = Config)
 ```
 
 _summary_
@@ -73,8 +75,9 @@ _summary_
   with information about the enzyme as values. The information included in this dict includes the turnover number for
   the forward and backward reaction (1/s), molar mass of the enzyme (mol/g), gene identifiers related to the enzyme,
   and with which other enzymes it forms a complex.
-- `configuration` _Config object, optional_ - Information about the general configuration of the model, including identifier conventions.
-  Default is as defined in the `PAModelpy.configuration` script for the E.coli iML1515 model.
+- `protein2gene` - dict
+  enzyme_id, gene_list key, value pairs for each enzyme.The gene_list value is a list of lists which indicates
+  'and' or 'or' relationships between the genes which code for the enzyme(complex).
 
 
 **Example**:
@@ -83,33 +86,62 @@ _summary_
     For the Parameter rxn2protein a dictionary may look like this:
     {
         'R1':
-            {
-                'E1': {'f': forward kcat, 'b': backward kcat, 'molmass': molar mass, 'genes': ['G1', 'G2'],
-                       'complex_with': 'E2'},
-                'E2': {'f': forward kcat, 'b': backward kcat, 'molmass': molar mass, 'genes': ['G3', 'G4'],
-                       'complex_with': 'E1'}
+            {E1:
+                        {'f': forward kcat, 'b': backward kcat, 'molmass': molar mass, 'genes': [G1, G2],
+                        'protein_reaction_association': [[E1, E2]]
+                        },
+                    E2:
+                        {'f': forward kcat, 'b': backward kcat, 'molmass': molar mass, 'genes': [G3, G4],
+                         'protein_reaction_association': [[E1, E2]]
             }
     }
+
+    For the Parameter protein2gene a dictionary may look like this:
+    {E1:
+            [[gene1], [gene2, gene3]],
+    E2:
+            [[gene4]]
+    }
+    where the gene-protein-reaction associations are the following:
+    E1: gene1 or (gene2 and gene3)
+    E2: gene4
     ```
 
+**Arguments**:
+
+  rxn2protein : nested dict
+  reaction id, enzymes_dict key, value pairs for each reaction in the active_enzyme sector.
+  The enzymes_dict contains the enzyme identifiers of the enzymes which are related to the specific reaction
+  as keys and a dict with information about the enzyme as values. The information included in this dict is:
+  turnover number for forward and backward reaction [1/s], molar mass of the enzyme [mol/g], gene identifiers
+  related to the enzyme, with which other enzymes it forms a complex.
+
+- `protein2gene` - dict
+  enzyme_id, gene_list key, value pairs for each enzyme.The gene_list value is a list of lists which indicates
+  'and' or 'or' relationships between the genes which code for the enzyme(complex).
+
+- `configuration` - Config object, optional
+  Information about general configuration of the model including identifier conventions.
+  Default as defined in the `PAModelpy.configuration` script for the E.coli iML1515 model.
+
 #### check\_kcat\_values
 
 ```python
-def check_kcat_values(model, reaction, kcat)
+def check_kcat_values(model, reaction, enzyme_dict)
 ```
 
-Function to check if the kcat values provided for an enzyme are consistent with the direction of the reaction.
+Function to check if the kcat values provided for an enzyme are consistent with the direction of the reaction
 
 **Arguments**:
 
 - `model` _cobra.Model or PAModel_ - Model to which the kcat values should be added.
 - `reaction` _cobra.Reaction_ - Reaction that is catalyzed with the enzyme related to the kcats.
-- `kcat` _dict_ - A dictionary with the turnover values for the forward and/or backward reaction for different enzymes [/s].
+- `enzyme_dict` _dict_ - A dictionary with the turnover values for the forward and/or backward reaction for different enzymes [/s].
 
 
 **Example**:
 
-  Example dictionary for the `kcat` parameter
+  Example dictionary for the `enzyme_dict` parameter
     ```
     {'E1': {'f': forward kcat, 'b': backward kcat}}
     ```