Query Methods

Query Distributions

SBMLKinetics.KineticAnalyzer.getKTypeDistribution(self)

Get the kinetics type distribution.

Returns:

df_gen_stat_final: dataFrame-kinetics type distribution. The column names are: “Classifications”, “Percentage”, “Percentage standard error”, “Percentage per model”, “Percentage per model standard error”.

The column of “Classifications” covers the ten kinetic law types.

SBMLKinetics.KineticAnalyzer.getKTypeDistributionPerRType(self, R_type)

Get the kinetics type distribution for the certein reaction type.

Args:

R_type: an object with attributes rct_num and prd_num representing the number of reactants and products.

rct_num: int-0, 1, 2, 3 (representing > 2).

prd_num: int-0, 1, 2, 3 (representing > 2).

Returns:

df_gen_stat_PR_final: dataFrame-the kinetics distribution for a reaction type.

The column names are: “Classifications”, “Percentage”, “Percentage standard error”, “Percentage per model”, “Percentage per model standard error”.

The column of “Classifications” covers the ten kinetic law types.

SBMLKinetics.KineticAnalyzer.getRTypeDistribution(self)

Get the distribution of reaction involved for each reaction type.

Returns:

df_table_PR_final: dataFrame-Reaction type distribution.

The column names represent number of reactants: “R = 0”, “R = 1”, “R = 2”, “R > 2”.

The row names represent number of products: “P = 0”, “P = 1”, “P = 2”, “P > 2”.

SBMLKinetics.KineticAnalyzer.getRTypeDistributionPerModel(self)

Get the distribution of reaction involved for each reaction type per model.

Returns:

df_table_PR_per_model final: dataFrame-Reaction type distribution.

The column names represent number of reactants: “R = 0”, “R = 1”, “R = 2”, “R > 2”.

The row names represent number of products: “P = 0”, “P = 1”, “P = 2”, “P > 2”.

Query Elements

SBMLKinetics.KineticAnalyzer.getTopKType(self)

Get the most frequent kinetics type.

Returns:

kinetic_type_list: list of K_type. Sometimes there could be more than one top kinetics type to make the length of kinetic_type_list larger than one.

K_type: an object with an attribute K_type_str representing the type of kinetics.

K_type_str: str-“ZERO” (Zeroth order), “UNDR” (Uni-directional mass action), “UNMO” (Uni-term with the moderator), “BIDR” (Bi-directional mass action), “BIMO” (Bi-terms with the moderator), “MM” (Michaelis-Menten kinetics without an explicit enzyme), “MMCAT” (Michaelis-Menten kinetics with an explicit enzyme), “HILL” (Hill equations), “FR” (Kinetic law in the format of fraction other than MM, MMCAT or HILL) and “NA” (not classified kinetics).

SBMLKinetics.KineticAnalyzer.getKTypeProb(self, K_type)

Get the probability value of the certain kinetics type.

Args:

K_type: an object with an attribute K_type_str representing the type of kinetic law.

K_type_str: str-“ZERO” (Zeroth order), “UNDR” (Uni-directional mass action), “UNMO” (Uni-term with the moderator), “BIDR” (Bi-directional mass action), “BIMO” (Bi-terms with the moderator), “MM” (Michaelis-Menten kinetics without an explicit enzyme), “MMCAT” (Michaelis-Menten kinetics with an explicit enzyme), “HILL” (Hill equations), “FR” (Kinetic law in the format of fraction other than MM, MMCAT or HILL) and “NA” (not classified kinetics).

Returns:

kinetics_value: float-the probability of the certain kinetics type.

SBMLKinetics.KineticAnalyzer.getTopKTypePerRType(self, R_type)

Get the most frequent kinetics type from a certain reaction type.

Args:

R_type: an object with attributes rct_num and prd_num representing the number of reactants and products.

rct_num: int-0, 1, 2, 3 (representing > 2).

prd_num: int-0, 1, 2, 3 (representing > 2).

Returns:

kinetic_type_list: list of k_type. Sometimes there could be more than one top kinetics type to make the length of kinetic_type_list larger than one.

K_type: an object with an attribute K_type_str representing the type of kinetic law.

K_type_str: str-“ZERO” (Zeroth order), “UNDR” (Uni-directional mass action), “UNMO” (Uni-term with the moderator), “BIDR” (Bi-directional mass action), “BIMO” (Bi-terms with the moderator), “MM” (Michaelis-Menten kinetics without an explicit enzyme), “MMCAT” (Michaelis-Menten kinetics with an explicit enzyme), “HILL” (Hill equations), “FR” (Kinetic law in the format of fraction other than MM, MMCAT or HILL) and “NA” (not classified kinetics).

SBMLKinetics.KineticAnalyzer.getKTypeProbPerRType(self, R_type, K_type)

Get the probability value of the certain kinetics type from a certain reaction type.

Args:

R_type: an object with attributes rct_num and prd_num representing the number of reactants and products.

rct_num: int-0, 1, 2, 3 (representing > 2).

prd_num: int-0, 1, 2, 3 (representing > 2).

K_type: an object with an attribute K_type_str representing the type of kinetics.

K_type_str: str-“ZERO” (Zeroth order), “UNDR” (Uni-directional mass action), “UNMO” (Uni-term with the moderator), “BIDR” (Bi-directional mass action), “BIMO” (Bi-terms with the moderator), “MM” (Michaelis-Menten kinetics without an explicit enzyme), “MMCAT” (Michaelis-Menten kinetics with an explicit enzyme), “HILL” (Hill equations), “FR” (Kinetic law in the format of fraction other than MM, MMCAT or HILL) and “NA” (not classified kinetics).

Returns:

kinetics_value: float-the probability of the certain kinetics type.

SBMLKinetics.KineticAnalyzer.getTopRType(self)

Get the most frequent reaction type (with the largest number of reactions involved in the certain reaction type).

returns:

rct_prd_num_list: list of R_type info with the most frequent reaction type. Sometimes there could be more than one top kinetics type to make the length of rct_prd_num_list larger than one.

R_type: an object with attributes rct_num and prd_num representing the number of reactants and products.

rct_num: int-0, 1, 2, 3 (representing > 2).

prd_num: int-0, 1, 2, 3 (representing > 2).

SBMLKinetics.KineticAnalyzer.getRTypeProb(self, R_type)

Args:

R_type: an object with attributes rct_num and prd_num representing the number of reactants and products.

rct_num: int-0, 1, 2, 3 (representing > 2).

prd_num: int-0, 1, 2, 3 (representing > 2).

Returns:

R_value: float-the probability of the certain reaction type.

SBMLKinetics.KineticAnalyzer.getNumSBMLModelsAnalyzed(self)

Get the number of SBML models analyzed.

Returns:

SBMLModels_num: int-number of SBML models.

SBMLKinetics.KineticAnalyzer.getNumRxnsAnalyzed(self)

Get the number of reactions analyzed.

Returns:

rxn_num: int-number of reactions.