Quick Start Guide

This guide provides a quick introduction to using ratesb_python.

Simple Example

Simple example using check_model

from ratesb_python import check_model
print(check_model("S->P;k1*S"))

Complex Example

Complex example using Analyzer

from ratesb_python import Analyzer

analyzer = Analyzer("Reaction1: S1->P1; k1 * S1")

# Analyze the model for rate law correctness
analyzer.check_all()

# Display all errors and warnings
print(analyzer.results)

# Check selected errors and warnings
analyzer.checks([1, 2, 1001, 1002])
results = analyzer.results
print(results)

# Display only warnings
warnings = results.get_warnings()
for reaction, messages in warnings.items():
    print(reaction, messages)

# Retrieve messages for a specific reaction
messages = results.get_messages_by_reaction("Reaction1")
print(messages)

# Remove messages for a specific reaction
results.remove_messages_by_reaction("Reaction1")

# Get number of errors and warnings
print("Num Errors: ", results.count_errors())
print("Num Warnings: ", results.count_warnings())

This example shows how to use the custom rate law checker to check a model for rate law correctness. The custom rate law checker allows for the creation of custom rate law checks. For detailed information on creating custom rate law checks, see the Custom Rate Law Checks section.

Here is the custom rate law file in JSON format:

[
    {
        "name": "Your rate law check (Here is Uni-Directional Mass Action, which is included)",
        "expression": "compartment * parameter * reactant1",
        "optional_symbols": ["compartment", "parameter"],
        "power_limited_species": []
    }
]

Here is the Python code to use the custom rate law checker:

from ratesb_python import check_model

# Load custom rate law checks
custom_rate_law_file = "custom_rate_law.json"
print(check_model("S1->P1; k1 * S1", custom_rate_law_file))

Or, you can use the Analyzer class to check a model for rate law correctness:

from ratesb_python import Analyzer

# Load custom rate law checks
custom_rate_law_file = "custom_rate_law.json"
analyzer = Analyzer("S1->P1; k1 * S1", custom_rate_law_file)

# Analyze the model for rate law correctness
analyzer.check_all()
print(analyzer.results)

ratesb_python provides more methods to analyze the model. For more information, see the API documentation.