guide.rst

User Guide

Description

The :mod:`SAGA_optimize` package provides a simple Python application programming interface for solving boundary-value inverse problem based on a simulated annealing and genetic algorithm.

Installation

SAGA_optimize runs under Python 3.6+ and is available through python3-pip. Install via pip or clone the git repo and install the following dependencies and you are ready to go!

Install on Linux

Pip installation (method 1)

pip3 install SAGA-optimize

GitHub Package installation (method 2)

Make sure you have git installed:

git clone https://github.com/MoseleyBioinformaticsLab/SAGA_optimize.git

Dependecies

SAGA_optimize requires the following Python libraries:

• JSONPickle for saving Python objects in a JSON serializable form and outputting to a file.

Basic usage

The :mod:`SAGA_optimize` package is used to find the optimal solutions to a set of parameters based on a given energy function calculated using the set of parameters.

Note

Read :doc:`tutorial` to learn more and see code examples on using the :mod:`SAGA_optimize` as a library.