00-example.py

#!/usr/bin/env python3
#
# Copyright © 2022 Christos Pavlatos, George Rassias, Christos Andrikos,
#                  Evangelos Makris, Aggelos Kolaitis
#
# Permission is hereby granted, free of charge, to any person obtaining a copy of
# this software and associated documentation files (the “Software”), to deal in
# the Software without restriction, including without limitation the rights to
# use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies
# of the Software, and to permit persons to whom the Software is furnished to do
# so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in all
# copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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# SOFTWARE.
#

"""
Script:         00-example.py
Author:         Angelos Kolaitis <neoaggelos@gmail.com>
Usage:          ./00-example.py
Description:
    This script gives an example of using Knotify directly from Python code.
"""

from datetime import datetime

# import knotify
from knotify import knotify


def main():
    # initialize knotify options
    options = knotify.new_options()

    # override any options. you will most likely need to set the C library paths.
    # refer to knotify.*_OPTS for defaults.
    #
    # For example,
    #
    # options.yaep_library_path = "/opt/knotify/lib/libpseudoknot.so"

    # load configuration from environment variables
    options(args=[])

    # initialize the knotify engine from options
    algorithm, config = knotify.from_options(options)

    # run knotify and get list of results
    start = datetime.now()
    results = algorithm.get_results("CGAAUCUCAAGCAAUCAAGCAUUCUACUUCUAUUGCA", **config)
    duration = datetime.now() - start

    # first result is our choice, the rest are candidates
    result = results.loc[0]

    print("Dot Bracket:", result.dot_bracket)
    print("Energy:", result.energy)
    print("Duration:", duration.total_seconds())


if __name__ == "__main__":
    main()