Source code for test_PyInteration

# -*- coding: utf-8 -*-
#  Copyright (c) 2016-2017, Zhijiang Yao, Jie Dong and Dongsheng Cao
#  All rights reserved.
#  This file is part of the PyBioMed.
#  The contents are covered by the terms of the BSD license
#  which is included in the file license.txt, found at the root
#  of the PyBioMed source tree.
"""
The script is used for testing.

Authors: Zhijiang Yao and Dongsheng Cao.

Date: 2016.06.14

Email: gadsby@163.com
"""


# Core Library modules
import os


def test_pyinteration():

    from PyBioMed.PyInteraction.PyInteraction import CalculateInteraction1
    from PyBioMed.PyInteraction.PyInteraction import CalculateInteraction2
    from PyBioMed.PyInteraction.PyInteraction import CalculateInteraction3

    from PyBioMed.PyDNA import PyDNAac

    print("...............................................................")
    print("testing the DNA descriptors")

    DNA_des = PyDNAac.GetTCC(
        "GACTGAACTGCACTTTGGTTTCATATTATTTGCTC",
        phyche_index=["Dnase I", "Nucleosome", "MW-kg"],
    )

    print(DNA_des)

    print("...............................................................")
    print("testing the protein descriptors")

    from PyBioMed.PyProtein import CTD

    protein = "ADGCGVGEGTGQGPMCNCMCMKWVYADEDAADLESDSFADEDASLESDSFPWSNQRVFCSFADEDAS"
    protein_des = CTD.CalculateCTD(protein)

    print("...............................................................")
    print("testing the molecular descriptors")

    from PyBioMed.PyMolecule import moe
    from rdkit import Chem

    smis = ["CCCC", "CCCCC", "CCCCCC", "CC(N)C(=O)O", "CC(N)C(=O)[O-].[Na+]"]
    m = Chem.MolFromSmiles(smis[3])
    mol_des = moe.GetMOE(m)

    print("...............................................................")
    print("testing the Interaction type 1 module")

    mol_mol_interaction1 = CalculateInteraction1(mol_des, mol_des)
    print(mol_mol_interaction1)

    pro_mol_interaction1 = CalculateInteraction1(mol_des, protein_des)
    print(pro_mol_interaction1)

    DNA_mol_interaction1 = CalculateInteraction1(DNA_des, mol_des)
    print(DNA_mol_interaction1)

    print("...............................................................")
    print("testing the Interaction type 2 module")

    mol_mol_interaction2 = CalculateInteraction2(mol_des, mol_des)
    print(mol_mol_interaction2)

    pro_mol_interaction2 = CalculateInteraction2(mol_des, protein_des)
    print(pro_mol_interaction2)

    DNA_mol_interaction2 = CalculateInteraction2(DNA_des, mol_des)
    print(DNA_mol_interaction2)

    print("...............................................................")
    print("testing the Interaction type 3 module")

    mol_mol_interaction3 = CalculateInteraction3(mol_des, mol_des)
    print(mol_mol_interaction3)


if __name__ == "__main__":
    test_pyinteration()