Chimie Théorique » scripts_chimie4psmn » DockOnSurf

import sys

import unittest

from rdkit.Chem import Mol, AllChem as Chem

from ase.atoms import Atoms

from modules.formats import adapt_format, confs_to_mol_list, \

    rdkit_mol_to_ase_atoms

mol = Chem.MolFromMolFile('acetic.mol', removeHs=False)

num_confs = 5

Chem.EmbedMultipleConfs(mol, num_confs)

class TestConfsToMolList(unittest.TestCase):

    def test_confs_to_mol_list(self):

        self.assertIsInstance(confs_to_mol_list(mol), list)

        self.assertEqual(len(confs_to_mol_list(mol)), num_confs)

        self.assertEqual(len(confs_to_mol_list(mol, [0, 2, 4])), 3)

class TestMolToAtoms(unittest.TestCase):

    def test_rdkit_mol_to_ase_atoms(self):

        self.assertIsInstance(rdkit_mol_to_ase_atoms(mol), Atoms)

        atoms = rdkit_mol_to_ase_atoms(mol)

        self.assertEqual(mol.GetNumAtoms(), atoms.get_global_number_of_atoms())

class TestAdaptFormat(unittest.TestCase):

    def test_rdkit_mol(self):

        self.assertIsInstance(

            adapt_format('rdkit', 'acetic.mol'),

            Mol)

    def test_rdkit_xyz(self):

        self.assertIsInstance(

            adapt_format('rdkit', 'acetic.xyz'), Mol)

    def test_ase_mol(self):

        self.assertIsInstance(

            adapt_format('ase', 'acetic.mol'),

            Atoms)

    def test_ase_xyz(self):

        self.assertIsInstance(

            adapt_format('ase', 'acetic.xyz'), Atoms)

    def test_not_adeq_req(self):

        self.assertRaises(NotImplementedError, adapt_format, 'hola',

                          'acetic.xyz')

    def test_wrong_file_type(self):

        self.assertRaises(NotImplementedError, adapt_format, 'ase', 'good.inp')

if __name__ == '__main__':

    unittest.main()