Exemplos de XYZ.from_string em Python

Exemplo n.º 1

    def test_from_string(self):
        ans = """5
H4 C1
C 0.000000 0.000000 0.000000
H 0.000000 0.000000 1.089000
H 1.026719 0.000000 -0.363000
H -0.513360 -0.889165 -0.363000
H -0.513360 0.889165 -0.363000"""
        xyz = XYZ.from_string(ans)
        mol = xyz.molecule
        sp = ["C", "H", "H", "H", "H"]
        for i, site in enumerate(mol):
            self.assertEqual(site.species_string, sp[i])
            self.assertEqual(len(site.coords), 3)
            if i == 0:
                self.assertTrue(all([c == 0 for c in site.coords]))

        mol_str = """2
Random
C 2.39132145462 -0.700993488928 -7.22293142224e-06
C 1.16730636786 -1.38166622735 -2.77112970359e-06
"""
        xyz = XYZ.from_string(mol_str)
        mol = xyz.molecule
        self.assertTrue(abs(mol[0].z) < 1e-5)
        self.assertTrue(abs(mol[1].z) < 1e-5)

Exemplo n.º 2

Arquivo: test_xyzio.py Projeto: ATNDiaye/pymatgen

    def test_from_string(self):
        ans = """5
H4 C1
C 0.000000 0.000000 0.000000
H 0.000000 0.000000 1.089000
H 1.026719 0.000000 -0.363000
H -0.513360 -0.889165 -0.363000
H -0.513360 0.889165 -0.363000"""
        xyz = XYZ.from_string(ans)
        mol = xyz.molecule
        sp = ["C", "H", "H", "H", "H"]
        for i, site in enumerate(mol):
            self.assertEqual(site.species_string, sp[i])
            self.assertEqual(len(site.coords), 3)
            if i == 0:
                self.assertTrue(all([c == 0 for c in site.coords]))

        mol_str = """2
Random
C 2.39132145462 -0.700993488928 -7.22293142224e-06
C 1.16730636786 -1.38166622735 -2.77112970359e-06
"""
        xyz = XYZ.from_string(mol_str)
        mol = xyz.molecule
        self.assertTrue(abs(mol[0].z) < 1e-5)
        self.assertTrue(abs(mol[1].z) < 1e-5)

Exemplo n.º 3

Arquivo: test_xyzio.py Projeto: jesuansito/pymatgen

    def test_from_string(self):
        ans = """5
H4 C1
C 0.000000 0.000000 0.000000
H 0.000000 0.000000 1.089000
H 1.026719 0.000000 -0.363000
H -0.513360 -0.889165 -0.363000
H -0.513360 0.889165 -0.363000"""
        xyz = XYZ.from_string(ans)
        mol = xyz.molecule
        sp = ["C", "H", "H", "H", "H"]
        for i, site in enumerate(mol):
            self.assertEqual(site.species_string, sp[i])

Exemplo n.º 4

Arquivo: test_xyzio.py Projeto: NadezhdaBzhilyanskaya/pymatgen

    def test_from_string(self):
        ans = """5
H4 C1
C 0.000000 0.000000 0.000000
H 0.000000 0.000000 1.089000
H 1.026719 0.000000 -0.363000
H -0.513360 -0.889165 -0.363000
H -0.513360 0.889165 -0.363000"""
        xyz = XYZ.from_string(ans)
        mol = xyz.molecule
        sp = ["C", "H", "H", "H", "H"]
        for i, site in enumerate(mol):
            self.assertEqual(site.species_string, sp[i])
            self.assertEqual(len(site.coords), 3)
            if i == 0:
                self.assertTrue(all([c == 0 for c in site.coords]))

Exemplo n.º 5

    def test_from_string(self):
        ans = """5
H4 C1
C 0.000000 0.000000 0.000000
H 0.000000 0.000000 1.089000
H 1.026719 0.000000 -0.363000
H -0.513360 -0.889165 -0.363000
H -0.513360 0.889165 -0.363000"""
        xyz = XYZ.from_string(ans)
        mol = xyz.molecule
        sp = ["C", "H", "H", "H", "H"]
        for i, site in enumerate(mol):
            self.assertEqual(site.species_string, sp[i])
            self.assertEqual(len(site.coords), 3)
            if i == 0:
                self.assertTrue(all([c == 0 for c in site.coords]))