Python XYZ示例

示例#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)

示例#2

文件： test_xyzio.py 项目： 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)

示例#3

    def test_init_from_structure(self):
        filepath = os.path.join(test_dir, 'POSCAR')
        poscar = Poscar.from_file(filepath)
        struct = poscar.structure
        xyz = XYZ(struct)
        ans = """24
Fe4 P4 O16
Fe 2.277347 4.550379 2.260125
Fe 2.928536 1.516793 4.639870
Fe 7.483231 4.550379 0.119620
Fe 8.134420 1.516793 2.499364
P 0.985089 1.516793 1.990624
P 4.220794 4.550379 4.370369
P 6.190973 1.516793 0.389120
P 9.426677 4.550379 2.768865
O 0.451582 4.550379 3.365614
O 1.006219 1.516793 3.528306
O 1.725331 0.279529 1.358282
O 1.725331 2.754057 1.358282
O 3.480552 3.313115 3.738027
O 3.480552 5.787643 3.738027
O 4.199665 4.550379 1.148562
O 4.754301 1.516793 0.985870
O 5.657466 4.550379 3.773620
O 6.212102 1.516793 3.610928
O 6.931215 0.279529 1.021463
O 6.931215 2.754057 1.021463
O 8.686436 3.313115 3.401208
O 8.686436 5.787643 3.401208
O 9.405548 4.550379 1.231183
O 9.960184 1.516793 1.393875"""
        self.assertEqual(str(xyz), ans)

示例#4

文件： smartio.py 项目： zacharygibbs/pymatgen

def write_mol(mol, filename):
    """
    Write a molecule to a file based on file extension. For example, anything
    ending in a "xyz" is assumed to be a XYZ file. Supported formats include
    xyz, Gaussian input (gjf|g03|g09|com|inp), and pymatgen's JSON serialized
    molecules.

    Args:
        mol (Molecule/IMolecule): Molecule to write
        filename (str): A filename to write to.
    """
    fname = os.path.basename(filename)
    if fnmatch(fname.lower(), "*.xyz*"):
        return XYZ(mol).write_file(filename)
    elif any([
            fnmatch(fname.lower(), "*.{}*".format(r))
            for r in ["gjf", "g03", "g09", "com", "inp"]
    ]):
        return GaussianInput(mol).write_file(filename)
    elif fnmatch(fname, "*.json*") or fnmatch(fname, "*.mson*"):
        with zopen(filename, "w") as f:
            return json.dump(mol, f, cls=PMGJSONEncoder)
    else:
        m = re.search("\.(pdb|mol|mdl|sdf|sd|ml2|sy2|mol2|cml|mrv)",
                      filename.lower())
        if m:
            return BabelMolAdaptor(mol).write_file(filename, m.group(1))

    raise ValueError("Unrecognized file extension!")

示例#5

 def setUp(self):
     coords = [[0.000000, 0.000000, 0.000000],
               [0.000000, 0.000000, 1.089000],
               [1.026719, 0.000000, -0.363000],
               [-0.513360, -0.889165, -0.363000],
               [-0.513360, 0.889165, -0.363000]]
     self.mol = Molecule(["C", "H", "H", "H", "H"], coords)
     self.xyz = XYZ(self.mol)

示例#6

文件： test_pointgroup.py 项目： akashneo/pymatgen

 def test_spherical(self):
     a = PointGroupAnalyzer(CH4)
     self.assertEqual(a.sch_symbol, "Td")
     self.assertEqual(len(a.get_pointgroup()), 24)
     a = PointGroupAnalyzer(PF6)
     self.assertEqual(a.sch_symbol, "Oh")
     self.assertEqual(len(a.get_pointgroup()), 48)
     xyz = XYZ.from_file(os.path.join(test_dir, "c60.xyz"))
     a = PointGroupAnalyzer(xyz.molecule)
     self.assertEqual(a.sch_symbol, "Ih")

示例#7

文件： test_pointgroup.py 项目： akashneo/pymatgen

 def test_dihedral(self):
     a = PointGroupAnalyzer(C2H4)
     self.assertEqual(a.sch_symbol, "D2h")
     self.assertEqual(len(a.get_pointgroup()), 8)
     a = PointGroupAnalyzer(BF3)
     self.assertEqual(a.sch_symbol, "D3h")
     self.assertEqual(len(a.get_pointgroup()), 12)
     xyz = XYZ.from_file(os.path.join(test_dir, "b12h12.xyz"))
     a = PointGroupAnalyzer(xyz.molecule)
     self.assertEqual(a.sch_symbol, "D5d")

示例#8

 def test_spherical(self):
     a = PointGroupAnalyzer(CH4)
     self.assertEqual(a.sch_symbol, "Td")
     self.assertEqual(len(a.get_pointgroup()), 24)
     a = PointGroupAnalyzer(PF6)
     self.assertEqual(a.sch_symbol, "Oh")
     self.assertEqual(len(a.get_pointgroup()), 48)
     xyz = XYZ.from_file(os.path.join(test_dir, "c60.xyz"))
     a = PointGroupAnalyzer(xyz.molecule)
     self.assertEqual(a.sch_symbol, "Ih")

示例#9

 def test_dihedral(self):
     a = PointGroupAnalyzer(C2H4)
     self.assertEqual(a.sch_symbol, "D2h")
     self.assertEqual(len(a.get_pointgroup()), 8)
     a = PointGroupAnalyzer(BF3)
     self.assertEqual(a.sch_symbol, "D3h")
     self.assertEqual(len(a.get_pointgroup()), 12)
     xyz = XYZ.from_file(os.path.join(test_dir, "b12h12.xyz"))
     a = PointGroupAnalyzer(xyz.molecule)
     self.assertEqual(a.sch_symbol, "D5d")

示例#10

文件： test_xyzio.py 项目： 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])

示例#11

文件： test_xyzio.py 项目： 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]))

示例#12

    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]))

示例#13

def read_mol(filename):
    """
    Reads a molecule based on file extension. For example, anything ending in
    a "xyz" is assumed to be a XYZ file. Supported formats include xyz,
    gaussian input (gjf|g03|g09|com|inp), Gaussian output (.out|and
    pymatgen's JSON serialized molecules. Using openbabel,
    many more extensions are supported but requires openbabel to be installed.

    Args:
        filename:
            A filename to read from.

    Returns:
        A Molecule object.
    """
    fname = os.path.basename(filename)
    if fnmatch(fname.lower(), "*.xyz*"):
        return XYZ.from_file(filename).molecule
    elif any([
            fnmatch(fname.lower(), "*.{}*".format(r))
            for r in ["gjf", "g03", "g09", "com", "inp"]
    ]):
        return GaussianInput.from_file(filename).molecule
    elif any([
            fnmatch(fname.lower(), "*.{}*".format(r))
            for r in ["out", "lis", "log"]
    ]):
        return GaussianOutput(filename).final_structure
    elif fnmatch(fname, "*.json*") or fnmatch(fname, "*.mson*"):
        with zopen(filename) as f:
            s = json.load(f, cls=PMGJSONDecoder)
            if type(s) != Molecule:
                raise IOError("File does not contain a valid serialized "
                              "molecule")
            return s
    else:
        m = re.search("\.(pdb|mol|mdl|sdf|sd|ml2|sy2|mol2|cml|mrv)",
                      filename.lower())
        if m:
            return BabelMolAdaptor.from_file(filename, m.group(1)).pymatgen_mol

    raise ValueError("Unrecognized file extension!")

示例#14

文件： smartio.py 项目： akashneo/pymatgen

def read_mol(filename):
    """
    Reads a molecule based on file extension. For example, anything ending in
    a "xyz" is assumed to be a XYZ file. Supported formats include xyz,
    gaussian input (gjf|g03|g09|com|inp), Gaussian output (.out|and
    pymatgen's JSON serialized molecules. Using openbabel,
    many more extensions are supported but requires openbabel to be installed.

    Args:
        filename:
            A filename to read from.

    Returns:
        A Molecule object.
    """
    fname = os.path.basename(filename)
    if fnmatch(fname.lower(), "*.xyz*"):
        return XYZ.from_file(filename).molecule
    elif any([fnmatch(fname.lower(), "*.{}*".format(r))
              for r in ["gjf", "g03", "g09", "com", "inp"]]):
        return GaussianInput.from_file(filename).molecule
    elif any([fnmatch(fname.lower(), "*.{}*".format(r))
              for r in ["out", "lis", "log"]]):
        return GaussianOutput(filename).final_structure
    elif fnmatch(fname, "*.json*") or fnmatch(fname, "*.mson*"):
        with zopen(filename) as f:
            s = json.load(f, cls=PMGJSONDecoder)
            if type(s) != Molecule:
                raise IOError("File does not contain a valid serialized "
                              "molecule")
            return s
    else:
        m = re.search("\.(pdb|mol|mdl|sdf|sd|ml2|sy2|mol2|cml|mrv)",
                      filename.lower())
        if m:
            return BabelMolAdaptor.from_file(filename,
                                             m.group(1)).pymatgen_mol

    raise ValueError("Unrecognized file extension!")

示例#15

文件： test_babelio.py 项目： zacharygibbs/pymatgen

 def test_from_string(self):
     xyz = XYZ(self.mol)
     adaptor = BabelMolAdaptor.from_string(str(xyz), "xyz")
     mol = adaptor.pymatgen_mol
     self.assertEqual(mol.formula, "H4 C1")