from pymatgen import Molecule
# Create a methane molecule.
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]]
mol = Molecule(["C", "H", "H", "H", "H"], coords)
print(mol)

# A Molecule is simply a list of Sites.
print(mol[0])
print(mol[1])

# Break a Molecule into two by breaking a bond.
for frag in mol.break_bond(0, 1):
    print(frag)

# Getting neighbors that are within 3 angstroms from C atom.
print(mol.get_neighbors(mol[0], 3))

#Detecting bonds
print(mol.get_covalent_bonds())

# If you need to run the molecule in a box with a periodic boundary condition
# code, you can generate the boxed structure as follows (in a 10Ax10Ax10A box)
structure = mol.get_boxed_structure(10, 10, 10)
print(structure)

# Writing to XYZ files (easy to open with many molecule file viewers)
from pymatgen.io.xyzio import XYZ
xyz = XYZ(mol)
xyz.write_file("methane.xyz")

"""
Explanation: Introduction
This notebook demonstrates pymatgen's functionality in terms of creating and editing molecules, as well as its integration with OpenBabel. For the latter, please note that you will need to have openbabel with python bindings installed. Please refer to pymatgen's documentation for installation details.
Molecules
End of explanation
"""


from pymatgen.io.babelio import BabelMolAdaptor
import pybel as pb
a = BabelMolAdaptor(mol)
# Create a pybel.Molecule, which simplifies a lot of access
pm = pb.Molecule(a.openbabel_mol)
# Print canonical SMILES representation (unique and comparable).
print("Canonical SMILES = {}".format(pm.write("can")))
# Print Inchi representation
print("Inchi= {}".format(pm.write("inchi")))
# pb.outformats provides a listing of available formats. 
# Let's do a write to the commonly used PDB file.
pm.write("pdb", filename="methane.pdb", overwrite=True)

# Generating ethylene carbonate (SMILES obtained from Wikipedia)
# And displaying the svg.
ec = pb.readstring("smi", "C1COC(=O)O1")
ec.make3D()
from IPython.core.display import SVG, display_svg
svg = SVG(ec.write("svg"))
display_svg(svg)

"""
Explanation: Openbabel interface
This section demonstrates pymatgen's integration with openbabel.
End of explanation
"""


print(mol.to(fmt="xyz"))
print(mol.to(fmt="g09"))
print(mol.to(fmt="pdb")) #Needs Openbabel.

mol.to(filename="methane.xyz")
mol.to(filename="methane.pdb") #Needs Openbabel.

print(Molecule.from_file("methane.pdb"))

"""
Explanation: Input/Output
Pymatgen has built-in support for the XYZ and Gaussian, NWchem file formats. It also has support for most other file formats if you have openbabel with Python bindings installed.
End of explanation
"""


from pymatgen.io.gaussianio import GaussianInput
gau = GaussianInput(mol, charge=0, spin_multiplicity=1, title="methane", 
                    functional="B3LYP", basis_set="6-31G(d)", 
                    route_parameters={'Opt': "", "SCF": "Tight"},
                    link0_parameters={"%mem": "1000MW"})
print(gau)

# A standard relaxation + SCF energy nwchem calculation input file for methane.
from pymatgen.io.nwchemio import NwTask, NwInput
tasks = [
    NwTask.dft_task(mol, operation="optimize", xc="b3lyp",
                    basis_set="6-31G"),
    NwTask.dft_task(mol, operation="freq", xc="b3lyp",
                    basis_set="6-31G"),
    NwTask.dft_task(mol, operation="energy", xc="b3lyp",
                    basis_set="6-311G"),
]
nwi = NwInput(mol, tasks, geometry_options=["units", "angstroms"])
print(nwi)

"""
Explanation: For more fine-grained control over output, you can use the underlying IO classes Gaussian and Nwchem, two commonly used computational chemistry programs.
End of explanation
"""


