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.
# Uncomment the subsequent lines in this cell to install dependencies for Google Colab.
# !pip install pymatgen==2022.7.19
from pymatgen.core 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)
Full Formula (H4 C1) Reduced Formula: H4C Charge = 0.0, Spin Mult = 1 Sites (5) 0 C 0.000000 0.000000 0.000000 1 H 0.000000 0.000000 1.089000 2 H 1.026719 0.000000 -0.363000 3 H -0.513360 -0.889165 -0.363000 4 H -0.513360 0.889165 -0.363000
# A Molecule is simply a list of Sites.
print(mol[0])
print(mol[1])
[0. 0. 0.] C [0. 0. 1.089] H
# Break a Molecule into two by breaking a bond.
for frag in mol.break_bond(0, 1):
print(frag)
Full Formula (H3 C1) Reduced Formula: H3C Charge = 0, Spin Mult = 2 Sites (4) 0 C 0.000000 0.000000 0.000000 1 H 1.026719 0.000000 -0.363000 2 H -0.513360 -0.889165 -0.363000 3 H -0.513360 0.889165 -0.363000 Full Formula (H1) Reduced Formula: H2 Charge = 0, Spin Mult = 2 Sites (1) 0 H 0.000000 0.000000 1.089000
# Getting neighbors that are within 3 angstroms from C atom.
print(mol.get_neighbors(mol[0], 3))
[Site: H (0.0000, 0.0000, 1.0890), Site: H (1.0267, 0.0000, -0.3630), Site: H (-0.5134, -0.8892, -0.3630), Site: H (-0.5134, 0.8892, -0.3630)]
# Detecting bonds
print(mol.get_covalent_bonds())
[Covalent bond between [0. 0. 0.] C and [0. 0. 1.089] H, Covalent bond between [0. 0. 0.] C and [ 1.026719 0. -0.363 ] H, Covalent bond between [0. 0. 0.] C and [-0.51336 -0.889165 -0.363 ] H, Covalent bond between [0. 0. 0.] C and [-0.51336 0.889165 -0.363 ] H]
# 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)
Full Formula (H4 C1) Reduced Formula: H4C abc : 10.000000 10.000000 10.000000 angles: 90.000000 90.000000 90.000000 Sites (5) # SP a b c --- ---- -------- -------- ------ 0 H 0.5 0.5 0.6089 1 H 0.602672 0.5 0.4637 2 H 0.448664 0.411083 0.4637 3 H 0.448664 0.588917 0.4637 4 C 0.5 0.5 0.5
# Writing to XYZ files (easy to open with many molecule file viewers)
from pymatgen.io.xyz import XYZ
xyz = XYZ(mol)
xyz.write_file("methane.xyz")
This section demonstrates pymatgen's integration with openbabel.
import pybel as pb
from pymatgen.io.babel import BabelMolAdaptor
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)
--------------------------------------------------------------------------- ModuleNotFoundError Traceback (most recent call last) <ipython-input-8-15cbf4a933be> in <module> 1 from pymatgen.io.babel import BabelMolAdaptor ----> 2 import pybel as pb 3 a = BabelMolAdaptor(mol) 4 # Create a pybel.Molecule, which simplifies a lot of access 5 pm = pb.Molecule(a.openbabel_mol) ModuleNotFoundError: No module named 'pybel'
# 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)
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.
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"))
For more fine-grained control over output, you can use the underlying IO classes Gaussian and Nwchem, two commonly used computational chemistry programs.
from pymatgen.io.gaussian 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.nwchem import NwInput, NwTask
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)