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.
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)
Molecule Summary (H4 C1) Reduced Formula: H4C Charge = 0, Spin Mult = 1 Sites (5) 1 C 0.000000 0.000000 0.000000 2 H 0.000000 0.000000 1.089000 3 H 1.026719 0.000000 -0.363000 4 H -0.513360 -0.889165 -0.363000 5 H -0.513360 0.889165 -0.363000
# A Molecule is simply a list of Sites.
print(mol[0])
print(mol[1])
[0.0, 0.0, 0.0] C [0.0, 0.0, 1.089] H
# Break a Molecule into two by breaking a bond.
for frag in mol.break_bond(0, 1):
print(frag)
Molecule Summary (H3 C1) Reduced Formula: H3C Charge = 0, Spin Mult = 2 Sites (4) 1 C 0.000000 0.000000 0.000000 2 H 1.026719 0.000000 -0.363000 3 H -0.513360 -0.889165 -0.363000 4 H -0.513360 0.889165 -0.363000 Molecule Summary (H1) Reduced Formula: H2 Charge = 0, Spin Mult = 2 Sites (1) 1 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), 1.089), (Site: H (1.0267, 0.0000, -0.3630), 1.0889999563640946), (Site: H (-0.5134, -0.8892, -0.3630), 1.0890004071739368), (Site: H (-0.5134, 0.8892, -0.3630), 1.0890004071739368)]
#Detecting bonds
print(mol.get_covalent_bonds())
[Covalent bond between [0.0, 0.0, 0.0] C and [0.0, 0.0, 1.089] H, Covalent bond between [0.0, 0.0, 0.0] C and [1.026719, 0.0, -0.363] H, Covalent bond between [0.0, 0.0, 0.0] C and [-0.51336, -0.889165, -0.363] H, Covalent bond between [0.0, 0.0, 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)
Structure Summary (H4 C1) Reduced Formula: H4C abc : 10.000000 10.000000 10.000000 angles: 90.000000 90.000000 90.000000 Sites (5) 1 H 0.500000 0.500000 0.608900 2 H 0.602672 0.500000 0.463700 3 H 0.448664 0.411083 0.463700 4 H 0.448664 0.588917 0.463700 5 C 0.500000 0.500000 0.500000
# 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")
This section demonstrates pymatgen's integration with openbabel.
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)
Canonical SMILES = C Inchi= InChI=1S/CH4/h1H4
# 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"))
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 #P HF/6-31G(d) Test H4 C1 0 1 C H 1 B1 H 1 B2 2 A2 H 1 B3 2 A3 3 D3 H 1 B4 2 A4 4 D4 B1=1.089000 B2=1.089000 A2=109.471221 B3=1.089000 A3=109.471213 D3=120.000017 B4=1.089000 A4=109.471213 D4=119.999966 COMPND UNNAMED AUTHOR GENERATED BY OPEN BABEL 2.3.2 HETATM 1 C LIG 1 0.000 0.000 0.000 1.00 0.00 C HETATM 2 H LIG 1 0.000 0.000 1.089 1.00 0.00 H HETATM 3 H LIG 1 1.027 0.000 -0.363 1.00 0.00 H HETATM 4 H LIG 1 -0.513 -0.889 -0.363 1.00 0.00 H HETATM 5 H LIG 1 -0.513 0.889 -0.363 1.00 0.00 H CONECT 1 3 4 5 2 CONECT 1 CONECT 2 1 CONECT 3 1 CONECT 4 1 CONECT 5 1 MASTER 0 0 0 0 0 0 0 0 5 0 5 0 END Molecule Summary (H4 C1) Reduced Formula: H4C Charge = 0, Spin Mult = 1 Sites (5) 1 C 0.000000 0.000000 0.000000 2 H 0.000000 0.000000 1.089000 3 H 1.027000 0.000000 -0.363000 4 H -0.513000 -0.889000 -0.363000 5 H -0.513000 0.889000 -0.363000
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.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)
%mem=1000MW #P B3LYP/6-31G(d) Opt SCF=Tight Test methane 0 1 C H 1 B1 H 1 B2 2 A2 H 1 B3 2 A3 3 D3 H 1 B4 2 A4 4 D4 B1=1.089000 B2=1.089000 A2=109.471221 B3=1.089000 A3=109.471213 D3=120.000017 B4=1.089000 A4=109.471213 D4=119.999966
# 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)
geometry units angstroms C 0.0 0.0 0.0 H 0.0 0.0 1.089 H 1.026719 0.0 -0.363 H -0.51336 -0.889165 -0.363 H -0.51336 0.889165 -0.363 end title "H4C1 dft optimize" charge 0 basis C library "6-31G" H library "6-31G" end dft mult 1 xc b3lyp end task dft optimize title "H4C1 dft freq" charge 0 basis C library "6-31G" H library "6-31G" end dft mult 1 xc b3lyp end task dft freq title "H4C1 dft energy" charge 0 basis C library "6-311G" H library "6-311G" end dft mult 1 xc b3lyp end task dft energy