Create a vmd movie from .xyz file

Create molecule and scan two coordinates

Here we create a molecule from a smiles string and visualize its graph and 3D representation. We select two bonds to rotate around and scan the coordinates. The scan is written to an xyz file which can be read by vmd.

from pathlib import Path

from tqchem.molgraph import molecularSystem
from tqchem.internal_coordinates import MolecularGrid
from tqchem.chem import xyz_contents
from tqchem.viewer import plot_3D_molecule
from itertools import product


molecule = molecularSystem("NCCCOC(CCNCC)CCCC")
n_gridpoints = 12
shift_by_reference = True
molecule_grid = MolecularGrid(molecule, shift_by_reference)
print(molecule_grid.variable_atom_indices())

molecule.draw()
view = plot_3D_molecule(molecule.ase)
view.show()

bond_index1 = 3
bond_index2 = -1

xyzs = []

grid = molecule_grid.shape()
superindex = [0] * molecule_grid.n_variables()
for i, j in product(grid[bond_index1], grid[bond_index2]):
    superindex[bond_index1] = i
    superindex[bond_index2] = j
    molecule = molecule_grid(superindex)
    xyzs.append(xyz_contents(molecule.ase))

output_name = "aminophenol_derivative"
output_dir = Path(".output_movie")
output_dir.mkdir(exist_ok=True)
trajectory_file = output_dir / f"{output_name}.xyz"
trajectory_file.write_text("".join(xyzs))

['Bond(0, 1)', 'Bond(1, 2)', 'Bond(2, 3)', 'Bond(3, 4)', 'Bond(4, 5)', 'Bond(5, 6)', 'Bond(5, 11)', 'Bond(6, 7)', 'Bond(7, 8)', 'Bond(7, 8)', 'Bond(8, 9)', 'Bond(11, 12)', 'Bond(12, 13)']

3Dmol.js failed to load for some reason. Please check your browser console for error messages.

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# 1.) make sure that vmd is installed and the path is set (e.g. softlink to /usr/local/bin/vmd)
# 2.) set VMDDIR to the path of the VMD installation. Without naming, the default is /usr/local/bin/scripts/vmd/vmdinit.tcl

# Set the VMDDIR environment variable to the path of the VMD installation
from pathlib import Path
import os

vmd_path = Path("/Applications/VMD_1.9.4a57-arm64-Rev12.app/Contents/vmd")
os.environ["vmd_path"] = str(vmd_path)

Path("vmd_movie").mkdir(exist_ok=True)

!$vmd_path/vmd_MACOSXARM64 -e movie.tcl > movie.out
!magick -delay 2 vmd_movie/snapshot.*.rgb movie.gif

2024-11-13 16:19:12.547 vmd_MACOSXARM64[47881:347395] +[IMKClient subclass]: chose IMKClient_Modern
2024-11-13 16:19:12.547 vmd_MACOSXARM64[47881:347395] +[IMKInputSession subclass]: chose IMKInputSession_Modern