tqchem.viewer

Functions

plot_3D_molecule(→ py3Dmol.view)

Plot molecule using py3Dmol

display_trajectory(→ py3Dmol.view)

Display trajectory using py3Dmol

coordinate_screener(→ None)

Display changes along coordinates using ipython sliders

coordinate_screener_from_grid(→ None)

Display changes along coordinates using ipython sliders

Module Contents

tqchem.viewer.plot_3D_molecule(molecule: pathlib.Path | str | ase.Atoms | rdkit.Chem.Mol, width: int = 300, height: int = 300) → py3Dmol.view

Plot molecule using py3Dmol

tqchem.viewer.display_trajectory(xyzs: list[str], time: int = 30, repetitions: int = 1, width: int = 500, height: int = 500) → py3Dmol.view

Display trajectory using py3Dmol

Parameters:

  • xyzs (list[str]) – list of xyz contents

  • time (int) – time for the animation to complete; larger number means slower animation

  • repetitions (int) – animation is repeated as many times; 0 indicated infinite loop

  • width (int) – width of the animation window

  • height (int) – height of the animation window

tqchem.viewer.coordinate_screener(mol: tqchem.molgraph.MolecularSystem, zoomTo: bool = False, shift_by_reference: bool = True) → None

Display changes along coordinates using ipython sliders

ipython widget displaying the molecule and allowing to change individual coordinates using sliders

Parameters:

  • mol (MolecularSystem) – tqchem representation of a molecule

  • zoomTo (bool, optional, default False) – zoom to molecule after each update

tqchem.viewer.coordinate_screener_from_grid(molecule_grid: tqchem.internal_coordinates.MolecularGrid, zoomTo: bool = False) → None

Display changes along coordinates using ipython sliders

ipython widget displaying the molecule and allowing to change individual coordinates using sliders

Parameters:

  • molecule_grid (MolecularSystem) – Representation of a molecule and discretization of the flexible coordinates

  • zoomTo (bool, optional, default False) – zoom to molecule after each update