tqchem.viewer
=============

.. py:module:: tqchem.viewer


Functions
---------

.. autoapisummary::

   tqchem.viewer.plot_3D_molecule
   tqchem.viewer.display_trajectory
   tqchem.viewer.coordinate_screener
   tqchem.viewer.coordinate_screener_from_grid


Module Contents
---------------

.. py:function:: plot_3D_molecule(molecule: pathlib.Path | str | ase.Atoms | rdkit.Chem.Mol, width: int = 300, height: int = 300) -> py3Dmol.view

   Plot molecule using py3Dmol


.. py:function:: display_trajectory(xyzs: list[str], time: int = 30, repetitions: int = 1, width: int = 500, height: int = 500) -> py3Dmol.view

   Display trajectory using py3Dmol

   :param xyzs: list of xyz contents
   :type xyzs: list[str]
   :param time: time for the animation to complete; larger number means slower animation
   :type time: int
   :param repetitions: animation is repeated as many times; 0 indicated infinite loop
   :type repetitions: int
   :param width: width of the animation window
   :type width: int
   :param height: height of the animation window
   :type height: int


.. py:function:: 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

   :param mol: tqchem representation of a molecule
   :type mol: MolecularSystem
   :param zoomTo: zoom to molecule after each update
   :type zoomTo: bool, optional, default False


.. py:function:: 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

   :param molecule_grid: Representation of a molecule and discretization of the flexible coordinates
   :type molecule_grid: MolecularSystem
   :param zoomTo: zoom to molecule after each update
   :type zoomTo: bool, optional, default False