{ "cells": [ { "cell_type": "markdown", "id": "14eaa959", "metadata": {}, "source": [ "## Conformer Search\n", "\n", "The goal in Conformer optimization is to find the most stable 3D structure of a molecule \n", "which differ by dihedral angles, bond angles and bond lengths.\n", "We use tensor trains to avoid the exponential complexity of the\n", "conformer search problem.\n", "\n", "A more detailed explanation can be found in our [paper](http://dx.doi.org/10.26434/chemrxiv-2024-jjns1)." ] }, { "cell_type": "markdown", "id": "92a0f518", "metadata": {}, "source": [ "### Representation of a molecule\n", "\n", "The internal representation of a molecule in TQchem is the MolecularSystem class,\n", "which can be initialized from a variety of popular molecule representations.\n", "TQchem supports conversion from:\n", "- rdkit.Mol\n", "- ase.Atoms\n", "- smiles string\n", "- xyz file/xyz block\n", "\n", "For example, below is an example of creating a MolecularSystem object from an xyz block:" ] }, { "cell_type": "code", "execution_count": 1, "id": "22aa403c-e34e-48ee-9862-96ee0875f226", "metadata": {}, "outputs": [ { "data": { "application/3dmoljs_load.v0": "
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