{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Example 3: Build a Combinatorial Library\n", "\n", "This notebook briefly introduces the `molli combine` workflow which allows to substitute attachment points on the molecules in a combinatorial fashion.\n", "\n", "## Hardware Specification for Rerun\n", "\n", "Desktop workstation with 2x (AMD EPYC 7702 64-Core) with total of 128 physical and 256 logical cores, 1024 GB DDR4 with Ubuntu 22.04 LTS operating system." ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [], "source": [ "import molli as ml\n", "ml.visual.configure()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Overview.\n", "\n", "We start with the file `phosphorus_core.mol2`, in which we define the three attached pseudoatoms labeled `AP1`, `AP2` and `AP3`. These are the \"attachment points\": the pseudoatoms that define the direction of the substitution. These atoms need to be replaced with the groups found in another file: `substituents.cdxml`.\n", "We will be generating two libraries: achiral and chiral phosphines." ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Atom(element=P, isotope=None, label='P', formal_charge=0, formal_spin=0)\n", "Atom(element=Unknown, isotope=None, label='AP1', formal_charge=0, formal_spin=0)\n", "Atom(element=Unknown, isotope=None, label='AP2', formal_charge=0, formal_spin=0)\n", "Atom(element=Unknown, isotope=None, label='AP3', formal_charge=0, formal_spin=0)\n" ] }, { "data": { "application/3dmoljs_load.v0": "
You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n jupyter labextension install jupyterlab_3dmol
You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n",
" jupyter labextension install jupyterlab_3dmol
You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n jupyter labextension install jupyterlab_3dmol
You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n",
" jupyter labextension install jupyterlab_3dmol