{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Jupyter Notebook Tutorial " ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Roughly, the design idea of ``mdciao`` is that:\n", "\n", "* The [CLI](http://proteinformatics.uni-leipzig.de/mdciao/cli_cli/cli_cli.html) offers pre-packaged analysis pipelines that are essentially *one-shot* tools. They are an entry-point for non-experts and do not require any Python scripting knowledge. CLI tools are still highly customizable (check ``mdc_*.py -h`` or ``mdc_examples.py``), but offer **only some** of the ``mdciao``-functionalities.\n", " \n", "* The [Python API](http://proteinformatics.uni-leipzig.de/mdciao/api/api.html), on the other hand, exposes:\n", " - **CLI-equivalent** functions via the ``mdciao.cli`` [submodule](http://proteinformatics.uni-leipzig.de/mdciao/cli_cli/cli_cli.html). Here you'll find evertying that the CLI offers, only as regular Python functions. This provides scripting flexibility, with the added value that now input and outputs are *normal* Python objects that can be further manipulated, by ``mdciao`` or any other Python module of your liking.\n", " - Other **standalone submodules** that the CLI uses *under the hood*, and that the user can access directly for any other scripting purpuse: plotting methods, alignment/sequence methods, nomenclature methods, PDB-methods etc.\n", "\n", "