Develop further documentation for PolyTop worked examples

polytop_examples/README.md

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+# PolyTop example scripts
+
+This folder contains a handful of example scripts demonstrating the use of
+*PolyTop*. All the files you need to run these examples are contained within
+this folder.
+
+For detailed documentation of all *PolyTop* methods, please refer to the
+[PolyConstruct ReadTheDocs](https://polyconstruct.readthedocs.io/en/latest/index.html).
+
+These tutorials are not intended as a primer on polymer design or
+stereochemistry. It is assumed that the reader is familiar with polymer
+chemistry and common types of copolymers.
+
+## Tutorial 01: Building a linear polyethyleneimine polymer topology using PolyTop
+
+The first tutorial is an example of how to make a linear 20 unit
+polyethyleneimine chain using *PolyTop*. It is contained in the file
+`linear_PEI.py`.
+
+This tutorial showcases several approaches, including:
+* loading in itp files to create Topology objects
+* defining appropriate Junctions for polymer extension
+* creating Monomer objects from a Topology and list of Junctions
+* building a polymer chain with `extend()`
+* saving the polymer to an itp file
+
+This tutorial is all contained in a single script, with detailed comments
+discussing the strategies used and the reasoning behind them or another method.
+You are encouraged to view the topologies generated by this script, and others
+you develop, to understand how the monomers are connected.
+
+## Tutorial 02: Building an ethlyamine dendrimer polymer topology using PolyTop
+
+The second tutorial shows strategies for making a more complex polymer with
+levels of branching building outwards from a central monomer. It is contained
+in the file `dendrimer_ethylamine.py`.
+
+This tutorial showcases several approaches, including:
+* breaking down a polymer structure into the monomers required to build it
+* loading in itp files to create Topology objects
+* defining appropriate, distinct Junctions for precise polymer extension
+* creating Monomer objects from a Topology and list of Junctions
+* building a polymer chain with `extend()`
+* saving the polymer to an itp file
+
+This tutorial is all contained in a single script, with detailed comments
+discussing the strategies used and the reasoning behind them or another method.
+You are encouraged to view the topologies generated by this script, and others
+you develop, to understand how the monomers are connected.
+
+## Tutorial 03: Building a 4-arm PEG star polymer topology using PolyTop
+
+The third tutorial shows strategies for making another complex polymer with
+long linear arms branching out from a central monomer. It is contained
+in the file `star_PEG.py`.
+
+This tutorial showcases several approaches, including:
+* breaking down a polymer structure into the monomers required to build it
+* discussing different approaches to create the same polymer structure
+* loading in itp files to create Topology objects
+* defining appropriate, distinct Junctions for precise polymer extension
+* creating Monomer objects from a Topology and list of Junctions
+* building a polymer chain with `extend()`
+* saving the polymer to an itp file
+
+This tutorial is all contained in a single script, with detailed comments
+discussing the strategies used and the reasoning behind them or another method.
+You are encouraged to view the topologies generated by this script, and others
+you develop, to understand how the monomers are connected.