Merge pull request #84 from OMaraLab/recombinatrix-patch-3

Update getting_started.rst again

Author: recombinatrix

docs/source/getting_started.rst

@@ -5,28 +5,27 @@ This page details how to get started with *PolyConstruct*.
 
 The design, testing, and validation of *PolyConstruct* is detailed in the manuscript "PolyConstruct: 
 adapting  biomolecular simulation pipelines for polymers with PolyBuild, PolyConf and PolyTop", by 
-**__Rangika Munaweera__**, **__Ada Quinn__**, Luna Morrow, Richard A Morris, Megan L O’Mara
+**Rangika Munaweera**, **Ada Quinn**, Luna Morrow, Richard A Morris, Megan L O’Mara
 
 Getting Started
 ===============
 
-
 **Installing PolyConstruct:**
 
-From your home directory, clone PolyConstruct from Git:
+From your home directory, clone *PolyConstruct* from GitHub:
 
 .. code-block:: python
 
     cd ~
     git clone https://github.com/OMaraLab/polyconstruct.git
 
-Then navigate to polyconstruct:
+Then navigate to `~/PolyConstruct`:
 
 .. code-block:: python
 
     cd polyconstruct
 
-To setup an environment for polyconstruct, run: 
+To setup an environment for *PolyConstruct*, run: 
 
 .. code-block:: python
 
@@ -35,7 +34,7 @@ To setup an environment for polyconstruct, run:
 
     pip install -r requirements.txt
 
-Then, build the PolyTop, PolyConf and PolyBuild packages:
+Then, build the *PolyTop*, *PolyConf* and *PolyBuild* packages:
 
 .. code-block:: python
 
@@ -87,8 +86,8 @@ Monomer design
 For both *PolyBuild* and *PolyTop*, monomer parameters should include all monomer atoms that will be present 
 in the simulation model of the final polymer, and dummy atoms correesponding to connectivity with adjacent monomers.  
 The method for preparing monomer .itp depends on the choice of force field, and a number of suitable automated tools 
-exist for small molecule parameterization such as the `Automated Topology Builder <https://atb.uq.edu.au>`, 
-`antechamber <https://ambermd.org/antechamber/ac.html>`, and `LigParGen https://zarbi.chem.yale.edu/ligpargen/`. 
+exist for small molecule parameterization such as the `Automated Topology Builder <https://atb.uq.edu.au>`_, 
+`antechamber <https://ambermd.org/antechamber/ac.html>`_, and `LigParGen <https://zarbi.chem.yale.edu/ligpargen/>_`. 
 
 Monomer coordinates and parameters used as inputs should be designed to reflect the state of the monomer 
 in the mature polymer chain, rather than the isolated monomer molecule prior to polymerization.  For example, 
@@ -99,9 +98,8 @@ and not the ammonium and carboxylate groups found in the precursor amino acids.
 Monomer parameters should be designed in a manner consistent with the desired force field.  We recommend you 
 do not combine monomer parameters from different force field families in a single polymer. 
 
-
 For *PolyConf* These coordinate files should represent a sensible monomer geometry as could be found in the final 
-polymer.  These might be created using tools like ChimeraX, with theoretical ideal bond lengths and 
+polymer.  These might be created using tools like `ChimeraX <https://www.cgl.ucsf.edu/chimerax/>`_, with theoretical ideal bond lengths and 
 angles, by geometry optimization, or generated by automated parameterization tools.  Additionally, 
 it is often convenient if the monomer is in a conformation where atoms corresponding to adjacent monomers 
 are as far as possible from other atoms, and pointed away from other attachment points.
@@ -114,7 +112,8 @@ Worked Examples
 PolyConf creates polymer coordinate files through the tiling and manipulation of monomer pdb files.
 
 There are several detailed examples of the use of PolyConf to create ensembles of starting 
-conformations for a series of increasingly complex polymer architectures.  These are contained in the PolyConf repository in the folder 'polyconstruct/polyconf_examples/' contained in the 
+conformations for a series of increasingly complex polymer architectures.  These are contained in the 
+*PolyConf* repository in the folder `polyconstruct/polyconf_examples/` contained in the 
 
 Here is one simple example, showing the construction of a linear polyethylenimine 128-mer.