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43 changes: 29 additions & 14 deletions docs/source/getting_started.rst
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Getting Started
PolyConstruct
===============

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:**

Expand Down Expand Up @@ -49,26 +53,37 @@ Then, build the PolyTop, PolyConf and PolyBuild packages:



Input files and monomer design
Input files
===============

**PolyConf**

*PolyConf* assembles polymer pdb files by tiling individual monomer pdb files. Monomer PDB files should
include all monomer atoms that will be present in the final polymer, dummy atoms corresponding to
connectivity with adjacent monomers, and `CONECT` records that describe the connectivity between
monomer atoms.

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
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.
*PolyConf* does not require any preprocessing of monomer .pdb files.

**PolyBuild**

*PolyBuild* requires monomer itp files, which are then converted into gromacs residue topology database
entries, and a coordinate file containing a complete structure of the intended polymer. This structure can
be created with PolyConf, manually, or by using other structure creation packages.

PolyBuild leverages GROMACS tools to automatically parameterise polymers. and requires
.itp files to be converted to RTP database entries using the provided `ITP2RTP` program.
For more infomation, see the :ref:`PolyBuild` documentation.

**PolyTop**

*PolyTop* requires monomer itp files describing all monomers that will be contained in the system.

*PolyTop* does not require any preprocessing of monomer .itp files.

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
Expand All @@ -84,12 +99,12 @@ 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 and PolyTop, monomer .itp and .pdb files do not need to be pre-processed.

PolyBuild leverages GROMACS tools to automatically parameterise polymers. and requires
.itp files to be converted to RTP database entries using the provided `ITP2RTP` program.
For more infomation, see the :ref:`PolyBuild` documentation.

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
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.

Worked Examples
==================
Expand Down Expand Up @@ -331,4 +346,4 @@ Find the above and additional worked examples as executable Python scripts or Ju
Notebooks on the `PolyConstruct GitHub repository <https://github.com/OMaraLab/polyconstruct>`_.
Examples for PolyTop are available at 'polyconstruct/paper_worked_examples.ipynb'
and for PolyConf at 'polyconstruct/polyconf_examples/'; while instructions to
use the two PolyBuild scripts are included under the :ref:`PolyBuild` documentation.
use the two PolyBuild scripts are included under the :ref:`PolyBuild` documentation.