mupt-examples

Installation

To obtain a copy of these examples, clone this repo and navigate into it, via:

git clone https://github.com/MuPT-hub/mupt-examples # this repo
cd mupt-examples

Then set up a virtual environment with the Multiscale Polymer Toolkit installed to run the notebooks bundled here. The mupt toolkit repo provides details on how to do so, but if you don't like clicking you can also run the commands below, assuming you have a package management systems such as Mamba (recommended) or Conda installed on your machine:

mamba env create -f conda-envs/release-env.yml
mamba activate mupt-env
git clone https://github.com/MuPT-hub/mupt # the toolkit 
cd mupt
pip install .

You can then safely remove the mupt directory from your file system if you wish to

Index of examples

System building examples (high-level):

0. Simple peptide example
   Assembles a MuPT representation component hierarchy for a peptide generated from your choice of FASTA string
   Depicts the topological and hierarchical organization of parts in a colorful graphic with 2D coordinates
1. Backmapped chain/melt building
   Shows how to perform a backmapping-like build procedure to go from nothing to an MD starting structure using MuPT tools
   Allows specification of arbitrary homopolymer or copolymer chemistry, number of chains, and distribution of chain length
2. Parameterization, export, and MD simulations with OpenFF
   Shows how to use the OpenFF toolkit to parameterize and export MD input files from a MuPT-build starting structure (obtained from the previous demo)
   Concludes by running a short MD simulation in OpenMM

MuPT Representation components tutorials (low-level):

0. "Molecule from scratch" - bare basics
   Shows how to initialize a basic "bond graph" hierarchy with no coordinates
1. "Molecule from scratch" - advanced usage
   "Kitchen sink" tutorial of how to build a molecule fragment with complete hierarchical info using nothing but MuPT representation components
   Generates physically-plausible coordinates and topology using no force fields or external coordinate embedding algorithms (just basic knowledge of point groups)
   and shows how one can leverage the concurrent, arbitrary resolutions structure of the representation to organize initialization around chemically-meaningful motifs
2. Molecule from SMILES/RDKit
   Shows how to instantiate MuPT representation hierarchies from RDKit Mols and SMILES string
3. Rigid body shapes
   Shows off that different kinds of shapes that MuPT Primitive objects can take on (PointClouds, Spheres, Ellipsoids, and Rods)
4. Inter-body spatial alignment Generates animated trajectories which illustrate the different kinds of inter-body alignment operations MuPT uses to spatially align all MuPT representation components