Eigencages: Learning a latent space of porous cage molecules

Jupyter Notebook to produce data for:

A. Sturluson, M. T. Huynh, A. H. P. York, C. M. Simon. Eigencages: Learning a latent space of porous cage molecules.

Source of cage structures:

• DOI: 10.1021/acs.jpcc.7b03848 (CDB41 database courtesy of Kim Jelf's group. See https://github.com/marcinmiklitz/CDB41.git.)
• SI of DOI: 10.1038/s41467-018-05271-9

Structure of repository

.
├── ...
├── svd.ipynb                             # A Julia v1.0 notebook used to illustrate the newly learned latent space of the 74 cages
├── explore_flexibility.ipynb             # A Julia v1.0 notebook used to showcase the effects of flexibility in the cages
├── MD_files                              # Contains all Molecular Dynamics (MD) files used for the fluctuating cages
├── all_cages                             # Contains all cage structures in a .xyz format
│   ├── all_cages.txt                     # A list containing the names of all 74 cages
│   └── flexible_cages.tar.gz             # A tarbar containing the 1600 fluctuating snapshots in a .xyz format
├── cc3                                   # Experimental data for Xe and Kr adsorption in CC3
├── centered_cages                        # Used for Alignment calculations
├── cpd_results                           # Stores results from Alignment calculations
├── data                                  # Stores data needed for Energy calculations in PorousMaterials
│   ├── forcefields                       # Stores the force field files, which contain the parameters for LJ potentials
│   ├── molecules                         # Stores the molecules used (He, Xe and Kr)
│   └── grids                             # Stores the energy grids saved
├── final_aligned_cages                   # Contains the final aligned cages
├── henry_coefs                           # Contains files needed to calculate henry coefficients for the cages in PorousMaterials
│   └── data                              # See ./data
├── noria                                 # Experimental data for Xe and Kr adsorption in noria (NC2)
├── paper                                 # LaTeX files for the paper
├── principal_axes_rotation_failure       # Images to illustrate the failure of alignment via principal axes of inertia
├── rotational_inertia_aligned_cages      # The cages after being aligned via principal axes of inertia
├── Explore_accessibility.ipynb           # A Julia v1.0 notebook used to calculate accessibility of the 74 cages
└── cage_descriptors.ipynb                # A Python 3 notebook used to calculate descriptors for both the original 74 cages and the fluctuating cages using pywindow