Table of contents

• General info
• Dependencies
• Setup
• Usage
• Status
• References
• Issues

General info

atomMKS is a tool for the analytics of porous molecular structures.

The Molecular Structure of DDR:

The pore region of DDR embedded within the molecular structure.

The pore region of DDR accessible by a 1.5A radius probe is visualized as below:

The skeleton of the pore structure overlayed on the pore volume is visualized as below:

The shortest paths for the probe through the pore structure are visualized as below:

Dependencies

Project is created with:

• ase==3.23.0
• scikit-image==0.24.0
• scipy==1.14.1
• numpy==1.26.4
• numba==0.60.0
• torch==2.5.0
• toolz==1.0.0

Setup

To run this project, install it locally using conda:

$ cd ../<project_directory>
$ conda create -n atom python=3.10
$ conda activate atom
$ pip install -r requirements.txt
$ pip install atommks

Conda is a package and environment manager bundled with anaconda python distribution. See, https://www.continuum.io/downloads for more details on installing and using Conda.

Windows Users need to install visual studio build tools, in order to the compile c/c++ files assosciated with some of the dependencies.

Usage

Refer to the jupyter notebook in the doc folder.

We provide two scripts to analyze structure files in bulk

1. Generate and save grid-representations to disc for a list of CIF files

Usage: gen_gridStructures.py [OPTIONS]

  Command-line tool to process structures in CIF format with parallel
  processing. # noqa: E501

Options:
  -i, --input-dir PATH     Input directory containing CIF files.  [required]
  -o, --output-dir TEXT    Output directory to save processed files.
                           [required]
  -l, --len-pixel INTEGER  Length of pixel grid (default is 10).
  -r, --rep TEXT           Repeat the structure (default is "1,1,1").
  -p, --processes INTEGER  Number of parallel processes to use (default is 1).
  --help                   Show this message and exit.

2. Used the saved grid-representations from prior set to compute and save pore characteristics

Usage: gen_poreMetrics.py [OPTIONS]

  Command-line tool to process MAT files for pore structure analysis.

Options:
  -i, --input-folder PATH   Input folder containing MAT files.  [required]
  -o, --output-folder PATH  Output folder to save processed files.  [required]
  -r, --r-probe FLOAT       Probe radius (default is 1.0).
  -l, --len-pixel INTEGER   Number of voxels per angstrom (default is 10).
  -p, --processes INTEGER   Number of parallel processes (default is 2).
  --help                    Show this message and exit.

Status

atomMKS is currently under active development.

References

EDT
scikit-image

Issues

Please send questions and issues about installation and usage of PyMKS to apaar92@gmail.com

Lint instructions

black --line-length 79 .
isort .
flake8 .

Docker set-up

docker network create nanoporous-network
# start the service
./start_db_service.sh
stop the service
./stop_db_service.sh