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for analytics on nanoporous molecular structures

Project description

Table of contents

General info

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

The Molecular Structure of DDR: DDR Structure

The pore region of DDR embedded within the molecular structure. All Admissible Pore Structure

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

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

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

Dependencies

Project is created with:

  • ase: 3.16.2
  • scikit-image version: 0.14.0
  • scipy version: 1.1.0
  • numpy version: 1.16.0
  • numba version: 0.39.0
  • pytorch version: 0.4.1
  • pytoolz version: 0.9.0

Setup

To run this project, install it locally using conda:

$ cd ../<project_directory>
$ conda create -n poremks python=3.6
$ conda activate poremks
$ pip install -r requirements.txt
$ conda install pytorch-cpu torchvision-cpu -c pytorch
$ pip install poremks

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.

Status

poreMKS is currently under active development.

References

EDT scikit-image ReadMe

Issues

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

Project details


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