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for analytics on nanoporous molecular structures

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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


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


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, 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.


Refer to the jupyter notebook in the doc folder.


poreMKS is currently under active development.


EDT scikit-image ReadMe


Please send questions and issues about installation and usage of PyMKS to

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