poremks 1.0.7

for analytics on nanoporous molecular structures

Table of contents

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

General info

poreMKS 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: 3.16.2
• 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 [e-mail]