MAFIA-MD: Molecular Arrangements and Fringe Identification and Analysis from Molecular Dynamics

To Find out the number of cyclic rings from molecular dynamics simulation.

Directory structure

a) parent directory

  - mafiamd.py: the main python code
  - Makefile: Makefile for Linux-like systems
  - requirements.yml: requirement file to build the conda environment
  - LICENSE: terms and condition of the license for this code
  - README.md: this "readme" file
  - callgraph.png: the callgraph of the code

b) external_tool : this directory contains the external tool xyz2mol from https://github.com/jensengroup/xyz2mol

  -xyz2mol.py: xyz2mol source code
  -LICENSE: terms and condition of the license for xyz2mol

c) input : this directory contains the example input files

  -set1_validation_demo : example input trajectory files for ring detection and chemical analysis segment of MAFIA-MD

      -fabricated.xyz 
      -fabricated2.xyz
      -real_MD.xyz

  -set2_fringe_analysis_demo: example input trajectory file for fringe analysis segment of MAFIA-MD

      -1769atoms.xyz

d) output : a blank directory for saving the output files from MAFIA-MD

e) ancillary_script : contains a bash script for splitting a large trajectory file containing multiple timesteps into a number of trajectory files containg one timestep each.

    - splitting.sh : the bash script
    - splitting_demo.xyz: a large trajectory file containg multiple timesteps. 

Requirements

rdkit is required for the chemical representations. Conda is required to install rdkit.

Installation guide

1. install conda : (large installation)

    https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html
   

   or Miniconda: (minimal installation)

    https://docs.conda.io/en/latest/miniconda.html#
   

2. create a virtual environment using the Makefile:

   a) Linux or MacOS systems:

    make
   

   b) for Windows systems, use the Anaconda prompt installed during anaconda or miniconda installation and execute the following in the desired directory:

    conda env create -f requirements.yml -p MAFIAMD
   

3. activate the virtual environment:

    conda activate ./MAFIAMD
   

4. run the code:

    python mafiamd.py
   

5. to deactivate the virtual environment:

    conda deactivate