FishMol

A python molecular dynamics data analysis tool.

Install

Requirements

• python3: >=3.8

Install

Fishmol is still under development, but you can install it locally:

1. Download the code from GitHub:

git clone https://github.com/Lei-Lei-alpha/fishmol.git

2. Change to the fishmol directory:

cd fishmol

3. Install fishmol

pip install -e ./

4. Run the following command in your terminal to see if fishmol is successfully installed:

fishmol

                  Welcome!                    ▄▄█▀                  FishMol
                                          ▄▄███▀                 version 0.0.1
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         ○                ▄▄▄████████████████████▄▄                     \ 
                    ▄▄▄██████▀███████████████████████▄▄                  ○--○           ▄
                ▄▄████████████ ██████████████████████████▄▄             /           ▄▄█▀
         ○   ▄█████████████████ ████████████████████████████▄▄         ○         ▄███▀
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         ▄████████▀   ○  ▀███████ █████████████████████████████████▄▄      ▄▄█████▀
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            ▀██████████████████ ████████████████████████████████████████████████▄
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                        ▀▀▀█████████████████▀▀▀▀        ▀■                    ▀█▀
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                                    ▀▀▄                Contact: Lei.Lei@durham.ac.uk

Usage

Please refer to docs for usage.

• I/O of trajectory files in xyz format
  • calibration of the trajectory file by fixing the centre of mass
  • Simple view function
  • Simple manipulate of trajectory: filter, select etc
• Calculation of mean square displacement (MSD) and diffusion coefficient
• the anisotropy of diffusion by calculating the projection of MSD and diffusion coefficient along specified directions
• hydrogen bond recognition and lifetime analysis
• the reorientation lifetime of vectors
• the distribution function of a range of scalars (including the radial distribution function, angular distribution function, dihedral angle distribution function)
• 2D combined distribution functions
• Van Hove correlation function
• dimer lifetime correlation function