About atomipy

What is atomipy?

atomipy is a modular Python toolbox for handling and analyzing molecular structures, particularly for mineral slabs with periodic boundary conditions. It's a lightweight version of the MATLAB atom Toolbox and specializes in generating molecular topology files for the MINFF forcefield.

About this Web Interface

This web interface simplifies the use of atomipy by providing an easy way to:

  • Upload molecular structure files (.gro or .pdb)
  • Process them to assign MINFF atom types
  • Generate structure files with the assigned atom types
  • Create topology files for three popular simulation packages:
    • GROMACS (.itp)
    • NAMD/CHARMM (.psf)
    • LAMMPS (.data)
Key Features of atomipy:
  • MINFF forcefield atom typing
  • Import/export PDB, XYZ and Gromacs GRO files
  • Topology file generation for multiple simulation packages
  • Handle both orthogonal and triclinic simulation cells with periodic boundary conditions
  • Calculate bond distances and angles
  • Element type assignment based on structural information
  • Coordinate transformations (orthogonal/triclinic, fractional/cartesian)

How It Works

  1. Upload - Select and upload a structure file (.gro or .pdb)
  2. Process - The file is processed through several atomipy functions to:
    • Assign elements based on atom and residue names
    • Calculate bonds and angles with periodic boundary conditions
    • Assign specialized MINFF atom types based on their chemical environment
  3. Download - Get the processed structure and topology files for your simulations

Technical Details

This web application uses:

  • Flask web framework
  • atomipy Python package for molecular processing
  • The MINFF forcefield for atom typing

For more detailed information about atomipy and its capabilities, please visit the GitHub repository.