RMSD Clustering

Clustering based on RMSD

Usage

  rmsd_clustering [-h] [options] INPUT [INPUT ...]

Installation

  pip install git+https://github.com/boneta/RMSD-Clustering.git

Requirements

• Fortran compiler (tested with gfortran)
• LAPACK-devel libraries
• Python 3.8+ and the following packages:
  • numpy
  • scipy
  • ase
  • rmsd
  • matplotlib
  • seaborn

Detailed usage

Input

Input files can be of any kind supported by ASE (e.g. xyz, pdb, vasp). The input can be either a single file or several. File formats can be mixed and they will be automatically inferred individually.
A format can be forced by using the --in-type option, in which case all input files must be of the same format.

Reordering

Atom order is assumed to be the same for all structures. If this is not the case, the --reorder option can be used to reorder the atoms using different methods: 'hungarian', 'inertia-hungarian', 'brute' or 'distance'.

Clustering

The clustering is performed based on the calculation of an RMSD matrix between all pairs of structures. Then they are grouped if the RMSD is below a given threshold set with the --cutoff option. If --n-clusters is used instead, the structures will be grouped into n clusters setting the cutoff accordingly.

Examples

  rmsd_clustering molecs.xyz
  rmsd_clustering POSCAR_01 POSCAR_02 POSCAR_03
  rmsd_clustering --in-type vasp --reorder brute CONTCAR_*
  rmsd_clustering --n-clusters 20 molecs.xyz