Cluster(1) Manual Page

Name

Cluster - Cluster structures using an RMSD matrix.

Cluster [-hVw] [-a=0] [-k=0] [--rs=-1] [-t=1000] [--td=2.0] [--tol=0.5] files…

Cluster structures using an RMSD matrix.

-a, --algorithm=0: Algorithm: Multi-K-Means++ (0), Hierarchical (1), or Iterative (2)
-h, --help: Print command help and exit.
-k, --clusters=0: Maximum number of k-means clusters.
--rs, --randomSeed=-1: Set the random seed for deterministic clustering (-1 uses the current time).
-t, --trials=1000: Number of trials for Multi-K-Means or iterative method.
--td, --threshold=2.0: The distance value where a hierarchical tree flattened into clusters.
--tol, --tolerance=0.5: Tolerance to determine if points are equivalent (iterative method).
-V, --version: Print the Force Field X version and exit.
-w, --write: Write an archive containing a representative from each cluster.

files…: The RMSD distance matrix and optionally the corresponding structure archive (required for --write).