Synopsis

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

Description

Cluster structures using an RMSD matrix.

Options

-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.

Arguments

files…​

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