Cluster structures using an RMSD matrix.
Cluster(1) Manual Page
Name
Cluster - Cluster structures using an RMSD matrix.
Synopsis
Cluster [-hVw] [-a=0] [-k=0] [--rs=-1] [-t=1000] [--td=2.0] [--tol=0.5] files…
Description
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).