mosaic

MoSAIC motion v0.4.1

Molecular systems automated identification of collective motion, is a correlation based feature selection framework for MD data. Copyright © 2021-2022, Georg Diez and Daniel Nagel

Usage:

mosaic [OPTIONS] COMMAND [ARGS]...

Options:

  --help  Show this message and exit.

Subcommands

• clustering: Clustering similarity matrix of coordinates.
• similarity: Creating similarity matrix of coordinates.
• tui: Open Textual TUI for interactive usage.

mosaic clustering

Clustering similarity matrix of coordinates.

Usage:

mosaic clustering [OPTIONS]

Options:

  --mode [modularity|linkage|CPM|kmedoids]
                                  Mode used for Leiden clustering.  [default:
                                  CPM]
  --n-neighbors INTEGER RANGE     If unequal to None, a knn-graph will be
                                  used. If None, for mode "CPM" the whole
                                  matrix is used, while for "modularity" the
                                  sqrt(n_features)  [x>=2]
  --resolution-parameter FLOAT RANGE
                                  Resolution parameter used for CPM.
                                  [0<=x<=1]
  --n-clusters INTEGER RANGE      Required for mode="kmedoids". The number of
                                  clusters to form.  [x>=2]
  -i, --input PATH                Path to input file. Needs to be of shape
                                  (n_features, n_features).  [required]
  -o, --output-basename PATH      Basename of output files.
  --weighted / --unweighted       Using an adjacency graph (not supported for
                                  CPM).  [default: weighted]
  --plot                          Plotting matrix.
  -n, --name PATH                 Path to file containing names of each colum.
                                  Needs to be of shape (n_features, ).
  --precision [half|single|double]
                                  Precision used for calculation. Lower
                                  precision reduces memory impact but may lead
                                  to overflow errors.  [default: single]
  -v, --verbose                   Activate verbose mode.
  --help                          Show this message and exit.

mosaic similarity

Creating similarity matrix of coordinates.

Usage:

mosaic similarity [OPTIONS]

Options:

  --metric [GY|JSD|correlation|NMI]
                                  Metric used to estimate similarity measure
                                  matrix.  [default: correlation]
  --normalize-method [joint|min|geometric|arithmetic|max]
                                  Only required for metric="NMI". Determines
                                  the normalization factor for the mutual
                                  information. See docs for help.
  --low-memory                    If set the correlation is calculated on-the-
                                  fly using the online Welford algorithm. This
                                  is much slower but needs less RAM and is
                                  preferable for larger files. This supports
                                  only metric=correlation.
  -i, --input PATH                Path to input file. Needs to be of shape
                                  (n_samples, n_features). All command lines
                                  need to start with "#". By default
                                  np.float16 is used for the datatype.
                                  [required]
  -o, --output PATH               Path to output file. Will be a matrix of
                                  shape (n_features, n_features).  [required]
  --knn_estimator                 Uses a parameter free estimate for the
                                  Gelfand-Yaglom mutualinformation based
                                  distance measure which yields more
                                  accurateresults, but is computationally more
                                  expensive.
  --precision [half|single|double]
                                  Precision used for calculation. Lower
                                  precision reduces memory impact but may lead
                                  to overflow errors.  [default: single]
  -v, --verbose                   Activate verbose mode.
  --help                          Show this message and exit.

mosaic tui

Open Textual TUI for interactive usage.

Usage:

mosaic tui [OPTIONS]

Options:

  --help  Show this message and exit.