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 [linkage|modularity|kmedoids|CPM]
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|NMI|correlation]
Metric used to estimate similarity measure
matrix. [default: correlation]
--normalize-method [max|arithmetic|joint|min|geometric]
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.