swamp-make-library options¶

SWAMP-MAKE-LIBRARY: Create an ensemble library for SWAMP

usage: swamp-make-library [-h] [-nprocs [NPROCS]] [-homologs [HOMOLOGS]]
                          [-overwrite_library] [-min_samples [MIN_SAMPLES]]
                          [-xi [XI]] [-cluster_method [CLUSTER_METHOD]]
                          [-max_eps [MAX_EPS]] [-eps [EPS]]
                          [-min_cluster_size [MIN_CLUSTER_SIZE]]
                          workdir

Positional Arguments¶

workdir

Working directory to perform ensemble clustering

Named Arguments¶

`-nprocs`	Number of processors to use Default: 1
`-homologs`	A file with the list of homolog structures to exclude
`-overwrite_library`
	If set, overwrite the SWAMP library with the new ensembles Default: False
`-min_samples`	sklearn.OPTICS: no. of samples in a neighborhood for a point to be considered as a core Default: 2
`-xi`	sklearn.OPTICS: min.steepness on the reachability plot to constitute a cluster boundary Default: 0.01
`-cluster_method`
	sklearn.OPTICS: extraction method using the calculated cluster reachability Default: “xi”
`-max_eps`	sklearn.OPTICS: max. dist. between points to consider within neighborhood of each other Default: 0.2
`-eps`	sklearn.OPTICS: max. dist. between points to consider within neighborhood of each other Default: 0.2
`-min_cluster_size`
	sklearn.OPTICS: min. no. of samples in a cluster Default: 2