run: Main function

In koziek713/PDBClusteR: PDBClusteR: an R package for structural clustering of proteins and other biomolecules.

Description

Main function

Usage

run(file_name = "", file_type = "list", save_files = F, skip_frames = 0,
  plots = T, protein_representation = "CA", chain = "",
  cluster_quantity = 10, receptor_peptide_mode = F,
  reference_structure_pdb_code = "", reference_structure_file = "",
  reference_chain_id = "", kmeans_algorithm = "Hartigan-Wong",
  output_directory = "")

Arguments

file_name	path to file
file_type	list or file
save_files	boolean
skip_frames	number how many first frames should be skipped
plots	boolean
protein_representation	CA or all
chain	chain ID
cluster_quantity	number
receptor_peptide_mode	boolean
reference_structure_pdb_code	code from PDB web repository
reference_structure_file	path to file
reference_chain_id	chain ID
kmeans_algorithm	Hartigan-Wong / MacQueen / Lloyd / Forgy
output_directory	path to directory

Value

return object with clusters data

koziek713/PDBClusteR documentation built on May 7, 2019, 3:20 p.m.