Creating edge list from atom matrix — PDB2connections • predatoR

Creates all the edges from the input atom matrix created by PDB_read.

Usage

PDB2connections(
  atom_matrix,
  filtered_info_df,
  n_threads = NULL,
  single_run = TRUE,
  distance_cutoff = 5
)

Arguments

atom_matrix: matrix that contains all the atoms in the PDB file
filtered_info_df: input data.frame which contain only one PDB entries
n_threads: number of threads (default = NULL)
single_run: should be set as TRUE when using PDB2connections function alone (default = TRUE)
distance_cutoff: distance cutoff for setting edges (default = 5)

Value

list contains separate edge data.frames for each chain

Details

This function calculates the distances between all the atoms in the atom matrix and create edges if the distance between two atoms is less than or equal to 7 Angstrom.