PDB2connections: Creating edge list from atom matrix

In berkgurdamar/predatoR: Mutation Impact Prediction Based on Network Properties

Creating edge list from atom matrix

Description

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)

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.

Value

list contains separate edge data.frames for each chain

berkgurdamar/predatoR documentation built on Jan. 10, 2023, 10:51 p.m.