do_sr_chain_loop: Match query sequence to chain in PDB file

In egmg726/crisscrosslinker: An R package for protein interaction analysis

Description

This function will go through all chains in the PDB file to output list of chains that match the sequence

Usage

do_sr_chain_loop(
  protein_name,
  fasta_seq,
  pdb_read,
  pdb_rl,
  pwa_score_threshold = 500,
  peptide_sequence = NULL,
  fasta_file = NULL
)

Arguments

protein_name	Protein name that will be used for the console output
fasta_seq	Sequence from FASTA file
pdb_read	PDB file as loaded by bio3d::seqinr()
pdb_rl	Name of PDB file
pwa_score_threshold	Minimum score to determine a match using Biostrings::pairwiseAlignment()
peptide_sequence	An optional peptide sequence to use for recommendations if trying to match a peptide to a structure. Defaults to NULL
fasta_file	Optional fasta file input

egmg726/crisscrosslinker documentation built on Jan. 23, 2021, 1:50 a.m.