do_sr_chain_loop: Match query sequence to chain in PDB file

Description Usage Arguments

View source: R/pdb_functions2.R

Description

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

Usage

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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 Sept. 8, 2018, 9:30 p.m.