arpeggio2rins.py

arpeggio2rins.py analyses an Arpeggio output file, extracts all contacts involving any seed atoms, and prepares res_atoms.dat files for the model trimming.

Help message 

usage: arpeggio2rins.py [-h] [-pdb PDB] [-f ARPFILE] [-s SEED] [-prox]

Generate interaction information from arpeggio file. Usage: arpeggio2rins.py -pdb pdb -f probe_file -s seed [-prox]

options:
  -h, --help           show this help message and exit
  -pdb PDB             pdb file
  -f ARPFILE           arpeggio contacts file
  -s SEED, -seed SEED  seed for selecting RIN, in the format of "A:300,A:301,A:302"
  -prox, -proximal     include proximal interactions

Inputs

  • -pdb: PDB file
    • Given as filename
    • Examples: -pdb 2cht_h.pdb
  • -f: Arpeggio contacts file
    • Given as filename
    • Example: -f 2cht_h.contacts
  • -s: Seed
    • Given as ch:ID pairs
    • Examples: -s A:203 or -seed A:301,A:302
  • -prox/-proximal: flag to specify that proximal interactions should be included
    • No corresponding argument (acts as t/f flag)
    • Examples: -prox

Outputs

  • FG_arpeggio_counts.dat: table listing arpeggio contact counts with seed for each FG
  • res_atoms.dat: res_atoms file ranked by total contact count
  • res_atoms_types.dat: res_atoms file ranked by number of different contact types