Using the RINRUS driver

The driver runs the entire RINRUS model building procedure from initial PDB structure to input file with one command (and potentially a few interactive inputs along the way). The structure pre-processing needs to be done before using the driver (except for protonation with reduce, although we strongly recommend doing that beforehand as well so the results can be checked).

Calling the driver:

# Usage of the RINRUS driver
python $HOME/git/RINRUS/bin/RINRUS_driver.py 

# Optional arguments:
-i FILE    rinrus driver input file (default: rinrus.inp)

Input file

The input file is a simple text file containing “keyword: value” lines that tell the driver which model building steps to run and what arguments to pass to the relevant scripts. All arguments for the individual scripts can be defined in the driver input file. A template rinrus.inp file containing all recognized keywords is provided in the template_files directory.

Syntax

The input file syntax is simply a set of “keyword: value” lines, for example:

pdb: 2cht_h_corrected_new.clean.pdb
seed: A:203
rin_program: probe
model: max
model_prot_ignore_ids: A:203
qm_input_format: orca
seed_charge: -2

Recognized keywords

The rinrus.inp file must contain the following options (only one of model and approx_model_size_limit required, approx_model_size_limit used if both are given):

keyword	value	function argument defined
PDB	starting PDB filename	`-pdb` for most functions
seed	ch:ID identifiers	`-s` for most functions
RIN_program	probe/arpeggio/distance/manual
model	all/max/maximal/[integer]	`-model` for rinrus_trim2_pdb.py
approx_model_size_limit	[integer]	`-approx_model_size_limit` for rinrus_trim2_pdb.py
qm_input_format	gaussian/gau-xtb/orca/qchem/psi4-fsapt/none	`-format` for write_input.py

The following optional keywords can also be read from rinrus.inp:

keyword	value	function argument defined
path_to_scripts	path to RINRUS bin directory
protonate_initial	true/t/y or false/f/n
res_atoms_file	res_atoms file to use with “RIN_program: manual”	`-ra` for rinrus_trim2_pdb.py
arpeggio_proximal	true/t/y or false/f/n	`-prox` for arpeggio2rins.py
arpeggio_rank	counts/types	`-ra` for rinrus_trim2_pdb.py
dist_type	closest/mass/avg	`-type` for dist_rank.py
dist_satom	seed atoms for distance calculations	`-satom` for dist_rank.py
dist_max	distance cutoff in Angstroms	`-max` for dist_rank.py
dist_noH	true/t/y or false/f/n	`-noH` for dist_rank.py
dist_byres	true/t/y or false/f/n	`-byres` for dist_rank.py
must_add	ch:ID[:S/C/N] of non-seed fragments that need to be in model	`-mustadd` for rinrus_trim2_pdb.py
unfrozen	ch:ID[:CA/CB] of atoms to avoid constraining	`-unfrozen` for rinrus_trim2_pdb.py
nc_res_info	non-canonical residue info file	`-ncres` for rinrus_trim2_pdb.py
model_prot_ignore_ids	ch:ID identifiers	`-ignore_ids` for pymol_protonate.py
model_prot_ignore_atoms	ch:ID:atom identifiers	`-ignore_atoms` for pymol_protonate.py
model_prot_ignore_atnames	atom names	`-ignore_atnames` for pymol_protonate.py
QM_input_template	path to input template	`-intmp` for write_input.py
Gaussian_basis_intmp	true/t/y or false/f/n	`-basisinfo` for write_input.py
QM_input_hopt	true/t/y or false/f/n	`-type hopt` for write_input.py
seed_charge	charge of seed fragment(s)	`-c` for write_input.py
multiplicity	total spin multiplicity	`-m` for write_input.py
fsapt_fA	ch:ID identifiers	`-seed` for write_input.py

Log file

The driver writes a log file called rinrus_log_[date].out which contains the details of the run:

Header containing the github version tag so that building procedure can be reproduced even if code is later changed
Python executable being used (for troubleshooting errors with python packages)
The raw contents of the driver input file
The options selected from parsing the driver input file
The commands run by the driver in each step of the model building procedure