Documentation of individual functions

See individual pages for each script for detailed documentation on usage, inputs and outputs.

External programs packaged with RINRUS:

• Reduce
• Probe
• Arpeggio
• pdb_clean.py (PDB processing script for Arpeggio)

RINRUS driver:

• RINRUS_driver.py

RIN analysis/active site selection:

• arpeggio2rins.py
• probe2rins.py
• dist_rank.py

QM-cluster model construction:

• rinrus_trim2_pdb.py
• pymol_protonate.py
• make_template_pdb.py
• check_duplicate_models.py

QM input file preparation

• write_input.py

QM output processing: FSAPT

• define_fA_fB.py
• fisapt_analysis.py

QM output processing: optimized geometries

• gopt_to_pdb.py
• xyz_to_pdb.py

Batch RIN analysis for sets of MD frames

• MD_batch_rin.py
• merge_MD_batches.py