analyze_trajectory_ppi.py Command Help

Command: $SCHRODINGER/run analyze_trajectory_ppi.py

usage: analyze_trajectory_ppi.py [-h]
                                 [-includeinteraction INTERACTION_TYPE [INTERACTION_TYPE ...]]
                                 [-excludeinteraction INTERACTION_TYPE [INTERACTION_TYPE ...]]
                                 [-s START:END:STEP]
                                 cms_file csv_file protein_asl1 protein_asl2

analyze_trajectory_ppi.py - Analyzes protein-protein interactions from molecular dynamics trajectories

This script provides functionality to:
- Identify and quantify different types of protein-protein interactions in trajectory data
- Analyze specific interaction types (hydrogen bonds, salt bridges, pi-pi, etc.)
- Calculate interaction persistence/occupancy across trajectory frames
- Generate comprehensive interaction reports in CSV format

NOTE: Side-chains involved in salt-bridges and hydrogen bonds are counted as salt-bridges only.

Usage examples:
- Basic usage: analyze_trajectory_ppi.py cms_file.cms output.csv protein1_asl protein2_asl
- Specific interactions: analyze_trajectory_ppi.py -includeinteraction hbond_sb hydrophobic cms_file.cms output.csv protein1_asl protein2_asl
- Exclude interactions: analyze_trajectory_ppi.py -excludeinteraction water_bridges cms_file.cms output.csv protein1_asl protein2_asl
- Trajectory slice: analyze_trajectory_ppi.py -s 1:100:5 cms_file.cms output.csv protein1_asl protein2_asl

Copyright Schrodinger, LLC. All rights reserved.

Note: To place options before positional arguments, use the -- separator.
Example: analyze_trajectory_ppi.py -includeinteraction hbond_self -- cms_file.cms output.csv protein1 protein2

positional arguments:
  cms_file              Input CMS structure file.
  csv_file              Name of output CSV file.
  protein_asl1          ASL of first protein.
  protein_asl2          ASL of second protein.

options:
  -h, --help            show this help message and exit
  -includeinteraction INTERACTION_TYPE [INTERACTION_TYPE ...]
                        Include only these types of interactions. By default
                        all interaction types (pi-cat, hbond_ss, hbond_bb,
                        salt-bridge, hbond_sb, hbond_self, pi-pi (face-to-face
                        displaced), pi-pi (face-to-face), pi-pi (edge-to-
                        face), water_bridges, hydrophobic, hbond_aromatic_sb,
                        hbond_aromatic_self, hbond_aromatic_ss) are included.
                        Specify multiple interaction types with spaces (NOT
                        commas). Examples: '-includeinteraction hbond_sb
                        hydrophobic salt-bridge' or use multiple flags:
                        '-includeinteraction hbond_sb -includeinteraction
                        hydrophobic'. -includeinteraction should not be used
                        with -excludeinteraction.
  -excludeinteraction INTERACTION_TYPE [INTERACTION_TYPE ...]
                        Exclude these specific types of interactions. These
                        are the same values as in -includeinteraction. Specify
                        multiple types with spaces (NOT commas). Example:
                        '-excludeinteraction water_bridges hydrophobic'.
                        -excludeinteraction should not be used with
                        -includeinteraction.
  -s START:END:STEP     Use the sliced trajectory. We use Python's slice
                        notation. START, END, and STEP should be integer
                        numbers.