These tools analyze the lifetimes and transition kinetics of hydrogen bonds and salt bridges observed during molecular dynamics simulations. It quantifies how long each contact persists, how frequently it forms and breaks, and reports kinetic parameters such as average lifetime, formation rate, and breaking rate.

• Objective: Characterize the stability and turnover dynamics of specific residue–residue interactions.
• Process:
  • Loads binary interaction matrices (e.g., hbonds_*.csv, salt_bridges_*.csv) created by the ▶️ (Run First) Extract Pairwise Interaction from Trajectory tool.
  • For each contact, calculates:
    • Average lifetime: Mean duration of continuous presence.
    • Formation rate: Number of formation events per unit time.
    • Breaking rate: Number of dissociation events per unit time.
    • Fraction of simulation time: Proportion of frames the interaction is present.
  • Applies a user-defined threshold to exclude low-occupancy interactions.
  • Visualizes these properties using bar plots.

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• Requires binary contact files (hbonds_*.csv, salt_bridges_*.csv) generated from the extraction tool.
• Selection labels and interaction mode must match those used in the extraction step.

• Selection Labels:

  • sel1_name, sel2_name: Used to locate the corresponding contact files.

• Interaction Mode:

  • interaction_mode: Must be consistent with previous analysis steps (interchain, intrachain, or both).

• Simulation Timing:

  • time_total: Total duration of the simulation.
  • time_unit: Time units for output (ns, ps, µs, etc.).

• Contact Filtering:

  • min_contact_percentage: Only interactions present in at least this percentage of frames are included.

• Plot Settings:

  • fig_width, min_fig_height, fig_height_factor: Control plot dimensions.
  • bar_color_palette: Sets bar color theme.
  • yticks_font_size, yticks_rotation: Format y-axis labels.

• Axis Labels:

  • lifetime_xlabel, formation_xlabel, breaking_xlabel: X-axis labels for each kinetic plot, auto-updated with selected time_unit.

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• CSV Summary:

  • <interaction_type>_<name>.csv: Table listing residue pairs and their lifetime statistics.
  • <interaction_type>_kinetics_<name>.csv: Table listing residue pairs and their lifetime statistics.

• Plots:

  • <interaction_type>_lifetime_bar_plot_<name>.png: Average lifetime per interaction.
  • <interaction_type>_formation_rate_bar_plot_<name>.png: Rate of bond formation.
  • <interaction_type>_breaking_rate_bar_plot_<name>.png: Rate of bond breaking.

• Console Output:

  • Prints warnings for missing or low-occupancy contacts.
  • Displays kinetic summary in a formatted table.
  • Notes on special cases like always-formed or never-reformed bonds.

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• Average Lifetime:

  • Longer lifetimes suggest more stable or persistent interactions.
  • Shorter lifetimes reflect transient contacts or dynamic rearrangements.

• Formation and Breaking Rates:

  • High formation rates indicate frequent interaction onset.
  • Low breaking rates imply sustained interactions once formed.
  • Zero rates may reflect contacts that only form once or never reform.

• Occupancy Threshold:

  • The min_contact_percentage helps filter out noisy, low-importance contacts.
  • Setting it too low may clutter plots with unstable interactions.

• Sidechain Interactions:

  • Residue labels with * indicate H-bonds involving protein side chains.

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• Scenario: Identify long-lived H-bonds between a ligand and protein.
• Selections:
  • sel1 = 'protein'
  • sel2 = 'resname LIG', sel2_is_ligand = True
• Observation:
  • A few residue pairs exhibit average lifetimes >100 ns and low breaking rates.
• Interpretation:
  • These are likely anchoring interactions essential for ligand affinity and can guide rational drug optimization.

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• Scenario: Assess how a mutation affects salt bridge stability at an interface.
• Selections:
  • sel1 = 'segid A'
  • sel2 = 'segid B'
• Observation:
  • In the wild-type, certain salt bridges show high occupancy and low breaking rates. In the mutant, they are short-lived or absent.
• Interpretation:
  • Suggests that the mutation weakens electrostatic coupling, which may impact folding, function, or binding energetics.

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• Scenario: Track interdomain H-bond exchange during a dynamic event.
• Selections:
  • sel1 = 'segid NTD'
  • sel2 = 'segid CTD'
• Observation:
  • Several contacts have short lifetimes but high formation rates.
• Interpretation:
  • Indicates rapid bond turnover consistent with flexible hinge motion or conformational switching between structural states.

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• Time Calibration:

  • Ensure time_total and time_unit match your simulation settings.

• Labeling Consistency:

  • Always match selection names and interaction modes with previous tools to locate the correct input files.

• Threshold Tuning:

  • Adjust min_contact_percentage to balance inclusion of key contacts versus plot clarity.

• Interpret Carefully:

  • Long lifetimes with low rates suggest persistent contacts.
  • High rates with short lifetimes point to dynamic and flexible regions.

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