Comparison and Plotting Reference

Use this page when you need lookup information for polyzymd compare, comparison.yaml, output files, or the plotting workflow.

Comparison Project Layout

polyzymd compare init -n my_study creates a workspace like this:

my_study/
├── comparison.yaml
├── results/
├── figures/
└── structures/

Core comparison.yaml Fields

name: "polymer_stability_study"
description: "Optional human-readable summary"
control: "No Polymer"  # optional

conditions:
  - label: "No Polymer"
    config: "../no_polymer/config.yaml"
    replicates: [1, 2, 3]

defaults:
  equilibration_time: "10ns"

analysis_settings:
  rmsf:
    selection: "protein and name CA"

comparison_settings:
  rmsf: {}

Stable Analysis Keys

Stable release workflows for v1.2.0:

  • rmsf

  • contacts

  • distances

  • catalytic_triad

  • secondary_structure

Experimental but still available:

  • binding preference through contacts

  • exposure

  • binding_free_energy

  • polymer_affinity

Path Rules

  • Relative paths in config: are resolved relative to comparison.yaml

  • Absolute paths are used as-is

  • replicates must be an explicit list such as [1, 2, 3]

Commands

Command

Purpose

polyzymd compare init -n NAME

Create a comparison workspace

polyzymd compare validate

Check comparison.yaml before running

polyzymd compare run TYPE

Run a single comparison through the registry

polyzymd compare run-all

Run every enabled comparison in one pass

polyzymd compare plot-all

Generate configured figures

polyzymd compare plot-all --list-available

List available plots and experimental labels

Common Stable Commands

polyzymd compare run rmsf
polyzymd compare run contacts
polyzymd compare run distances
polyzymd compare run triad
polyzymd compare run-all
polyzymd compare plot-all

Experimental Commands

polyzymd compare exposure
polyzymd compare binding-free-energy
polyzymd compare polymer-affinity

These remain callable, but PolyzyMD labels them as experimental in CLI output, docs, and generated figures.

Output Locations

  • comparison JSON files are written to results/

  • figures are written under the configured plot_settings.output_dir

  • default project scaffolds create a figures/ directory next to comparison.yaml

Typical result filenames:

results/rmsf_comparison_<study>.json
results/contacts_comparison_<study>.json
results/distances_comparison_<study>.json
results/triad_comparison_<study>.json

Plotting Smoke Test

For a final smoke test after comparisons finish:

polyzymd compare plot-all --list-available
polyzymd compare plot-all

Statistical Terms

  • p-value: significance of the observed difference under the null hypothesis

  • Cohen's d: effect size magnitude

  • ANOVA: omnibus test across multiple conditions

  • SEM: standard error of the mean across replicates

For interpretation guidance rather than lookup, see: