Analysis Plugin Settings Reference

This page is a complete YAML key reference for plugin settings under comparison.yaml:

plugins:
  <plugin_name>:
    ...settings...

Use this as a lookup table for field names, types, defaults, and meanings.

FDR thresholds for comparison workflows are configured through top-level defaults.fdr_alpha in comparison.yaml where supported, not through plugin-local settings unless a plugin explicitly lists its own fdr_alpha field below.

rmsf

Key	Type	Default	Description
selection	str	"protein and name CA"	MDAnalysis selection used for RMSF calculation
reference_mode	str	"centroid"	Reference mode: centroid, average, frame, or external
reference_frame	int | null	null	Frame number used when reference_mode: frame (1-indexed)
reference_file	str | null	null	External PDB path used when reference_mode: external
alignment_selection	str	"protein and name CA"	Selection used for trajectory alignment
centroid_selection	str	"protein"	Selection used to find centroid frame

catalytic_triad

Key	Type	Default	Description
name	str	"catalytic_triad"	Name of the triad/active-site definition
pairs	list[TriadPairSettings]	required	Distance pairs to monitor
threshold	float	3.5	Contact threshold in Å
description	str | null	null	Optional human-readable description

TriadPairSettings entries in pairs:

Key	Type	Default	Description
label	str	required	Human-readable pair name
selection_a	str	required	First atom/point selection
selection_b	str	required	Second atom/point selection

distances

Key	Type	Default	Description
threshold	float | null	3.5	Global distance threshold (Å) for contact-style state analysis
pairs	list[DistancePairSettings]	[] (must be non-empty)	Distance pairs to monitor
use_pbc	bool	true	Use minimum-image PBC-aware distances
align_trajectory	bool	true	Align trajectory before distance calculations
alignment_selection	str	"protein and name CA"	Selection for alignment
alignment_mode	str	"centroid"	Alignment reference mode: centroid, average, or frame
alignment_frame	int | null	null	Frame index (1-indexed) when alignment_mode: frame

DistancePairSettings entries in pairs:

Key	Type	Default	Description
label	str	required	Human-readable pair name
selection_a	str	required	First atom/point selection
selection_b	str	required	Second atom/point selection
threshold	float | null	null	Per-pair threshold override (falls back to global threshold)
below_label	str | null	null	Display label for below-threshold state
above_label	str | null	null	Display label for above-threshold state

contacts

Key	Type	Default	Description
polymer_selection	str	"chainid C"	MDAnalysis selection for polymer atoms
protein_selection	str	"chainid A"	MDAnalysis selection for protein atoms
cutoff	float	4.5	Contact cutoff distance in Å
polymer_types	list[str] | null	null	Optional polymer residue-name filter
grouping	str	"aa_class"	Grouping mode: aa_class, secondary_structure, or none
compute_residence_times	bool	true	Compute aggregate residence-time summaries and plots; per-replicate contact events remain stored when disabled
protein_groups	dict[str, list[int]] | null	null	Custom residue groups, e.g. {name: [resid, ...]}
protein_partitions	dict[str, list[str]] | null	null	Partition definitions over custom protein_groups
fdr_alpha	float	0.05	Benjamini-Hochberg false-discovery-rate alpha
min_effect_size	float	0.5	Minimum Cohen’s d highlighted in output
top_residues	int	10	Number of top-contact residues shown in summaries

secondary_structure

Key	Type	Default	Description
chain_id	str	"A"	Protein chain letter to analyze (PolyzyMD convention: chain A)

sasa

Key	Type	Default	Description
runs	list[SASARunSettings]	[] (must be non-empty)	SASA runs to compute
probe_radius_nm	float	0.14	MDTraj Shrake-Rupley probe radius (nm)
n_sphere_points	int	960	MDTraj Shrake-Rupley sphere point count
chunk_size	int	100	Frames per chunk for SASA computation

SASARunSettings entries in runs:

Key	Type	Default	Description
label	str	required	Human-readable run label
target_selection	str	required	Selection whose SASA is reported
context_selection	str | null	null	Environment/context selection for SASA computation (null defaults to target_selection)
stride	int	1	Frame stride (1 means every frame)

hydrogen_bonds

Key	Type	Default	Description
groups	dict[str, str]	{protein: "chainid A", polymer: "chainid C"}	Named MDAnalysis selections used by summaries
summaries	list[HydrogenBondSummarySettings]	[{name: protein_polymer, between: [protein, polymer]}]	Summary definitions to compute
distance_cutoff	float	3.0	Donor-acceptor cutoff (Å)
angle_cutoff	float	150.0	D-H…A angle cutoff (degrees)
update_selections	bool	true	Re-evaluate selections each frame
top_n_pairs	int	15	Number of top residue pairs reported
allow_empty_groups	bool	true	Warn/skip empty groups instead of raising
allow_overlapping_composition	bool	false	Allow overlapping composition partitions (otherwise raise)
composition	HydrogenBondCompositionSettings | null	null	Optional partitioning for composition analysis
timestep_ps	float | null	null	Optional timestep override (ps) for time-axis plots

Time-axis plots assume uniformly saved frames. PolyzyMD maps frame index to time as frame_index * timestep_ps; variable-timestep concatenated trajectories are not supported.

HydrogenBondSummarySettings entries in summaries:

Key	Type	Default	Description
name	str	required	Unique summary name
between	tuple[str, str] | null	null	Cross-group summary mode
within	str | null	null	Intra-group summary mode

Exactly one of between or within must be set for each summary.

Hydrogen detection uses MDAnalysis HydrogenBondAnalysis with hydrogens selected as (<group union>) and element H; explicit hydrogens and reliable element metadata are required for meaningful counts.

HydrogenBondCompositionSettings:

Key	Type	Default	Description
partitions	dict[str, str]	{}	Named composition partitions as MDAnalysis selections

rg

Key	Type	Default	Description
runs	list[RgRunSettings]	[] (must be non-empty)	Named Rg runs to compute

RgRunSettings entries in runs:

Key	Type	Default	Description
label	str	required	Human-readable run label
selection	str	required	MDAnalysis selection for Rg calculation
calculation_mode	"selection" | "fragments"	"selection"	Whole-selection vs fragment-reduced Rg mode
fragment_weighting	"equal" | "mass"	"equal"	Fragment reduction weighting (fragment mode)
save_fragment_distribution	bool	true	Save per-fragment distribution sidecar outputs
histogram_bins	int	50	Histogram bins for fragment distribution summaries

rmsd

Key	Type	Default	Description
runs	list[RMSDRunSettings]	[] (must be non-empty)	Named RMSD runs to compute

RMSDRunSettings entries in runs:

Key	Type	Default	Description
label	str	required	Human-readable run label
selection	str	"protein and name CA"	Selection used for RMSD calculation
alignment_selection	str	"protein and name CA"	Selection used for alignment
reference_mode	str	"centroid"	Reference mode: centroid, average, frame, or external
reference_frame	int	0	0-indexed frame index for reference_mode: frame
reference_file	str | null	null	External PDB path for reference_mode: external
centroid_selection	str | null	null	Optional centroid-mode selection (falls back to alignment_selection)