AAMut.run

AAMut.run(from_aa=None, to_aa=None, scales=None)[source]

Compute the signed per-scale impact of amino acid substitutions.

For every from_aa -> to_aa pair and every scale, the impact is the signed difference delta = df_scales.loc[to_aa, scale] - df_scales.loc[from_aa, scale]. With both from_aa and to_aa unset, all 20x19 ordered substitution pairs are returned (a long, AAontology-annotated substitution table).

Parameters:

from_aa (str or list of str, optional) – Amino acid(s) to substitute from. If None, all canonical amino acids are used.
to_aa (str or list of str, optional) – Amino acid(s) to substitute to. If None, all canonical amino acids are used.
scales (list of str, optional) – Subset of scale ids to evaluate. If None, all scales of df_scales are used.

Returns:

df_impact – Tidy substitution-impact table with columns from_aa, to_aa, scale_id, category, subcategory, delta (signed), and abs_delta (magnitude).

Return type:

pd.DataFrame, shape (n_pairs * n_scales, 7)

Examples

AAMut quantifies how substituting one amino acid for another shifts each physicochemical scale, independent of any sequence or task. :meth:AAMut.run returns a tidy per-scale substitution-impact table; here we restrict to the M -> V / M -> A substitutions.

import aaanalysis as aa
aamut = aa.AAMut()
df_impact = aamut.run(from_aa="M", to_aa=["V", "A"])
aa.display_df(df_impact, n_rows=10, show_shape=True)

DataFrame shape: (1172, 7)

	from_aa	to_aa	scale_id	category	subcategory	delta	abs_delta
1	M	V	ANDN920101	Structure-Activity	Backbone-dynamics (-CH)	-0.704000	0.704000
2	M	V	ARGP820101	Polarity	Hydrophobicity	0.053000	0.053000
3	M	V	ARGP820102	Polarity	Amphiphilicity (α-helix)	-0.500000	0.500000
4	M	V	ARGP820103	ASA/Volume	Buried	-0.645000	0.645000
5	M	V	BEGF750101	Conformation	α-helix	-0.191000	0.191000
6	M	V	BEGF750102	Conformation	β-sheet	0.000000	0.000000
7	M	V	BEGF750103	Conformation	β-turn	-0.450000	0.450000
8	M	V	BHAR880101	Structure-Activity	Flexibility	0.365000	0.365000
9	M	V	BIGC670101	ASA/Volume	Volume	-0.128000	0.128000
10	M	V	BIOV880101	ASA/Volume	Buried	-0.003000	0.003000

Leaving from_aa / to_aa unset returns all 20x19 ordered pairs; scales restricts to a subset of scale ids.