Amino-Acid Property Profiles (AAindex)

sparrow ships the AAindex1 database: 500+ published indices that each assign a numerical value to every amino acid (hydropathy, volume, secondary-structure propensity, flexibility, and many more). sparrow.protein.Protein.linear_property_profile() maps a sequence onto any of these indices and returns a smoothed, windowed profile – the property-based analogue of linear_sequence_profile().

Quick start

from sparrow import Protein

p = Protein("MEEEKKKKSSSTTTDDDQQQQNNNNGGGGSSSS")

# window-averaged Kyte-Doolittle hydropathy along the sequence
hydropathy = p.linear_property_profile("hydropathy-kyte-1982", window_size=9)

# any index works; e.g. a volume or flexibility scale
volume = p.linear_property_profile("KYTJ820101")  # accession also accepted

linear_property_profile takes the same arguments as linear_sequence_profile (window_size, end_mode, smooth); only mode differs – here it selects an AAindex property.

Choosing an index (identifiers)

Each index is addressable two ways:

• a readable slug of the form <meaning>-<first-author>-<year>, where <meaning> is the first informative word of the index description (for example hydropathy-kyte-1982); and

• the canonical AAindex accession (for example KYTJ820101).

When several indices share the same meaning, author, and year, a -N increment is appended to every member of that group (ordered by accession), so identifiers are always unique – for example positional-aurora-1998-1 through positional-aurora-1998-20.

Discovering indices programmatically:

from sparrow.data import aaindex

# list every (identifier, accession, description)
all_indices = aaindex.list_property_indices()

# metadata for one index
aaindex.get_property_metadata("hydropathy-kyte-1982")

# the raw amino-acid -> value mapping
aaindex.get_property_values("hydropathy-kyte-1982")

Notes

• A few indices have no value for one or more residues in the source database. Requesting such an index for a sequence that contains an affected residue raises a ProteinException rather than returning a misleading number.

• The profile is the mean index value within each window_size window; end_mode and smooth behave exactly as in linear_sequence_profile.

Module reference

Access to the AAindex1 amino-acid property database.

AAindex1 is a collection of 500+ published indices that each map the 20 standard amino acids to a numerical value (hydropathy, volume, secondary-structure propensity, etc.). The raw database ships with sparrow as sparrow/data/properties/aaindex1.json; this module loads it and exposes each index under a readable, unique identifier.

Identifier scheme

Every index is addressable by a slug of the form:

<meaning>-<first-author>-<year>

where <meaning> is the first informative word of the index description (for example hydropathy). When several indices share the same meaning, author, and year, a -N increment is appended to every member of that group (ordered by accession), so identifiers are always unique, e.g. positional-aurora-1998-1 through positional-aurora-1998-20. The canonical AAindex accession (e.g. KYTJ820101) is also always accepted.

Use list_property_indices() to enumerate all available identifiers.

list_property_indices()

List every available property index.

Returns:

Sorted list of (identifier, accession, description) tuples.

Return type:

list[tuple[str, str, str]]

resolve_identifier(identifier)

Resolve a property identifier or accession to its AAindex accession.

Parameters:

identifier (str) – A <meaning>-<author>-<year>[-N] slug or a raw AAindex accession.

Returns:

The canonical AAindex accession.

Return type:

str

Raises:

sparrow.sparrow_exceptions.SparrowException – If the identifier matches neither a known slug nor an accession.

get_property_values(identifier)

Return the amino-acid -> value mapping for a property index.

Parameters:

identifier (str) – Property slug or AAindex accession.

Returns:

Mapping from each of the 20 standard amino acids to its value. Some indices have None for one or more residues (missing in the source database).

Return type:

dict[str, float or None]

get_property_metadata(identifier)

Return descriptive metadata for a property index.

Parameters:

identifier (str) – Property slug or AAindex accession.

Returns:

Keys: identifier (canonical slug), accession, description, authors, reference, title, journal.

Return type:

dict

Property Index Reference

The full list of available indices is below. The Description is the original AAindex summary of what each score measures; use the Identifier (or Accession) as the mode argument to linear_property_profile().