AAindex1
The AAindex1 section currently contains 566 amino acid indices representing the various physicochemical, structural and biochemical properties of amino acids. Each entry consists of an accession number, a short description on the index, the reference information, notes, PMID (pubmed ID) and the numerical values for the property of 20 amino acids. In addition, it contains neighbour information; namely, the cross-links to other entries with an absolute value for the correlation coefficient of 0.8 or larger, allowing users to identify entries describing similar properties.
Record format
************************************************************************
* *
* H Accession number *
* D Data description *
* R Pub med article ID (PMID) *
* A Author(s) *
* T Title of the article *
* J Journal reference *
* * Comment or missing *
* C Accession numbers of similar entries with the correlation *
* coefficients of 0.8 (-0.8) or more (less). *
* Notice: The correlation coefficient is calculated with zeros *
* filled for missing values. *
* I Amino acid index data in the following order *
* Ala Arg Asn Asp Cys Gln Glu Gly His Ile *
* Leu Lys Met Phe Pro Ser Thr Trp Tyr Val *
* // *
************************************************************************
- class aaindex.aaindex1.AAIndex1[source]
Bases:
objectPython parser for AAindex1: Amino Acid Index Database.
The AAindex is a database of numerical indices representing various physicochemical and biochemical properties of amino acids. This class stores the amino acid index of 20 numerical values for the 20 amino acids — AAindex1 (http://www.genome.jp/aaindex/).
- aaindex_module_path
Absolute path to the aaindex package directory.
- data_dir
Subdirectory name containing raw and cached data files.
- aaindex_filename
Base filename for this database (no extension).
- aaindex_json
Parsed database keyed by accession number.
- categories
Dict mapping each record code to its category.
- last_updated
Date string of the last published database update.
- __getitem__(record_code: str) Map[source]
Return a record by accession number wrapped in a Map (dot-notation dict).
- Parameters:
record_code – AAindex accession number (case-insensitive, leading/trailing whitespace is stripped).
- Returns:
Record data as a Map, accessible via dict or dot notation.
- Raises:
TypeError – If record_code is not a string.
ValueError – If record_code is not found in the database.
- amino_acids() list[str][source]
Return sorted list of amino acid single-letter codes.
Includes the
-placeholder for absent/gap amino acids.- Returns:
Sorted list of amino acid codes including
-.
- get_all_categories(category_file: str = 'aaindex_to_category.txt') dict[source]
Return dict mapping every record code to its category.
Delegates to
_parse_categories().- Parameters:
category_file – Bare filename or absolute path of the category mapping file. Defaults to
aaindex_to_category.txtin the data directory.- Returns:
Dict mapping each record code to its category string.
- get_record_by_category(category: str) dict[source]
Return all records belonging to a given category.
- Parameters:
category – Category name to filter records by (case-insensitive).
- Returns:
Dict of matching records keyed by accession number.
- Raises:
TypeError – If category is not a string.
- num_records() int[source]
Return the total number of records in the database.
- Returns:
Number of records as int.
- parse_aaindex() dict[source]
Deprecated: use _parse_aaindex() instead.
Deprecated since version This: method is an internal implementation detail and will be removed in a future version.
- parse_categories(aaindex_category_file: str = 'aaindex_to_category.txt') dict[source]
Deprecated: use _parse_categories() instead.
Deprecated since version This: method is an internal implementation detail and will be removed in a future version.
- record_codes() list[str][source]
Return sorted list of all accession numbers in the database.
- Returns:
Sorted list of accession number strings.
- record_names() list[str][source]
Return a list of description strings for all records.
- Returns:
List of description strings in database insertion order.
- search(query: str | list[str]) dict[source]
Search records by keyword(s) across all text fields.
Searches the description, accession code, PMID, references, and notes fields of each record. Matching is case-insensitive. Results are returned sorted by accession number.
- Parameters:
query – Keyword string or list of keyword strings.
- Returns:
Dict of matching records keyed by accession number, sorted alphabetically. Returns an empty dict if no records match.
- Raises:
TypeError – If query is not a str or list.
- values(record_code: str) dict[source]
Return the amino acid values dict for a given record.
Shortcut to avoid accessing the full record when only the values are needed.
- Parameters:
record_code – AAindex accession number.
- Returns:
Dict of amino acid values for the specified record.
- Raises:
ValueError – If record_code is not found in the database.
References
[1] Kawashima, S. and Kanehisa, M.; AAindex: amino acid index database. Nucleic Acids Res. 28, 374 (2000).