Metadata-Version: 2.4
Name: aaindex
Version: 1.2.0
Summary: A lightweight Python software package for accessing the data in the various AAIndex databases, which represent the physicochemical, biochemical and structural properties of amino acids as numerical indices.
Author-email: AJ McKenna <amckenna41@qub.ac.uk>
Maintainer: AJ McKenna
License-Expression: MIT
Project-URL: Homepage, https://github.com/amckenna41/aaindex
Project-URL: Download, https://github.com/amckenna41/aaindex/archive/refs/heads/main.zip
Project-URL: Issue Tracker, https://github.com/amckenna41/aaindex/issues
Project-URL: Documentation, https://aaindex.readthedocs.io/en/latest/
Project-URL: Changelog, https://github.com/amckenna41/aaindex/blob/main/CHANGELOG.md
Keywords: amino acid index,aaindex,bioinformatics,protein engineering,python,pypi,physicochemical properties,biochemical properties,proteins,protein structure prediction,pysar
Classifier: Development Status :: 5 - Production/Stable
Classifier: Environment :: Console
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Healthcare Industry
Classifier: Intended Audience :: Information Technology
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: Implementation :: PyPy
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Mathematics
Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENSE
Provides-Extra: test
Requires-Dist: pytest; extra == "test"
Requires-Dist: pytest-cov; extra == "test"
Requires-Dist: pytest-timeout; extra == "test"
Provides-Extra: docs
Requires-Dist: sphinx; extra == "docs"
Requires-Dist: sphinx-rtd-theme; extra == "docs"
Dynamic: license-file

## Python package for working with the AAindex database (https://www.genome.jp/aaindex/) 

[![AAindex](https://img.shields.io/pypi/v/aaindex)](https://pypi.org/project/aaindex/)
[![pytest](https://github.com/amckenna41/aaindex/workflows/Building%20and%20Testing/badge.svg)](https://github.com/amckenna41/aaindex/actions?query=workflowBuilding%20and%20Testing)
[![PythonV](https://img.shields.io/pypi/pyversions/aaindex?logo=2)](https://pypi.org/project/aaindex/)
[![Platforms](https://img.shields.io/badge/platforms-linux%2C%20macOS%2C%20Windows-green)](https://pypi.org/project/aaindex/)

[![License: MIT](https://img.shields.io/badge/License-MIT-red.svg)](https://opensource.org/licenses/MIT)
[![Issues](https://img.shields.io/github/issues/amckenna41/aaindex)](https://github.com/amckenna41/aaindex/issues)

Table of Contents
-----------------

  * [Introduction](#introduction)
  * [Requirements](#requirements)
  * [Installation](#installation)
  * [Usage](#usage)
  * [Tests](#tests)
  * [Contact](#contact)
  * [License](#license)
  * [References](#References)

Introduction
------------
The AAindex is a database of numerical indices representing various physicochemical, structural and biochemical properties of amino acids and pairs of amino acids 🧬. The AAindex consists of three sections: AAindex1 for the amino acid index of 20 numerical values, AAindex2 for the amino acid mutation matrix and AAindex3 for the statistical protein contact potentials. All data are derived from published literature [[1]](#references). 

This `aaindex` Python software package is a very lightweight way of accessing the data represented in the various AAindex databases, requiring no additional external library installations. Any record within the 3 databases and their associated data/numerical indices can be accessed in one simple command. The package supports all three AAindex databases: AAindex1 (amino acid property indices), AAindex2 (substitution matrices), and AAindex3 (contact potential matrices).

* A quick Colab notebook demo of `aaindex` is available [here][demo]. 
* A **Medium** article that dives deeper into the AAindex and the `aaindex` software itself is available [here][medium].




Background
----------

**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. With the links the user can identify a set of entries describing similar properties An example of the format of an AAindex1 record can be seen within the [aaindex](https://github.com/amckenna41/aaindex/tree/main/aaindex) folder [[1]](#references).

  ```python
  ************************************************************************
  *                                                                      *
  * 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 *
  * //                                                                   *
  ************************************************************************
  ```

**AAindex2:**

The AAindex2 section currently contains 66 amino acid mutation matrices: 47 symmetric matrices and 19 non-symmetric matrices. The format of the entry is almost the same as that of AAindex1 except that it contains 210 numerical values (20 diagonal and 20 × 19/2 off-diagonal elements) for a symmetric matrix and 400 or more numerical values for a non-symmetric matrix (some matrices include a gap or distinguish two states of cysteine). An example of the format of an AAindex2 record can be seen within the [aaindex](https://github.com/amckenna41/aaindex/tree/main/aaindex) folder.

**AAindex3:**

The AAindex3 section contains 47 statistical protein contact potentials and follows the same record format to that of the AAindex2. An example of the format of an AAindex3 record can be seen within the [aaindex](https://github.com/amckenna41/aaindex/tree/main/aaindex) folder.



  ```python  
  ************************************************************************
  *                                                                      *
  * Each entry has the following format.                                 *
  *                                                                      *
  * H Accession number                                                   *
  * D Data description                                                   *
  * R PMID                                                               *
  * A Author(s)                                                          *
  * T Title of the article                                               *
  * J Journal reference                                                  *
  * * Comment or missing                                                 *
  * M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV           *
  *   AA                                                                 *
  *   AR RR                                                              *
  *   AN RN NN                                                           *
  *   AD RD ND DD                                                        *
  *   AC RC NC DC CC                                                     *
  *   AQ RQ NQ DQ CQ QQ                                                  *
  *   AE RE NE DE CE QE EE                                               *
  *   AG RG NG DG CG QG EG GG                                            *
  *   AH RH NH DH CH QH EH GH HH                                         *
  *   AI RI NI DI CI QI EI GI HI II                                      *
  *   AL RL NL DL CL QL EL GL HL IL LL                                   *
  *   AK RK NK DK CK QK EK GK HK IK LK KK                                *
  *   AM RM NM DM CM QM EM GM HM IM LM KM MM                             *
  *   AF RF NF DF CF QF EF GF HF IF LF KF MF FF                          *
  *   AP RP NP DP CP QP EP GP HP IP LP KP MP FP PP                       *
  *   AS RS NS DS CS QS ES GS HS IS LS KS MS FS PS SS                    *
  *   AT RT NT DT CT QT ET GT HT IT LT KT MT FT PT ST TT                 *
  *   AW RW NW DW CW QW EW GW HW IW LW KW MW FW PW SW TW WW              *
  *   AY RY NY DY CY QY EY GY HY IY LY KY MY FY PY SY TY WY YY           *
  *   AV RV NV DV CV QV EV GV HV IV LV KV MV FV PV SV TV WV YV VV        *
  * //                                                                   *
  ************************************************************************
```

Installation
-----------------
Install the latest version of `aaindex` using pip:

```bash
pip3 install aaindex --upgrade
```

Install by cloning the repository:

```bash
git clone https://github.com/amckenna41/aaindex.git
cd aaindex
pip install .
```

Usage
-----
The `aaindex` package is made up of three modules for each AAindex database, with each having a Python class of the same name, when importing the package you should import the required database module:

```python
from aaindex import aaindex1
# from aaindex import aaindex2
# from aaindex import aaindex3
```

## AAIndex1 Usage

### Get record from AAindex1
The AAindex1 class offers diverse functionalities for obtaining any element from any record in the database. The records are imported from a parsed json in the data folder of the package. You can search for a particular record by its record code/accession number or its name/description. You can also get the record category, references, notes, correlation coefficients, PMID and importantly its associated amino acid values:
```python
from aaindex import aaindex1

full_record = aaindex1['CHOP780206']   #get full AAI record
''' full_record ->
{'category': 'sec_struct', 
'correlation_coefficients': {}, 
'description': 'Normalized frequency of N-terminal non helical region (Chou-Fasman, 1978b)', 
'notes': '', 
'pmid': '364941', 
'references': "Chou, P.Y. and Fasman, G.D. 'Prediction of the secondary structure of proteins from their amino acid sequence' Adv. Enzymol. 47, 45-148 (1978)", 
'values': {'-': 0, 'A': 0.7, 'C': 0.65, 'D': 0.98, 'E': 1.04, 'F': 0.93, 'G': 1.41, 'H': 1.22, 'I': 0.78, 'K': 1.01, 'L': 0.85, 'M': 0.83, 'N': 1.42, 'P': 1.1, 'Q': 0.75, 'R': 0.34, 'S': 1.55, 'T': 1.09, 'V': 0.75, 'W': 0.62, 'Y': 0.99}}
'''

#get individual elements of AAindex record
record_values = aaindex1['CHOP780206']['values'] 
record_values = aaindex1['CHOP780206'].values
#'values': {'-': 0, 'A': 0.7, 'C': 0.65, 'D': 0.98, 'E': 1.04, 'F': 0.93, 'G': 1.41, 'H': 1.22, 'I': 0.78, 'K': 1.01, 'L': 0.85, 'M': 0.83, 'N': 1.42, 'P': 1.1, 'Q': 0.75, 'R': 0.34, 'S': 1.55, 'T': 1.09, 'V': 0.75, 'W': 0.62, 'Y': 0.99}

record_description = aaindex1['CHOP780206']['description']
record_description = aaindex1['CHOP780206'].description
#'description': 'Normalized frequency of N-terminal non helical region (Chou-Fasman, 1978b)'

record_references = aaindex1['CHOP780206']['references']
record_references = aaindex1['CHOP780206'].references
#'references': "Chou, P.Y. and Fasman, G.D. 'Prediction of the secondary structure of proteins from their amino acid sequence' Adv. Enzymol. 47, 45-148 (1978)"

record_notes = aaindex1['CHOP780206']['notes']
record_notes = aaindex1['CHOP780206'].notes
#""

record_correlation_coefficients = aaindex1['CHOP780206']['correlation_coefficients']
record_correlation_coefficients = aaindex1['CHOP780206'].correlation_coefficients
#{}

record_pmid = aaindex1['CHOP780206']['pmid']  
record_pmid = aaindex1['CHOP780206'].pmid
#364941

record_category = aaindex1['CHOP780206']['category']
record_category = aaindex1['CHOP780206'].category
#sec_struct
```

### Get total number of AAindex1 records
```python
aaindex1.num_records()
```

### Get list of all AAindex1 record codes
```python
aaindex1.record_codes()
```

### Get list of all AAindex1 record names
```python
aaindex1.record_names()
```

## AAIndex2 Usage
```python
from aaindex import aaindex2

# Get number of records, record codes, and record names
aaindex2.num_records()            # 94
aaindex2.record_codes()           # sorted list of all accession numbers
aaindex2.record_names()           # list of all record descriptions

# Get a full record by accession number
record = aaindex2['ALTS910101']
record.description                # 'The PAM-120 matrix (Altschul, 1991)'
record.matrix                     # nested dict of 20x20 substitution scores

# Look up a pairwise substitution score (symmetric)
aaindex2.get('ALTS910101', 'A', 'R')   # -3.0
aaindex2.get('ALTS910101', 'R', 'A')   # -3.0

# Get just the matrix dict for a record
aaindex2.values('ALTS910101')

# Search records by keyword
aaindex2.search('substitution')   # dict of matching records
```

## AAIndex3 Usage
```python
from aaindex import aaindex3

# Get number of records, record codes, and record names
aaindex3.num_records()            # 47
aaindex3.record_codes()           # sorted list of all accession numbers
aaindex3.record_names()           # list of all record descriptions

# Get a full record by accession number
record = aaindex3['TANS760101']
record.description                # 'Statistical contact potential derived from 25 x-ray protein structures'
record.matrix                     # nested dict of 20x20 contact potential scores

# Look up a pairwise contact potential (symmetric)
aaindex3.get('TANS760101', 'A', 'A')   # -2.6
aaindex3.get('TANS760101', 'A', 'R')   # -3.4

# Get just the matrix dict for a record
aaindex3.values('TANS760101')

# Search records by keyword
aaindex3.search('contact potential')   # dict of matching records
```

Directories 📁
--------------
* `/tests` - unit and integration tests for `aaindex` package.
* `/aaindex` - source code and all required external data files for package.
* `/images` - images used throughout README.
* `/docs` - `aaindex` documentation.
 
Tests 🧪
--------
To run all tests, from the main `aaindex` folder run:
```
python3 -m unittest discover tests
```

Contact ✉️
---------
If you have any questions or comments, please contact amckenna41@qub.ac.uk or raise an issue on the [Issues][Issues] tab.

License
-------
Distributed under the MIT License. See `LICENSE` for more details.  

References
----------
\[1\]: Shuichi Kawashima, Minoru Kanehisa, AAindex: Amino Acid index database, Nucleic Acids Research, Volume 28, Issue 1, 1 January 2000, Page 374, https://doi.org/10.1093/nar/28.1.374 
\[2\]: https://www.genome.jp/aaindex/ 

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[python]: https://www.python.org/downloads/release/python-360/
[aaindex]: https://github.com/amckenna41/aaindex
[requests]: https://requests.readthedocs.io/en/latest/
[numpy]: https://numpy.org/
[PyPi]: https://pypi.org/project/aaindex/
[demo]: https://colab.research.google.com/drive/1dccV_n1BRMiU8W13F9PPXbSaFzvOdQLC?usp=sharing
[medium]: https://medium.com/@ajmckenna69/aaindex-a63de37ec118
[Issues]: https://github.com/amckenna41/aaindex/issues
