Metadata-Version: 2.1
Name: aaindex
Version: 0.0.1
Summary: A Python package 
Home-page: https://github.com/amckenna41/aaindex
Author: MIT
Author-email: amckenna41@qub.ac.uk
License: MIT
Description: # aaindex (In Development)
        ![alt text](https://raw.githubusercontent.com/amckenna41/aaindex/main/images/aaindex_logo.png)
        
        Python package for working with AAIndex database (https://www.genome.jp/aaindex/)
        
        # AAIndex <a name="TOP"></a>
        [![AAIndex](https://img.shields.io/pypi/v/aaindex)](https://pypi.org/project/aaindex/)
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        [![PythonV](https://img.shields.io/pypi/pyversions/pySAR?logo=2)](https://pypi.org/project/aaindex/)
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        Table of Contents
        -----------------
        
          * [Introduction](#introduction)
          * [Requirements](#requirements)
          * [Installation](#installation)
          * [Usage](#usage)
          * [Tests](#tests)
          * [Contact](#contact)
        
        Introduction
        ------------
        
        Requirements
        ------------
        * [Python][python] >= 3.6
        * [numpy][numpy] >= 1.16.0
        * [pandas][pandas] >= 1.1.0
        * [sklearn][sklearn] >= 0.24
        * [requests][requests] >= 2.24.0
        
        
        Installation
        -----------------
        Install the latest version of aaindex using pip:
        
        ```bash
        pip3 install aaindex
        ```
        
        Install by cloning repository:
        ```bash
        git clone https://github.com/amckenna41/aaindex.git
        python3 setup.py install
        ```
        
        
        Usage
        -----
        
        The AAIndex module is made up of the AAIndex class which itself has all the functions/attributes of the package, so when importing the module you have to import the class as well.
        
        ```python
        from aaindex.aaindex import aaindex
        
        ```
        
        ### Get record from AAIndex module
        The AAIndex class offers diverse functionalities for obtaining any element from any record in the database. Each record is stored in json format in a class attribute called <em>aaindex_json</em>. You can search for a particular record by its index/record code, description or reference. You can also get the index category, and importantly its associated amino acid values.
        
        ```python
        from aaindex.aaindex import aaindex
        
        full_record = aaindex['CHOP780206']   #get full AAI record
        ''' Above statement will return -> 
        {'description': 'Normalized frequency of N-terminal non helical region (Chou-Fasman, 1978b)', 'notes': '', 'refs': "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); Kawashima, S. and Kanehisa, M.                     'AAindex: amino acid index database.'  Nucleic Acids Res. 28, 374 (2000).", '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 = aaindex['CHOP780206']['values']
        record_description = aaindex['CHOP780206']['description']
        record_references = aaindex['CHOP780206']['refs']
        
        ```
        
        ### Get category from AAIndex record 
        ```python
        
        """
        Categories: 
        Each AAIndex record is classified into 1 of 8 categories: Charge, Composition, Flexibility, Geometry, Hydrophobic, Meta, 
        Observable, Polar and Secondary Structure. The record categories are parsed from the aaindex_categories.txt file and can be accessed for each record via the get_category_from_record() function.
        """
        category = aaindex.get_category_from_record('CHOP780206')
        
        ```
        
        ### Get total number of AAIndex records
        ```python
        #get total number of records in AAI database
        print(aaindex.get_num_records())
        
        ```
        
        ### Get list of all AAIndex record names
        ```python
        #get list of all AAIndex record names
        print(aaindex.get_record_names())
        
        ```
        
        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.
        
        Tests
        -----
        To run all tests, from the main aaindex folder run:
        ```
        python3 -m unittest discover
        ```
        
        To run main test module, from the main aaindex folder run:
        ```
        python -m unittest tests.test_aaindex -v
        ```
        
        Contact
        -------
        If you have any questions or comments, please contact amckenna41@qub.ac.uk or raise an issue on the [Issues][Issues] tab.
        
        [Back to top](#TOP)
        
        
        [python]: https://www.python.org/downloads/release/python-360/
        [numpy]: https://numpy.org/
        [pandas]: https://pandas.pydata.org/
        [sklearn]: https://scikit-learn.org/stable/
        [requests]: https://docs.python-requests.org/en/latest/
        [Issues]: https://github.com/amckenna41/pySAR/issues
        
        
Platform: UNKNOWN
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: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: Implementation :: PyPy
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: Implementation :: PyPy
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
Classifier: Topic :: Scientific/Engineering :: Mathematics
Description-Content-Type: text/markdown
