2019-Research-R-E

This repo contain all of Hieu's script and Supercharging Algorithm.

Inside Main.py, you will find:

• Super_seq class

This class is made to classify all the sequence as an object with features (sequence, charge, file location,etc) and functions related to supercharging the protein.

       Parameters

    seq a str format of the sequence of the protein

    __raw_seq raw format of the sequence (before formatting)

    charge a list that contain the charge of every 20 amino acid

    consurf (work in-progress) read the consurf scoring file obtained from the server of the protein

    name name of the protein ex) TNFb

    location location of the file containing the protein (default "")

       Functions

    format_seq format the input string of sequence

    seq_charge obtain a list of the total charge of every 20 amino acid from the input sequence

    consurf_reader read the scoring of the input .grade file of the protein

    display_lcd draw the linear charge density graph of the protein

    compare_lcd draw the linear charge density graph of the protein and another protein

    ---------------------------------------------

• Functions outside Super_seq class

    binding_site_converter convert input binding site into a list ex) "10-14+17+19+21-23" -> [10,11,12,13,14,17,19,21,22,23]

    the rest of the function is still in early development stages