PepToCodes (1.1.0) - Peptides to Codes

Script developed to transform the amino acid smiles to one letter code or three letter code for later analysis.

Illustrative image

Requirements

• pandas - a Python package that provides fast, flexible, and expressive data structures designed to make working with "relational" or "labeled" data both easy and intuitive.

• art - ART is a Python lib for text converting to ASCII art fancy. ;-)

Libraries were used in a Miniconda3 environment using python 3.6.13

Instalation

Miniconda3: Installation

pandas:

conda install -c anaconda pandas

art:

conda install -c sepandhaghighi art

How to use

• Download the code and unzip it on the desirable directory

• It is possible to use two databases to analyze aminoacids. One is the native database which only recognizes 20 aminoacids (canonical and isomeric). The other is the Norine Database with 544 aminoacids.

  • To use the native database use the following command:

    python main.py peptocodes True False
    

    To obtain one letter code. And,

    python main.py peptocodes False True
    

    To obtain three letter code.

  • To use the Norine Database use the following command:

    python main.py norine
    

    For now, this database is only available for three letter code analysis.

• Regarding the analysis for string or file:

  • For one aminoacid analysis:

    • Type your peptide smiles as an input

    i.e. NC@@(CCCNC(=N)N)C(=O)NC@@(C@(O)C)C(=O)NC@@(CCCCN)C(=O)NC@@(CCCNC(=N)N)C(=O)O

    • The answer will pop-up at your terminal screen

    i.e. RTKR

      * This example onyl works with the native database.
    

  • For more than one aminoacid analysis:

    • Use the file smiles.txt as example on how to format input data

• Asteriscs in your code answer means the software could not recognize the input. Please, keep in mind that the native database only recognizes 20 aminoacids (canonical and isomeric). If you need a bigger database please use norine option.

Observations

According to its website, Norine database is freely available to everybody, under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0). No changes were made on its structure or data.

Authorship

• Author: Brenda Ferrari (brendaferrari)

Social preview original photo by Brenda Ferrari (brendaferrari)