projest 0.0.7

Description:

projest 0.0.7

Projest
Made by [Esther Vendrell]
Last updated: July 2019
Introduction
Projest is my first program. Consist in introduce the name of a protein and obtain information about that as the most similar protein, the differents models it has or the atoms. All the information you can obtain comes from: https://www.rcsb.org/
Description
The main file is protein.py. In spite of main functions are in extract_atoms_information.py - load protein pdb or load protein fasta - the rest of functions are in protein.
In this way we will have functions directly linked to protein like:
Protein("2ki5").get_similar_protein() -> We will obtain fasta file, pdb file, all the information of protein in mongodb (in the init) and the similar protein of each chain.
Functions
There are 7 functions:

get_sequence_aminoacids: in Protein. Returns a list with chain and the sequence of aminoacids (1 letter). From fasta file.
get_chain_list: in Protein. Return a list with the differents chains there are.
get_aminoacid_list: in Protein. Return a list with the differents aminoacids (3 letters) with the differents sequence numbers classified in chains
get_similar_protein: in Protein. Return a dictionary with differents chains and the most similar protein of that chain of the protein.
general_dictionary: in Protein. Any return. It inserts in mongodb all the information classified. It is not callable.
load_protein_pdb: in extract_atoms_information. Returns the pdb file of the protein. Download the pdb file of the protein in the same directory of the files.
load_protein_fasta: in extract_atoms_information. Returns the fasta file of the protein.Download the fasta file of the protein in the same directory of the files.

MongoDB
I could have used an other structure to upload all the information to MongoDB:
Protein - Model - residue_sequence_number - atom_number - information atom.
Class Model:
def init(self, model_identifier, model_dict):
self.model_identifier = model_identifier
self.chain_list = []
for chain_identifier, value in model_dict:
self.chain_list.append(Chain(chain_identifier))
In this way we obtain information from mongodb. This would be easier but I haven't had enough time since I have realized.
The structure of my project is:
Portein - Model - residue_name - residue_sequence_number - element_name - atom_name - information atom.
This is more easy to understand the information we are getting and classified it. This is why I have used this structure. Visually is better but for obtaining this information internally it is worse.