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peptide_function.py
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from __future__ import division
# Goal: Make a fragment list of peptides from proteins
# Author: Bruno Santos
# Comment: Viva la revolucion.
import argparse
import csv
import sys
import math
import pandas as pd
import time
import pickle
import seaborn as sns
import matplotlib.pyplot as plt
from classes import *
from sharedstuff import *
for arquivo in sequencia:
seq_string = sequencia
while '' in seq_string:
seq_string.remove('')
setting_protein.nome_proteina(arquivo)
setting_protein.nested_dic(seq_string)
for i in range(0, len(arquivo)):
exec("dic_frag%d = %s" % (i + 1, {}));
##----------------------------------------------------------------------------------------------
## Calcular massa monoisotópica
##----------------------------------------------------------------------------------------------
#Dicionário contém lista de resíduos (aa - 18 Da)
setting_protein.monoisotopic_mass(seq_string)
##----------------------------------------------------------------------------------------------
## Isoeletric point
##----------------------------------------------------------------------------------------------
setting_peptide.pka_residues3(seq_string)
setting_peptide.resulting_charge_ph0_3(seq_string)
setting_peptide.charged_residues_quantity_3(seq_string)
setting_peptide.CR_list_3(seq_string)
setting_peptide.pI_3(seq_string)
##----------------------------------------------------------------------------------------------
## Calcular massa monoisotópica dos peptideos
##----------------------------------------------------------------------------------------------
setting_peptide.massa_amidada_3(seq_string)
setting_peptide.m_h_3(seq_string)
##----------------------------------------------------------------------------------------------
## Hydrophobicity Calculation - GRAVY
##----------------------------------------------------------------------------------------------
setting_peptide.hydropathicity_3(seq_string)
setting_peptide.hydrophobic_moment_3(seq_string)
##----------------------------------------------------------------------------------------------
## More
##----------------------------------------------------------------------------------------------
setting_peptide.aromatic_3(seq_string)
setting_peptide.cf_alpha_3(seq_string)
setting_peptide.cf_beta_3(seq_string)
setting_peptide.cf_turn_3(seq_string)
setting_peptide.volume_3(seq_string)
setting_peptide.charge_3(seq_string)
setting_peptide.pct_buried_3(seq_string)
setting_peptide.asa_mainchain_3(seq_string)
setting_peptide.asa_mainchain_nonpolar_3(seq_string)
setting_peptide.asa_mainchain_polar_3(seq_string)
##----------------------------------------------------------------------------------------------
## Amino acids residues percentage
##----------------------------------------------------------------------------------------------
setting_peptide.aa_percentage_3(seq_string)
##----------------------------------------------------------------------------------------------
## New dictionary with the attributes that shall be exported
##----------------------------------------------------------------------------------------------
setting_peptide.nested_dic3_2(seq_string)
setting_peptide.attributes_exportation_3(seq_string)