projet_court_nz/src/projet8.py

#!/bin/python3

import pandas as pd
import numpy as np
import pbxplore as pbx
import sys

class Conformations:
    """
    An instance of the class conformations contains differents conformations of
    the same protein, encoded as 1D sequences of protein bloc, in a pandas
    dataframe.
    """
    pass

    def __init__(self, filename):
        """
        df : pd.DataFrame object
        Each row of the dataframe is a conformation and each column a position
        of the sequence.
        """
        self.df = pd.DataFrame()
        for chain_name, chain in pbx.chains_from_files([filename]): 
                dihedrals = chain.get_phi_psi_angles() 
                pb_seq = pbx.assign(dihedrals) 
                self.df = self.df.append(pd.Series(list(pb_seq)), ignore_index=True)
    
    def dissimilarity(self):
        """
        computes the dissimilarity matrix of the intance's df
        """
        matrix = pd.DataFrame(index=np.arange(self.df.shape[0]),
                              columns=np.arange(self.df.shape[0]))
        matrix = matrix.fillna(0)
        return matrix

if __name__ == "__main__":
    if len(sys.argv) != 2:
        print("Error : usage $ python3 projet8 md.pdb")
        exit()

    confs = Conformations(sys.argv[1])


    print(confs.df)