projet_court/src/dssp.py

import pdb
import sys
from structure import *
from chem import *
import argparse

from datetime import date

def print_dssp(pdb_file, verbose=False, raw_ladd=False):
    # gets export date
    export_date = date.today().strftime("%d/%m/%Y")
      
    ################### OUTPUT ####################
    # print DSSP-style formatted header of PDB file
    print("################### DSSP OUTPUT ####################\n####",
          "Exported on",export_date,
          "\n####################################################")
    for elem in pdb_file.get_header() : 
        print(pdb_file.get_header()[elem], end="")

    # Get preliminary data for print loop
    residues = pdb_file.residues
    bridges = get_bridges(residues)
    ladders = get_ladders(bridges, residues)
    sheets = get_sheets(ladders)  
    helix = build_helix_patterns(residues)
    # iterating over residues
    # print header of table
    print('   # RESIDUE AA  STRUCTURE     BP1   TCO   KAPPA  ALPHA   ' \
    'PHI    PSI    X-CA   Y-CA   Z-CA')
    for i,res in enumerate(residues):
        #res.get_turns(residues, turns)
        kappa = res.get_bends(residues)[0]
        bend_symbol = res.get_bends(residues)[1]
        t_co = res.get_tco(residues)
        alpha = res.get_chirality(residues)[0]
        chirality = res.get_chirality(residues)[1]
        phi = res.get_phi_psi(residues)[0]
        psi = res.get_phi_psi(residues)[1]
        x_ca = res.atoms["CA"].coord_x
        y_ca = res.atoms["CA"].coord_y
        z_ca = res.atoms["CA"].coord_z
        turns = build_turns_patterns(residues)
        turn_3 = print_turn_pattern(residues, res, turns[0])
        turn_4 = print_turn_pattern(residues, res, turns[1])
        turn_5 = print_turn_pattern(residues, res, turns[2])
        helix_3 = print_helix_pattern(residues, res, helix[0])
        helix_4 = print_helix_pattern(residues, res, helix[1])
        helix_5 = print_helix_pattern(residues, res, helix[2])
        if i in bridges.keys():
            bp1 = bridges[i].j
        else:
            bp1 = 0
       
        print('{0: >5}{1: >5}{2: >2}{3: >2}{4: >2}{5: >2}{6: >2}{7: >2}'\
              '{8: >2}{9: >2}{10: >2}{11: >1}{12: >5}{13: >7}{14: >7}' \
              '{15: >7}{16: >7}{17: >7}{18: >7}{19: >7}'\
              '{20: >7}'.format(i+1, res.resid,
                                res.chain_id,
                                res.res_letter,
                                helix_3, helix_4,
                                helix_5, turn_3,
                                turn_4, turn_5, bend_symbol,
                                chirality, bp1,round(t_co, 3),
                                round(kappa,1), round(alpha, 1),
                                round(phi, 1), round(psi,1),
                                round(x_ca,1), round(y_ca,1),
                                round(z_ca,1)))
    if(raw_ladd):
        raw_ladders_print(ladders)

parser = argparse.ArgumentParser()
if(len(sys.argv)<2):
    print("Not enough arguments! Run with --help to learn more about proper"
          "call structure and parameters.")
else:
    parser.add_argument("file", type=str, help="input file in PDB format")
    parser.add_argument("-v","--verbose", help="add ladders verbose output",
                        action="store_true")
    args = parser.parse_args()
    pdb_file = pdb.PDBFile(sys.argv[1])
    if(args.verbose):
        print_dssp(pdb_file, raw_ladd=True)
    else:
        print_dssp(pdb_file)