Source code for

#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Python parser to 3dna <>.


  # install the code from
  Create a copy of the (remove "_sample") present in rna-tools/rna_tools/tools/rna_x3dna folder.
  Edit this line :
  BINARY_PATH = <path to your x3dna-dssr file>
  matching the path with the path of your x3dna-dssr file.
  e.g. in my case: BINARY_PATH = ~/bin/x3dna-dssr.bin

For one structure you can run this script as::

    [mm] py3dna$ git:(master) ✗ ./ test_data/1xjr.pdb
    >1xjr nts=47 [1xjr] -- secondary structure derived by DSSR

For multiple structures in the folder, run the script like this::

    [mm] py3dna$ git:(master) ✗ ./ test_data/*
    >1xjr nts=47 [1xjr] -- secondary structure derived by DSSR
    >6TNA nts=76 [6TNA] -- secondary structure derived by DSSR
    >rp2_bujnicki_1_rpr nts=100 [rp2_bujnicki_1_rpr] -- secondary structure derived by DSSR

.. warning:: This script should not be used in this given form with Parallel because it process output files from x3dna that are named always in the same way, e.g. dssr-torsions.txt. #TODO

import re
import argparse

from subprocess import Popen, PIPE
import os
from rna_tools.rna_tools_config import X3DNA, X3DNA_FP
# x3dna-dssr-64bit

[docs] class x3DNAMissingFile(Exception): pass
[docs] def get_parser(): parser = argparse.ArgumentParser( description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter) parser.add_argument('-c', '--compact', action='store_true') parser.add_argument('-x', '--rerun', action='store_true') parser.add_argument('-s', '--show', action='store_true', help="show results") parser.add_argument('--pymol', action='store_true', help='get resi to color code puckers in PyMOL') parser.add_argument('-l', '--show-log', action='store_true', help="show full log") parser.add_argument('-v', '--verbose', action='store_true', help="show full log") parser.add_argument('files', help='file', nargs='+') return parser
[docs] class x3DNA(object): """ Atributes: **curr_fn** **report** """ def __init__(self, pdbfn, show_log=False): """Set self.curr_fn based on pdbfn""" self.curr_fn = pdbfn self.run_x3dna(show_log) self.clean_up() def __get_report(self): """Off right now. Run find_pair ..warning:: To get modification use get_modifications() """ cmd = X3DNA_FP + ' ' + self.curr_fn + ' stdout | analyze stdin' # hack out = Popen([cmd], stderr=PIPE, stdout=PIPE, shell=True) stdout = outerr = text = '' for l in outerr.split('\n'): if l.startswith('Time used') or l.startswith('..') or l.startswith('handling') or l.startswith('uncommon residue'): continue if l.strip(): text += l + '\n' return text.strip()
[docs] def get_modifications(self): """Run find_pair to find modifications. """ cmd = X3DNA_FP + ' -p ' + self.curr_fn + ' /tmp/fpout' # hack out = Popen([cmd], stderr=PIPE, stdout=PIPE, shell=True) outerr = text = '' for l in outerr.split('\n'): if l.startswith('uncommon residue'): text += l.replace('uncommon residue ', '') + '\n' return text.strip()
[docs] def run_x3dna(self, show_log=False, verbose=False): """ """ cmd = X3DNA + ' -i=' + self.curr_fn out = Popen([cmd], stderr=PIPE, stdout=PIPE, shell=True) stdout = str( outerr = str( f = open('py3dna.log', 'w') if verbose: print(f'cmd: {cmd}') f.write(cmd + '\n' + stdout) if show_log: print(stdout) f.close() if outerr.find('does not exist!') > -1: # not very pretty raise x3DNAMissingFile if outerr.find('not found') > -1: # not very pretty raise Exception('x3dna not found!') rx = re.compile('no. of DNA/RNA chains:\s+(?P<no_DNARNAchains>\d+)\s').search(stdout) if rx: no_of_DNARNA_chains = int('no_DNARNAchains')) msg = 'py3dna::no of DNARNA chains' = msg + '\n' + msg + '\n' # hack! else: raise Exception('no_of_DNARNA_chains not found') if no_of_DNARNA_chains: = stdout.strip()
[docs] def get_ion_water_report(self): """@todo File name: /tmp/tmp0pdNHS no. of DNA/RNA chains: 0 [] no. of nucleotides: 174 no. of waters: 793 no. of metals: 33 [Na=29, Mg=1, K=3] """ pass
[docs] def clean_up(self, verbose=False): files_to_remove = [ 'dssr-helices.pdb', 'dssr-pairs.pdb', 'dssr-torsions.dat', 'dssr-hairpins.pdb', 'dssr-multiplets.pdb', 'dssr-stems.pdb', 'dssr-Aminors.pdb', 'hel_regions.pdb', 'bp_order.dat', 'bestpairs.pdb', ] for f in files_to_remove: try: os.remove(f) pass except OSError: if verbose: print('error: can not remove %s' % f)
[docs] def get_seq(self): """Get sequence. Somehow 1bzt_1 x3dna UCAGACUUUUAAPCUGA, what is P? P -> u """ return'\n')[-2].replace('P', 'u').replace('I', 'a')
[docs] def get_secstruc(self): """Get secondary structure. """ hits ="as a whole and per chain.*?\n(?P<ss>.+?)\n\*",, re.DOTALL|re.MULTILINE) if hits: return'ss').strip() else:'\n')[-1] # tofix
[docs] def get_torsions(self, outfn) -> str: """Get torsion angles into 'torsion.csv' file:: nt,id,res,alpha,beta,gamma,delta,epsilon,zeta,e-z,chi,phase-angle,sugar-type,ssZp,Dp,splay,bpseq 1,g,A.GTP1,nan,nan,142.1,89.5,-131.0,-78.3,-53(BI),-178.2(anti),358.6(C2'-exo),~C3'-endo,4.68,4.68,29.98,0 2,G,A.G2,-75.8,-167.0,57.2,79.5,-143.4,-69.7,-74(BI),-169.2(anti),5.8(C3'-endo),~C3'-endo,4.68,4.76,25.61,0 """ angles = '' save = False c2pendo = [] c3pendo = [] if not os.path.isfile('dssr-torsions.txt'): print(f'Problem to get torsion angles for {self.curr_fn}') return f'Problem to get torsion angles for {self.curr_fn}' for l in open('dssr-torsions.txt'): if 'nt alpha beta' in l: save = True l = l.replace('nt', 'nt id res ') if '***************' in l and save: save = False if save: if "~C2'-endo" in l: c2pendo.append(l.split()[0]) if "~C3'-endo" in l: c3pendo.append(l.split()[0]) angles += l c2 = 'color pink, resi ' + '+'.join(c2pendo) c3 = 'color blue, resi ' + '+'.join(c3pendo) if args.pymol: print(c2) print(c3) return import re nangles = '' #'9 C 41', #'10 C 0', bpseq = ['bpseq'] + [x.strip().split()[2] for x in open('dssr-2ndstrs.bpseq').readlines()] for i, l in enumerate(angles.split('\n')): if l.strip(): l = re.sub(r'\s+', ',', l, 0, re.MULTILINE) if bpseq[i] == '0': bpseq[i] = 'no paired' else: bpseq[i] = 'paired' l = l[1:] + ',' + bpseq[i] + '\n' nangles += l nangles = re.sub(r'---', 'nan', nangles, 0, re.MULTILINE) with open(outfn, 'w') as f: f.write(nangles.strip()) if import pandas as pd df = pd.read_csv(outfn) print(df) return nangles.strip()
# name if __name__ == '__main__': if not X3DNA: raise Exception( 'Set up BINARY_PATH in, .e.g "/Users/magnus/work/opt/x3dna/x3dna-dssr"') # get parser and arguments parser = get_parser() args = parser.parse_args() # try: # compact = sys.argv[2] # if compact == '-c': # compact = True # # except IndexError: # compact = False for f in args.files: if args.compact: p = x3DNA(f) print((f, p.get_secstruc())) else: print(f'input: {f}') outfn = os.path.basename(f.replace('.pdb', '')) + '-torsion-paired.csv' if not args.rerun: if os.path.isfile(outfn): print(f'skip: {f}, use --rerun to run analysis again') continue p = x3DNA(f, args.show_log, args.verbose) s = p.get_seq() print(s) s = p.get_secstruc() print(s) s = p.get_torsions(outfn) if args.verbose: print(s) p.clean_up(args.verbose)