#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Python parser to 3dna <http://x3dna.org/>.
Installation::
# install the code from http://forum.x3dna.org/downloads/3dna-download/
Create a copy of the rna_x3dna_config_local_sample.py (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) ✗ ./rna_x3dna.py test_data/1xjr.pdb
test_data/1xjr.pdb
>1xjr nts=47 [1xjr] -- secondary structure derived by DSSR
gGAGUUCACCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAUU
..(((((((...((((.((((.....))..))..))).).)))))))
For multiple structures in the folder, run the script like this::
[mm] py3dna$ git:(master) ✗ ./rna_x3dna.py test_data/*
test_data/1xjr.pdb
>1xjr nts=47 [1xjr] -- secondary structure derived by DSSR
gGAGUUCACCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAUU
..(((((((...((((.((((.....))..))..))).).)))))))
test_data/6TNA.pdb
>6TNA nts=76 [6TNA] -- secondary structure derived by DSSR
GCGGAUUUAgCUCAGuuGGGAGAGCgCCAGAcUgAAgAPcUGGAGgUCcUGUGtPCGaUCCACAGAAUUCGCACCA
(((((((..((((.....[..)))).((((.........)))).....(((((..]....))))))))))))....
test_data/rp2_bujnicki_1_rpr.pdb
>rp2_bujnicki_1_rpr nts=100 [rp2_bujnicki_1_rpr] -- secondary structure derived by DSSR
CCGGAGGAACUACUG&CCGGCAGCCU&CCGGAGGAACUACUG&CCGGCAGCCU&CCGGAGGAACUACUG&CCGGCAGCCU&CCGGAGGAACUACUG&CCGGCAGCCU
[[[[(((.....(((&{{{{))))))&(((((((.....(.(&]]]]).))))&[[[[[[......[[[&))))]]].]]&}}}}(((.....(((&]]]]))))))
"""
import re
import argparse
from subprocess import Popen, PIPE
from os import remove, path
from rna_tools.rna_tools_config import X3DNA, X3DNA_FP
[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('-l', '--show-log', 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 = out.stdout.read()
outerr = out.stderr.read()
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 = out.stderr.read()
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):
"""
"""
cmd = X3DNA + ' -i=' + self.curr_fn
out = Popen([cmd], stderr=PIPE, stdout=PIPE, shell=True)
stdout = str(out.stdout.read().decode())
outerr = str(out.stderr.read().decode())
f = open('py3dna.log', 'w')
f.write(cmd + '\n' + stdout)
if args.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(rx.group('no_DNARNAchains'))
msg = 'py3dna::no of DNARNA chains'
self.report = msg + '\n' + msg + '\n' # hack!
else:
raise Exception('no_of_DNARNA_chains not found')
if no_of_DNARNA_chains:
self.report = 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:
remove(f)
except OSError:
if verbose:
print('can not remove %s' % f)
[docs] def get_seq(self):
"""Get sequence.
Somehow 1bzt_1 x3dna UCAGACUUUUAAPCUGA, what is P?
P -> u
"""
return self.report.split('\n')[-2].replace('P', 'u').replace('I', 'a')
[docs] def get_secstruc(self):
"""Get secondary structure.
"""
return open('dssr-2ndstrs.dbn').read().strip() # self.report.split('\n')[-1]
# name
if __name__ == '__main__':
if not X3DNA:
raise Exception(
'Set up BINARY_PATH in rna_x3dna_config_local.py, .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)
p = x3DNA(f, args.show_log)
# s = p.get_seq()
# print s
s = p.get_secstruc()
print(s)