#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""This module contains functions for computing Dfire potential
Installation:
git clone https://github.com/tcgriffith/dfire_rna.git
make
# add DFIRE_RNA_HOME to .bashrc
"""
from __future__ import print_function
import argparse
import os
from shutil import copyfile
from rna_tools.tools.mq.lib.wrappers.SubprocessUtils import run_command
from rna_tools.tools.pdb_formatix.PDBFile import PDBFile#resname_check_and_3to1, set_residues_bfactor
from rna_tools.tools.mq.lib.wrappers.base_wrappers import ProgramWrapper
from rna_tools.rna_tools_config import dfire_PATH
[docs]
class Dfire(ProgramWrapper):
"""
Wrapper class for Dfire.
"""
def __init__(self):
super(Dfire, self).__init__()
[docs]
def run(self, path_to_pdb, verbose=False):
copyfile(path_to_pdb, self.sandbox_dir + os.sep + 'query.pdb')
old_pwd = os.getcwd()
os.chdir(self.sandbox_dir)
self.log('dfire::start for %s' % self.sandbox_dir + '/query.pdb')
cmd = "export DFIRE_RNA_HOME=" + dfire_PATH + "; "
cmd += dfire_PATH + '/bin/DFIRE_RNA ' + self.sandbox_dir + '/query.pdb >' + self.sandbox_dir + '/log.txt.dfire.rna'
if verbose: print(cmd)
os.system(cmd)
self.log('dfire::Run finished')
for line in open(self.sandbox_dir + '/log.txt.dfire.rna'):
score = line.strip().split()[1] # /tmp/tmplDNztf/query.pdb -12480.188898
if verbose: print(open(self.sandbox_dir + '/log.txt.dfire.rna').read())
os.chdir(old_pwd)
return float(score)
[docs]
def get_parser():
parser = argparse.ArgumentParser(
description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument("-v", "--verbose",
action="store_true", help="be verbose")
parser.add_argument("--test", action="store_true")
parser.add_argument("--file", help="", default="") # nargs='+')
return parser
[docs]
def test(verbose):
wrapper = Dfire()
try:
result = wrapper.run('../test' + os.sep + '1a9n.pdb', verbose)
if result:
print(result)
except Exception as e:
print(e)
finally:
#wrapper.cleanup()
pass
print((wrapper.run('../../../input/mq/' + os.sep + '1a9nR.pdb', verbose)))
print((wrapper.run('../../../input/mq/' + os.sep + '3b58ABC.pdb', verbose)))
print((wrapper.run('../../../input/mq/' + os.sep + '5e3hBC.pdb', verbose)))
print((wrapper.run('../../../input/mq/' + os.sep + 'S_000001_000.pdb', verbose)))
if __name__ == '__main__':
parser = get_parser()
args = parser.parse_args()
if args.test:
test(args.verbose)
else:
wrapper = Dfire()
result = wrapper.run(args.file, args.verbose)
print(result)