Source code for rna_tools.tools.mq.Dfire.Dfire

#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""This module contains functions for computing Dfire potential
"""
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)