Replace calls to GREP with python equivalent

[Andreas Scheck]

feature request

io.open_rosetta_file

    symm = False
    files = _gather_file_list( filename, multi )
    for file_count, f in enumerate( files ):
        if check_symmetry:
            cmd = "zgrep SYMMETRY_INFO {} |wc" if f.endswith(".gz") else "grep SYMMETRY_INFO {} |wc"
            process = subprocess.Popen(cmd.format(f), stdout=subprocess.PIPE, shell=True)
            symm = int(process.communicate()[0].strip().split()[0]) > 0
        fd = gzip.open( f ) if f.endswith(".gz") else open( f )
        for line in fd:
            line = line.decode('utf8') if f.endswith(".gz") else line
            if line.strip().split()[0].strip(":") in _headers:
                yield line, line.strip().split()[-1] == "description", file_count, symm
        fd.close()

Problem description

When checking for symmetry info in silent files, the open_rosetta_file function calls grep. This would potentially be faster when calling it just inside python and not spawning a new shell process.

Expected Output

The output remains the same, but the time required for parsing should be less.