/usr/lib/python3/dist-packages/csb/bio/io/vasco.py is in python3-csb 1.2.3+dfsg-3.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 | """
VASCO Chemical Shift format parser.
"""
import csb.core
class ShiftInfo(object):
def __init__(self, residue_id, amino_acid, nucleus,
shift, element, secondary_structure):
self.residue_id = residue_id
self.nucleus = nucleus
self.element = element
self.amino_acid = amino_acid
self.shift = shift
self.secondary_structure = secondary_structure
def __str__(self):
return '{0.amino_acid} {0.nucleus} {0.shift}'.format(self)
__repr__ = __str__
class ChemicalShiftContainer(csb.core.DictionaryContainer):
def __init__(self, bmrb_id='', pdb_id='', sequence='',
chain='', exptype=''):
self.bmrb_id = bmrb_id
self.pdb_id = pdb_id
self.sequence = sequence
self.chain = chain
self.exptype = exptype
super(ChemicalShiftContainer, self).__init__()
class VascoStructureParser(object):
"""
Simple Vasco Parser
"""
def __init__(self):
self._stream = None
def parse(self, file_name, ignore_outliers=True):
"""
@param file_name: source file to parse
@type file_name: str
@return: a L{ChemicalShiftContainer} of L{ShiftInfo} objects
@rtype: dict
"""
self._stream = open(file_name)
shifts = self._parse_header()
self._parse_shifts(shifts, ignore_outliers=ignore_outliers)
self._stream.close()
return shifts
def _parse_header(self):
bmrb_id = ''
pdb_id = ''
sequence = ''
chain = ''
exptype = ''
self._stream.seek(0)
while True:
try:
line = next(self._stream)
except StopIteration :
break
if line.startswith('#'):
if line[2:].startswith('BMRB ORIGIN'):
bmrb_id = line[20:].strip()
elif line[2:].startswith('PDB ORIGIN'):
pdb_id = line[20:].strip()
elif line[2:].startswith('SEQUENCE PDB'):
sequence = line[20:].strip()
chain = line[17]
elif line[2:].startswith('PDB EXPTYPE'):
exptype = line[20:].strip()
else:
break
return ChemicalShiftContainer(bmrb_id, pdb_id, chain,
sequence, exptype )
def _parse_shifts(self, data, ignore_outliers=True):
while True:
try:
line = next(self._stream)
except StopIteration:
break
if ignore_outliers and "Shift outlier" in line:
continue
chain_id = line[7]
res_code = line[9:14].strip()
res_label = line[16:19].strip()
res_ss = line[21]
nucleus_name = line[23:28].strip()
nucleus_element = line[41]
shift = float(line[43:52])
info = ShiftInfo(res_code, res_label,
nucleus_name, shift,
nucleus_element, res_ss)
if not chain_id in data:
data.append(chain_id, csb.core.OrderedDict())
if not res_code in data[chain_id]:
data[chain_id][res_code] = {}
data[chain_id][res_code][nucleus_name] = info
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