/usr/lib/python3/dist-packages/csb/bio/io/cs.py is in python3-csb 1.2.3+dfsg-3.
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Simple NMR STAR chemical shift readers.
"""
from csb.bio.nmr import ChemShiftInfo
class ChemShiftFormatError(ValueError):
pass
class ChemShiftReader(object):
"""
Simple NMR STAR v2 chemical shift reader.
@note: This is not a full-fledged, semantic NMR STAR parser. It handles
only the chemical shift table.
"""
FRAME = 'save_assigned_chemical_shifts'
RANK = '_Residue_seq_code'
RESIDUE = '_Residue_label'
ATOM = '_Atom_name'
ELEMENT = '_Atom_type'
SHIFT = '_Chem_shift_value'
@staticmethod
def create(frame=FRAME, version=2):
"""
Parser factory: create a new parser, given a saveframe name
and format verison.
@param frame: name of the saveframe to read
@type frame: str
@param version: NMR STAR format version
@type version: int
@return: an instance of any L{ChemShiftReader} class
@rtype: L{ChemShiftReader}
"""
if version == 3:
return ChemShift3Reader(frame=frame)
elif version == 2:
return ChemShiftReader(frame=frame)
else:
raise ValueError('Unknown NMR-STAR version')
@staticmethod
def guess(file, frame=FRAME):
"""
Parser factory: try to guess the correct NMR STAR version from a given
file and create an appropriate parser.
@param file: NMR STAR path and file name
@type file: str
@param frame: name of the saveframe to read
@type frame: str
@return: an instance of any L{ChemShiftReader} class
@rtype: L{ChemShiftReader}
@raise ChemShiftFormatError: on failure to determine the NMR STAR version
"""
with open(file) as cs:
content = cs.read()
if not content.strip():
return ChemShiftReader.create()
elif ChemShift3Reader.SHIFT3 in content:
return ChemShiftReader.create(frame, version=3)
elif ChemShiftReader.SHIFT in content:
return ChemShiftReader.create(frame, version=2)
else:
raise ChemShiftFormatError("Can't guess NMR-STAR version")
def __init__(self, frame=FRAME):
self._frame = frame
def read_file(self, filename):
"""
Parse the specified file.
@param filename: file path and name
@type filename: str
@rtype: tuple of L{ChemShiftInfo}
"""
with open(filename) as input:
return self.read_shifts(input.read())
def read_shifts(self, star_table):
"""
Parse a given NMR STAR chemical shift table.
@param star_table: NMR STAR chemical shift table
@type star_table: str
@rtype: tuple of L{ChemShiftInfo}
@raise ChemShiftFormatError: on parse error
"""
shifts = []
init = False
in_shifts = False
fields = []
lines = iter(star_table.splitlines())
if self._frame in star_table:
self._scroll(lines, self._frame)
for l in lines:
ls = l.strip()
if not in_shifts:
if ls == 'loop_':
assert in_shifts is False and not fields and init is False
init = True
continue
elif init and ls.startswith('_'):
assert in_shifts is False
fields.append(l.strip())
continue
elif init and not ls:
if len(fields) < 1:
raise ChemShiftFormatError("No fields found in the CS table")
in_shifts = True
continue
else:
if ls == 'stop_':
break
elif ls.startswith('#'):
continue
elif ls:
values = l.split()
if len(values) < len(fields):
raise ChemShiftFormatError("Insufficient number of values: {0}".format(l))
data = dict(zip(fields, values))
shifts.append(self._create_shift(data))
return tuple(shifts)
def _scroll(self, iterator, field):
for line in iterator:
if line.lstrip().startswith(field):
break
def _create_shift(self, data):
try:
position = int(data[ChemShiftReader.RANK])
residue = data[ChemShiftReader.RESIDUE]
name = data[ChemShiftReader.ATOM]
element = data[ChemShiftReader.ELEMENT]
shift = float(data[ChemShiftReader.SHIFT])
except KeyError as ke:
raise ChemShiftFormatError("Required field {0} not found".format(str(ke)))
except ValueError as ve:
raise ChemShiftFormatError("Can't parse value: {0}".format(str(ve)))
return ChemShiftInfo(position, residue, name, element, shift)
class ChemShift3Reader(ChemShiftReader):
"""
Simple NMR STAR v3 chemical shift reader.
@note: This is not a full-fledged, semantic NMR STAR parser. It handles
only the chemical shift table.
"""
RANK3 = '_Atom_chem_shift.Seq_ID'
RESIDUE3 = '_Atom_chem_shift.Comp_ID'
ATOM3 = '_Atom_chem_shift.Atom_ID'
ELEMENT3 = '_Atom_chem_shift.Atom_type'
SHIFT3 = '_Atom_chem_shift.Val'
def _create_shift(self, data):
try:
position = data[ChemShift3Reader.RANK3]
residue = data[ChemShift3Reader.RESIDUE3]
name = data[ChemShift3Reader.ATOM3]
element = data[ChemShift3Reader.ELEMENT3]
shift = data[ChemShift3Reader.SHIFT3]
except KeyError as ke:
raise ChemShiftFormatError("Required field {0} not found".format(str(ke)))
except ValueError as ve:
raise ChemShiftFormatError("Can't parse value: {0}".format(str(ve)))
return ChemShiftInfo(position, residue, name, element, shift)
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