/usr/lib/python2.7/dist-packages/csb/bio/io/noe.py is in python-csb 1.2.2+dfsg-2ubuntu1.
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Simple XEASY and Sparky peak list parsers.
"""
from abc import ABCMeta, abstractmethod
from csb.bio.nmr import NOESpectrum
class PeakListFormatError(ValueError):
pass
class BasePeakListReader(object):
__metaclass__ = ABCMeta
@abstractmethod
def read(self, table):
"""
Parse a peak list table.
@param table: input peak list table
@type table: str
@rtype: L{NOESpectrum}
"""
pass
def read_file(self, filename):
"""
Parse a peak list file.
@param filename: input file name
@type filename: str
@rtype: L{NOESpectrum}
"""
with open(filename) as input:
return self.read(input.read())
def read_all(self, filenames):
"""
Parse a list of peak list files and merge the resulting spectra.
All spectra must have identical dimensions.
@param filenames: input file names
@type filenames: iterable of str
@return: joint spectrum
@rtype: L{NOESpectrum}
"""
spectra = [self.read_file(f) for f in filenames]
return NOESpectrum.join(*spectra)
class SparkyPeakListReader(BasePeakListReader):
"""
Sparky NOE peak list parser.
@param elements: list of element names for each dimension
@type elements: list of (str or L{EnumItem})
@param connected: list of covalently connected dimension indices in the
format: [(i1,i2),...]
@type connected: list of (int,int) tuples
"""
def __init__(self, elements, connected):
self._elements = list(elements)
self._connected = [(d1, d2) for d1, d2 in connected]
if len(self._elements) < 1:
raise ValueError("Can't parse a 0-dimensional peak list")
def read(self, table):
"""
Parse a Sparky peak list table.
@param table: input peak list
@type table: str
@rtype: L{NOESpectrum}
"""
offset = 0
spectrum = NOESpectrum(self._elements)
for d1, d2 in self._connected:
spectrum.connect(d1, d2)
for l in table.splitlines():
if not l.strip() or ('w1' in l and 'w2' in l):
if l.lstrip().lower().startswith('assignment'):
offset = 1
continue
line = l.split()[offset:]
try:
float(line[-1]) # last item may or may not be a comment
except ValueError:
if len(line) > 0:
line.pop()
items = list(map(float, line))
intensity = items[-1]
dimensions = items[:-1]
if len(dimensions) != len(self._elements):
raise PeakListFormatError("Expected {0} dimensional spectrum, got {1}".format(
len(self._elements), len(dimensions)))
spectrum.add(intensity, dimensions)
return spectrum
class XeasyPeakListReader(BasePeakListReader):
"""
XEASY NOE peak list parser.
"""
def __init__(self):
pass
def read(self, table):
"""
Parse an XEASY peak list table.
@param table: input peak list
@type table: str
@rtype: L{NOESpectrum}
"""
lines = table.splitlines()
spectrum = self._read_header(lines)
for l in lines:
if not l.strip() or l.startswith('#'):
continue
parts = l.split()[1:]
peak = parts[:spectrum.num_dimensions]
height = parts[spectrum.num_dimensions + 2]
intensity = float(height)
dimensions = map(float, peak)
spectrum.add(intensity, dimensions)
return spectrum
def _read_header(self, lines):
num = 0
dim = {}
el = {}
el2 = {}
connectivity = None
for l in lines:
if l.startswith('#'):
if l[1:].lstrip().lower().startswith('number of dimensions'):
num = int(l.split()[-1])
if l.startswith('#INAME'):
parts = l.split()[1:]
if len(parts) != 2:
raise PeakListFormatError("Invalid Xeasy header")
index = int(parts[0]) - 1
if index < 0:
raise PeakListFormatError("Invalid Xeasy header: dimension index < 1")
element = ''.join(i for i in parts[1] if i.isalpha())
el[parts[1]] = index
el2[element] = index
dim[index] = element
if l.startswith('#CYANAFORMAT'):
connectivity = l.split()[1]
if len(dim) != num or num == 0:
raise PeakListFormatError("Invalid Xeasy header")
elements = tuple(dim[i] for i in sorted(dim))
spectrum = NOESpectrum(elements)
if connectivity:
# cyanaformat - explicitly defines connected dimensions:
# upper case dimensions are connected, e.g. "#CYANAFORMAT hCH" => 2-3
if connectivity.upper() != ''.join(elements).upper():
raise ValueError("Invalid XEASY/CYANA header")
for i1 in range(len(connectivity)):
for i2 in range(len(connectivity)):
e1, e2 = connectivity[i1], connectivity[i2]
if i1 != i2 and e1.isupper() and e2.isupper():
spectrum.connect(i1, i2)
else:
# dimension labels starting with a number are connected, e.g. "1A B2 3C" => 1-3
if len(el) != num:
raise PeakListFormatError("Invalid XEASY header")
for e1 in el:
for e2 in el:
if e1 != e2:
element1 = dim[el[e1]]
element2 = dim[el[e2]]
num1 = e1.replace(element1, '')
num2 = e2.replace(element2, '')
if e1.startswith(num1) and e2.startswith(num2):
spectrum.connect(el[e1], el[e2])
return spectrum
class XeasyFileBuilder(object):
"""
XEASY output format builder.
@param stream: destination stream, were the output is written
@type stream: file
"""
def __init__(self, stream):
self._out = stream
def add_spectrum(self, spectrum):
self.add_header(spectrum)
self.add_peaks(spectrum)
def add_header(self, spectrum):
"""
Write the XEASY header.
@param spectrum: NOE spectrum
@type spectrum: L{NOESpectrum}
"""
self._out.write(
'# Number of dimensions {0}\n'.format(spectrum.num_dimensions))
conn = ''
for en, e in enumerate(spectrum.dimensions, start=1):
element = repr(e).upper()
self._out.write('#INAME {0} {1}{0}\n'.format(en, element))
if spectrum.has_connected_dimensions(en - 1):
conn += element.upper()
else:
conn += element.lower()
self._out.write(
'#CYANAFORMAT {0}\n'.format(conn))
def add_peaks(self, spectrum):
"""
Write all peaks from C{spectrum}.
@param spectrum: NOE spectrum
@type spectrum: L{NOESpectrum}
"""
for pn, peak in enumerate(spectrum, start=1):
self._out.write("{0:5} ".format(pn))
for dim in range(spectrum.num_dimensions):
data = "{0:7.3f} ".format(peak.get(dim))
self._out.write(data)
self._out.write("2 U ")
self._out.write("{0:18e} ".format(peak.intensity))
self._out.write("0.00e+00 m 0 0 0 0 0\n")
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