def readPeakList(self, fn, status='keep'):
""" Six lines per peak
1,1,2,99,1,2,'Jurgen','20-HG1|20-HN'
^ assignment info
2.340,0.050,0.041,9.049,0.026,0.026,2.000
^ Chemical shift 1
^ Chemical shift 2
26
0
0.0000E+00,8.0715E+06
^ peak volume
20,5,20,1
"""
nTmessage("Reading: %s" % fn)
txt = readTextFromFile(fn)
_path,name,_ext = nTpath( fn )
peakList = PeakList( name=name, status=status )
splitLineList = txt.splitlines()
# Init here after some content is added; can't be done in constructor of class.
self.chainName = self.project.molecule.allChains()[0].name
i = 0
while i < len(splitLineList):
# nTdebug("Working on line %d (line 1 in block)" % i)
# 1,1,2,99,1,2,'Jurgen','20-HG1|20-HN'
# ^ assignment info
line = splitLineList[i]
wordList = line.split(',')
assignmentListStr = wordList[ - 1]
assignmentListStr = assignmentListStr.replace("'", '')
barIdx = assignmentListStr.find('|')
resonances = []
if barIdx > 0:
assignmentListStrList = assignmentListStr.split('|')
for loc in assignmentListStrList:
resId, atomName = loc.split('-')
resId = int(resId)
resonanceListAtomName = self.getResonanceListForLoc(resId, atomName)
resonances.append(resonanceListAtomName)
# work on line 2 for peak positions
# 2.340,0.050,0.041,9.049,0.026,0.026,2.000
# ^ Chemical shift 1
# ^ Chemical shift 2
i += 1
line = splitLineList[i]
# nTdebug("Working on CS line 2: [%s]" % line)
wordList = line.split(',')
peakPosition1 = float(wordList[0])
peakPosition2 = float(wordList[3])
positions = [peakPosition1, peakPosition2]
# work on line 5 for peak volume
i += 3
line = splitLineList[i]
wordList = line.split(',')
volume = float(wordList[ -1])
# nTdebug("Working on volume [%s] from line 5 (%d) : [%s]" % (volume, i,line))
peak = Peak(self.dimension,
positions = positions,
height = volume, # this is a work around the fact that later on xeasy only uses height and misses volume.
volume = volume,
resonances = resonances)
# Use the Lister class for a string representation.
# nTdebug("Found peak: %r" % peak)
peakList.append( peak )
# skip to next line 1
i += 2
return peakList
def importPeaks( self, molecule, peakFile, status='keep') :
"""Read Xeasy peak file
returns a PeaksList instance or None on error
JFD: description of XEASY peak list format:
43 1.760 3.143 1 T 0.000e+00 0.00e+00 - 0 2260 2587 0
46 1.649 4.432 1 T 1.035e+05 0.00e+00 r 0 2583 2257 0
^ peak id ^ height
^ chemical shifts ^ height dev ^ resonance ids
^ ? ^ ? ^ ?
^ ? ^ ?
resonance id is zero for unassigned.
"""
#print '>>', molecule, peakFile
self.map2molecule( molecule )
_path,name,_ext = nTpath( peakFile )
peaks = PeakList( name=name, status=status )
dimension = 0
# f stands for field.
for f in AwkLike( peakFile ):
if (f.NR == 1 and f.NF == 5):
dimension = f.int(5)
elif (not f.isComment('#') ):
# if (f.NF == 12):
# dimension = 2
# elif (f.NF == 13 or f.NF == 14 or (f.NF>):
# dimension = 3
# else:
# nTerror('Xeasy.importPeaks: invalid number of fields (%d) in file "%s" on line %d (%s)',
# f.NF, peakFile, f.NR, f.dollar[0]
# )
# return None
# #end if
if not dimension:
nTerror('Xeasy.importPeaks: invalid dimensionality in file "%s" (line %d, "%s")'%(
peakFile, f.NR, f.dollar[0]))
return None
#end if
cur = 1
# preserve the Xeasy peak id
peakId = f.int( cur )
if (peakId == None):
return None
cur += 1
peakpos = []
for _i in range(X_AXIS, dimension):
p = f.float( cur )
if (p == None):
return None
peakpos.append( p )
cur += 1
#end if
cur += 2 # skip two fields
height = f.float( cur )
if height == None:
return None
cur += 1
heightError = f.float( cur )
if heightError == None:
return None
cur += 1
resonances = []
error = 0
cur += 2 # skip two fields
for _i in range(X_AXIS, dimension):
aIndex = f.int( cur )
if aIndex == None:
return None
cur += 1
# 0 means unassigned according to Xeasy convention
if aIndex == 0:
resonances.append( None )
else:
if not aIndex in self.prot:
nTerror('Xeasy.importPeaks: invalid atom id %d on line %d (%s)',
aIndex, f.NR, f.dollar[0]
)
error = 1
break
else:
atom = self.prot[ aIndex].atom
if atom != None:
resonances.append( atom.resonances() )
else:
resonances.append( None )
#end if
#end if
#end for
if not error:
peak = Peak( dimension=dimension,
positions=peakpos,
height=height, heightError=heightError,
resonances = resonances,
)
# store original peak id
peak.xeasyIndex = peakId
peaks.append( peak )
#end if
#end if
#end for
nTmessage('Xeasy.importPeaks: extracted %d peaks from %s', len(peaks), peakFile )
#end if
return peaks
def readPeakList(self, fn, status='keep'):
""" Six lines per peak
1,1,2,99,1,2,'Jurgen','20-HG1|20-HN'
^ assignment info
2.340,0.050,0.041,9.049,0.026,0.026,2.000
^ Chemical shift 1
^ Chemical shift 2
26
0
0.0000E+00,8.0715E+06
^ peak volume
20,5,20,1
"""
nTmessage("Reading: %s" % fn)
txt = readTextFromFile(fn)
_path, name, _ext = nTpath(fn)
peakList = PeakList(name=name, status=status)
splitLineList = txt.splitlines()
# Init here after some content is added; can't be done in constructor of class.
self.chainName = self.project.molecule.allChains()[0].name
i = 0
while i < len(splitLineList):
# nTdebug("Working on line %d (line 1 in block)" % i)
# 1,1,2,99,1,2,'Jurgen','20-HG1|20-HN'
# ^ assignment info
line = splitLineList[i]
wordList = line.split(',')
assignmentListStr = wordList[-1]
assignmentListStr = assignmentListStr.replace("'", '')
barIdx = assignmentListStr.find('|')
resonances = []
if barIdx > 0:
assignmentListStrList = assignmentListStr.split('|')
for loc in assignmentListStrList:
resId, atomName = loc.split('-')
resId = int(resId)
resonanceListAtomName = self.getResonanceListForLoc(
resId, atomName)
resonances.append(resonanceListAtomName)
# work on line 2 for peak positions
# 2.340,0.050,0.041,9.049,0.026,0.026,2.000
# ^ Chemical shift 1
# ^ Chemical shift 2
i += 1
line = splitLineList[i]
# nTdebug("Working on CS line 2: [%s]" % line)
wordList = line.split(',')
peakPosition1 = float(wordList[0])
peakPosition2 = float(wordList[3])
positions = [peakPosition1, peakPosition2]
# work on line 5 for peak volume
i += 3
line = splitLineList[i]
wordList = line.split(',')
volume = float(wordList[-1])
# nTdebug("Working on volume [%s] from line 5 (%d) : [%s]" % (volume, i,line))
peak = Peak(
self.dimension,
positions=positions,
height=
volume, # this is a work around the fact that later on xeasy only uses height and misses volume.
volume=volume,
resonances=resonances)
# Use the Lister class for a string representation.
# nTdebug("Found peak: %r" % peak)
peakList.append(peak)
# skip to next line 1
i += 2
return peakList
def importPeaks(self, molecule, peakFile, status='keep'):
"""Read Xeasy peak file
returns a PeaksList instance or None on error
JFD: description of XEASY peak list format:
43 1.760 3.143 1 T 0.000e+00 0.00e+00 - 0 2260 2587 0
46 1.649 4.432 1 T 1.035e+05 0.00e+00 r 0 2583 2257 0
^ peak id ^ height
^ chemical shifts ^ height dev ^ resonance ids
^ ? ^ ? ^ ?
^ ? ^ ?
resonance id is zero for unassigned.
"""
#print '>>', molecule, peakFile
self.map2molecule(molecule)
_path, name, _ext = nTpath(peakFile)
peaks = PeakList(name=name, status=status)
dimension = 0
# f stands for field.
for f in AwkLike(peakFile):
if (f.NR == 1 and f.NF == 5):
dimension = f.int(5)
elif (not f.isComment('#')):
# if (f.NF == 12):
# dimension = 2
# elif (f.NF == 13 or f.NF == 14 or (f.NF>):
# dimension = 3
# else:
# nTerror('Xeasy.importPeaks: invalid number of fields (%d) in file "%s" on line %d (%s)',
# f.NF, peakFile, f.NR, f.dollar[0]
# )
# return None
# #end if
if not dimension:
nTerror(
'Xeasy.importPeaks: invalid dimensionality in file "%s" (line %d, "%s")'
% (peakFile, f.NR, f.dollar[0]))
return None
#end if
cur = 1
# preserve the Xeasy peak id
peakId = f.int(cur)
if (peakId == None):
return None
cur += 1
peakpos = []
for _i in range(X_AXIS, dimension):
p = f.float(cur)
if (p == None):
return None
peakpos.append(p)
cur += 1
#end if
cur += 2 # skip two fields
height = f.float(cur)
if height == None:
return None
cur += 1
heightError = f.float(cur)
if heightError == None:
return None
cur += 1
resonances = []
error = 0
cur += 2 # skip two fields
for _i in range(X_AXIS, dimension):
aIndex = f.int(cur)
if aIndex == None:
return None
cur += 1
# 0 means unassigned according to Xeasy convention
if aIndex == 0:
resonances.append(None)
else:
if not aIndex in self.prot:
nTerror(
'Xeasy.importPeaks: invalid atom id %d on line %d (%s)',
aIndex, f.NR, f.dollar[0])
error = 1
break
else:
atom = self.prot[aIndex].atom
if atom != None:
resonances.append(atom.resonances())
else:
resonances.append(None)
#end if
#end if
#end for
if not error:
peak = Peak(
dimension=dimension,
positions=peakpos,
height=height,
heightError=heightError,
resonances=resonances,
)
# store original peak id
peak.xeasyIndex = peakId
peaks.append(peak)
#end if
#end if
#end for
nTmessage('Xeasy.importPeaks: extracted %d peaks from %s', len(peaks),
peakFile)
#end if
return peaks
