def midge(argServer=None):
assert argServer
(resonances, noesyPeaks,
intensityFactors) = getCloudsResonanceList(argServer)
# now make the noesy F2 assignments!
print len(resonances), 'Resonances'
print len(noesyPeaks), 'Noesy peaks'
constraintList = optimiseRelaxation(resonances,
noesyPeaks,
intensityMax=36000000,
intensityFactors=intensityFactors,
tmix=60,
sf=500,
tcor=3,
rleak=2)
structure = argServer.getStructure()
if structure:
for constraint in constraintList.constraints:
resonances = list(constraint, findFirstItem().resonances)
atomSets1 = list(resonances[0].resonanceSet.atomSets)
atomSets2 = list(resonances[1].resonanceSet.atomSets)
distance = getAtomSetsDistance(atomSets1, atomSets2, structure)
constraint.setDetails('Known Dist: %4.3f' % (distance))
return constraintList
def within_distance_on_structure(structure, resonances, maxDist):
'''Check whether the distance between two resonances
is within the maximum allowed distance.
'''
atomSets1 = resonances[0].resonanceSet.atomSets
atomSets2 = resonances[1].resonanceSet.atomSets
distance = getAtomSetsDistance(atomSets1, atomSets2,
structure, method='noe')
if distance > maxDist:
return False
else:
return True
def showResonancesConnection(self, resonance1, resonance2):
if resonance1.resonanceSet and resonance2.resonanceSet:
atomSets1 = resonance1.resonanceSet.atomSets
atomSets2 = resonance2.resonanceSet.atomSets
value = getAtomSetsDistance(atomSets1,
atomSets2,
self.structure,
self.model,
method=self.distMethod)
color = self.getNoeColor(value)
self.showAtomSetsConnection(atomSets1,
atomSets2,
value,
color=color)
def setModel(self, model):
if model is not self.model:
self.model = model
oldConn = self.connections[:]
drawConn = self.showAtomSetsConnection
self.connections = []
self.structFrame.clearConnections()
self.update()
for atomSets1, atomSets2, cBond, color, value in oldConn:
value = getAtomSetsDistance(atomSets1,
atomSets2,
self.structure,
self.model,
method=self.distMethod)
drawConn(atomSets1, atomSets2, value, color)
def setDistMethod(self, name):
distMethod = distanceMethods.get(name, 'noe')
if distMethod != self.distMethod:
self.distMethod = distMethod
for i, data in enumerate(self.connections):
atomSets1, atomSets2, cBond, oldColor, oldVal = data
value = getAtomSetsDistance(atomSets1,
atomSets2,
self.structure,
self.model,
method=self.distMethod)
color = self.getNoeColor(value)
cBond.setColor(color)
cBond.setAnnotation('%.3f' % value)
self.connections[i][3] = color
self.connections[i][4] = value
self.updateAfter()
def cheatForTesting(self, atomSelection='H'):
""" Makes a perfect cloud from a structure. """
project = self.project
structure = self.guiParent.argumentServer.getStructure()
constraintStore = makeNmrConstraintStore(project)
distConstraintList = NmrConstraint.DistanceConstraintList(
constraintStore)
chain = structure.findFirstCoodChain()
structureGeneration.hydrogenResonances = []
molSystem = structure.molSystem
atomSets = []
resonances = []
i = 0
for resonance in project.currentNmrProject.resonances:
if resonance.isotopeCode == '1H':
if resonance.resonanceSet:
atomSet = resonance.resonanceSet.findFirstAtomSet()
atom = atomSet.findFirstAtom()
seqId = atom.residue.seqId
if (seqId < 9) or (seqId > 78):
continue
if atom.residue.chain.molSystem is molSystem:
if atomSelection == 'methyl':
if len(atomSet.atoms) == 3:
if atom.residue.ccpCode not in ('Ala', 'Val',
'Ile', 'Leu',
'Thr', 'Met'):
continue
elif atom.name != 'H':
continue
elif atomSelection == 'amide':
if atom.name != 'H':
continue
if atom.name == 'H':
resonance.name = 'HN'
else:
resonance.name = 'H'
resonances.append(resonance)
atomSets.append(list(resonance.resonanceSet.atomSets))
i += 1
print "Found %d atomSets" % (len(atomSets))
weight = 1
adcWeight = 1
constrDict = {}
N = len(atomSets)
for i in range(N - 1):
atomSets0 = atomSets[i]
residue0 = atomSets0[0].findFirstAtom().residue.seqId
print "R", residue0
for j in range(i + 1, N):
if j == i:
continue
atomSets1 = atomSets[j]
dist = getAtomSetsDistance(atomSets0, atomSets1, structure)
if not dist:
continue
if dist < 5.5:
fixedResonance0 = getFixedResonance(
constraintStore, resonances[i])
fixedResonance1 = getFixedResonance(
constraintStore, resonances[j])
constrDict[i] = 1
constrDict[j] = 1
constraint = NmrConstraint.DistanceConstraint(
distConstraintList,
weight=weight,
targetValue=dist,
upperLimit=dist + (dist / 10),
lowerLimit=dist - (dist / 10),
error=dist / 5)
item = NmrConstraint.DistanceConstraintItem(
constraint,
resonances=[fixedResonance0, fixedResonance1])
elif (atomSets1[0].findFirstAtom().name
== 'H') and (atomSets0[0].findFirstAtom().name
== 'H') and (dist > 7):
#else:
fixedResonance0 = getFixedResonance(
constraintStore, resonances[i])
fixedResonance1 = getFixedResonance(
constraintStore, resonances[j])
constrDict[i] = 1
constrDict[j] = 1
constraint = NmrConstraint.DistanceConstraint(
distConstraintList,
weight=adcWeight,
targetValue=75,
upperLimit=175,
lowerLimit=5.0,
error=94.5)
item = NmrConstraint.DistanceConstraintItem(
constraint,
resonances=[fixedResonance0, fixedResonance1])
return (distConstraintList, resonances)
def calculateDistances(self):
# setup normalisation factor intensityMax
# self.maxIter
# what if failure ?
resDict = {}
for resonance in self.project.currentNmrProject.resonances:
resDict[resonance.serial] = resonance
self.resonances = self.origResonances
intensityFactors = [1.0 for x in range(len(self.resonances))]
# optimiseRelaxation will remove unconstrained resonances
self.distanceConstraintList = optimiseRelaxation(
self.resonances,
self.noesyPeaks,
intensityMax=self.maxIntens,
intensityFactors=intensityFactors,
tmix=self.mixTime,
sf=self.specFreq,
tcor=self.corrTime,
rleak=self.leakRate)
constrainSpinSystems(self.distanceConstraintList)
# for testing calculate distances from structure overrides any resonances: uses assigned ones
#(self.distanceConstraintList, self.resonances) = self.cheatForTesting()
#self.antiDistConstraintList = self.distanceConstraintList
protonNumbs = {'CH3': 3, 'Haro': 2, 'HN': 1, 'H': 1}
PI = 3.1415926535897931
GH = 2.6752e4
HB = 1.05459e-27
CONST = GH * GH * GH * GH * HB * HB
tc = 1.0e-9 * self.corrTime
wh = 2.0 * PI * self.specFreq * 1.0e6
j0 = CONST * tc
j1 = CONST * tc / (1.0 + wh * wh * tc * tc)
j2 = CONST * tc / (1.0 + 4.0 * wh * wh * tc * tc)
#jself = 6.0*j2 + 3.0*j1 + j0
jcross = 6.0 * j2 - j0
if self.distanceConstraintList:
constraintStore = self.distanceConstraintList.nmrConstraintStore
dict = {
'HN': ['H'],
'HN HA': ['H', 'HA', 'HA1', 'HA2'],
'HN HA HB': ['H', 'HA', 'HA1', 'HA2', 'HB', 'HB2', 'HB3']
}
self.antiDistConstraintList = makeNoeAdcs(
self.resonances,
self.noesyPeakList.dataSource,
constraintStore,
allowedAtomTypes=dict[self.adcAtomTypes])
if self.structure:
N = len(self.resonances)
sigmas = [[] for i in range(N)]
for i in range(N):
sigmas[i] = [0.0 for j in range(N)]
for constraint in self.distanceConstraintList.constraints:
resonances = list(constraint, findFirstItem().resonances)
ri = resDict[resonances[0].resonanceSerial]
rj = resDict[resonances[1].resonanceSerial]
i = self.resonances.index(ri)
j = self.resonances.index(rj)
atomSets1 = list(ri.resonanceSet.atomSets)
atomSets2 = list(rj.resonanceSet.atomSets)
if atomSets1 == atomSets2:
ass = list(atomSets1)
atomSets1 = [
ass[0],
]
atomSets2 = [
ass[-1],
]
distance = getAtomSetsDistance(atomSets1, atomSets2,
self.structure)
r = distance * 1e-8
nhs = protonNumbs[rj.name]
sigma = 0.1 * jcross * nhs / (r**6)
sigmas[i][j] = sigma
constraint.setDetails('Known Dist: %4.3f' % (distance))
#for constraint in self.antiDistConstraintList.constraints:
# atomSets1 = list(resonances[0].resonanceSet.atomSets)
# atomSets2 = list(resonances[1].resonanceSet.atomSets)
# distance = getAtomSetsDistance(atomSets1, atomSets2, self.structure)
# constraint.setDetails('Known Dist: %4.3f' % (distance))
fp = open('sigmas.out', 'w')
for i in range(N - 1):
for j in range(i + 1, N):
if sigmas[i][j] != 0.0:
fp.write('%3.1d %3.1d %9.2e\n' %
(i, j, sigmas[i][j]))
#fp.write('\n')
fp.close()
self.setButtonStates()
def showPeakConnection(self, peak):
peakContribs = peak.peakContribs
dimAtomSets = []
dimIsotopes = []
for peakDim in peak.sortedPeakDims():
isotope = None
for contrib in peakDim.peakDimContribs:
resonance = contrib.resonance
resonanceSet = resonance.resonanceSet
if resonanceSet:
atomSets = resonanceSet.atomSets
isotope = resonance.isotopeCode
dimAtomSets.append(
(peakDim, contrib.peakContribs, atomSets, isotope))
dimIsotopes.append(isotope)
M = len(dimAtomSets)
atomSetsPairs = set()
if dimIsotopes.count('1H') > 1:
hOnly = True
else:
hOnly = False
for i in range(M - 1):
peakDimI, peakContribsI, atomSetsI, isotopeI = dimAtomSets[i]
if hOnly and (isotopeI != '1H'):
continue
for j in range(i + 1, M):
peakDimJ, peakContribsJ, atomSetsJ, isotopeJ = dimAtomSets[j]
if peakDimJ is peakDimI:
continue
if isotopeI != isotopeJ:
continue
if hOnly and (isotopeJ != '1H'):
continue
if atomSetsI == atomSetsJ:
continue
if peakContribs:
for peakContrib in peakContribsJ:
if peakContrib in peakContribsI:
atomSetsPairs.add(frozenset([atomSetsI,
atomSetsJ]))
break
else:
atomSetsPairs.add(frozenset([atomSetsI, atomSetsJ]))
if len(atomSetsPairs):
for atomSetsI, atomSetsJ in atomSetsPairs:
value = getAtomSetsDistance(atomSetsI,
atomSetsJ,
self.structure,
self.model,
method=self.distMethod)
color = self.getNoeColor(value)
self.showAtomSetsConnection(atomSetsI,
atomSetsJ,
value,
color=color)
# If the AtomSets could not be paired just highlight the respective atoms.
else:
for i in range(M):
peakDimI, peakContribsI, atomSetsI, isotopeI = dimAtomSets[i]
self.highlightAtoms(atomSetsI)
def makeConstraintsFromStructure(argServer,
structure=None,
atomRoots=None,
threshold=5.5,
tolerance=0.1,
adcThreshold=7.0,
atomTypes=('H', ),
adcAtoms=('H', )):
# find all NMR visible atom pairs within a specified distance to
# generate distance constraints
if not structure:
structure = argServer.getStructure()
from ccpnmr.analysis.core.AssignmentBasic import newResonance
from ccpnmr.analysis.core.StructureBasic import getAtomSetsDistance
from ccpnmr.analysis.core.ConstraintBasic import getFixedResonance, makeNmrConstraintHead
notVisible = {
'Lys': ["H''", "HZ1", "HZ2", "HZ3"],
'Arg': ["H''", "HH11", "HH12", "HH21", "HH22", "CZ"],
'Ser': [
"H''",
"HG",
],
'Cys': [
"H''",
"HG",
],
'His': ["H''", "HD1", "CG"],
'Thr': [
"H''",
"HG1",
],
'Tyr': ["H''", "HH", "CG"],
'Phe': ["H''", "CG"],
'Glu': [
"H''",
"HE2",
],
'Asp': [
"H''",
"HD2",
],
'Trp': ["H''", "CG", "CD2", "CE2"],
}
project = structure.root
chain = structure.findFirstCoordChain().chain
atomSetDict = {}
anchorAtomSets = {}
amideAtomSets = []
resonanceDict = {}
adcAtomSets = {}
print "Getting atomSets and resonances"
for residue in chain.residues:
atomSetDict[residue] = []
exclude = notVisible.get(residue.ccpCode) or [
"H''",
]
for atom in residue.atoms:
if atom.name[0] not in atomTypes:
continue
if atom.name in exclude:
continue
atomSet = atom.atomSet
if atomSet:
if resonanceDict.get(atomSet) is None:
if atomSet.resonanceSets:
resonanceSet = atomSet.findFirstResonanceSet()
i = list(resonanceSet.atomSets).index(atomSet)
if i >= len(resonanceSet.resonances):
i = 0
resonance = resonanceSet.resonances[i]
else:
resonance = newResonance(project, isotopeCode='1H')
resonanceDict[atomSet] = resonance
atomSetDict[residue].append(atomSet)
if atom.name in ('H', 'H1'):
amideAtomSets.append(atomSet)
elif (residue.ccpCode == 'PRO') and (atom.name == 'HD2'):
amideAtomSets.append(atomSet)
if atomRoots:
if atom.name in atomRoots:
anchorAtomSets[atomSet] = 1
else:
anchorAtomSets[atomSet] = 1
if adcAtoms and (atom.name in adcAtoms):
adcAtomSets[atomSet] = 1
print "Calculating distances"
resonanceDists = []
resonanceDists2 = []
for amide1 in amideAtomSets:
residue1 = amide1.finsFirstAtom().residue
print " %d %s" % (residue1.seqCode, residue1.ccpCode)
for amide2 in amideAtomSets:
residue2 = amide2.findFirstAtom().residue
if amide1 is amide2:
amideDist = 0.0
else:
amideDist = getAtomSetsDistance((amide1, ), (amide2, ),
structure)
if (amideDist is not None) and (amideDist <= 25.0):
for atomSet1 in atomSetDict[residue1]:
if anchorAtomSets.get(atomSet1) is None:
continue
for atomSet2 in atomSetDict[residue2]:
if atomSet1 is atomSet2:
continue
dist = getAtomSetsDistance((atomSet1, ), (atomSet2, ),
structure)
if dist and dist <= threshold:
resonanceDists.append(
(dist, resonanceDict[atomSet1],
resonanceDict[atomSet2]))
if adcAtoms:
for atomSet1 in atomSetDict[residue1]:
if anchorAtomSets.get(atomSet1) is None:
continue
if adcAtomSets.get(atomSet1) is None:
continue
for atomSet2 in atomSetDict[residue2]:
if adcAtomSets.get(atomSet2) is None:
continue
if atomSet1 is atomSet2:
continue
dist = getAtomSetsDistance((atomSet1, ), (atomSet2, ),
structure)
if dist >= adcThreshold:
resonanceDists2.append(
(dist, resonanceDict[atomSet1],
resonanceDict[atomSet2]))
print "Generating constraints"
if resonanceDists:
constraintHead = makeNmrConstraintHead(project)
constraintList = constraintHead.newDistanceConstraintList()
for dist, resonance1, resonance2, in resonanceDists:
if resonance1 is resonance2:
continue
fixedResonance1 = getFixedResonance(constraintHead, resonance1)
fixedResonance2 = getFixedResonance(constraintHead, resonance2)
delta = tolerance * dist
minDist = max(0.0, dist - delta)
maxDist = dist + delta
constraint = constraintList.newDistanceConstraint(
weight=1.0,
origData=dist,
targetValue=dist,
upperLimit=maxDist,
lowerLimit=minDist,
error=delta)
item = constraint.newDistanceConstraintItem(
resonances=[fixedResonance1, fixedResonance2])
if adcAtoms:
constraintList2 = constraintHead.newDistanceConstraintList()
# make ADCs
for dist, resonance1, resonance2, in resonanceDists2:
if resonance1 is resonance2:
continue
dist = 75.0
fixedResonance1 = getFixedResonance(constraintHead, resonance1)
fixedResonance2 = getFixedResonance(constraintHead, resonance2)
minDist = 5.0
maxDist = 150
delta = maxDist - minDist
constraint = constraintList2.newDistanceConstraint(
weight=1.0,
origData=dist,
targetValue=dist,
upperLimit=maxDist,
lowerLimit=minDist,
error=delta)
item = constraint.newDistanceConstraintItem(
resonances=[fixedResonance1, fixedResonance2])
print "Done"
def calculateDistances(self):
resonances = list(self.resonances)
resDict = {}
for resonance in resonances:
resDict[resonance.serial] = resonance
ratioHD = self.ratioHDEntry.get() or self.ratioHD
tmix1 = self.tmix1Entry.get() or 60
tmix2 = self.tmix2Entry.get() or 120
tmix3 = self.tmix3Entry.get() or 200
data = [(tmix1, self.noesyPeakList1), (tmix2, self.noesyPeakList2),
(tmix3, self.noesyPeakList3)]
data.sort()
mixingTimes = [x[0] for x in data]
peakLists = [x[1] for x in data]
# get a clean, symmetric and normalised NOE matrix
noeMatrix = getNoeMatrixFromPeaks(self.noesyPeaks,
resonances,
peakLists,
mixingTimes,
ratioHD=ratioHD,
analysis=self.guiParent)
# optimiseRelaxation will remove unconstrained resonances
self.distanceConstraintList, resonances = optimiseRelaxation(
resonances,
noeMatrix,
self.mixTime,
self.specFreq,
self.corrTime,
self.leakRate,
self.carbonLabel,
self.nitrogenLabel,
maxIter=self.maxIter)
#constrainSpinSystems(self.distanceConstraintList)
# for testing calculate distances from structure overrides any resonances: uses assigned ones
#(self.distanceConstraintList, self.resonances) = self.cheatForTesting()
#self.antiDistConstraintList = self.distanceConstraintList
protonNumbs = {'CH3': 3, 'Haro': 2, 'HN': 1, 'H': 1}
PI = 3.1415926535897931
GH = 2.6752e4
HB = 1.05459e-27
CONST = GH * GH * GH * GH * HB * HB
tc = 1.0e-9 * self.corrTime
wh = 2.0 * PI * self.specFreq * 1.0e6
j0 = CONST * tc
j1 = CONST * tc / (1.0 + wh * wh * tc * tc)
j2 = CONST * tc / (1.0 + 4.0 * wh * wh * tc * tc)
#jself = 6.0*j2 + 3.0*j1 + j0
jcross = 6.0 * j2 - j0
if self.distanceConstraintList and self.noesyPeakList:
constraintHead = self.distanceConstraintList.nmrConstraintStore
if self.adcAtomTypes:
adcDict = {
'HN': ['H'],
'HN HA': ['H', 'HA', 'HA1', 'HA2'],
'HN HA HB': ['H', 'HA', 'HA1', 'HA2', 'HB', 'HB2', 'HB3']
}
allowedAtomTypes = adcDict[self.adcAtomTypes]
print "Making ADCs"
self.antiDistConstraintList = makeNoeAdcs(
resonances[:],
self.noesyPeakList.dataSource,
constraintHead,
allowedAtomTypes=allowedAtomTypes)
print "Done ADCs"
if self.structure:
N = len(self.resonances)
sigmas = [[] for i in range(N)]
for i in range(N):
sigmas[i] = [0.0 for j in range(N)]
for constraint in self.distanceConstraintList.constraints:
item = constraint.findFirstItem()
resonances = list(item.resonances)
ri = resDict[resonances[0].resonanceSerial]
rj = resDict[resonances[1].resonanceSerial]
i = self.resonances.index(ri)
j = self.resonances.index(rj)
atomSets1 = list(ri.resonanceSet.atomSets)
atomSets2 = list(rj.resonanceSet.atomSets)
if atomSets1 == atomSets2:
ass = list(atomSets1)
atomSets1 = [
ass[0],
]
atomSets2 = [
ass[-1],
]
distance = getAtomSetsDistance(atomSets1, atomSets2,
self.structure)
r = distance * 1e-8
nhs = protonNumbs[rj.name]
sigma = 0.1 * jcross * nhs / (r**6)
sigmas[i][j] = sigma
constraint.setOrigData(distance)
self.update()
def update(self,
contrib,
peakDim,
aliasing=False,
structure=None,
limitedResonances=None,
molSystems=None,
component=None,
noDisplay=False,
doubleTol=False,
resetScrollbars=True,
showMolSystem=False):
self.aliasing = aliasing
self.contrib = contrib
self.resonances = []
self.jCouplings = []
self.structure = structure
self.component = component
atomSets1 = []
if peakDim:
self.peakDim = peakDim
elif contrib:
self.peakDim = None
peakDim = contrib.peakDim
else:
self.scrolledMatrix.update(objectList=[], textMatrix=[
[],
])
return
if component and (component.dataDimRef.expDimRef.unit != 'ppm'):
headingList = ['#', 'Names', 'Delta', 'Coupling', 'SD']
tipTexts = TIP_TEXTS2
isCoupling = True
else:
tipTexts = TIP_TEXTS
headingList = ['#', 'Name', 'Delta', 'Shift', 'SD', 'Dist']
isCoupling = False
if showMolSystem:
tipTexts = tipTexts[:]
tipText = 'Mol System of resonance'
if isCoupling:
tipText += 's'
tipTexts.append(tipText)
headingList.append('MS')
dataDimRef = peakDim.dataDimRef
expDimRef = dataDimRef.expDimRef
dataDim = dataDimRef.dataDim
textMatrix = []
colorMatrix = []
if isCoupling:
ppm = getAnalysisDataDim(peakDim.dataDim).assignTolerance
points = peakDim.dataDimRef.valueToPoint(ppm)
tolerance = component.dataDimRef.pointToValue(points)
if doubleTol:
tolerance *= 2
# get couplings that might match the splitting
for delta, coupling in findMatchingCouplings(component, tolerance):
resonanceA, resonanceB = coupling.resonances
nameA = makeResonanceGuiName(resonanceA)
nameB = makeResonanceGuiName(resonanceB)
self.jCouplings.append(coupling)
colors = [None, None, None, None, None]
if coupling.error >= tolerance:
colors[4] = '#d0a0a0'
textMatrix.append([
'%d,%d' % (resonanceA.serial, resonanceB.serial),
'%s-%s' % (nameA, nameB),
'%5.3f' % round(delta, 3), coupling.value,
'%5.3f' % round(coupling.error, 3)
])
colorMatrix.append(colors)
if showMolSystem:
molSystemA = getResonanceMolSystem(resonanceA) or ''
molSystemB = getResonanceMolSystem(resonanceB) or ''
if molSystemA == molSystemB:
texts.append(molSystemA and molSystemA.code)
else:
texts.append('%s,%s' %
(molSystemA and molSystemA.code,
molSystemB and molSystemB.code))
colors.append(None)
objectList = self.jCouplings
else:
# set up atomSets for distance calculations where possible
if self.structure:
for expTransfer in expDimRef.expTransfers:
if expTransfer.transferType in longRangeTransfers:
expDimRefs = list(expTransfer.expDimRefs)
expDimRefs.remove(expDimRef)
for peakDim1 in peakDim.peak.sortedPeakDims():
if peakDim1.dataDimRef.expDimRef is expDimRefs[0]:
for contrib1 in peakDim1.peakDimContribs:
resonance1 = contrib1.resonance
if resonance1 and resonance1.resonanceSet:
for atomSet in resonance1.resonanceSet.atomSets:
atomSets1.append(atomSet)
if component:
# E.g. MQ or reduced dimensionality
dataDimRef2 = component.dataDimRef
if dataDimRef is dataDimRef2:
ppm = abs(peakDim.value - peakDim.realValue)
else:
realPoint = ppm2pnt(peakDim.realValue, dataDimRef)
deltaPoints = abs(peakDim.position - realPoint)
ppm = abs(component.scalingFactor *
dataDimRef2.pointToValue(deltaPoints))
peakUnit = dataDimRef2.expDimRef.unit or 'point'
else:
ppm = peakDim.realValue
peakUnit = expDimRef.unit or 'point'
shiftList = peakDim.peak.peakList.dataSource.experiment.shiftList
shiftUnit = shiftList.unit
tolerance = getAnalysisDataDim(dataDim).assignTolerance
if doubleTol:
tolerance *= 2
shifts = self.givePossAssignments(peakDim, tolerance, ppm)
if len(shifts) > 0: # resonance matches
temp = []
for shift in shifts:
resonance = shift.resonance
if limitedResonances is not None:
if resonance not in limitedResonances:
continue
if molSystems:
molSystem = getResonanceMolSystem(resonance)
if molSystem and (molSystem not in molSystems):
continue
# Kludge until chain states
if (
not molSystem
) and resonance.resonanceGroup and resonance.resonanceGroup.chains:
molSystems2 = set([
ch.molSystem
for ch in resonance.resonanceGroup.chains
])
if not molSystems2.intersection(molSystems):
continue
if peakUnit != shiftUnit:
shiftValue = unit_converter[(shiftUnit,
peakUnit)](shift.value,
dataDimRef)
else:
shiftValue = shift.value
points = unit_converter[(peakUnit, 'point')](shiftValue,
dataDimRef)
numAliasing = findNumAliasing(dataDimRef, points)
deltaAliasing = numAliasing - peakDim.numAliasing
if deltaAliasing:
points -= dataDim.numPointsOrig * deltaAliasing
shiftValue = unit_converter[('point',
peakUnit)](points,
dataDimRef)
shift.isDiffAliasing = 1
else:
shift.isDiffAliasing = 0
delta = abs(ppm - shiftValue)
temp.append((delta, shift))
shift.delta = delta
temp.sort()
shifts = [x[1] for x in temp]
textMatrix = []
colorMatrix = []
for shift in shifts:
resonance = shift.resonance
if limitedResonances is not None:
if resonance not in limitedResonances:
continue
# wb104, 13 Apr 2016, added below (could check this instead in if statement
# but the problem is that shift.delta also needs to exist further down
# and also both attributes get deleted at bottom of the loop)
if not hasattr(shift, 'isDiffAliasing'):
continue
if shift.isDiffAliasing:
colors = [None, None, '#d0d0a0', None, None, None]
else:
colors = [None, None, None, None, None, None]
name = makeResonanceGuiName(resonance)
self.resonances.append(resonance)
if shift.error >= tolerance:
colors[4] = '#d0a0a0'
if self.structure and atomSets1:
if resonance.resonanceSet:
atomSets2 = list(resonance.resonanceSet.atomSets)
dist = getAtomSetsDistance(atomSets1,
atomSets2,
self.structure,
method='noe')
else:
dist = None
else:
dist = None
texts = [
resonance.serial, name,
'%5.3f' % round(shift.delta, 3), shift.value,
'%5.3f' % round(shift.error, 3), dist or ' '
]
if showMolSystem:
molSystem = getResonanceMolSystem(resonance)
texts.append(molSystem and molSystem.code)
colors.append(None)
textMatrix.append(texts)
colorMatrix.append(colors)
del shift.isDiffAliasing
del shift.delta
objectList = self.resonances
if not noDisplay:
self.scrolledMatrix.update(headingList=headingList,
tipTexts=tipTexts,
objectList=objectList,
textMatrix=textMatrix,
colorMatrix=colorMatrix,
resetScrollbars=resetScrollbars)