def getTableObjects(self):
objs = []
if self.project:
objs = getThroughSpacePeakLists(self.project)
if self.constraintSet:
objs.extend(list(self.constraintSet.constraintLists))
return objs
def getSpectra(self):
spectra = set()
peakLists = getThroughSpacePeakLists(self.nmrProject)
for peakList in peakLists:
spectra.add(peakList.dataSource)
spectra = list(spectra)
spectra.sort()
return spectra
def getNoesys(self):
peakLists = getThroughSpacePeakLists(self.project)
names = [
'<None>',
]
for peakList in peakLists:
spectrum = peakList.dataSource
name = '%s:%s:%s' % (spectrum.experiment.name, spectrum.name,
peakList.serial)
names.append(name)
self.peakListDict[name] = peakList
if not self.noesyPeakList:
self.noesyPeakList = peakList
return names
def showPeaks(self):
if not self.selectedAtoms:
msg = 'No atoms selected'
showWarning('Warning', msg, parent=self)
return
if self.peakList:
peakLists = [
self.peakList,
]
else:
peakLists = set(getThroughSpacePeakLists(self.project))
resonances = []
for coordAtom in self.selectedAtoms:
atom = coordAtom.atom
atomSet = atom.atomSet
if not atomSet:
continue
for resonanceSet in atomSet.resonanceSets:
for resonance in resonanceSet.resonances:
resonances.append(resonance)
peaks = set([])
for resonance in resonances:
for contrib in resonance.peakDimContribs:
peak = contrib.peakDim.peak
if peak.peakList in peakLists:
peaks.add(peak)
self.connections = []
self.structFrame.clearConnections()
self.structFrame.clearHighlights()
if peaks:
for peak in peaks:
self.showPeakConnection(peak)
self.guiParent.viewPeaks(list(peaks))
self.updateAfter()
def updatePeakLists(self, obj=None):
index = 0
names = []
peakLists = getThroughSpacePeakLists(self.project)
if peakLists:
if self.peakList not in peakLists:
self.peakList = peakLists[0]
index = peakLists.index(self.peakList)
names = ['%s:%s:%d' % (pl.dataSource.experiment.name, \
pl.dataSource.name, pl.serial) for pl in peakLists ]
peakLists.append(None)
names.append('<All Avail>')
else:
self.peakList = None
self.peakListPulldown.setup(names, peakLists, index)
def analyseNoeAssignments(molSystem, peakLists=None):
# Row per residue - cols are num NOES: total, intra, inter,
# seq, short, short non-seq, long, inter chain, intra chain, contacted res
project = molSystem.root
if not peakLists:
peakLists = getThroughSpacePeakLists(project)
total = {}
intra = {}
inter = {}
seqen = {}
short = {}
nonSeqShort = {}
longr = {}
interCh = {}
intraCh = {}
contact = {}
for peakList in peakLists:
dataDims = getThroughSpaceDataDims(peakList.dataSource)
if not dataDims:
initExpTransfers(peakList.dataSource.experiment)
dataDims = getThroughSpaceDataDims(peakList.dataSource)
if not dataDims:
experiment = peakList.dataSource.experiment
print "Something is wrong with ExpTransfer setup for experiment %s" % (experiment.name)
continue
dims = set([dd.dim for dd in dataDims])
for peak in peakList.peaks:
dict = {}
peakDims = [pd for pd in peak.peakDims if pd.dim in dims]
dimGrouped = []
dimUngrouped = []
for peakDim in peakDims:
grouped = []
ungrouped = []
for contrib in peakDim.peakDimContribs:
resonanceSet = contrib.resonance.resonanceSet
if not resonanceSet:
continue
if contrib.peakContribs:
grouped.append((contrib, resonanceSet))
else:
ungrouped.append((contrib, resonanceSet))
dimGrouped.append(grouped)
dimUngrouped.append(ungrouped)
for contribs in dimGrouped:
for contrib, resonanceSet in contribs:
residue = resonanceSet.findFirstAtomSet().findFirstAtom().residue
for peakContrib in contrib.peakContribs:
if dict.get(peakContrib) is None:
dict[peakContrib] = []
dict[peakContrib].append(residue)
if (len(dimUngrouped[0]) < 2) or (len(dimUngrouped[-1]) < 2):
for contribs in dimUngrouped:
for contrib, resonanceSet in contribs:
residue = resonanceSet.findFirstAtomSet().findFirstAtom().residue
if dict.get(None) is None:
dict[None] = []
dict[None].append(residue)
for peakContrib in dict.keys():
residues = dict[peakContrib]
if len(residues) > 1:
for i in range(len(residues)-1):
residueI = residues[i]
chainI = residueI.chain
if contact.get(residueI) is None:
contact[residueI] = {}
for j in range(i+1,len(residues)):
residueJ = residues[j]
chainJ = residueJ.chain
delta = abs(residueI.seqCode-residueJ.seqCode)
if contact.get(residueJ) is None:
contact[residueJ] = {}
total[chainI] = total.get(chainI, 0) + 1
if chainI is not chainJ:
total[chainJ] = total.get(chainJ, 0) + 1
if residueI is residueJ:
intra[residueI] = intra.get(residueI, 0) + 1
total[residueI] = total.get(residueI, 0) + 1
intra[chainI] = intra.get(chainI, 0) + 1
else:
contact[residueJ][residueI] = True
contact[residueI][residueJ] = True
total[residueI] = total.get(residueI, 0) + 1
total[residueJ] = total.get(residueJ, 0) + 1
inter[residueI] = inter.get(residueI, 0) + 1
inter[residueJ] = inter.get(residueJ, 0) + 1
inter[chainI] = inter.get(chainI, 0) + 1
if chainI is not chainJ:
inter[chainJ] = inter.get(chainJ, 0) + 1
if chainI is chainJ:
intraCh[chainI] = intraCh.get(chainI, 0) + 1
intraCh[residueI] = intraCh.get(residueI, 0) + 1
if residueI is not residueJ:
intraCh[residueJ] = intraCh.get(residueJ, 0) + 1
if delta < 5:
if delta > 0:
short[chainI] = short.get(chainI, 0) + 1
short[residueI] = short.get(residueI, 0) + 1
if residueI is not residueJ:
short[residueJ] = short.get(residueJ, 0) + 1
if delta > 1:
nonSeqShort[chainI] = nonSeqShort.get(chainI, 0) + 1
nonSeqShort[residueI] = nonSeqShort.get(residueI, 0) + 1
nonSeqShort[residueJ] = nonSeqShort.get(residueJ, 0) + 1
elif delta == 1:
seqen[residueI] = seqen.get(residueI, 0) + 1
seqen[residueJ] = seqen.get(residueJ, 0) + 1
seqen[chainI] = seqen.get(chainI, 0) + 1
else:
longr[chainI] = longr.get(chainI, 0) + 1
longr[residueI] = longr.get(residueI, 0) + 1
longr[residueJ] = longr.get(residueJ, 0) + 1
else:
longr[residueI] = longr.get(residueI, 0) + 1
longr[residueJ] = longr.get(residueJ, 0) + 1
longr[chainI] = longr.get(chainI, 0) + 1
longr[chainJ] = longr.get(chainJ, 0) + 1
interCh[residueI] = interCh.get(residueI, 0) + 1
interCh[residueJ] = interCh.get(residueJ, 0) + 1
interCh[chainI] = interCh.get(chainI, 0) + 1
interCh[chainJ] = interCh.get(chainJ, 0) + 1
if len(molSystem.chains) > 1:
residues = [('%s%5.5d' % (r.chain.code,r.seqCode),
'%s%d%s'% (r.chain.code,r.seqCode,r.ccpCode),r) for r in contact.keys()]
else:
residues = [('%5.5d' % (r.seqCode,),
'%d%s' % (r.seqCode,r.ccpCode),r) for r in contact.keys()]
residues.sort()
data = []
for key, name, residue in residues:
datum = [name,
total.get(residue, 0),
intra.get(residue, 0),
inter.get(residue, 0),
seqen.get(residue, 0),
short.get(residue, 0),
nonSeqShort.get(residue, 0),
longr.get(residue, 0),
intraCh.get(residue, 0),
interCh.get(residue, 0),
contact[residue].keys()]
data.append([residue, datum])
if len(molSystem.chains) > 1:
for residue, datum in data:
residues2 = [('%s%5.5d' % (r.chain.code,r.seqCode),
'%s%d'% (r.chain.code,r.seqCode)) for r in datum[-1]]
residues2.sort()
datum[-1] = ' '.join([x[1] for x in residues2])
else:
for residue, datum in data:
residues2 = [('%5.5d' % (r.seqCode),
'%d' % (r.seqCode)) for r in datum[-1]]
residues2.sort()
datum[-1] = ' '.join([x[1] for x in residues2])
chains = [(chain.code, chain) for chain in molSystem.chains]
chains.sort()
chains.reverse()
for code, chain in chains:
datum = ['Chain %s' % code,]
datum.append(total.get(chain, 0))
datum.append(intra.get(chain, 0))
datum.append(inter.get(chain, 0))
datum.append(seqen.get(chain, 0))
datum.append(short.get(chain, 0))
datum.append(nonSeqShort.get(chain, 0))
datum.append(longr.get(chain, 0))
datum.append(intraCh.get(chain, 0))
datum.append(interCh.get(chain, 0))
datum.append(None)
data.insert(0, [None, datum])
return data
def getPeakLists(self): # overwrites superclass return getThroughSpacePeakLists(self.project)
def runRpf(self,
doAlised=DEFAULT_CONSIDER_ALIASED_POSITIONS,
distThreshold=DEFAULT_DISTANCE_THRESHOLD,
prochiralExclusion=DEFAULT_PROCHIRAL_EXCLUSION_SHIFT,
diagonalExclusion=DEFAULT_DIAGONAL_EXCLUSION_SHIFT):
"""
Return None on error.
It's not an error to have no peak list.
If pyRpf crashes the exception will be propagated up from here.
"""
nTmessage("Starting cing.PluginCode.Analysis#runRpf")
if not hasattr(self.project, CCPN_LOWERCASE_STR):
# nTdebug("Failed to find ccpn attribute project. Happens when no CCPN project was read first.") # TODO: change when cing to ccpn code works.
return
# end if
self.ccpnProject = self.project[CCPN_LOWERCASE_STR]
ccpnProject = self.ccpnProject
if not ccpnProject:
nTmessage("Failed to find ccpn project.")
return
# Find and print this peakList in the CCPN data model.
peakLists = getThroughSpacePeakLists(ccpnProject)
if not peakLists:
nTwarning("No peak list found; skipping runRpf")
return
nTmessage('Peaklists: [%s]' % peakLists)
# peakLists = [pl for pl in self.peakListTable.objectList if pl.rpfUse]
# ensembles = [e for e in self.ensembleTable.objectList if e.rpfUse]
ensembles = getEnsembles(ccpnProject)
if not ensembles:
nTwarning("No ensemble found; skipping runRpf")
return
for ensemble in ensembles:
nTdebug("Using ensemble: %s " % str(ensemble))
ensemble.rpfUse = True # set the selection automatically.
# end for
tolerances = []
for peakList in peakLists:
try:
tolerance = getNoeTolerances(peakList)
except:
nTexception(format_exc())
nTerror(
"Analysis: Crashed on getNoeTolerances and unknown how to be taking default tolerances."
)
return
tolerances.append(tolerance)
nTdebug("Using peakList.dataSource.name: %s with tolerance: %s" %
(peakList.dataSource.name, str(tolerance)))
# peakList[RPF_USE] = True # set the selection automatically.
peakList.rpfUse = True # set the selection automatically.
# end for
#Instead of polluting the RPF code simply prevent it from crashing CING by wrapping the functionality in a try block.
validResultStores = calcRPF(
ensembles,
peakLists,
tolerances,
distThreshold,
prochiralExclusion,
diagonalExclusion,
doAlised,
verbose=cing.verbosity == cing.verbosityDebug)
# self.updateResultsTable()
nTdebug("validResultStores: %s" % str(validResultStores))
return validResultStores
