def body(self, guiFrame):
ProgressBar.body(self, guiFrame)
guiFrame.expandGrid(2,3)
self.stepLabel = Label(guiFrame, text='Best step: ', grid=(0,3))
frame = LabelFrame(guiFrame, text='Best mappings', grid=(1,0), gridSpan=(1,4))
row = 0
for i in range(self.ensembleSize):
label = Label(frame, text='', pady=0, font='Courier 10',
borderwidth=0, grid=(row,0), sticky='ew')
self.labels.append(label)
row +=1
guiFrame.grid_rowconfigure(2, weight=1)
self.graph = ScrolledGraph(guiFrame, width=450, height=300,
graphType='scatter', title='Typing Scores',
xLabel='Spin System', yLabel='Score',
grid=(2,0), gridSpan=(1,4))
self.buttonList = ButtonList(guiFrame, texts=['Close',], commands=[self.done],
grid=(3,0), gridSpan=(1,4))
self.buttonList.buttons[0].disable()
def __init__(self, parent, ensembleSize=20, *args, **kw):
self.guiParent = parent
self.ensembleSize = ensembleSize or 20
self.labels = []
ProgressBar.__init__(self, parent, title="Highest Scoring Mappings", text=' Progress', **kw)
def update(self):
if self.progress == self.total:
width = int(self.cWidth)
self.canvas.coords(self.bar,self.bw,self.bw,width,self.cHeight)
self.percent.set( ' %3.1d %%' % 100)
self.buttonList.buttons[0].enable()
else:
ProgressBar.update(self)
def getProgressBar(self, text='', progress=0, total=100,
width=200, height=15, transient=True):
if self.inGui:
from memops.gui.ProgressBar import ProgressBar
return ProgressBar(self.parent, text=text, progress=progress, total=total,
width=width, height=height, transient=transient)
def run(self):
if self.chain:
pattern = self.filenameEntry.get()
nSteps = self.numStepsEntry.get() or 4000
pdbFile = self.pdbEntry.get()
dist = self.distEntry.get() or 3.0
pgb = ProgressBar(self, text='Searching', total=nSteps)
files = getFileNamesFromPattern(pattern , '.')
if not files:
return
clouds = getCloudsFromFile(files, self.chain.root)
score, self.scores, self.assignment = cloudHomologueAssign(self.chain, clouds, pdbFile, dist, nSteps, self.graph, pgb)
pgb.destroy()
self.globalScoreLabel.set(str(score))
self.update()
def readPredictions(self, predictions, gleScores):
progressBar = ProgressBar(self, text='Reading DANGLE predictions')
progressBar.total = len(predictions) - 2 # 2 header lines
residues = self.dangleChain.chain.sortedResidues()
getDangleResidue = self.dangleChain.findFirstDangleResidue
newDangleResidue = self.dangleChain.newDangleResidue
for residue in residues:
seqId = residue.seqId
prediction = predictions.get(seqId)
if prediction is None:
continue
gleMatrix = gleScores[seqId]
progressBar.increment()
#resNum, resName = prediction[:2];
numIsland = prediction[2]
ss = prediction[10]
angles = [min(179.9999, a) for a in prediction[3:10]]
phi, phiUpper, phiLower, psi, psiUpper, psiLower, omega = angles
# Normalise to max
maxVal = max(gleMatrix)
gleMatrix = [
max(0, int(val / maxVal * 65535)) / 65535.0
for val in gleMatrix
]
dangleResidue = getDangleResidue(residue=residue)
if not dangleResidue:
dangleResidue = newDangleResidue(
phiPsiLikelihoodMatrix=gleMatrix, residue=residue)
else:
dangleResidue.phiPsiLikelihoodMatrix = gleMatrix
dangleResidue.numIslands = numIsland
dangleResidue.phiValue = phi
dangleResidue.phiUpper = phiUpper
dangleResidue.phiLower = phiLower
dangleResidue.psiValue = psi
dangleResidue.psiUpper = psiUpper
dangleResidue.psiLower = psiLower
dangleResidue.omegaValue = omega
dangleResidue.secStrucCode = ss
progressBar.destroy()
def updateChemCompVarTable(self, *extra):
textMatrix = []
allChemComps = []
if (self.chemCompEntries is None):
selected = self.chem_comp_buttons.getSelected()
else:
selected = self.chemCompEntries
numberToLoad = self.numberChemCompsToLoad()
if (selected and (numberToLoad > 1)):
use_progress_bar = True
p = ProgressBar(self, text='loading', total=numberToLoad)
else:
use_progress_bar = False
try:
n = 0
for (molType, ccpCode) in self.chemCompInfoList:
chemCompInfo = self.chemCompInfoDict[(molType,ccpCode)]
isShown = self.chem_comps_shown.has_key((molType, ccpCode))
has_been_loaded = False
if (isShown):
chemComp = chemCompInfo.chemComp
if not chemComp:
chemComp = getChemComp(self.project, molType, ccpCode,
showError=showError)
chemCompAndVars = [chemComp] + list(chemComp.chemCompVars)# this loads data, if needed
for chemCompOrVar in chemCompAndVars:
if (self.chemCompShown(chemCompOrVar)):
n = n + 1
text = [n]
for heading in self.chem_comp_var_headings:
if hasattr(chemCompOrVar,heading):
text.append(getattr(chemCompOrVar, heading))
elif hasattr(chemCompOrVar,'chemComp') and hasattr(chemCompOrVar.chemComp,heading):
text.append(getattr(chemCompOrVar.chemComp, heading))
else:
text.append("n/a")
textMatrix.append(text)
allChemComps.append(chemCompOrVar)
if (use_progress_bar and has_been_loaded):
p.increment()
finally:
if (use_progress_bar):
p.destroy()
self.chem_comp_var_table.update(objectList=allChemComps, textMatrix=textMatrix)
def done(self): self.progress = self.total ProgressBar.update(self)
def readPredictionFile(self, filename, chain):
try:
fopen = open(filename, 'r')
except:
showError('File Reading Error',
'DANGLE prediction file %s cannot be open.' % filename,
parent=self)
return
lines = fopen.readlines()
progressBar = ProgressBar(self, text='Reading DANGLE predictions')
progressBar.total = len(lines) - 2 # 2 header lines
lines = lines[2:]
for line in lines:
progressBar.increment()
if (line == '\n'):
continue
array = line.split() # keep everything as string
resNum = int(array[0])
resName = array[1]
numIsland = int(array[2])
phi = array[3]
phiUpper = array[4]
phiLower = array[5]
psi = array[6]
psiUpper = array[7]
psiLower = array[8]
omega = array[9]
ss = array[10]
if (phi == 'None'):
phi = None
else:
phi = float(phi)
if (psi == 'None'):
psi = None
else:
psi = float(psi)
if (omega == 'None'):
omega = None
else:
omega = float(omega)
if omega == 180:
omega = 179.9
if (phiUpper == 'None'):
phiUpper = None
else:
phiUpper = float(phiUpper)
if (phiLower == 'None'):
phiLower = None
else:
phiLower = float(phiLower)
if (psiUpper == 'None'):
psiUpper = None
else:
psiUpper = float(psiUpper)
if (psiLower == 'None'):
psiLower = None
else:
psiLower = float(psiLower)
if (ss == 'None'):
ss = None
path = os.path.join(self.dangleDir, 'Res_%d.pgm' % resNum)
gleMatrix = self.readGLE(path)
residue = chain.findFirstResidue(seqId=int(resNum))
dangleResidue = self.dangleChain.findFirstDangleResidue(
residue=residue)
if not dangleResidue:
dangleResidue = self.dangleChain.newDangleResidue(
phiPsiLikelihoodMatrix=gleMatrix, residue=residue)
else:
dangleResidue.phiPsiLikelihoodMatrix = gleMatrix
dangleResidue.numIslands = numIsland
dangleResidue.phiValue = phi
dangleResidue.phiUpper = phiUpper
dangleResidue.phiLower = phiLower
dangleResidue.psiValue = psi
dangleResidue.psiUpper = psiUpper
dangleResidue.psiLower = psiLower
dangleResidue.omegaValue = omega
dangleResidue.secStrucCode = ss
# Delete temp pgm files to save space once data is in CCPN
os.unlink(path)
fopen.close()
progressBar.destroy()
def runDangle(self):
chain = self.chain
shiftList = self.shiftList
if (not chain) or (not shiftList):
showError('Cannot Run DANGLE',
'Please specify a chain and a shift list.',
parent=self)
return
# check if there is a DangleChain available
self.checkDangleStore()
dangleStore = self.dangleStore
if not dangleStore:
return
dangleChain = dangleStore.findFirstDangleChain(chain=chain)
if dangleChain:
data = (chain.code, dangleChain.shiftList.serial)
msg = 'Predictions for Chain %s using Shift List %d already exist.\nReplace data?' % data
if not showYesNo('Replace Data', msg, parent=self):
return
else:
self.dangleChain = dangleChain
dangleChain.shiftList = shiftList
else:
self.dangleChain = dangleStore.newDangleChain(chain=chain,
shiftList=shiftList)
#dangleStore.packageLocator.repositories[0].url.dataLocation = '/home/msc51/ccpn/NexusTestGI'
#dangleStore.packageName = 'cambridge.dangle'
repository = dangleStore.packageLocator.repositories[0]
array = dangleStore.packageName.split('.')
path = os.path.join(repository.url.dataLocation, *array)
path = os.path.join(path, dangleStore.name,
chain.code) # Dangle_dir/dangleStoreName/chainCode
if not os.path.exists(path):
os.makedirs(path)
self.dangleDir = path
inputFile = os.path.join(self.dangleDir, 'dangle_cs.inp')
if os.path.isfile(inputFile):
os.unlink(inputFile)
outputFile = os.path.join(self.dangleDir, 'danglePred.txt')
if os.path.isfile(outputFile):
os.unlink(outputFile)
numShift = self.makeDangleInput(inputFile, chain, shiftList)
if not os.path.isfile(inputFile):
msg = 'No DANGLE input has been generated.\nPlease check shift lists.'
showError('File Does Not Exist', msg, parent=self)
return
if numShift == 0:
msg = 'No shift data in input file.\nPerhaps shifts are not assigned.\nContinue prediction anyway?'
if not showYesNo('Empty DANGLE input', msg, parent=self):
return
rejectThresh = self.rejectPulldown.getObject()
# Use the Reference info from the main installation
# location must be absolute because DANGLE could be run from anywhere
location = os.path.dirname(dangleModule.__file__)
progressBar = ProgressBar(self)
self.update_idletasks()
dangle = Dangle(location,
inputFile=inputFile,
outputDir=self.dangleDir,
reject=rejectThresh,
angleOnly=False,
progressBar=progressBar,
writePgm=False)
#self.dangleDir = '/home/msc51/nexus/gItest/DanglePred/'
#outputFile = '/home/msc51/nexus/gItest/DanglePred/danglePred.txt'
predictions = dangle.predictor.predictions
gleScores = dangle.predictor.gleScores
self.readPredictions(predictions, gleScores)
self.updatePredictionMatrix()