def test_Procheck(self):
cingDirTmpTest = os.path.join(cingDirTmp, getCallerName())
mkdirs(cingDirTmpTest)
self.failIf(os.chdir(cingDirTmpTest),
msg="Failed to change to test directory for files: " +
cingDirTmpTest)
runAqua = True
showProcheckResults = False
#entryId = "1ai0" # Most complex molecular system in any PDB NMR entry
entryId = "1bus"
# entryId = "1brv_1model" # Small much studied PDB NMR entry
ranges = None
if entryId.startswith("1brv"):
ranges = "173-186"
if entryId.startswith("1ai0"):
ranges = "2-20"
if entryId == "2hgh":
# in the case of 2hgh this is not a problem because the residue numbering doesn't
# overlap between the chain A protein and chain B RNA.
ranges = "2-11,13-33,35-54"
# 1 and 55 are 5' and 3' terminii which are a little looser.
# 12, and 34 are bases that are not basepaired.
ranges += ",104-105,115-136,145-190"
# 106-114 is a loop
# 137-144 is a loop
# 191-193 are 3 Zn ions.
#This leads to a procheck ranges file like:
# RESIDUES 2 B 11 B
# RESIDUES 13 B 33 B
# RESIDUES 35 B 54 B
# RESIDUES 104 A 105 A
# RESIDUES 115 A 136 A
# RESIDUES 145 A 190 A
cingDirTmpTest = os.path.join(cingDirTmp, getCallerName())
mkdirs(cingDirTmpTest)
self.failIf(os.chdir(cingDirTmpTest),
msg="Failed to change to test directory for files: " +
cingDirTmpTest)
project = Project(entryId)
self.failIf(project.removeFromDisk())
project = Project.open(entryId, status='new')
cyanaFile = os.path.join(cingDirTestsData, "cyana",
entryId + ".cyana.tgz")
self.assertTrue(project.initCyana(cyanaFolder=cyanaFile))
project.molecule.setRanges(ranges)
project.save()
self.failIf(
project.runProcheck(createPlots=True, runAqua=runAqua) is None)
if showProcheckResults:
for res in project.molecule.allResidues():
nTdebug(repr(res) + " " + repr(res.procheck.secStruct))
def testMolgrapRunFromPdbFile(self):
# SETUP FIRST
# entryId = "1ai0" # Most complex molecular system in any PDB NMR entry
# entryId = "1a4d" # Small much studied PDB NMR entry
# entryId = "1zwj" # X-ray entry of CESG interest.
entryId = "1brv" # Small much studied PDB NMR entry
# entryId = "2hgh_1model"
# does it matter to import it just now?
project = Project(entryId)
self.failIf(project.removeFromDisk())
project = Project.open(entryId, status='new')
cyanaFile = os.path.join(cingDirTestsData, "cyana",
entryId + ".cyana.tgz")
self.assertTrue(project.initCyana(cyanaFolder=cyanaFile))
project.save()
gifFileName = entryId + ".gif"
pathGif = os.path.join(self.cingDirTmpTest, gifFileName)
self.assertFalse(project.molecule.export2gif(pathGif, project=project))
self.assertTrue(os.path.exists(pathGif))
pathMolGifPinup = pathGif[:-4] + '_pin.gif'
self.assertTrue(os.path.exists(pathMolGifPinup))
pathGifDefault = os.path.join(cingPythonCingDir, 'PluginCode',
DATA_STR, 'UnknownImage.gif')
self.assertFalse(
os.path.getsize(pathGif) == os.path.getsize(pathGifDefault))
nTmessage("Created new molecular imagery at: %s" % self.cingDirTmpTest)
def test_Procheck(self):
cingDirTmpTest = os.path.join( cingDirTmp, getCallerName() )
mkdirs( cingDirTmpTest )
self.failIf(os.chdir(cingDirTmpTest), msg =
"Failed to change to test directory for files: " + cingDirTmpTest)
runAqua = True
showProcheckResults = False
#entryId = "1ai0" # Most complex molecular system in any PDB NMR entry
entryId = "1bus"
# entryId = "1brv_1model" # Small much studied PDB NMR entry
ranges = None
if entryId.startswith("1brv"):
ranges = "173-186"
if entryId.startswith("1ai0"):
ranges = "2-20"
if entryId == "2hgh":
# in the case of 2hgh this is not a problem because the residue numbering doesn't
# overlap between the chain A protein and chain B RNA.
ranges = "2-11,13-33,35-54"
# 1 and 55 are 5' and 3' terminii which are a little looser.
# 12, and 34 are bases that are not basepaired.
ranges += ",104-105,115-136,145-190"
# 106-114 is a loop
# 137-144 is a loop
# 191-193 are 3 Zn ions.
#This leads to a procheck ranges file like:
# RESIDUES 2 B 11 B
# RESIDUES 13 B 33 B
# RESIDUES 35 B 54 B
# RESIDUES 104 A 105 A
# RESIDUES 115 A 136 A
# RESIDUES 145 A 190 A
cingDirTmpTest = os.path.join( cingDirTmp, getCallerName() )
mkdirs( cingDirTmpTest )
self.failIf(os.chdir(cingDirTmpTest), msg =
"Failed to change to test directory for files: " + cingDirTmpTest)
project = Project( entryId )
self.failIf( project.removeFromDisk() )
project = Project.open( entryId, status='new' )
cyanaFile = os.path.join(cingDirTestsData, "cyana", entryId + ".cyana.tgz")
self.assertTrue(project.initCyana(cyanaFolder = cyanaFile))
project.molecule.setRanges(ranges)
project.save()
self.failIf(project.runProcheck(createPlots=True, runAqua=runAqua) is None)
if showProcheckResults:
for res in project.molecule.allResidues():
nTdebug(repr(res) +" "+ repr(res.procheck.secStruct))
def _testCreateCcpn(self):
'Disabled test because...'
cingDirTmpTest = os.path.join( cingDirTmp, getCallerName() )
mkdirs( cingDirTmpTest )
self.failIf(os.chdir(cingDirTmpTest), msg =
"Failed to change to test directory for files: " + cingDirTmpTest)
for entryId in AllChecks.entryList:
# Allow pdb files to be of different naming systems for this test.
project = Project(entryId)
self.failIf(project.removeFromDisk())
project = Project.open(entryId, status = 'new')
cyanaFolder = os.path.join(cingDirTestsData,"cyana", entryId+".cyana.tgz")
nTdebug("Reading files from: " + cyanaFolder)
project.initCyana( cyanaFolder)
project.save()
nTmessage( "Project: %s" % project)
ccpnFolder = entryId + "New"
self.assertTrue(project.saveCcpn(ccpnFolder))
def _testCreateCcpn(self):
'Disabled test because...'
cingDirTmpTest = os.path.join(cingDirTmp, getCallerName())
mkdirs(cingDirTmpTest)
self.failIf(os.chdir(cingDirTmpTest),
msg="Failed to change to test directory for files: " +
cingDirTmpTest)
for entryId in AllChecks.entryList:
# Allow pdb files to be of different naming systems for this test.
project = Project(entryId)
self.failIf(project.removeFromDisk())
project = Project.open(entryId, status='new')
cyanaFolder = os.path.join(cingDirTestsData, "cyana",
entryId + ".cyana.tgz")
nTdebug("Reading files from: " + cyanaFolder)
project.initCyana(cyanaFolder)
project.save()
nTmessage("Project: %s" % project)
ccpnFolder = entryId + "New"
self.assertTrue(project.saveCcpn(ccpnFolder))
def test_shiftx(self):
# entryId = "1brv" # Small much studied PDB NMR entry
# entryId = "2hgh_1model" RNA-protein complex.
entryId = "1brv"
# entryId = "1tgq_1model" # withdrawn entry
cingDirTmpTest = os.path.join( cingDirTmp, getCallerName() )
mkdirs( cingDirTmpTest )
self.failIf(os.chdir(cingDirTmpTest), msg =
"Failed to change to test directory for files: " + cingDirTmpTest)
project = Project( entryId )
self.failIf( project.removeFromDisk())
project = Project.open( entryId, status='new' )
cyanaFile = os.path.join(cingDirTestsData, "cyana", entryId + ".cyana.tgz")
self.assertTrue(project.initCyana(cyanaFolder = cyanaFile))
project.runShiftx()
def test_shiftx(self):
# entryId = "1brv" # Small much studied PDB NMR entry
# entryId = "2hgh_1model" RNA-protein complex.
entryId = "1brv"
# entryId = "1tgq_1model" # withdrawn entry
cingDirTmpTest = os.path.join(cingDirTmp, getCallerName())
mkdirs(cingDirTmpTest)
self.failIf(os.chdir(cingDirTmpTest),
msg="Failed to change to test directory for files: " +
cingDirTmpTest)
project = Project(entryId)
self.failIf(project.removeFromDisk())
project = Project.open(entryId, status='new')
cyanaFile = os.path.join(cingDirTestsData, "cyana",
entryId + ".cyana.tgz")
self.assertTrue(project.initCyana(cyanaFolder=cyanaFile))
project.runShiftx()
def testMolgrapRunFromPdbFile(self):
# SETUP FIRST
# entryId = "1ai0" # Most complex molecular system in any PDB NMR entry
# entryId = "1a4d" # Small much studied PDB NMR entry
# entryId = "1zwj" # X-ray entry of CESG interest.
entryId = "1brv" # Small much studied PDB NMR entry
# entryId = "2hgh_1model"
# does it matter to import it just now?
project = Project( entryId )
self.failIf( project.removeFromDisk())
project = Project.open( entryId, status='new' )
cyanaFile = os.path.join(cingDirTestsData, "cyana", entryId + ".cyana.tgz")
self.assertTrue(project.initCyana(cyanaFolder = cyanaFile))
project.save()
gifFileName = entryId+".gif"
pathGif = os.path.join( self.cingDirTmpTest, gifFileName)
self.assertFalse(project.molecule.export2gif(pathGif, project=project))
self.assertTrue(os.path.exists(pathGif))
pathMolGifPinup = pathGif[:-4] + '_pin.gif'
self.assertTrue(os.path.exists(pathMolGifPinup))
pathGifDefault = os.path.join( cingPythonCingDir, 'PluginCode', DATA_STR, 'UnknownImage.gif' )
self.assertFalse(os.path.getsize(pathGif) == os.path.getsize(pathGifDefault))
nTmessage("Created new molecular imagery at: %s" % self.cingDirTmpTest)
def testResPlot(self):
actuallyRunProcheck = False
actuallyRunWhatif = False
showValues = False
modelNum = 1 # Only used when simulating data
#entryId = "1ai0" # Most complex molecular system in any PDB NMR entry
# entryId = "2hgh" # Small much studied PDB NMR entry; 48 models
# entryId = "1bus" # Small much studied PDB NMR entry: 5 models of 57 AA.: 285 residues.
entryId = "1brv"
ranges = None
if entryId.startswith("2hgh"):
# Compile a NTlist instance with residue objects.
ranges = "2-54,111-136,145-193"
# 1 and 55 are 5' and 3' terminii which are a little looser.
# 12, and 34 are bases that are not basepaired.
# 191-193 are bound ZN ions.
elif entryId.startswith("1brv"):
# Truncate from Val171-Glu189 to:
ranges = "176-188"
project = Project( entryId )
project.removeFromDisk()
project = Project.open( entryId, status='new' )
cyanaFolder = os.path.join(cingDirTestsData,"cyana", entryId+".cyana.tgz")
nTdebug("Reading files from: " + cyanaFolder)
project.initCyana( cyanaFolder )
project.runDssp()
rangeList = project.molecule.getFixedRangeList(
max_length_range = ResPlot.MAX_WIDTH_IN_RESIDUES, ranges=ranges )
if actuallyRunProcheck:
self.failIf(project.procheck(createPlots=False, runAqua=False) is None)
if actuallyRunWhatif:
self.assertFalse(runWhatif(project))
pointsANGCHK = [] # list per res in rangeList of lists
pointsBNDCHK = []
pointsQUACHK = []
pointsRAMCHK = []
pointsC12CHK = []
pointsBBCCHK = []
resNumb = 0
for resList in rangeList:
for res in resList:
resNumb += 1
# nTdebug(repr(res))
# if random() < 0.2: # Skip a 10%
# continue
whatifResDict = res.setdefault(WHATIF_STR, NTdict())
procheckResDict = res.setdefault(PROCHECK_STR, NTdict())
# if not whatifResDict: # empty dict
# continue
angList = NTlist()
bndList = NTlist()
quaList = NTlist()
ramList = NTlist()
c12List = NTlist()
bbcList = NTlist()
accList = NTlist()
sstList = NTlist()
sstListPossibilities='SH' # secondary structure elements.
for _modelID in range(modelNum):
if not actuallyRunWhatif:
angList.append(random()*10-0) # Simulate abs max of Z-scores.
bndList.append(random()*5+1) # offset by 1 but still want to start from zero?
quaList.append(random()*5+1)
ramList.append(random()*5+1)
c12List.append(random()*5+1)
bbcList.append(random()*5+1)
accList.append(random()*4-2)
if not actuallyRunProcheck:
sstList.append( sstListPossibilities[ int(random()*2)]) # Simulate secondary structure
if not actuallyRunWhatif:
self.assertFalse ( whatifResDict.setDeepByKeys(angList, ANGCHK_STR,VALUE_LIST_STR) )
self.assertFalse ( whatifResDict.setDeepByKeys(bndList, BNDCHK_STR,VALUE_LIST_STR) )
self.assertFalse ( whatifResDict.setDeepByKeys(quaList, QUACHK_STR,VALUE_LIST_STR) )
self.assertFalse ( whatifResDict.setDeepByKeys(ramList, RAMCHK_STR,VALUE_LIST_STR) )
self.assertFalse ( whatifResDict.setDeepByKeys(c12List, C12CHK_STR,VALUE_LIST_STR) )
self.assertFalse ( whatifResDict.setDeepByKeys(bbcList, BBCCHK_STR,VALUE_LIST_STR) )
self.assertFalse ( whatifResDict.setDeepByKeys(accList, INOCHK_STR,VALUE_LIST_STR) )
if not actuallyRunProcheck:
self.assertFalse ( procheckResDict.setDeepByKeys(sstList, SECSTRUCT_STR) )
for d in [whatifResDict, procheckResDict]:
checkIDList = d.keys()
for checkID in checkIDList:
if d==whatifResDict:
valueList = d.getDeepByKeys(checkID,VALUE_LIST_STR)
else:
valueList = d.getDeepByKeys(checkID)
if checkID == ANGCHK_STR:
zScore = valueList.average()[0]
pointsANGCHK.append( (resNumb-.5, zScore) )
elif checkID == BNDCHK_STR:
zScore = valueList.average()[0]
pointsBNDCHK.append( (resNumb-.5, zScore) )
elif checkID == QUACHK_STR:
zScore = valueList.average()[0]
pointsQUACHK.append( (resNumb-.5, zScore) )
elif checkID == RAMCHK_STR:
zScore = valueList.average()[0]
pointsRAMCHK.append( (resNumb-.5, zScore) )
elif checkID == C12CHK_STR:
zScore = valueList.average()[0]
pointsC12CHK.append( (resNumb-.5, zScore) )
elif checkID == BBCCHK_STR:
zScore = valueList.average()[0]
pointsBBCCHK.append( (resNumb-.5, zScore) )
# nTdebug("pointsBBCCHK: %s", pointsBBCCHK)
if showValues:
nTdebug("%10s valueList: %-80s" % ( checkID, valueList))
fileNameList =[]
ps = None
r = 0
for resList in rangeList:
r += 1
# nTdebug("resList: %s" % resList)
ps = NTplotSet() # closes any previous plots
ps.hardcopySize = (600,600)
nrows = 2
ntPlotList = []
for i in range(nrows):
ntPlotList.append( ps.createSubplot(nrows,1,i+1,useResPlot=True,molecule=project.molecule,resList=resList) )
ps.subplotsAdjust(hspace = .1) # no height spacing between plots.
ps.subplotsAdjust(top = 0.9) # Accommodate icons and res types.
ps.subplotsAdjust(left = 0.15) # Accommodate extra Y axis label.
attr = fontVerticalAttributes()
attr.fontColor = 'blue'
# Left of actual yLabel.
labelAxesExtraList = [
'Backbone',
'Quality',
'Angle',
'',
'' ]
labelAxesList = [
'Ramachandr. Z',
'Chi 1/2. Z',
'Bond max Z',
'Restraint RMSD',
'' ]
for i in range(nrows):
position = (-0.12, 0.5)
ntPlotList[i].labelAxes( position, labelAxesExtraList[i], attributes=attr)
ntPlotList[i].yLabel = labelAxesList[i]
if i != nrows-1:
ntPlotList[i].xLabel = None
plusPoint = pointAttributes( type='plus', size=1.5, color='black' )
circlePoint = pointAttributes( type='circle', size=1.5, color='blue')
plusPoint.lineColor = 'black'
circlePoint.lineColor = 'blue'
length = ntPlotList[0].MAX_WIDTH_IN_RESIDUES
start = (r-1)*length
# pointsBBCCHK = removeNulls(pointsBBCCHK)
# buildin max is overridden by matplotlib
# end = NTmin(start + ntPlot1.MAX_WIDTH_IN_RESIDUES,len(pointsANGCHK))
pointsANGCHKOffset = convertPointsToPlotRange(pointsANGCHK, xOffset=-start, yOffset=0, start=0, length=length)
pointsBNDCHKOffset = convertPointsToPlotRange(pointsBNDCHK, xOffset=-start, yOffset=0, start=0, length=length)
pointsQUACHKOffset = convertPointsToPlotRange(pointsQUACHK, xOffset=-start, yOffset=0, start=0, length=length)
pointsRAMCHKOffset = convertPointsToPlotRange(pointsRAMCHK, xOffset=-start, yOffset=0, start=0, length=length)
pointsC12CHKOffset = convertPointsToPlotRange(pointsC12CHK, xOffset=-start, yOffset=0, start=0, length=length)
pointsBBCCHKOffset = convertPointsToPlotRange(pointsBBCCHK, xOffset=-start, yOffset=0, start=0, length=length)
pointsOffsetList = [pointsRAMCHKOffset,
pointsQUACHKOffset,
pointsANGCHKOffset ]
pointsOffsetList2 = [pointsBBCCHKOffset,
pointsC12CHKOffset,
pointsBNDCHKOffset ]
# nTdebug("pointsRAMCHKOffset: %s" % pointsRAMCHKOffset)
# nTdebug("start:end: %s %s" % (start,end))
for i in range(nrows):
if i >= len( pointsOffsetList ):
continue
ntPlotList[i].lines(pointsOffsetList[i], plusPoint)
ntPlotList[i].lines(pointsOffsetList2[i], circlePoint)
ntPlotList[i].autoScaleY( pointsOffsetList[i]+pointsOffsetList2[i] )
if i == 2: # by chance
ntPlotList[i].setYrange((.0, ntPlotList[i].yRange[1]))
ySpaceAxisResTypes = .02 + (nrows-1) * .01
ntPlotList[0].drawResTypes(ySpaceAxis=ySpaceAxisResTypes) # Weirdly can only be called after yRange is set.
for i in range(nrows):
showLabels = False
if i == nrows-1:
showLabels = True
# also sets the grid lines for major. Do last as it won't rescale with plot yet.
ntPlotList[i].drawResNumbers( showLabels=showLabels)
# Draw secondary structure elements and accessibility
# Set x range and major ticker.
# The major ticker determines the grid layout.
# leave space for res types but get it right on top.
# .18 at nrows = 4
# Needs to be done before re-scaling the y axis from [0,1] ???????
ySpaceAxisResIcons = .06 + (nrows-1) * .04
ntPlotList[0].iconBoxYheight = 0.16 * nrows / 3. # .16 at nrows=3
ntPlotList[0].drawResIcons( ySpaceAxis=ySpaceAxisResIcons )
# Set the grid and major tickers
fileNameList.append( 'residuePlotSet%03d.pdf' % r)
ps.hardcopy(fileNameList[r-1])
# end for resList in rangeList:
self.assertFalse( joinPdfPages( fileNameList, 'residuePlotSetAll.pdf' ))
for fileName in fileNameList:
os.unlink( fileName )
