def test_Whatif(self):
#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" # DEFAULT is not to do more than 2 models because it takes quite a while.
# entryId = "1brv_cs_pk_2mdl"
# entryId = "1tgq_1model"
# pdbConvention = IUPAC
parseOnly = False # normal is False
showValues = True
ranges='cv'
# ranges='172-177'
# ranges='6-13,29-45'
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 )
if not parseOnly:
project.removeFromDisk()
project = Project.open( entryId, status='new' )
inputArchiveDir = os.path.join(cingDirTestsData, "ccpn")
ccpnFile = os.path.join(inputArchiveDir, entryId + ".tgz")
if not os.path.exists(ccpnFile):
ccpnFile = os.path.join(inputArchiveDir, entryId + ".tar.gz")
if not os.path.exists(ccpnFile):
self.fail("Neither %s or the .tgz exist" % ccpnFile)
self.assertTrue(project.initCcpn(ccpnFolder = ccpnFile, modelCount=2))
self.assertFalse(runWhatif(project, ranges=ranges, parseOnly=False))
else:
project = Project.open( entryId, status='old' )
# print project.cingPaths.format()
project.save()
if showValues:
for res in project.molecule.allResidues():
nTdebug(repr(res))
whatifResDict = res.getDeepByKeys(WHATIF_STR)
if not whatifResDict:
continue
# checkIDList = whatifResDict.keys()
checkIDList = 'RAMCHK'.split()
for checkID in checkIDList:
valueList = whatifResDict.getDeepByKeys(checkID,VALUE_LIST_STR)
qualList = whatifResDict.getDeepByKeys(checkID,QUAL_LIST_STR)
nTdebug("%10s valueList: %-80s qualList: %-80s" % ( checkID, valueList, qualList))
# Do not leave the old CCPN directory laying around since it might get added to by another test.
if os.path.exists(entryId):
self.assertFalse(shutil.rmtree(entryId))
def testMoleculePlot(self):
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 = "2hgh_1model"
# entryId = "1brv_1model"
# ranges = None
ranges = 'cv'
if entryId.startswith("2hgh"):
# Compile a NTlist instance with residue objects.
ranges = "2-54,111-136,145-193"
ranges = None
# 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 = "175-188"
# ranges = None
elif entryId.startswith("1bus"):
ranges = "6-13,29-45"
project = Project.open(entryId, status='new')
cyanaFile = os.path.join(cingDirTestsData, "cyana", entryId + ".cyana.tgz")
self.assertTrue(project.initCyana(cyanaFolder = cyanaFile))
# project.validate(parseOnly=False, htmlOnly=True, doProcheck=False, doWhatif=False, doWattos=False, doTalos=False) # needed?
self.assertFalse( project.molecule.setRanges(ranges) )
from cing.PluginCode.dssp import runDssp # Triggers checks. @UnusedImport # pylint: disable=W0612,W0404
project.runDssp()
if actuallyRunWhatif:
from cing.PluginCode.Whatif import runWhatif # Triggers checks. # pylint: disable=W0612,W0404
self.assertFalse(runWhatif(project))
else:
rangeList = project.molecule.getFixedRangeList(
max_length_range=ResPlot.MAX_WIDTH_IN_RESIDUES)
_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()
rotList = NTlist()
bbcList = NTlist()
accList = NTlist()
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()*100 + 1)
ramList.append(random()*5 + 1)
c12List.append(random()*5 + 1)
rotList.append(random()*5 + 1)
bbcList.append(random()*5 + 1)
accList.append(random()*4 - 2)
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(rotList, ROTCHK_STR, VALUE_LIST_STR))
self.assertFalse (whatifResDict.setDeepByKeys(bbcList, BBCCHK_STR, VALUE_LIST_STR))
self.assertFalse (whatifResDict.setDeepByKeys(accList, INOCHK_STR, VALUE_LIST_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 showValues:
nTdebug("%10s valueList: %-80s" % (checkID, valueList))
#end if actuallyRunWhatif:
# The following object will be responsible for creating a (png/pdf) file with
# possibly multiple pages
# Level 1: row
# Level 2: against main or alternative y-axis
# Level 3: plot parameters dictionary (extendable).
keyLoLoL = []
plotAttributesRowMain = NTdict()
plotAttributesRowAlte = NTdict()
plotAttributesRowMain[ KEY_LIST_STR] = [ PHI_STR, CV_STR ]
plotAttributesRowMain[ KEY_LIST2_STR] = [ PSI_STR, CV_STR ]
plotAttributesRowAlte[ KEY_LIST_STR] = [ 'cv_backbone' ]
plotAttributesRowMain[ YLABEL_STR] = 'cv phi/psi'
plotAttributesRowAlte[ YLABEL_STR] = 'cv backbone'
plotAttributesRowMain[ USE_ZERO_FOR_MIN_VALUE_STR] = True
# plotAttributesRowMain[ USE_MAX_VALUE_STR] = 0.2
keyLoLoL.append([ [plotAttributesRowMain], [plotAttributesRowAlte] ])
plotAttributesRowMain = NTdict()
plotAttributesRowMain[ KEY_LIST_STR] = [ CHK_STR, RAMACHANDRAN_CHK_STR, VALUE_STR ]
plotAttributesRowMain[ YLABEL_STR] = 'Z phi/psi'
keyLoLoL.append([ [plotAttributesRowMain]])
plotAttributesRowMain = NTdict()
plotAttributesRowAlte = NTdict()
plotAttributesRowMain[ KEY_LIST_STR] = [ CHI1_STR, CV_STR ]
plotAttributesRowMain[ KEY_LIST2_STR] = [ CHI2_STR, CV_STR ]
plotAttributesRowAlte[ KEY_LIST_STR] = [ 'cv_sidechain' ]
plotAttributesRowMain[ YLABEL_STR] = 'cv chi1/2'
plotAttributesRowAlte[ YLABEL_STR] = 'cv sidechain'
plotAttributesRowMain[ USE_ZERO_FOR_MIN_VALUE_STR] = True
# plotAttributesRowMain[ USE_MAX_VALUE_STR] = 1.0
keyLoLoL.append([ [plotAttributesRowMain], [plotAttributesRowAlte] ])
plotAttributesRowMain = NTdict()
plotAttributesRowAlte = NTdict()
plotAttributesRowMain[ KEY_LIST_STR] = [ RMSD_STR, BACKBONE_AVERAGE_STR, VALUE_STR ]
plotAttributesRowAlte[ KEY_LIST_STR] = [ RMSD_STR, HEAVY_ATOM_AVERAGE_STR, VALUE_STR ]
plotAttributesRowMain[ YLABEL_STR] = BACKBONE_AVERAGE_STR
plotAttributesRowAlte[ YLABEL_STR] = HEAVY_ATOM_AVERAGE_STR
plotAttributesRowMain[ USE_ZERO_FOR_MIN_VALUE_STR] = True
keyLoLoL.append([ [plotAttributesRowMain], [plotAttributesRowAlte] ])
plotAttributesRowMain = NTdict()
plotAttributesRowAlte = NTdict()
plotAttributesRowMain[ KEY_LIST_STR] = [ WHATIF_STR, C12CHK_STR, VALUE_LIST_STR ]
plotAttributesRowAlte[ KEY_LIST_STR] = [ WHATIF_STR, ROTCHK_STR, VALUE_LIST_STR ]
plotAttributesRowAlte[ KEY_LIST2_STR] = [ WHATIF_STR, RAMCHK_STR, VALUE_LIST_STR ]
plotAttributesRowMain[ YLABEL_STR] = C12CHK_STR
plotAttributesRowAlte[ YLABEL_STR] = ROTCHK_STR
plotAttributesRowMain[ USE_ZERO_FOR_MIN_VALUE_STR] = True
# plotAttributesRowMain[ USE_MAX_VALUE_STR] = 10.0
keyLoLoL.append([ [plotAttributesRowMain], [plotAttributesRowAlte] ])
plotAttributesRowMain = NTdict()
plotAttributesRowMain[ KEY_LIST_STR] = [ QSHIFT_STR, ALL_ATOMS_STR]
plotAttributesRowMain[ KEY_LIST2_STR] = [ QSHIFT_STR, BACKBONE_STR]
plotAttributesRowMain[ KEY_LIST3_STR] = [ QSHIFT_STR, HEAVY_ATOMS_STR]
plotAttributesRowMain[ KEY_LIST4_STR] = [ QSHIFT_STR, PROTONS_STR]
plotAttributesRowMain[ YLABEL_STR] = 'QCS all/bb/hvy/prt'
plotAttributesRowMain[ USE_ZERO_FOR_MIN_VALUE_STR] = True
# plotAttributesRowMain[ USE_VERBOSE_Y_LOCATOR_STR ] = True
plotAttributesRowMain[ USE_MAX_VALUE_STR] = 0.5
keyLoLoL.append([ [plotAttributesRowMain] ])
#BACKBONE_STR = 'backbone'
#HEAVY_ATOMS_STR = 'heavyAtoms'
#PROTONS_STR = 'protons'
nTdebug("Instantiating moleculePlotSet")
moleculePlotSet = MoleculePlotSet(project=project, keyLoLoL=keyLoLoL)
pdfPath = '%s/test_NTMoleculePlot.pdf' % self.cingDirTmpTest
moleculePlotSet.renderMoleculePlotSet(pdfPath, createPngCopyToo=True)
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 )
def testMoleculePlot(self):
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 = "2hgh_1model"
# entryId = "1brv_1model"
# ranges = None
ranges = 'cv'
if entryId.startswith("2hgh"):
# Compile a NTlist instance with residue objects.
ranges = "2-54,111-136,145-193"
ranges = None
# 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 = "175-188"
# ranges = None
elif entryId.startswith("1bus"):
ranges = "6-13,29-45"
project = Project.open(entryId, status='new')
cyanaFile = os.path.join(cingDirTestsData, "cyana",
entryId + ".cyana.tgz")
self.assertTrue(project.initCyana(cyanaFolder=cyanaFile))
# project.validate(parseOnly=False, htmlOnly=True, doProcheck=False, doWhatif=False, doWattos=False, doTalos=False) # needed?
self.assertFalse(project.molecule.setRanges(ranges))
from cing.PluginCode.dssp import runDssp # Triggers checks. @UnusedImport # pylint: disable=W0612,W0404
project.runDssp()
if actuallyRunWhatif:
from cing.PluginCode.Whatif import runWhatif # Triggers checks. # pylint: disable=W0612,W0404
self.assertFalse(runWhatif(project))
else:
rangeList = project.molecule.getFixedRangeList(
max_length_range=ResPlot.MAX_WIDTH_IN_RESIDUES)
_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()
rotList = NTlist()
bbcList = NTlist()
accList = NTlist()
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() * 100 + 1)
ramList.append(random() * 5 + 1)
c12List.append(random() * 5 + 1)
rotList.append(random() * 5 + 1)
bbcList.append(random() * 5 + 1)
accList.append(random() * 4 - 2)
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(
rotList, ROTCHK_STR, VALUE_LIST_STR))
self.assertFalse(
whatifResDict.setDeepByKeys(
bbcList, BBCCHK_STR, VALUE_LIST_STR))
self.assertFalse(
whatifResDict.setDeepByKeys(
accList, INOCHK_STR, VALUE_LIST_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 showValues:
nTdebug("%10s valueList: %-80s" %
(checkID, valueList))
#end if actuallyRunWhatif:
# The following object will be responsible for creating a (png/pdf) file with
# possibly multiple pages
# Level 1: row
# Level 2: against main or alternative y-axis
# Level 3: plot parameters dictionary (extendable).
keyLoLoL = []
plotAttributesRowMain = NTdict()
plotAttributesRowAlte = NTdict()
plotAttributesRowMain[KEY_LIST_STR] = [PHI_STR, CV_STR]
plotAttributesRowMain[KEY_LIST2_STR] = [PSI_STR, CV_STR]
plotAttributesRowAlte[KEY_LIST_STR] = ['cv_backbone']
plotAttributesRowMain[YLABEL_STR] = 'cv phi/psi'
plotAttributesRowAlte[YLABEL_STR] = 'cv backbone'
plotAttributesRowMain[USE_ZERO_FOR_MIN_VALUE_STR] = True
# plotAttributesRowMain[ USE_MAX_VALUE_STR] = 0.2
keyLoLoL.append([[plotAttributesRowMain], [plotAttributesRowAlte]])
plotAttributesRowMain = NTdict()
plotAttributesRowMain[KEY_LIST_STR] = [
CHK_STR, RAMACHANDRAN_CHK_STR, VALUE_STR
]
plotAttributesRowMain[YLABEL_STR] = 'Z phi/psi'
keyLoLoL.append([[plotAttributesRowMain]])
plotAttributesRowMain = NTdict()
plotAttributesRowAlte = NTdict()
plotAttributesRowMain[KEY_LIST_STR] = [CHI1_STR, CV_STR]
plotAttributesRowMain[KEY_LIST2_STR] = [CHI2_STR, CV_STR]
plotAttributesRowAlte[KEY_LIST_STR] = ['cv_sidechain']
plotAttributesRowMain[YLABEL_STR] = 'cv chi1/2'
plotAttributesRowAlte[YLABEL_STR] = 'cv sidechain'
plotAttributesRowMain[USE_ZERO_FOR_MIN_VALUE_STR] = True
# plotAttributesRowMain[ USE_MAX_VALUE_STR] = 1.0
keyLoLoL.append([[plotAttributesRowMain], [plotAttributesRowAlte]])
plotAttributesRowMain = NTdict()
plotAttributesRowAlte = NTdict()
plotAttributesRowMain[KEY_LIST_STR] = [
RMSD_STR, BACKBONE_AVERAGE_STR, VALUE_STR
]
plotAttributesRowAlte[KEY_LIST_STR] = [
RMSD_STR, HEAVY_ATOM_AVERAGE_STR, VALUE_STR
]
plotAttributesRowMain[YLABEL_STR] = BACKBONE_AVERAGE_STR
plotAttributesRowAlte[YLABEL_STR] = HEAVY_ATOM_AVERAGE_STR
plotAttributesRowMain[USE_ZERO_FOR_MIN_VALUE_STR] = True
keyLoLoL.append([[plotAttributesRowMain], [plotAttributesRowAlte]])
plotAttributesRowMain = NTdict()
plotAttributesRowAlte = NTdict()
plotAttributesRowMain[KEY_LIST_STR] = [
WHATIF_STR, C12CHK_STR, VALUE_LIST_STR
]
plotAttributesRowAlte[KEY_LIST_STR] = [
WHATIF_STR, ROTCHK_STR, VALUE_LIST_STR
]
plotAttributesRowAlte[KEY_LIST2_STR] = [
WHATIF_STR, RAMCHK_STR, VALUE_LIST_STR
]
plotAttributesRowMain[YLABEL_STR] = C12CHK_STR
plotAttributesRowAlte[YLABEL_STR] = ROTCHK_STR
plotAttributesRowMain[USE_ZERO_FOR_MIN_VALUE_STR] = True
# plotAttributesRowMain[ USE_MAX_VALUE_STR] = 10.0
keyLoLoL.append([[plotAttributesRowMain], [plotAttributesRowAlte]])
plotAttributesRowMain = NTdict()
plotAttributesRowMain[KEY_LIST_STR] = [QSHIFT_STR, ALL_ATOMS_STR]
plotAttributesRowMain[KEY_LIST2_STR] = [QSHIFT_STR, BACKBONE_STR]
plotAttributesRowMain[KEY_LIST3_STR] = [QSHIFT_STR, HEAVY_ATOMS_STR]
plotAttributesRowMain[KEY_LIST4_STR] = [QSHIFT_STR, PROTONS_STR]
plotAttributesRowMain[YLABEL_STR] = 'QCS all/bb/hvy/prt'
plotAttributesRowMain[USE_ZERO_FOR_MIN_VALUE_STR] = True
# plotAttributesRowMain[ USE_VERBOSE_Y_LOCATOR_STR ] = True
plotAttributesRowMain[USE_MAX_VALUE_STR] = 0.5
keyLoLoL.append([[plotAttributesRowMain]])
#BACKBONE_STR = 'backbone'
#HEAVY_ATOMS_STR = 'heavyAtoms'
#PROTONS_STR = 'protons'
nTdebug("Instantiating moleculePlotSet")
moleculePlotSet = MoleculePlotSet(project=project, keyLoLoL=keyLoLoL)
pdfPath = '%s/test_NTMoleculePlot.pdf' % self.cingDirTmpTest
moleculePlotSet.renderMoleculePlotSet(pdfPath, createPngCopyToo=True)