def _testPlotModelHisto(self):
ps = NTplotSet() # closes any previous plots
outliersPerModel = { 0:2, 1:3 }
valueList = outliersPerModel.values()
modelCount = len(outliersPerModel.keys())
plot = NTplot( xLabel = 'Model',
xRange = (0, modelCount),
# yRange = (0, 5),
yLabel = 'Outliers',
hardcopySize= (600,300),
# aspectRatio = 0.5
)
ps.addPlot(plot)
plot.autoScaleYByValueList(valueList,
startAtZero=True,
useIntegerTickLabels=True
)
plot.barChart( outliersPerModel.items(),
0.05, 0.95,
attributes = boxAttributes(fillColor='green' ) )
ps.hardcopy( 'testPlotModelHisto.png' )
def plotDihedralD1D2byResType():
showDataPoints = False
dihedralName1 = 'Cb4N'
dihedralName2 = 'Cb4C'
# graphicsFormat = "png"
outputDir = os.path.join(cingDirTmp, 'd1d2')
if not os.path.exists(outputDir):
os.mkdir(outputDir)
# outputDir = cingDirTmp
os.chdir(outputDir)
# ssType = 'E'
# resType = 'GLY'
# for ssType in histRamaBySsAndResType.keys():
# ssTypeForFileName = ssType.replace(' ', '_')
ssTypeFixed = 'H'
resTypeListSkip = [
'CSB', 'GLUH', 'HISE', 'HISH', 'MSE', '', '', '', '', ''
]
for resType in hPlot.histd1BySs0AndResTypes[ssTypeFixed].keys(
): # TODO: check UNTESTED code for attribute histd1BySs0AndResTypes
# if resType != 'ARG': # for testing enable filtering.
# continue
if resType in resTypeListSkip:
continue
titleStr = 'd1d2 ' + resType
nTmessage("plotting: %s" % titleStr)
# hist = histd1d2BySsAndResType[ssType][resType]
ps = NTplotSet() # closes any previous plots
ps.hardcopySize = (500, 500)
# residueName = resType + ""
x = NTlist(-45, -80, 125) # outside the range.
y = NTlist(-65, -63, -125)
# important to switch to temp space before starting to generate files for the project.
project = Project('testPlotHistoDihedrald1d2')
plotparams1 = project.plotParameters.getdefault(
dihedralName1, 'dihedralDefault')
plotparams2 = project.plotParameters.getdefault(
dihedralName2, 'dihedralDefault')
x.limit(plotparams1.min, plotparams1.max)
y.limit(plotparams2.min, plotparams2.max)
plot = NTplot(title=titleStr,
xRange=(plotparams1.min, plotparams1.max),
xTicks=range(int(plotparams1.min),
int(plotparams1.max + 1),
plotparams1.ticksize),
xLabel=dihedralName1,
yRange=(plotparams2.min, plotparams2.max),
yTicks=range(int(plotparams2.min),
int(plotparams2.max + 1),
plotparams2.ticksize),
yLabel=dihedralName2)
ps.addPlot(plot)
# Plot a density background
histList = []
ssTypeList = hPlot.histd1BySs0AndResTypes.keys(
) # TODO: test this untested histd1BySs0AndResTypes parameter
ssTypeList.sort() # in place sort to: space, H, S
for ssType in ssTypeList:
hist = getDeepByKeys(hPlot.histd1BySs0AndResTypes, ssType, resType)
if hist != None:
nTdebug('appending [%s]' % ssType)
histList.append(hist)
if histList:
plot.dihedralComboPlot(histList)
if showDataPoints:
myPoint = plusPoint.copy()
myPoint.pointColor = 'green'
myPoint.pointSize = 6.0
myPoint.pointEdgeWidth = 1.0
myPoint.fill = False
if resType == 'GLY':
myPoint.pointType = 'triangle'
if resType == 'PRO':
myPoint.pointType = 'square'
plot.points(zip(x, y), attributes=myPoint)
# fn = os.path.join('bySsAndResType', ( ssTypeForFileName+"_"+resType+"."+graphicsFormat))
# fn = os.path.join('byResType', ( resType+"."+graphicsFormat))
# fn = resType + "_d1d2." + graphicsFormat
# ps.hardcopy(fn, graphicsFormat)
plot.show()
def plotDihedralD1D2():
dihedralName1 = 'Cb4N'
dihedralName2 = 'Cb4C'
graphicsFormat = "png"
entryId = "1brv" # Small much studied PDB NMR entry
# entryId = "1hy8" # small, single model, very low scoring entry
pdbDirectory = os.path.join(cingDirTestsData, "pdb", entryId)
pdbFileName = "pdb" + entryId + ".ent"
pdbFilePath = os.path.join(pdbDirectory, pdbFileName)
# does it matter to import it just now?
project = Project(entryId)
project.removeFromDisk()
project = Project.open(entryId, status='new')
project.initPDB(pdbFile=pdbFilePath, convention=IUPAC)
# ssType = 'E'
# resType = 'GLY'
# for ssType in histRamaBySsAndResType.keys():
# ssTypeForFileName = ssType.replace(' ', '_')
titleStr = 'd1d2 all resType'
nTmessage("plotting: %s" % titleStr)
# hist = histd1d2BySsAndResType[ssType][resType]
ps = NTplotSet() # closes any previous plots
ps.hardcopySize = (500, 500)
# residueName = resType + ""
x = NTlist(-45, -80, 125) # outside the range.
y = NTlist(-65, -63, -125)
# important to switch to temp space before starting to generate files for the project.
# project = Project('testPlotHistoDihedrald1d2')
plotparams1 = project.plotParameters.getdefault(dihedralName1,
'dihedralDefault')
plotparams2 = project.plotParameters.getdefault(dihedralName2,
'dihedralDefault')
x.limit(plotparams1.min, plotparams1.max)
y.limit(plotparams2.min, plotparams2.max)
plot = NTplot(title=titleStr,
xRange=(plotparams1.min, plotparams1.max),
xTicks=range(int(plotparams1.min), int(plotparams1.max + 1),
plotparams1.ticksize),
xLabel=dihedralName1,
yRange=(plotparams2.min, plotparams2.max),
yTicks=range(int(plotparams2.min), int(plotparams2.max + 1),
plotparams2.ticksize),
yLabel=dihedralName2)
ps.addPlot(plot)
# Plot a density background
histList = []
ssTypeList = hPlot.histd1BySs0.keys(
) # TODO: check this histd1BySs0 attribute. UNTESTED.
ssTypeList.sort() # in place sort to: space, H, S
for ssType in ssTypeList:
hist = getDeepByKeys(hPlot.histd1BySs0, ssType)
if hist != None:
nTdebug('appending [%s]' % ssType)
histList.append(hist)
if histList:
plot.dihedralComboPlot(histList)
# fn = os.path.join('bySsAndResType', ( ssTypeForFileName+"_"+resType+"."+graphicsFormat))
# fn = os.path.join('byResType', ( resType+"."+graphicsFormat))
fpGood = open(project.name + '.testCb2Good.out', 'w')
fpBad = open(project.name + '.testCb2Bad.out', 'w')
mCount = project.molecule.modelCount
for res in project.molecule.A.allResidues():
triplet = NTlist()
for i in [-1, 0, 1]:
triplet.append(res.sibling(i))
if None in triplet:
nTdebug('Skipping ' % res)
else:
ca_atms = triplet.zap('CA')
cb_atms = triplet.zap('CB')
nTdebug("%s %s %s %s" % (res, triplet, ca_atms, cb_atms))
if None in cb_atms: # skip Gly for now
nTdebug('Skipping %s' % res)
else:
d1 = Dihedral(res, 'Cb4N', range=[0.0, 360.0])
d1.atoms = [cb_atms[0], ca_atms[0], ca_atms[1], cb_atms[1]]
d1.calculateValues()
res['Cb4N'] = d1 # append dihedral to residue
d2 = Dihedral(res, 'Cb4C', range=[0.0, 360.0])
d2.atoms = [cb_atms[1], ca_atms[1], ca_atms[2], cb_atms[2]]
d2.calculateValues()
res['Cb4C'] = d2 # append dihedral to residue
bb = getDeepByKeys(res, WHATIF_STR, BBCCHK_STR, VALUE_LIST_STR,
0) # check first one.
if bb == None:
nTdebug('Skipping without BB %s' % res)
continue
if d1.cv < 0.03 and d2.cv < 0.03: # Only include structured residues
for i in range(mCount): # Consider each model individually
# bb = res.Whatif.bbNormality.valueList[i]
bb = getDeepByKeys(res, WHATIF_STR, BBCCHK_STR,
VALUE_LIST_STR, i)
if bb == None:
nTdebug('Skipping without BB %s' % res)
continue
angles = NTlist() # store phi, psi, chi1, chi2
for angle in ['PHI', 'PSI', 'CHI1', 'CHI2']:
if res.has_key(angle):
angles.append(res[angle][i])
else:
angles.append(0.0)
#end for
if bb < 20.0: # Arbitrary 20 bb occurences as cuttoff for now
fprintf(fpBad,
'%4d %7.2f %7.2f %7.2f %s %s %s\n',
res.resNum, d1[i], d2[i], bb,
angles.format("%7.2f "), res,
res.dssp.consensus)
else:
fprintf(fpGood,
'%4d %7.2f %7.2f %7.2f %s %s %s\n',
res.resNum, d1[i], d2[i], bb,
angles.format("%7.2f "), res,
res.dssp.consensus)
#end if
#end if
#end if
#end for
fpBad.close()
fpGood.close()
fn = "allRestype_d1d2." + graphicsFormat
ps.hardcopy(fn, graphicsFormat)
def plotHisBySsTypeResTypes():
graphicsFormat = "png"
doOnlyOverall = False
# If set it will do a single ssType otherwise the overall.
# for doOverall in [ False, True ]:
for doOverall in [True]:
if doOverall:
ssTypeList = [None]
else:
ssTypeList = [' ', 'S', 'H']
for ssType in ssTypeList:
#met-asp-leu
for _i, resType in enumerate(common20AAList):
if resType != 'PHE':
continue
for _j, resTypePrev in enumerate(common20AAList):
if resTypePrev != 'SER':
continue
for _k, resTypeNext in enumerate(common20AAList):
if resTypeNext != 'VAL':
continue
resTypeListBySequenceOrder = (resTypePrev, resType,
resTypeNext)
myHistList = getTripletHistogramList(
resTypeListBySequenceOrder,
doOnlyOverall=doOnlyOverall,
ssTypeRequested=ssType,
doNormalize=True)
if myHistList == None:
nTwarning(
"Encountered an error getting the D1D2 hist for %s; skipping"
% str(resTypeListBySequenceOrder))
continue
if len(myHistList) != 1:
nTdebug(
"Expected exactly one but Found %s histogram for %s; skipping"
% (len(myHistList),
str(resTypeListBySequenceOrder)))
continue
myHist = deepcopy(myHistList[0])
# nTdebug("myHist: %s" % str(myHist))
myList = numpy.asarray(myHist).flatten()
maxl = numpy.max(myList)
sdl = numpy.std(myList)
avl = numpy.average(myList)
suml = numpy.sum(myList)
n = 36
suml2 = avl * n * n
if math.fabs(suml2 - suml) > 1:
# Perhaps because sum is misinterpreted?
msg = "Math is off for suml != suml2: %s != %s" % (
suml, suml2)
nTerror(msg)
if maxl > suml:
msg = "Math is off for maxl > suml : %s != %s" % (
maxl, suml)
nTerror(msg)
vL = []
for value in (avl, sdl, maxl, suml):
vL.append(locale.format('%12.3f', value, True))
strTitle = "av: %s sd: %s\nmax: %s sum: %s" % (
vL[0], vL[1], vL[2], vL[3])
nTdebug("myHist: %s" % strTitle)
if True: # plot distribution itself too?
clf()
ps = NTplotSet() # closes any previous plots
ps.hardcopySize = (500, 500)
plotparams1 = plotParameters.getdefault(
dihedralName1, 'dihedralDefault')
plotparams2 = plotParameters.getdefault(
dihedralName2, 'dihedralDefault')
myplot = NTplot(
title=strTitle,
xRange=(plotparams1.min, plotparams1.max),
xTicks=range(int(plotparams1.min),
int(plotparams1.max + 1),
plotparams1.ticksize),
xLabel=dihedralName1,
yRange=(plotparams2.min, plotparams2.max),
yTicks=range(int(plotparams2.min),
int(plotparams2.max + 1),
plotparams2.ticksize),
yLabel=dihedralName2)
ps.addPlot(myplot)
myplot.dihedralComboPlot([myHist],
minPercentage=MIN_Z_D1D2,
maxPercentage=MAX_Z_D1D2,
scaleBy=SCALE_BY_Z,
ssType=ssType)
fn = 'd1d2_%s_%s-%s-%s' % (ssType, resTypePrev,
resType, resTypeNext)
if doOverall:
fn += '_ov_'
fn += "." + graphicsFormat
ps.hardcopy(fn, graphicsFormat)
if True:
clf()
hist(myList, 40)
xlabel('triplet count')
ylabel('number of occurrences')
title(strTitle)
fn = "plotHistOfHist_%s_%s_d1d2.%s" % (
ssType,
str('-'.join(resTypeListBySequenceOrder)),
graphicsFormat)
savefig(fn)
# end loop over ssType
# end over ssType overall
return
def plotDihedralD1_2d(doOnlyOverall=True):
graphicsFormat = "png"
# minPercentage = MIN_Z_D1D2
# maxPercentage = MAX_Z_D1D2
# scaleBy = SCALE_BY_Z
minPercentage = MIN_PERCENTAGE_D1D2
maxPercentage = MAX_PERCENTAGE_D1D2
scaleBy = SCALE_BY_SUM
for resType in common20AAList:
for resTypePrev in common20AAList:
for resTypeNext in common20AAList:
if resType != 'PHE':
continue
if resTypePrev != 'SER':
continue
if resTypeNext != 'VAL':
continue
# Plot a density background
histList = []
resTypeListBySequenceOrder = [
resTypePrev, resType, resTypeNext
]
titleStr = 'd1d2 %s-%s-%s' % (resTypePrev, resType,
resTypeNext)
# nTmessage("plotting: %s" % titleStr)
# important to switch to temp space before starting to generate files for the project.
# project = Project('testPlotHistoDihedrald1d2')
plotparams1 = plotParameters.getdefault(
dihedralName1, 'dihedralDefault')
plotparams2 = plotParameters.getdefault(
dihedralName2, 'dihedralDefault')
hist1 = getDeepByKeys(hPlot.histd1ByResTypes, resType,
resTypePrev) #
hist2 = getDeepByKeys(hPlot.histd1ByResTypes, resTypeNext,
resType) #L
if hist1 == None:
nTdebug('skipping for hist1 is empty for [%s] [%s]' %
(resType, resTypePrev))
continue
if hist2 == None:
nTdebug('skipping for hist2 is empty for [%s] [%s]' %
(resType, resTypeNext))
continue
sumh1 = sum(hist1)
sumh2 = sum(hist2)
titleStr += ' %d-%d' % (sumh1, sumh2)
# if doOnlyOverall:
histList = getTripletHistogramList(
resTypeListBySequenceOrder,
doOnlyOverall=doOnlyOverall,
ssTypeRequested=None,
doNormalize=False,
normalizeSeparatelyToZ=False)
# else:
# titleStr += '\n'
# histList = getTripletHistogramList(resTypeListBySequenceOrder, doOnlyOverall = doOnlyOverall,
#ssTypeRequested = None, doNormalize = True, normalizeSeparatelyToZ = True)
# scaleBy = SCALE_BY_ONE
ps = NTplotSet() # closes any previous plots
ps.hardcopySize = (500, 500)
myplot = NTplot(title=titleStr,
xRange=(plotparams1.min, plotparams1.max),
xTicks=range(int(plotparams1.min),
int(plotparams1.max + 1),
plotparams1.ticksize),
xLabel=dihedralName1,
yRange=(plotparams2.min, plotparams2.max),
yTicks=range(int(plotparams2.min),
int(plotparams2.max + 1),
plotparams2.ticksize),
yLabel=dihedralName2)
ps.addPlot(myplot)
myplot.dihedralComboPlot(histList,
minPercentage=minPercentage,
maxPercentage=maxPercentage,
scaleBy=scaleBy)
fn = 'd1d2_%s-%s-%s' % (resTypePrev, resType, resTypeNext)
if doOnlyOverall:
fn += '_ov_'
fn += "." + graphicsFormat
# savefig(fn)
ps.hardcopy(fn, graphicsFormat)
def plotDihedralD1_1d():
dihedralName = 'Cb4N'
graphicsFormat = "png"
nTmessage("Starting plotDihedralD1_1d")
# interestingResTypeList = [ 'GLY' ]
interestingResTypeList = common20AAList
# interestingResTypeList = [ 'GLY', 'ALA' ]
# interestingResTypeList = [ 'CYS', 'PRO' ]
for resType in common20AAList:
for resTypePrev in common20AAList:
# nTmessage("Looking at %s %s" % ( resType, resTypePrev))
if resType not in interestingResTypeList:
continue
if resTypePrev not in interestingResTypeList:
continue
if resType != 'GLY':
continue
# if resTypePrev != 'ALA':
# continue
titleStr = 'd1 %s(i-1) %s(i)' % (resTypePrev, resType)
nTmessage("plotting: %s" % titleStr)
plotparams = plotParameters.getdefault(dihedralName,
'dihedralDefault')
ps = NTplotSet() # closes any previous plots
ps.hardcopySize = (600, 369)
plot = NTplot(title=titleStr,
xRange=(plotparams.min, plotparams.max),
yRange=(0, 50),
xTicks=range(int(plotparams.min),
int(plotparams.max + 1),
plotparams.ticksize),
xLabel=dihedralName,
yLabel='Occurrence (%)')
ps.addPlot(plot)
h = getDeepByKeys(hPlot.histd1ByResTypes, resType, resTypePrev)
if h == None:
continue
sumh = sum(h)
plot.title += ' tot: %d' % sumh
x = range(5, 360, 10)
y = 100.0 * h / sumh # mod inplace
points = zip(x, y)
lAttr = solidLine(color='black')
plot.lines(points, attributes=lAttr)
ssTypeList = hPlot.histd1BySs0.keys()
ssTypeList.sort() # in place sort to: space, H, S
colorList = ['green', 'blue', 'yellow']
for isI in (1, 0):
if isI:
# histd1BySs = hPlot.histd1BySs0
histd1BySsAndResTypes = hPlot.histd1BySs0AndResTypes
else:
# histd1BySs = hPlot.histd1BySs1
histd1BySsAndResTypes = hPlot.histd1BySs1AndResTypes
for i, ssType in enumerate(ssTypeList):
h = getDeepByKeys(histd1BySsAndResTypes, ssType, resType,
resTypePrev)
sumh = sum(h)
plot.title += ' %s: %d' % (ssType, sumh)
if h == None:
continue
# nTdebug('appending [%s]' % ssType)
y = 100.0 * h / sumh
points = zip(x, y)
lAttr = solidLine(color=colorList[i])
plot.lines(points, attributes=lAttr)
fn = "d1 %s %s_d1d2." % (resTypePrev, resType)
fn += graphicsFormat
ps.hardcopy(fn, graphicsFormat)
def plotDihedral2DJanin():
showRestraints = True
showDataPoints = True
dihedralName1 = "CHI1"
dihedralName2 = "CHI2"
graphicsFormat = "png"
outputDir = os.path.join(cingDirTmp, 'janin')
if not os.path.exists(outputDir):
os.mkdir(outputDir)
# outputDir = cingDirTmp
os.chdir(outputDir)
# ssType = 'E'
# resType = 'GLY'
# for ssType in histRamaBySsAndResType.keys():
# ssTypeForFileName = ssType.replace(' ', '_')
ssTypeFixed = 'H'
for resType in hPlot.histRamaBySsAndResType[ssTypeFixed].keys():
if resType != 'ARG': # for testing enable filtering.
continue
# titleStr = ssType + ' ' + resType
titleStr = resType
nTmessage("plotting: %s" % titleStr)
# hist = histRamaBySsAndResType[ssType][resType]
ps = NTplotSet() # closes any previous plots
ps.hardcopySize = (500, 500)
# residueName = resType + ""
x = NTlist(-45, -80, 125) # outside the range.
y = NTlist(-65, -63, -125)
# 4 boxes:
lower1, upper1 = 120, 0
lower2, upper2 = 130, 20
# left/right boxes:
# lower1, upper1 = 90, 270
# lower2, upper2 = 0, 70
# upper/lower boxes:
# lower1, upper1 = 0, 70
# lower2, upper2 = 80, 270
# borring one box
# lower1, upper1 = 0, 70
# lower2, upper2 = 10, 60
# important to switch to temp space before starting to generate files for the project.
project = Project('testPlotHistoDihedralJanin')
plotparams1 = project.plotParameters.getdefault(
dihedralName1, 'dihedralDefault')
plotparams2 = project.plotParameters.getdefault(
dihedralName2, 'dihedralDefault')
x.limit(plotparams1.min, plotparams1.max)
y.limit(plotparams2.min, plotparams2.max)
plot = NTplot(title=titleStr,
xRange=(plotparams1.min, plotparams1.max),
xTicks=range(int(plotparams1.min),
int(plotparams1.max + 1),
plotparams1.ticksize),
xLabel=dihedralName1,
yRange=(plotparams2.min, plotparams2.max),
yTicks=range(int(plotparams2.min),
int(plotparams2.max + 1),
plotparams2.ticksize),
yLabel=dihedralName2)
ps.addPlot(plot)
if showRestraints:
plot.plotDihedralRestraintRanges2D(lower1, upper1, lower2, upper2)
# Plot a Ramachandran density background
histList = []
ssTypeList = histJaninBySsAndResType.keys() #@UndefinedVariable
ssTypeList.sort() # in place sort to: space, H, S
for ssType in ssTypeList:
hist = getDeepByKeys(hPlot.histJaninBySsAndResType, ssType,
resType)
if hist != None:
nTdebug('appending [%s]' % ssType)
histList.append(hist)
if histList:
if plot.dihedralComboPlot(histList):
nTerror("Failed plot.plotDihedralRestraintRanges2D -b-")
sys.exit(1)
if showDataPoints:
myPoint = plusPoint.copy()
myPoint.pointColor = 'green'
myPoint.pointSize = 6.0
myPoint.pointEdgeWidth = 1.0
myPoint.fill = False
if resType == 'GLY':
myPoint.pointType = 'triangle'
if resType == 'PRO':
myPoint.pointType = 'square'
plot.points(zip(x, y), attributes=myPoint)
# fn = os.path.join('bySsAndResType', ( ssTypeForFileName+"_"+resType+"."+graphicsFormat))
# fn = os.path.join('byResType', ( resType+"."+graphicsFormat))
fn = resType + "_janin." + graphicsFormat
ps.hardcopy(fn, graphicsFormat)
def plotDihedral2DRama():
showRestraints = False
showDataPoints = False
dihedralName1 = "PHI"
dihedralName2 = "PSI"
graphicsFormat = "png"
# ssType = 'E'
# resType = 'GLY'
# for ssType in histRamaBySsAndResType.keys():
# ssTypeForFileName = ssType.replace(' ', '_')
ssTypeFixed = 'H'
for resType in hPlot.histRamaBySsAndResType[ssTypeFixed].keys():
if resType != 'ALA': # for testing enable filtering.
continue
# titleStr = ssType + ' ' + resType
titleStr = resType
# nTmessage("plotting: %s" % titleStr)
# hist = histRamaBySsAndResType[ssType][resType]
ps = NTplotSet() # closes any previous plots
ps.hardcopySize = (500, 500)
# residueName = resType + ""
x = NTlist(-45, -80, 125) # outside the range.
y = NTlist(-65, -63, -125)
# 1 SMALL boxe
lower1, upper1 = -120.00, -125.05 # if within 0.1 they're considered the same and order shouldn't matter.
lower2, upper2 = 0, 100
# 4 boxes:
# lower1, upper1 = 120, 0
# lower2, upper2 = 130, 20
# left/right boxes:
# lower1, upper1 = 90, 270
# lower2, upper2 = 0, 70
# upper/lower boxes:
# lower1, upper1 = 0, 70
# lower2, upper2 = 80, 270
# borring one box
# lower1, upper1 = 0, 70
# lower2, upper2 = 10, 60
# important to switch to temp space before starting to generate files for the project.
project = Project('testPlotHistoDihedral2D')
plotparams1 = project.plotParameters.getdefault(
dihedralName1, 'dihedralDefault')
plotparams2 = project.plotParameters.getdefault(
dihedralName2, 'dihedralDefault')
x.limit(plotparams1.min, plotparams1.max)
y.limit(plotparams2.min, plotparams2.max)
plot = NTplot(title=titleStr,
xRange=(plotparams1.min, plotparams1.max),
xTicks=range(int(plotparams1.min),
int(plotparams1.max + 1),
plotparams1.ticksize),
xLabel=dihedralName1,
yRange=(plotparams2.min, plotparams2.max),
yTicks=range(int(plotparams2.min),
int(plotparams2.max + 1),
plotparams2.ticksize),
yLabel=dihedralName2)
ps.addPlot(plot)
if showRestraints:
if plot.plotDihedralRestraintRanges2D(lower1, upper1, lower2,
upper2):
nTerror("Failed plot.plotDihedralRestraintRanges2D")
sys.exit(1)
# Plot a Ramachandran density background
histList = []
ssTypeList = hPlot.histRamaBySsAndResType.keys() #@UndefinedVariable
ssTypeList.sort() # in place sort to: space, H, S
for ssType in ssTypeList:
# nTdebug('appending [%s]' % ssType )
hist = hPlot.histRamaBySsAndResType[ssType][resType]
histList.append(hist)
if plot.dihedralComboPlot(histList):
nTerror("Failed plot.plotDihedralRestraintRanges2D -b-")
sys.exit(1)
if showDataPoints:
myPoint = plusPoint.copy()
myPoint.pointColor = 'green'
myPoint.pointSize = 6.0
myPoint.pointEdgeWidth = 1.0
myPoint.fill = False
if resType == 'GLY':
myPoint.pointType = 'triangle'
if resType == 'PRO':
myPoint.pointType = 'square'
plot.points(zip(x, y), attributes=myPoint)
# fn = os.path.join('bySsAndResType', ( ssTypeForFileName+"_"+resType+"."+graphicsFormat))
# fn = os.path.join('byResType', ( resType+"."+graphicsFormat))
# fn = resType + "_rama." + graphicsFormat
fnBase = resType + "_rama"
if True:
fn = fnBase + '.png'
else:
i = 0
fn = None
while not fn or os.path.exists(fn):
i += 1
fn = fnBase + '_' + str(i) + '.png'
ps.hardcopy(fn, graphicsFormat)
def plotDihedralD1D2byResType():
showDataPoints = False
dihedralName1 = 'Cb4N'
dihedralName2 = 'Cb4C'
# graphicsFormat = "png"
outputDir = os.path.join(cingDirTmp, 'd1d2')
if not os.path.exists(outputDir):
os.mkdir(outputDir)
# outputDir = cingDirTmp
os.chdir(outputDir)
# ssType = 'E'
# resType = 'GLY'
# for ssType in histRamaBySsAndResType.keys():
# ssTypeForFileName = ssType.replace(' ', '_')
ssTypeFixed = 'H'
resTypeListSkip = ['CSB', 'GLUH', 'HISE', 'HISH', 'MSE', '', '', '', '', '']
for resType in hPlot.histd1BySs0AndResTypes[ssTypeFixed].keys(): # TODO: check UNTESTED code for attribute histd1BySs0AndResTypes
# if resType != 'ARG': # for testing enable filtering.
# continue
if resType in resTypeListSkip:
continue
titleStr = 'd1d2 ' + resType
nTmessage("plotting: %s" % titleStr)
# hist = histd1d2BySsAndResType[ssType][resType]
ps = NTplotSet() # closes any previous plots
ps.hardcopySize = (500, 500)
# residueName = resType + ""
x = NTlist(-45, -80, 125) # outside the range.
y = NTlist(-65, -63, -125)
# important to switch to temp space before starting to generate files for the project.
project = Project('testPlotHistoDihedrald1d2')
plotparams1 = project.plotParameters.getdefault(dihedralName1, 'dihedralDefault')
plotparams2 = project.plotParameters.getdefault(dihedralName2, 'dihedralDefault')
x.limit(plotparams1.min, plotparams1.max)
y.limit(plotparams2.min, plotparams2.max)
plot = NTplot(title=titleStr,
xRange=(plotparams1.min, plotparams1.max),
xTicks=range(int(plotparams1.min), int(plotparams1.max + 1), plotparams1.ticksize),
xLabel=dihedralName1,
yRange=(plotparams2.min, plotparams2.max),
yTicks=range(int(plotparams2.min), int(plotparams2.max + 1), plotparams2.ticksize),
yLabel=dihedralName2)
ps.addPlot(plot)
# Plot a density background
histList = []
ssTypeList = hPlot.histd1BySs0AndResTypes.keys() # TODO: test this untested histd1BySs0AndResTypes parameter
ssTypeList.sort() # in place sort to: space, H, S
for ssType in ssTypeList:
hist = getDeepByKeys(hPlot.histd1BySs0AndResTypes, ssType, resType)
if hist != None:
nTdebug('appending [%s]' % ssType)
histList.append(hist)
if histList:
plot.dihedralComboPlot(histList)
if showDataPoints:
myPoint = plusPoint.copy()
myPoint.pointColor = 'green'
myPoint.pointSize = 6.0
myPoint.pointEdgeWidth = 1.0
myPoint.fill = False
if resType == 'GLY':
myPoint.pointType = 'triangle'
if resType == 'PRO':
myPoint.pointType = 'square'
plot.points(zip(x, y), attributes=myPoint)
# fn = os.path.join('bySsAndResType', ( ssTypeForFileName+"_"+resType+"."+graphicsFormat))
# fn = os.path.join('byResType', ( resType+"."+graphicsFormat))
# fn = resType + "_d1d2." + graphicsFormat
# ps.hardcopy(fn, graphicsFormat)
plot.show()
def plotDihedralD1D2():
dihedralName1 = 'Cb4N'
dihedralName2 = 'Cb4C'
graphicsFormat = "png"
entryId = "1brv" # Small much studied PDB NMR entry
# entryId = "1hy8" # small, single model, very low scoring entry
pdbDirectory = os.path.join(cingDirTestsData, "pdb", entryId)
pdbFileName = "pdb" + entryId + ".ent"
pdbFilePath = os.path.join(pdbDirectory, pdbFileName)
# does it matter to import it just now?
project = Project(entryId)
project.removeFromDisk()
project = Project.open(entryId, status='new')
project.initPDB(pdbFile=pdbFilePath, convention=IUPAC)
# ssType = 'E'
# resType = 'GLY'
# for ssType in histRamaBySsAndResType.keys():
# ssTypeForFileName = ssType.replace(' ', '_')
titleStr = 'd1d2 all resType'
nTmessage("plotting: %s" % titleStr)
# hist = histd1d2BySsAndResType[ssType][resType]
ps = NTplotSet() # closes any previous plots
ps.hardcopySize = (500, 500)
# residueName = resType + ""
x = NTlist(-45, -80, 125) # outside the range.
y = NTlist(-65, -63, -125)
# important to switch to temp space before starting to generate files for the project.
# project = Project('testPlotHistoDihedrald1d2')
plotparams1 = project.plotParameters.getdefault(dihedralName1, 'dihedralDefault')
plotparams2 = project.plotParameters.getdefault(dihedralName2, 'dihedralDefault')
x.limit(plotparams1.min, plotparams1.max)
y.limit(plotparams2.min, plotparams2.max)
plot = NTplot(title=titleStr,
xRange=(plotparams1.min, plotparams1.max),
xTicks=range(int(plotparams1.min), int(plotparams1.max + 1), plotparams1.ticksize),
xLabel=dihedralName1,
yRange=(plotparams2.min, plotparams2.max),
yTicks=range(int(plotparams2.min), int(plotparams2.max + 1), plotparams2.ticksize),
yLabel=dihedralName2)
ps.addPlot(plot)
# Plot a density background
histList = []
ssTypeList = hPlot.histd1BySs0.keys() # TODO: check this histd1BySs0 attribute. UNTESTED.
ssTypeList.sort() # in place sort to: space, H, S
for ssType in ssTypeList:
hist = getDeepByKeys(hPlot.histd1BySs0, ssType)
if hist != None:
nTdebug('appending [%s]' % ssType)
histList.append(hist)
if histList:
plot.dihedralComboPlot(histList)
# fn = os.path.join('bySsAndResType', ( ssTypeForFileName+"_"+resType+"."+graphicsFormat))
# fn = os.path.join('byResType', ( resType+"."+graphicsFormat))
fpGood = open(project.name + '.testCb2Good.out', 'w')
fpBad = open(project.name + '.testCb2Bad.out', 'w')
mCount = project.molecule.modelCount
for res in project.molecule.A.allResidues():
triplet = NTlist()
for i in [-1, 0, 1]:
triplet.append(res.sibling(i))
if None in triplet:
nTdebug('Skipping ' % res)
else:
ca_atms = triplet.zap('CA')
cb_atms = triplet.zap('CB')
nTdebug("%s %s %s %s" % (res, triplet, ca_atms, cb_atms))
if None in cb_atms: # skip Gly for now
nTdebug('Skipping %s' % res)
else:
d1 = Dihedral(res, 'Cb4N', range=[0.0, 360.0])
d1.atoms = [cb_atms[0], ca_atms[0], ca_atms[1], cb_atms[1]]
d1.calculateValues()
res['Cb4N'] = d1 # append dihedral to residue
d2 = Dihedral(res, 'Cb4C', range=[0.0, 360.0])
d2.atoms = [cb_atms[1], ca_atms[1], ca_atms[2], cb_atms[2]]
d2.calculateValues()
res['Cb4C'] = d2 # append dihedral to residue
bb = getDeepByKeys(res, WHATIF_STR, BBCCHK_STR, VALUE_LIST_STR, 0) # check first one.
if bb == None:
nTdebug('Skipping without BB %s' % res)
continue
if d1.cv < 0.03 and d2.cv < 0.03: # Only include structured residues
for i in range(mCount): # Consider each model individually
# bb = res.Whatif.bbNormality.valueList[i]
bb = getDeepByKeys(res, WHATIF_STR, BBCCHK_STR, VALUE_LIST_STR, i)
if bb == None:
nTdebug('Skipping without BB %s' % res)
continue
angles = NTlist() # store phi, psi, chi1, chi2
for angle in ['PHI', 'PSI', 'CHI1', 'CHI2']:
if res.has_key(angle):
angles.append(res[angle][i])
else:
angles.append(0.0)
#end for
if bb < 20.0: # Arbitrary 20 bb occurences as cuttoff for now
fprintf(fpBad, '%4d %7.2f %7.2f %7.2f %s %s %s\n',
res.resNum, d1[i], d2[i], bb, angles.format("%7.2f "), res, res.dssp.consensus)
else:
fprintf(fpGood, '%4d %7.2f %7.2f %7.2f %s %s %s\n',
res.resNum, d1[i], d2[i], bb, angles.format("%7.2f "), res, res.dssp.consensus)
#end if
#end if
#end if
#end for
fpBad.close()
fpGood.close()
fn = "allRestype_d1d2." + graphicsFormat
ps.hardcopy(fn, graphicsFormat)
def plotHisBySsTypeResTypes():
graphicsFormat = "png"
doOnlyOverall = False
# If set it will do a single ssType otherwise the overall.
# for doOverall in [ False, True ]:
for doOverall in [ True ]:
if doOverall:
ssTypeList = [ None ]
else:
ssTypeList = [' ', 'S', 'H']
for ssType in ssTypeList:
#met-asp-leu
for _i, resType in enumerate(common20AAList):
if resType != 'PHE':
continue
for _j, resTypePrev in enumerate(common20AAList):
if resTypePrev != 'SER':
continue
for _k, resTypeNext in enumerate(common20AAList):
if resTypeNext != 'VAL':
continue
resTypeListBySequenceOrder = (resTypePrev, resType , resTypeNext)
myHistList = getTripletHistogramList(resTypeListBySequenceOrder, doOnlyOverall=doOnlyOverall,
ssTypeRequested=ssType, doNormalize = True)
if myHistList == None:
nTwarning("Encountered an error getting the D1D2 hist for %s; skipping" % str(resTypeListBySequenceOrder))
continue
if len(myHistList) != 1:
nTdebug("Expected exactly one but Found %s histogram for %s; skipping" % (len(myHistList),
str(resTypeListBySequenceOrder)))
continue
myHist = deepcopy(myHistList[0])
# nTdebug("myHist: %s" % str(myHist))
myList = numpy.asarray(myHist).flatten()
maxl = numpy.max(myList)
sdl = numpy.std(myList)
avl = numpy.average(myList)
suml = numpy.sum(myList)
n = 36
suml2 = avl * n * n
if math.fabs(suml2 - suml) > 1:
# Perhaps because sum is misinterpreted?
msg = "Math is off for suml != suml2: %s != %s" % (suml, suml2)
nTerror(msg)
if maxl > suml:
msg = "Math is off for maxl > suml : %s != %s" % (maxl, suml)
nTerror(msg)
vL = []
for value in (avl, sdl, maxl, suml):
vL.append( locale.format('%12.3f', value, True))
strTitle = "av: %s sd: %s\nmax: %s sum: %s" % (vL[0],vL[1],vL[2],vL[3])
nTdebug("myHist: %s" % strTitle)
if True: # plot distribution itself too?
clf()
ps = NTplotSet() # closes any previous plots
ps.hardcopySize = (500, 500)
plotparams1 = plotParameters.getdefault(dihedralName1, 'dihedralDefault')
plotparams2 = plotParameters.getdefault(dihedralName2, 'dihedralDefault')
myplot = NTplot(title=strTitle,
xRange=(plotparams1.min, plotparams1.max),
xTicks=range(int(plotparams1.min), int(plotparams1.max + 1), plotparams1.ticksize),
xLabel=dihedralName1,
yRange=(plotparams2.min, plotparams2.max),
yTicks=range(int(plotparams2.min), int(plotparams2.max + 1), plotparams2.ticksize),
yLabel=dihedralName2)
ps.addPlot(myplot)
myplot.dihedralComboPlot([myHist], minPercentage=MIN_Z_D1D2, maxPercentage=MAX_Z_D1D2, scaleBy=SCALE_BY_Z,
ssType = ssType)
fn = 'd1d2_%s_%s-%s-%s' % (ssType, resTypePrev, resType, resTypeNext)
if doOverall:
fn += '_ov_'
fn += "." + graphicsFormat
ps.hardcopy(fn, graphicsFormat)
if True:
clf()
hist(myList, 40)
xlabel('triplet count')
ylabel('number of occurrences')
title(strTitle)
fn = "plotHistOfHist_%s_%s_d1d2.%s" % (ssType, str('-'.join(resTypeListBySequenceOrder)), graphicsFormat)
savefig(fn)
# end loop over ssType
# end over ssType overall
return
def plotDihedralD1_2d(doOnlyOverall=True):
graphicsFormat = "png"
# minPercentage = MIN_Z_D1D2
# maxPercentage = MAX_Z_D1D2
# scaleBy = SCALE_BY_Z
minPercentage = MIN_PERCENTAGE_D1D2
maxPercentage = MAX_PERCENTAGE_D1D2
scaleBy = SCALE_BY_SUM
for resType in common20AAList:
for resTypePrev in common20AAList:
for resTypeNext in common20AAList:
if resType != 'PHE':
continue
if resTypePrev != 'SER':
continue
if resTypeNext != 'VAL':
continue
# Plot a density background
histList = []
resTypeListBySequenceOrder = [ resTypePrev, resType, resTypeNext ]
titleStr = 'd1d2 %s-%s-%s' % ( resTypePrev, resType, resTypeNext )
# nTmessage("plotting: %s" % titleStr)
# important to switch to temp space before starting to generate files for the project.
# project = Project('testPlotHistoDihedrald1d2')
plotparams1 = plotParameters.getdefault(dihedralName1, 'dihedralDefault')
plotparams2 = plotParameters.getdefault(dihedralName2, 'dihedralDefault')
hist1 = getDeepByKeys(hPlot.histd1ByResTypes, resType, resTypePrev) #
hist2 = getDeepByKeys(hPlot.histd1ByResTypes, resTypeNext, resType) #L
if hist1 == None:
nTdebug('skipping for hist1 is empty for [%s] [%s]' % (resType, resTypePrev))
continue
if hist2 == None:
nTdebug('skipping for hist2 is empty for [%s] [%s]' % (resType, resTypeNext))
continue
sumh1 = sum(hist1)
sumh2 = sum(hist2)
titleStr += ' %d-%d' % (sumh1, sumh2)
# if doOnlyOverall:
histList = getTripletHistogramList(resTypeListBySequenceOrder, doOnlyOverall = doOnlyOverall,
ssTypeRequested = None, doNormalize = False, normalizeSeparatelyToZ = False)
# else:
# titleStr += '\n'
# histList = getTripletHistogramList(resTypeListBySequenceOrder, doOnlyOverall = doOnlyOverall,
#ssTypeRequested = None, doNormalize = True, normalizeSeparatelyToZ = True)
# scaleBy = SCALE_BY_ONE
ps = NTplotSet() # closes any previous plots
ps.hardcopySize = (500, 500)
myplot = NTplot(title=titleStr,
xRange=(plotparams1.min, plotparams1.max),
xTicks=range(int(plotparams1.min), int(plotparams1.max + 1), plotparams1.ticksize),
xLabel=dihedralName1,
yRange=(plotparams2.min, plotparams2.max),
yTicks=range(int(plotparams2.min), int(plotparams2.max + 1), plotparams2.ticksize),
yLabel=dihedralName2)
ps.addPlot(myplot)
myplot.dihedralComboPlot(histList, minPercentage=minPercentage, maxPercentage=maxPercentage, scaleBy=scaleBy)
fn = 'd1d2_%s-%s-%s' % (resTypePrev, resType, resTypeNext)
if doOnlyOverall:
fn += '_ov_'
fn += "." + graphicsFormat
# savefig(fn)
ps.hardcopy(fn, graphicsFormat)
def plotDihedralD1_1d():
dihedralName = 'Cb4N'
graphicsFormat = "png"
nTmessage("Starting plotDihedralD1_1d")
# interestingResTypeList = [ 'GLY' ]
interestingResTypeList = common20AAList
# interestingResTypeList = [ 'GLY', 'ALA' ]
# interestingResTypeList = [ 'CYS', 'PRO' ]
for resType in common20AAList:
for resTypePrev in common20AAList:
# nTmessage("Looking at %s %s" % ( resType, resTypePrev))
if resType not in interestingResTypeList:
continue
if resTypePrev not in interestingResTypeList:
continue
if resType != 'GLY':
continue
# if resTypePrev != 'ALA':
# continue
titleStr = 'd1 %s(i-1) %s(i)' % (resTypePrev, resType)
nTmessage("plotting: %s" % titleStr)
plotparams = plotParameters.getdefault(dihedralName, 'dihedralDefault')
ps = NTplotSet() # closes any previous plots
ps.hardcopySize = (600, 369)
plot = NTplot(title=titleStr,
xRange=(plotparams.min, plotparams.max),
yRange=(0, 50),
xTicks=range(int(plotparams.min), int(plotparams.max + 1), plotparams.ticksize),
xLabel=dihedralName,
yLabel='Occurrence (%)')
ps.addPlot(plot)
h = getDeepByKeys(hPlot.histd1ByResTypes, resType, resTypePrev)
if h == None:
continue
sumh = sum(h)
plot.title += ' tot: %d' % sumh
x = range(5, 360, 10)
y = 100.0 * h / sumh # mod inplace
points = zip(x, y)
lAttr = solidLine(color='black')
plot.lines(points, attributes=lAttr)
ssTypeList = hPlot.histd1BySs0.keys()
ssTypeList.sort() # in place sort to: space, H, S
colorList = [ 'green', 'blue', 'yellow']
for isI in (1, 0):
if isI:
# histd1BySs = hPlot.histd1BySs0
histd1BySsAndResTypes = hPlot.histd1BySs0AndResTypes
else:
# histd1BySs = hPlot.histd1BySs1
histd1BySsAndResTypes = hPlot.histd1BySs1AndResTypes
for i, ssType in enumerate(ssTypeList):
h = getDeepByKeys(histd1BySsAndResTypes, ssType, resType, resTypePrev)
sumh = sum(h)
plot.title += ' %s: %d' % (ssType, sumh)
if h == None:
continue
# nTdebug('appending [%s]' % ssType)
y = 100.0 * h / sumh
points = zip(x, y)
lAttr = solidLine(color=colorList[i])
plot.lines(points, attributes=lAttr)
fn = "d1 %s %s_d1d2." % (resTypePrev, resType)
fn += graphicsFormat
ps.hardcopy(fn, graphicsFormat)
def plotDihedral2DJanin():
showRestraints = True
showDataPoints = True
dihedralName1 = "CHI1"
dihedralName2 = "CHI2"
graphicsFormat = "png"
outputDir = os.path.join(cingDirTmp, 'janin')
if not os.path.exists(outputDir):
os.mkdir(outputDir)
# outputDir = cingDirTmp
os.chdir(outputDir)
# ssType = 'E'
# resType = 'GLY'
# for ssType in histRamaBySsAndResType.keys():
# ssTypeForFileName = ssType.replace(' ', '_')
ssTypeFixed = 'H'
for resType in hPlot.histRamaBySsAndResType[ssTypeFixed].keys():
if resType != 'ARG': # for testing enable filtering.
continue
# titleStr = ssType + ' ' + resType
titleStr = resType
nTmessage("plotting: %s" % titleStr)
# hist = histRamaBySsAndResType[ssType][resType]
ps = NTplotSet() # closes any previous plots
ps.hardcopySize = (500, 500)
# residueName = resType + ""
x = NTlist(-45, -80, 125) # outside the range.
y = NTlist(-65, -63, -125)
# 4 boxes:
lower1, upper1 = 120, 0
lower2, upper2 = 130, 20
# left/right boxes:
# lower1, upper1 = 90, 270
# lower2, upper2 = 0, 70
# upper/lower boxes:
# lower1, upper1 = 0, 70
# lower2, upper2 = 80, 270
# borring one box
# lower1, upper1 = 0, 70
# lower2, upper2 = 10, 60
# important to switch to temp space before starting to generate files for the project.
project = Project('testPlotHistoDihedralJanin')
plotparams1 = project.plotParameters.getdefault(dihedralName1, 'dihedralDefault')
plotparams2 = project.plotParameters.getdefault(dihedralName2, 'dihedralDefault')
x.limit(plotparams1.min, plotparams1.max)
y.limit(plotparams2.min, plotparams2.max)
plot = NTplot(title=titleStr,
xRange=(plotparams1.min, plotparams1.max),
xTicks=range(int(plotparams1.min), int(plotparams1.max + 1), plotparams1.ticksize),
xLabel=dihedralName1,
yRange=(plotparams2.min, plotparams2.max),
yTicks=range(int(plotparams2.min), int(plotparams2.max + 1), plotparams2.ticksize),
yLabel=dihedralName2)
ps.addPlot(plot)
if showRestraints:
plot.plotDihedralRestraintRanges2D(lower1, upper1, lower2, upper2)
# Plot a Ramachandran density background
histList = []
ssTypeList = histJaninBySsAndResType.keys() #@UndefinedVariable
ssTypeList.sort() # in place sort to: space, H, S
for ssType in ssTypeList:
hist = getDeepByKeys(hPlot.histJaninBySsAndResType, ssType, resType)
if hist != None:
nTdebug('appending [%s]' % ssType)
histList.append(hist)
if histList:
if plot.dihedralComboPlot(histList):
nTerror("Failed plot.plotDihedralRestraintRanges2D -b-")
sys.exit(1)
if showDataPoints:
myPoint = plusPoint.copy()
myPoint.pointColor = 'green'
myPoint.pointSize = 6.0
myPoint.pointEdgeWidth = 1.0
myPoint.fill = False
if resType == 'GLY':
myPoint.pointType = 'triangle'
if resType == 'PRO':
myPoint.pointType = 'square'
plot.points(zip(x, y), attributes=myPoint)
# fn = os.path.join('bySsAndResType', ( ssTypeForFileName+"_"+resType+"."+graphicsFormat))
# fn = os.path.join('byResType', ( resType+"."+graphicsFormat))
fn = resType + "_janin." + graphicsFormat
ps.hardcopy(fn, graphicsFormat)
def plotDihedral2DRama():
showRestraints = False
showDataPoints = False
dihedralName1 = "PHI"
dihedralName2 = "PSI"
graphicsFormat = "png"
# ssType = 'E'
# resType = 'GLY'
# for ssType in histRamaBySsAndResType.keys():
# ssTypeForFileName = ssType.replace(' ', '_')
ssTypeFixed = 'H'
for resType in hPlot.histRamaBySsAndResType[ssTypeFixed].keys():
if resType != 'ALA': # for testing enable filtering.
continue
# titleStr = ssType + ' ' + resType
titleStr = resType
# nTmessage("plotting: %s" % titleStr)
# hist = histRamaBySsAndResType[ssType][resType]
ps = NTplotSet() # closes any previous plots
ps.hardcopySize = (500, 500)
# residueName = resType + ""
x = NTlist(-45, -80, 125) # outside the range.
y = NTlist(-65, -63, -125)
# 1 SMALL boxe
lower1, upper1 = -120.00, -125.05 # if within 0.1 they're considered the same and order shouldn't matter.
lower2, upper2 = 0, 100
# 4 boxes:
# lower1, upper1 = 120, 0
# lower2, upper2 = 130, 20
# left/right boxes:
# lower1, upper1 = 90, 270
# lower2, upper2 = 0, 70
# upper/lower boxes:
# lower1, upper1 = 0, 70
# lower2, upper2 = 80, 270
# borring one box
# lower1, upper1 = 0, 70
# lower2, upper2 = 10, 60
# important to switch to temp space before starting to generate files for the project.
project = Project('testPlotHistoDihedral2D')
plotparams1 = project.plotParameters.getdefault(dihedralName1, 'dihedralDefault')
plotparams2 = project.plotParameters.getdefault(dihedralName2, 'dihedralDefault')
x.limit(plotparams1.min, plotparams1.max)
y.limit(plotparams2.min, plotparams2.max)
plot = NTplot(title=titleStr,
xRange=(plotparams1.min, plotparams1.max),
xTicks=range(int(plotparams1.min), int(plotparams1.max + 1), plotparams1.ticksize),
xLabel=dihedralName1,
yRange=(plotparams2.min, plotparams2.max),
yTicks=range(int(plotparams2.min), int(plotparams2.max + 1), plotparams2.ticksize),
yLabel=dihedralName2)
ps.addPlot(plot)
if showRestraints:
if plot.plotDihedralRestraintRanges2D(lower1, upper1, lower2, upper2):
nTerror("Failed plot.plotDihedralRestraintRanges2D")
sys.exit(1)
# Plot a Ramachandran density background
histList = []
ssTypeList = hPlot.histRamaBySsAndResType.keys() #@UndefinedVariable
ssTypeList.sort() # in place sort to: space, H, S
for ssType in ssTypeList:
# nTdebug('appending [%s]' % ssType )
hist = hPlot.histRamaBySsAndResType[ssType][resType]
histList.append(hist)
if plot.dihedralComboPlot(histList):
nTerror("Failed plot.plotDihedralRestraintRanges2D -b-")
sys.exit(1)
if showDataPoints:
myPoint = plusPoint.copy()
myPoint.pointColor = 'green'
myPoint.pointSize = 6.0
myPoint.pointEdgeWidth = 1.0
myPoint.fill = False
if resType == 'GLY':
myPoint.pointType = 'triangle'
if resType == 'PRO':
myPoint.pointType = 'square'
plot.points(zip(x, y), attributes=myPoint)
# fn = os.path.join('bySsAndResType', ( ssTypeForFileName+"_"+resType+"."+graphicsFormat))
# fn = os.path.join('byResType', ( resType+"."+graphicsFormat))
# fn = resType + "_rama." + graphicsFormat
fnBase = resType + "_rama"
if True:
fn = fnBase + '.png'
else:
i = 0
fn = None
while not fn or os.path.exists(fn):
i += 1
fn = fnBase + '_' + str(i) + '.png'
ps.hardcopy(fn, graphicsFormat)