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 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_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)
