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 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 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)
