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 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)
triplet = NTlist()
for i in [-1,0,1]:
triplet.append( res.sibling(i) )
if None in triplet:
print 'Skipping ', res
else:
CA_atms = triplet.zap('CA')
CB_atms = triplet.zap('CB')
# print res, triplet, CA_atms, CB_atms
if None in CB_atms: # skip Gly for now
print 'Skipping ', 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:
print 'Skipping without BB', res
continue
if d1.cv < 0.03 and d2.cv < 0.03: # Only include structured residues
