for pdd in pdbList:
print(pdd)
print('*****************\n')
#This is all the data we are going to be looking at
geoList = [
'N:N+1', 'TAU', 'PSI', 'PHI', 'N:C', 'CA:C', 'C:O', 'N:CA', 'C-1:N',
'C:N+1', 'OMEGA', 'CA:C:O:N+1', 'O:N+1', 'CA:O', 'CA:N+1', 'CA:C:N+1',
'C-1:N:CA'
]
hueList = ['aa', 'rid', 'bfactor', 'pdbCode', 'bfactorRatio', 'disordered']
if SaveAgain:
print('Creating CSV files anew')
#Load original csv unrestricted on occupant and bfactor
pdbmanager = geopdb.GeoPdbs(pdbOriginalPath, edDataPath, False, False,
True)
georep = psu.GeoReport(pdbList,
pdbOriginalPath,
edDataPath,
printPath,
ed=False,
dssp=False,
includePdbs=False,
keepDisordered=True)
print('Create unrestricted csv')
dataUnrestricted = georep.getGeoemtryCsv(geoList, hueList, -1)
dataUnrestricted.to_csv(printPath + "Results14_UnrestrictedStats.csv",
index=False)
#Load good csv
pdbmanager.clear()
def createGeosFileOld(pdbSet, cutOff):
print('Running CreateGeosFile on', pdbSet)
setName = 'BEST'
#pdbDataPath = 'F:/Code/ProteinDataFiles/pdb_out/NCACO_001_05/'
pdbDataPath = 'F:/Code/ProteinDataFiles/pdb_out/' + pdbSet + '/'
keepDisordered = False
bFactorFactor = -1 #no need to restrict on bfactor and electron density but we do not want occupant verions
if pdbSet == 'RESTRICTED':
pdbDataPath = 'F:/Code/ProteinDataFiles/pdb_data/'
keepDisordered = False
bFactorFactor = 1.3
elif pdbSet == 'UNRESTRICTED':
pdbDataPath = 'F:/Code/ProteinDataFiles/pdb_data/'
keepDisordered = True
bFactorFactor = -1
edDataPath = 'F:/Code/ProteinDataFiles/ccp4_data/'
printPath = 'F:/Code/BbkProject/PhDThesis/0.Papers/3.DefensibleGeometry/EvidencedSet/DataA/'
#TIMER
print('----------start report 14----------')
startx = time.time()
#This gets the list of pdbs
pdbdata = pd.read_csv(
'../../PdbLists/Pdbs_Evidenced.csv'
) # This is a list of pdbs <= 1.1A non homologous to 90%
pdbListIn = pdbdata['PDB'].tolist()[0:]
if cutOff > 0:
pdbListIn = pdbdata['PDB'].tolist()[0:cutOff]
pdbList = []
for pdb in pdbListIn:
import os.path
if os.path.isfile((pdbDataPath + 'pdb' + pdb + '.ent').lower()):
pdbList.append(pdb.lower())
else:
print('No file:', (pdbDataPath + 'pdb' + pdb + '.ent').lower())
#Clear the pdb manager cache
pdbmanager = geopdb.GeoPdbs(pdbDataPath, edDataPath, False, False,
keepDisordered)
pdbmanager.clear()
#This is all the data we are going to be looking at
geoLists = []
#geoLists.append(['TAU'])#for dssp from linux only
#geoLists.append(['0', ['TAU']])
#We currently have these
geoLists.append(['1BOND', ['N:CA', 'CA:C', 'C:O', 'C-1:N', 'C:N+1']])
geoLists.append([
'2ANGS',
['TAU', 'C-1:N:CA', 'CA:C:N+1', 'CA:C:O', 'O:C:N+1', 'CA:C:N+1']
])
geoLists.append(['3DIHS', ['PHI', 'PSI', 'OMEGA', 'CA-1:C-1:N:CA']])
geoLists.append(['4DIST', ['N:N+1', 'N:C']])
geoLists.append(['5HB', ['N:O-2', 'C:O-2', 'N:CA:C:O-2', 'N:CA:N+1:O-2']])
geoLists.append(['6HB', ['N:O-3', 'C:O-3', 'N:CA:C:O-3', 'N:CA:N+1:O-3']])
#geoLists.append(['9HBO', ['N:{O}','C:{O}','N:CA:C:{O}','N:CA:N+1:{O}']])
#geoLists.append(['10CIS', ['CA-1:C-1:N:CA', 'CA-1:CA']])
# geoLists.append(['7HB', ['N:O-4', 'C:O-4', 'N:CA:C:O-4', 'N:CA:N+1:O-4']])
# geoLists.append(['8HB', ['N:O-5', 'C:O-5', 'N:CA:C:O-5', 'N:CA:N+1:O-5']])
# Water
#geoLists.append(['7WAT', ['N:HOH','C:HOH','N:CA:C:HOH','N:CA:N+1:HOH']])
# Other!
#geoLists.append(['8XTRA', ['N:HETATM']])
hueList = ['aa', 'rid', 'bfactor', 'pdbCode', 'bfactorRatio', 'disordered']
aas = ['ALL']
print('Creating CSV files anew')
for geoListT in geoLists:
geoList = geoListT[1]
set = geoListT[0]
for aa in aas:
tag = 'Set' + set + aa + '_' + pdbSet
georep = psu.GeoReport(pdbList,
pdbDataPath,
edDataPath,
printPath,
ed=False,
dssp=False,
includePdbs=False,
keepDisordered=keepDisordered)
print('Create csv', pdbDataPath, geoList)
dataUnrestricted = georep.getGeoemtryCsv(geoList,
hueList,
bFactorFactor,
allAtoms=True,
restrictedAa=aa)
dataUnrestricted.to_csv(printPath + 'CsvGeos_' + setName + '_' +
tag + '.csv',
index=False)
print('----------Finished----------')
endx = time.time()
time_diff = endx - startx
timestring = str(int(time_diff / 60)) + "m " + str(int(
time_diff % 60)) + "s"
print(timestring)
calcList = [self.geoX, self.geoY]
hueList = hues
if hues == None:
hueList = [self.hue]
for rest in self.restrictions:
if rest not in hueList:
hueList.append(rest)
dfs = []
if self.parent != None:
<<<<<<< Updated upstream
=======
>>>>>>> Stashed changes
from PsuGeometry import GeoPdb as geopdb
pdbmanager = geopdb.GeoPdbs(self.parent.pdbDataPath, self.parent.edDataPath, self.parent.ed, self.parent.dssp)
for pdb in self.parent.pdbCodes:
apdb = pdbmanager.getPdb(pdb)
data = apdb.getGeoemtryCsv(calcList, hueList)
dfs.append(data)
self.data = pd.concat(dfs, ignore_index=True)
else:
print('PSU: cannot create data, pass in report parent to plots')
def applyRestrictions(self):
# now the data can be restricted as per the restrictions, which is a dictionary of restrictions, eg aa:'THR,PRO'
if len(self.restrictions)>0 and not self.data.empty:
dfs = []
for rest in self.restrictions:
allowed = self.restrictions[rest]
allows = allowed.split(',')
geoList = ['N:N+1','TAU','PSI']
hueList = ['aa', 'rid', 'bfactor']
aas = ['GLY']
###################################################################################
pdbDataPath = '/home/rachel/Documents/Bioinformatics/ProteinDataFiles/pdb_data/'
edDataPath = '/home/rachel/Documents/Bioinformatics/ProteinDataFiles/ccp4_data/'
printPath = '/home/rachel/Documents/Bioinformatics/ProteinDataFiles/results_psu/Paper02/'
if myWindowsLaptop:
pdbDataPath = 'F:/Code/ProteinDataFiles/pdb_data/'
edDataPath = 'F:/Code/ProteinDataFiles/ccp4_data/'
printPath = 'F:/Code/ProteinDataFiles/results_psu/Paper02/'
###########################################################################################
georep = psu.GeoReport(pdbList, pdbDataPath, edDataPath, printPath, ed=False, dssp=False, includePdbs=True,keepDisordered=keepDisordered)
pdbmanager = geopdb.GeoPdbs(georep.pdbDataPath, georep.edDataPath, georep.ed, georep.dssp)
data = georep.getGeoemtryCsv(geoList, hueList,bfactorFactor)
#data = data.query('TAU > 100')
#data = data.query('TAU < 125')
dataPsiRange = data.query('PSI > -50')
dataPsiRange = dataPsiRange.query('PSI < 50')
#for pd in pdbList:
# apdb = pdbmanager.getPdb(pd, True)
# atomData = apdb.getDataFrame()
# fullFileName = printPath + 'Results10_' + pd + '.csv'
# atomData.to_csv(fullFileName, index=False)
for aa in aas:
def printReport(self, reportName,fileName):
print('PSU: create report',reportName,'for',fileName)
self.flush()
printList = []
if reportName == 'BackboneOutliers': # Sp2Planarity, DensityAtomCompare, OmegaCis
atomData = self.getReportCsv(reportName)
title = 'Backbone Outliers Report'
cols = 3
printList = []
#printList.append(GeoQuery(['Bonds', atomData, 'C-1:N', 'N:CA','aa', '2FoFc', 'viridis_r', False, 0, 0])
self.addScatter(data=atomData,geoX='C-1:N',geoY='N:CA',title='Bonds',ghost=True)
self.addScatter(data=atomData, geoX='CA:C', geoY='C:N+1', title='Bonds',ghost=True)
self.addScatter(data=atomData, geoX='C-1:N', geoY='C:N+1', title='Bonds',ghost=True)
self.addScatter(data=atomData, geoX='C-1:N:CA', geoY='N:CA:C', title='Angles',ghost=True)
self.addScatter(data=atomData, geoX='N:CA:C', geoY='CA:C:N+1', title='Angles',ghost=True)
self.addScatter(data=atomData, geoX='C-1:N:CA', geoY='CA:C:N+1', title='Angles',ghost=True)
self.printToHtml(title, cols, fileName)
elif reportName == 'RachelsChoice' or reportName == 'RachelsChoiceNonXRay' :
atomData = self.getReportCsv(reportName)
# We want the dummy trace correlation plot so we can see if there are areas of interest
title = "Rachel's Choice of Correlations"
cols = 4
printList = []
densityHue = '2FoFc'
if reportName == 'RachelsChoiceNonXRay':
densityHue = 'bfactor'
self.addScatter(geoX='C-1:N:CA:C', geoY='N:CA:C:N+1', title='', hue='dssp',palette='gist_rainbow',ghost=True)
self.addScatter(geoX='C-1:N:CA:C', geoY='N:CA:C:N+1', title='', hue=densityHue, palette='cubehelix_r',ghost=True)
self.addScatter(geoX='C-1:N:CA:C', geoY='N:CA:C:N+1', title='', hue='aa', palette='gist_rainbow',ghost=True,categorical=True)
self.addScatter(geoX='C-1:N:CA:C', geoY='N:CA:C:N+1', title='', hue='pdbCode', palette='gist_rainbow',ghost=True,categorical=True)
self.addScatter(geoX='N:CA:CB:CG', geoY='CA:CB:CG:CD', title='', hue='dssp', palette='gist_rainbow', ghost=True)
self.addScatter(geoX='N:CA:CB:CG', geoY='CA:CB:CG:CD', title='', hue=densityHue, palette='cubehelix_r',ghost=True)
self.addScatter(geoX='N:CA:CB:CG', geoY='CA:CB:CG:CD', title='', hue='aa', palette='gist_rainbow',ghost=True,categorical=True)
self.addScatter(geoX='N:CA:CB:CG', geoY='CA:CB:CG:CD', title='', hue='pdbCode', palette='gist_rainbow',ghost=True,categorical=True)
self.addScatter(geoX='N:CA', geoY='CA:C', title='', hue='dssp', palette='gist_rainbow',ghost=True)
self.addScatter(geoX='N:CA', geoY='CA:C', title='', hue=densityHue, palette='cubehelix_r', ghost=True)
self.addScatter(geoX='N:CA', geoY='CA:C', title='', hue='aa', palette='gist_rainbow', ghost=True,categorical=True)
self.addScatter(geoX='N:CA', geoY='CA:C', title='', hue='pdbCode', palette='gist_rainbow', ghost=True,categorical=True)
self.addScatter(geoX='CA:CA+1', geoY='CA-1:CA', title='', hue='dssp', palette='gist_rainbow', ghost=True)
self.addScatter(geoX='CA:CA+1', geoY='CA-1:CA', title='', hue=densityHue, palette='cubehelix_r', ghost=True)
self.addScatter(geoX='CA:CA+1', geoY='CA-1:CA', title='', hue='aa', palette='gist_rainbow', ghost=True,categorical=True)
self.addScatter(geoX='CA:CA+1', geoY='CA-1:CA', title='', hue='pdbCode', palette='gist_rainbow', ghost=True,categorical=True)
self.addScatter(geoX='CA:C:N+1:CA+1', geoY='N:CA:C', title='', hue='dssp', palette='gist_rainbow', ghost=True)
self.addScatter(geoX='CA:C:N+1:CA+1', geoY='N:CA:C', title='', hue=densityHue, palette='cubehelix_r', ghost=True)
self.addScatter(geoX='CA:C:N+1:CA+1', geoY='N:CA:C', title='', hue='aa', palette='gist_rainbow', ghost=True,categorical=True)
self.addScatter(geoX='CA:C:N+1:CA+1', geoY='N:CA:C', title='', hue='pdbCode', palette='gist_rainbow', ghost=True,categorical=True)
self.addScatter(geoX='N:O', geoY='CB:O', title='', hue='dssp', palette='gist_rainbow', ghost=True)
self.addScatter(geoX='N:O', geoY='CB:O', title='', hue=densityHue, palette='cubehelix_r', ghost=True)
self.addScatter(geoX='N:O', geoY='CB:O', title='', hue='aa', palette='gist_rainbow', ghost=True,categorical=True)
self.addScatter(geoX='N:O', geoY='CB:O', title='', hue='pdbCode', palette='gist_rainbow', ghost=True,categorical=True)
self.addScatter(geoX='N:CA:C:N+1', geoY='N:O', title='', hue='dssp', palette='gist_rainbow', ghost=True)
self.addScatter(geoX='N:CA:C:N+1', geoY='N:O', title='', hue=densityHue, palette='cubehelix_r', ghost=True)
self.addScatter(geoX='N:CA:C:N+1', geoY='N:O', title='', hue='aa', palette='gist_rainbow', ghost=True,categorical=True)
self.addScatter(geoX='N:CA:C:N+1', geoY='N:O', title='', hue='pdbCode', palette='gist_rainbow', ghost=True,categorical=True)
self.addScatter(geoX='N:CA:C:N+1', geoY='CB:O', title='', hue='dssp', palette='gist_rainbow', ghost=True)
self.addScatter(geoX='N:CA:C:N+1', geoY='CB:O', title='', hue=densityHue, palette='cubehelix_r', ghost=True)
self.addScatter(geoX='N:CA:C:N+1', geoY='CB:O', title='', hue='aa', palette='gist_rainbow', ghost=True,categorical=True)
self.addScatter(geoX='N:CA:C:N+1', geoY='CB:O', title='', hue='pdbCode', palette='gist_rainbow', ghost=True,categorical=True)
self.addScatter(geoX='N:CA:C:N+1', geoY='N:CA:C:O', title='', hue='dssp', palette='gist_rainbow', ghost=True)
self.addScatter(geoX='N:CA:C:N+1', geoY='N:CA:C:O', title='', hue=densityHue, palette='cubehelix_r', ghost=True)
self.addScatter(geoX='N:CA:C:N+1', geoY='N:CA:C:O', title='', hue='aa', palette='gist_rainbow', ghost=True,categorical=True)
self.addScatter(geoX='N:CA:C:N+1', geoY='N:CA:C:O', title='', hue='pdbCode', palette='gist_rainbow', ghost=True,categorical=True)
self.addScatter(geoX='N:CA:C:N+1', geoY='CA-1:CA:CA+1', title='', hue='dssp', palette='gist_rainbow', ghost=True)
self.addScatter(geoX='N:CA:C:N+1', geoY='CA-1:CA:CA+1', title='', hue=densityHue, palette='cubehelix_r',ghost=True)
self.addScatter(geoX='N:CA:C:N+1', geoY='CA-1:CA:CA+1', title='', hue='aa', palette='gist_rainbow',ghost=True,categorical=True)
self.addScatter(geoX='N:CA:C:N+1', geoY='CA-1:CA:CA+1', title='', hue='pdbCode', palette='gist_rainbow',ghost=True,categorical=True)
self.addScatter(geoX='C-1:N:CA:C', geoY='C-1:C', title='', hue='dssp', palette='gist_rainbow', ghost=True)
self.addScatter(geoX='C-1:N:CA:C', geoY='C-1:C', title='', hue=densityHue, palette='cubehelix_r', ghost=True)
self.addScatter(geoX='C-1:N:CA:C', geoY='C-1:C', title='', hue='aa', palette='gist_rainbow', ghost=True,categorical=True)
self.addScatter(geoX='C-1:N:CA:C', geoY='C-1:C', title='', hue='pdbCode', palette='gist_rainbow', ghost=True,categorical=True)
self.addScatter(geoX='C-1:N:CA:C', geoY='C-1:CB', title='', hue='dssp', palette='gist_rainbow', ghost=True)
self.addScatter(geoX='C-1:N:CA:C', geoY='C-1:CB', title='', hue=densityHue, palette='cubehelix_r', ghost=True)
self.addScatter(geoX='C-1:N:CA:C', geoY='C-1:CB', title='', hue='aa', palette='gist_rainbow', ghost=True,categorical=True)
self.addScatter(geoX='C-1:N:CA:C', geoY='C-1:CB', title='', hue='pdbCode', palette='gist_rainbow', ghost=True,categorical=True)
self.addScatter(geoX='CA:C:N+1:CA+1', geoY='CA-1:C-1:N:CA', title='', hue='dssp', palette='gist_rainbow', ghost=True)
self.addScatter(geoX='CA:C:N+1:CA+1', geoY='CA-1:C-1:N:CA', title='', hue=densityHue, palette='cubehelix_r',ghost=True)
self.addScatter(geoX='CA:C:N+1:CA+1', geoY='CA-1:C-1:N:CA', title='', hue='aa', palette='gist_rainbow',ghost=True,categorical=True)
self.addScatter(geoX='CA:C:N+1:CA+1', geoY='CA-1:C-1:N:CA', title='', hue='pdbCode', palette='gist_rainbow',ghost=True,categorical=True)
self.addScatter(geoX='CA-2:CA-1:CA', geoY='CA:CA+1:CA+2', title='', hue='dssp', palette='gist_rainbow', ghost=True)
self.addScatter(geoX='CA-2:CA-1:CA', geoY='CA:CA+1:CA+2', title='', hue=densityHue, palette='cubehelix_r',ghost=True)
self.addScatter(geoX='CA-2:CA-1:CA', geoY='CA:CA+1:CA+2', title='', hue='aa', palette='gist_rainbow',ghost=True,categorical=True)
self.addScatter(geoX='CA-2:CA-1:CA', geoY='CA:CA+1:CA+2', title='', hue='pdbCode', palette='gist_rainbow',ghost=True,categorical=True)
self.addScatter(geoX='C-1:N:CA', geoY='CA:C:N+1', title='', hue='dssp', palette='gist_rainbow', ghost=True)
self.addScatter(geoX='C-1:N:CA', geoY='CA:C:N+1', title='', hue=densityHue, palette='cubehelix_r', ghost=True)
self.addScatter(geoX='C-1:N:CA', geoY='CA:C:N+1', title='', hue='aa', palette='gist_rainbow', ghost=True,categorical=True)
self.addScatter(geoX='C-1:N:CA', geoY='CA:C:N+1', title='', hue='pdbCode', palette='gist_rainbow', ghost=True,categorical=True)
self.printToHtml(title, cols, fileName)
elif reportName == 'MainChainHistograms': # Sp2Planarity, DensityAtomCompare, OmegaCis
atomData = self.getReportCsv(reportName)
title = 'Main Chain Histograms'
cols = 3
printList = []
self.addHistogram(data=atomData,geoX='C-1:N',title='C-1:N',hue='rid',ghost=True)
self.addHistogram(data=atomData,geoX='N:CA',title='O:C:N+1',hue='rid',ghost=True)
self.addHistogram(data=atomData,geoX='CA:C',title='N+1:C:CA',hue='rid',ghost=True)
self.addHistogram(data=atomData, geoX='C:O', title='C:0', hue='rid',ghost=True)
self.addHistogram(data=atomData, geoX='CA-1:CA', title='CA-1:CA', hue='rid',ghost=True)
self.addHistogram(data=atomData, geoX='CA:CA+1', title='CA:CA+1', hue='rid',ghost=True)
self.addHistogram(data=atomData, geoX='C-1:N:CA', title='Tau-1', hue='rid',ghost=True)
self.addHistogram(data=atomData, geoX='N:CA:C', title='Tau', hue='rid',ghost=True)
self.addHistogram(data=atomData, geoX='CA:C:N+1', title='Tau+1', hue='rid',ghost=True)
self.addHistogram(data=atomData, geoX='C-1:N:CA:C', title='PHI', hue='rid',ghost=True)
self.addHistogram(data=atomData, geoX='N:CA:C:N+1', title='PSI', hue='rid',ghost=True)
self.addHistogram(data=atomData, geoX='CA:C:N+1:CA+1', title='AbsVal OMEGA', hue='rid', operation='ABS',ghost=True)
self.printToHtml(title, cols, fileName)
elif reportName == 'Sp2Planarity': # Sp2Planarity, DensityAtomCompare, OmegaCis
atomData = self.getReportCsv(reportName)
title = 'Sp2 Planarity'
cols = 4
printList = []
self.addHistogram(data=atomData,geoX='N+1:O:C:CA',title='AbsVal Dihedral',hue='rid',operation='ABS')
self.addHistogram(data=atomData,geoX='CA:C:O',title='CA:C:O',hue='rid')
self.addHistogram(data=atomData,geoX='O:C:N+1',title='O:C:N+1',hue='rid')
self.addHistogram(data=atomData,geoX='N+1:C:CA',title='N+1:C:CA',hue='rid')
self.addScatter(data=atomData, geoX='N+1:O:C:CA', geoY='CA:C:O',hue='dssp')
self.addScatter(data=atomData, geoX='N+1:O:C:CA', geoY='O:C:N+1')
self.addScatter(data=atomData, geoX='N+1:O:C:CA', geoY='N+1:C:CA',hue='bfactor')
self.addScatter(data=atomData, geoX='N+1:C:CA', geoY='O:C:N+1',hue='FoFc', palette='Spectral',centre=True)
self.printToHtml(title, cols, fileName)
elif reportName == 'DataPerPdb':
pdbmanager = geopdb.GeoPdbs(self.pdbDataPath, self.edDataPath, self.ed, self.dssp)
for pdb in self.pdbCodes:
print('\tPSU:', reportName, 'for', pdb)
apdb = pdbmanager.getPdb(pdb,True)
atomData = apdb.getDataFrame()
title = 'General Data Report'
cols = 3
self.addScatter(data=atomData, geoX='atomNo', geoY='aa', hue='aa', categorical=True,palette='gist_rainbow')
self.addScatter(data=atomData, geoX='atomNo', geoY='dssp',hue= 'aa',categorical=True,palette='gist_rainbow')
self.addScatter(data=atomData, geoX='2FoFc', geoY='bfactor',hue= 'element',palette='jet_r',categorical=True)
self.addScatter(data=atomData, geoX='atomNo', geoY='bfactor',hue= 'element',palette='jet_r',categorical=True)
self.addScatter(data=atomData, geoX='atomNo', geoY='2FoFc',hue='element',palette='jet_r',categorical=True)
self.addScatter(data=atomData, geoX='atomNo', geoY='FoFc',hue='element',palette='jet_r',categorical=True)
self.addScatter(data=atomData, geoX='x', geoY='y',hue='atomNo', palette='plasma_r')
self.addScatter(data=atomData, geoX='y', geoY='z',hue='atomNo', palette='plasma_r')
self.addScatter(data=atomData, geoX='z', geoY='x',hue='atomNo', palette='plasma_r')
self.printToHtml(title, cols, fileName + '_' + apdb.pdbCode)
elif reportName == 'Slow_DensityPointsPerPdb' or reportName == 'Slow_DensityPeaksPerPdb': # this can only be done per pdb
for pdb in self.pdbCodes:
pdbmanager = geopdb.GeoPdbs(self.pdbDataPath, self.edDataPath, self.ed, self.dssp)
apdb = pdbmanager.getPdb(pdb,True)
if apdb.hasDensity:
print('\tPSU:', reportName, 'for', apdb.pdbCode)
allPoints = True
maintitle = 'Density Points and Atoms Comparison'
if reportName == 'Slow_DensityPeaksPerPdb':
allPoints = False
maintitle = 'Density Peaks and Atoms Comparison'
peaksData = apdb.getStructureDensity(allPoints,10,self.pdbDataPath,self.edDataPath)
atomData = apdb.getDataFrame()
atomData['FoFc2'] = atomData['FoFc'] ** 2
cols = 3
printList = []
self.addScatter(data=peaksData, geoX='c', geoY='r', title='Density CR Fo',hue='Fo',palette='gist_gray_r')
self.addScatter(data=peaksData, geoX='r', geoY='s',title='Density RS Fo',hue='Fo',palette='gist_gray_r')
self.addScatter(data=peaksData, geoX='s', geoY='c',title='Density SC Fo',hue='Fo',palette='gist_gray_r')
self.addScatter(data=peaksData, geoX='c', geoY='r',title='Density CR Fo',hue='Fo',palette='cubehelix_r')
self.addScatter(data=peaksData, geoX='r', geoY='s',title='Density RS Fo',hue='Fo',palette='cubehelix_r')
self.addScatter(data=peaksData, geoX='s', geoY='c',title='Density SC Fo',hue='Fo',palette='cubehelix_r')
self.addScatter(data=peaksData, geoX='c', geoY='r',title='Density CR 2FoFC',hue='2FoFc',palette='cubehelix_r')
self.addScatter(data=peaksData, geoX='r', geoY='s',title='Density RS 2FoFC',hue='2FoFc',palette='cubehelix_r')
self.addScatter(data=peaksData, geoX='s', geoY='c',title='Density SC 2FoFC',hue='2FoFc',palette='cubehelix_r')
self.addScatter(data=peaksData, geoX='c', geoY='r',title='Density CR FC',hue='Fc',palette='cubehelix_r')
self.addScatter(data=peaksData, geoX='r', geoY='s',title='Density RS FC',hue='Fc',palette='cubehelix_r')
self.addScatter(data=peaksData, geoX='s', geoY='c',title='Density SC FC',hue='Fc',palette='cubehelix_r')
self.addScatter(data=peaksData, geoX='c', geoY='r',title='Density CR FoFC',hue='FoFc',palette='PiYG',centre=True)
self.addScatter(data=peaksData, geoX='r', geoY='s',title='Density RS FoFC',hue='FoFc',palette='PiYG',centre=True)
self.addScatter(data=peaksData, geoX='s', geoY='c',title='Density SC FoFC',hue='FoFc',palette='PiYG',centre=True)
self.addScatter(data=peaksData, geoX='x', geoY='y',title='Density XY Fo',hue='Fo',palette='cubehelix_r')
self.addScatter(data=peaksData, geoX='y', geoY='z',title='Density YZ Fo',hue='Fo',palette='cubehelix_r')
self.addScatter(data=peaksData, geoX='z', geoY='x',title='Density ZX Fo',hue='Fo',palette='cubehelix_r')
self.addScatter(data=peaksData, geoX='x', geoY='y',title='Density XY FoFC',hue='FoFc',palette='PiYG',centre=True)
self.addScatter(data=peaksData, geoX='y', geoY='z',title='Density YZ FoFC',hue='FoFc',palette='PiYG',centre=True)
self.addScatter(data=peaksData, geoX='z', geoY='x', title='Density ZX FoFC',hue='FoFc',palette='PiYG',centre=True)
self.addScatter(data=peaksData, geoX='x', geoY='y',title='Density XY 2FoFC',hue='2FoFc',palette='cubehelix_r')
self.addScatter(data=peaksData, geoX='y', geoY='z',title='Density YZ 2FoFC',hue='2FoFc',palette='cubehelix_r')
self.addScatter(data=peaksData, geoX='z', geoY='x',title='Density ZX 2FoFC',hue='2FoFc',palette='cubehelix_r')
self.addScatter(data=atomData, geoX='x', geoY='y',title='PDB XY 2FoFc',hue='2FoFc',palette='cubehelix_r')
self.addScatter(data=atomData, geoX='y', geoY='z',title='PDB YZ 2FoFc',hue='2FoFc',palette='cubehelix_r')
self.addScatter(data=atomData, geoX='z', geoY='x',title='PDB ZX 2FoFc',hue='2FoFc',palette='cubehelix_r')
self.addScatter(data=atomData, geoX='x', geoY='y',title='PDB XY Electrons',hue='electrons',palette='Spectral_r',categorical=True)
self.addScatter(data=atomData, geoX='y', geoY='z',title='PDB YZ Electrons',hue='electrons',palette='Spectral_r',categorical=True)
self.addScatter(data=atomData, geoX='z', geoY='x',title='PDB ZX Electrons',hue='electrons',palette='Spectral_r',categorical=True)
self.addScatter(data=atomData, geoX='x', geoY='y',title='PDB XY FoFc',hue='FoFc',palette='PiYG',centre=True)
self.addScatter(data=atomData, geoX='y', geoY='z',title='PDB YZ FoFc',hue='FoFc',palette='PiYG',centre=True)
self.addScatter(data=atomData, geoX='z', geoY='x',title='PDB ZX FoFc',hue='FoFc',palette='PiYG',centre=True)
self.addScatter(data=atomData, geoX='x', geoY='y',title='PDB XY bfactor',hue='bfactor',palette='cubehelix_r')
self.addScatter(data=atomData, geoX='y', geoY='z',title='PDB YZ bfactor',hue='bfactor',palette='cubehelix_r')
self.addScatter(data=atomData, geoX='z', geoY='x',title='PDB ZX bfactor',hue='bfactor',palette='cubehelix_r')
self.addScatter(data=atomData, geoX='x', geoY='y',title='PDB XY atom nos',hue='atomNo',palette='gist_ncar')
self.addScatter(data=atomData, geoX='y', geoY='z',title='PDB YZ atom nos',hue='atomNo',palette='gist_ncar')
self.addScatter(data=atomData, geoX='z', geoY='x',title='PDB ZX atom nos',hue='atomNo',palette='gist_ncar')
self.addScatter(data=atomData, geoX='x', geoY='y',title='PDB XY amino acids',hue='aa',palette='nipy_spectral',categorical=True)
self.addScatter(data=atomData, geoX='y', geoY='z',title='PDB YZ amino acids',hue='aa',palette='nipy_spectral',categorical=True)
self.addScatter(data=atomData, geoX='z', geoY='x',title='PDB ZX amino acids',hue='aa',palette='nipy_spectral',categorical=True)
self.addScatter(data=atomData, geoX='bfactor', geoY='2FoFc',title='PDB bfactor vs 2FoFc',hue='electrons',palette='viridis_r',categorical=True)
self.addScatter(data=atomData, geoX='Fc', geoY='Fo',title='PDB Fc vs Fc',hue='electrons',palette='viridis_r',categorical=True)
self.addScatter(data=atomData, geoX='electrons', geoY='2FoFc',title='PDB electrons vs 2FoFc',hue='element',palette='viridis_r',categorical=True)
self.addHistogram(data=atomData, geoX='aa',title='Amino Acids')
self.addHistogram(data=atomData, geoX='element',title='Atoms')
self.addHistogram(data=atomData, geoX='2FoFc',title='Peaks in 2FoFc')
self.printToHtml(maintitle, cols, fileName + '_' + apdb.pdbCode)
else:
print('\tPSU:',apdb.pdbCode,'has no density matrix')
def addDataView(self, pdbCode, geoX, geoY, palette='viridis', hue='2FoFc', categorical=False, title='',centre=False,sort='ASC'):
pdbmanager = geopdb.GeoPdbs(self.pdbDataPath, self.edDataPath, self.ed, self.dssp)
apdb = pdbmanager.getPdb(pdbCode,True)
df = apdb.getDataFrame()
self.addScatter(data=df, geoX=geoX, geoY=geoY, title=title, hue=hue, palette=palette,categorical=categorical,centre=centre,sort=sort)