def importEXP(request):
#load db with an initial value, if first time user
defEXP = dbEXPupload(username=request.user.username, EXPupload='none chosen')
defEXP.save()
#get loaded Results data, if any, for the Testing Refresh, otherwise it will blank
rerun = getLoadDict(request.user.username)
# maybe use UploadDataForm and have def to chunk: https://docs.djangoproject.com/en/1.8/topics/http/file-uploads/
if request.method == 'GET':
EXP = EXPuploadForm(initial={'username': request.user.username,'EXPupload': 'none chosen'})
else:
EXP = EXPuploadForm(request.POST, request.FILES)
if EXP.is_valid():
entry=dbEXPupload(username = request.POST.get('username'),
EXPupload = request.FILES['EXPupload']
) #this is name of col in DB
entry.save()
else:
EXP = EXPuploadForm(initial={'username': request.user.username,'EXPupload': 'none chosen'})
#update newrundict.txt (to-be-run-parameters) via the toberun function
query = 'SELECT * FROM Inputs_dbexpupload WHERE username = "******" ORDER BY id DESC LIMIT 1'
object = dbEXPupload.objects.raw(query)[0]
ToBeRunDict = toberun(object)
return render(request, 'main.html',
{'EXPHTML' : EXP,
'ToBeRunHTML' : ToBeRunDict, 'resultsHTML': rerun})
def importPDBup(request):
#load db with an initial value, if first time user
defUp = dbPDBup(username=request.user.username, PDBup='none chosen')
defUp.save()
#get loaded Results data, if any, for the Testing Refresh, otherwise it will blank
rerun = getLoadDict(request.user.username)
# maybe use UploadDataForm and have def to chunk: https://docs.djangoproject.com/en/1.8/topics/http/file-uploads/
if request.method == 'GET':
PDBup = PDBupForm(initial={'username': request.user.username,'PDBup': 'none chosen'})
else:
PDBup = PDBupForm(request.POST, request.FILES)
if PDBup.is_valid():
entry=dbPDBup(username = request.POST.get('username'),
PDBup = request.FILES['PDBup']
) #obj containing files
entry.save()
else:
PDBup = PDBupForm(initial={'username': request.user.username,'PDBup': 'none chosen'})
#update dbtoberun via the toberun function
query = 'SELECT * FROM Inputs_dbpdbup WHERE username = "******" ORDER BY id DESC LIMIT 1'
object = dbPDBup.objects.raw(query)[0]
ToBeRunDict = toberun(object)
return render(request, 'main.html',
{'PDBupHTML' : PDBup,
'ToBeRunHTML' : ToBeRunDict, 'resultsHTML': rerun})
def Clear(request):
#get -loaded- Results data, if any, for the Refresh, otherwise it will blank
rerun = getLoadDict(request.user.username)
if request.method == 'POST': #if clear is pressed....
#default all possible choices, save to appropriate db
defDown = dbPDBdown(username=request.user.username, PDBdown='none chosen')
defDown.save()
defUp = dbPDBup(username=request.user.username, PDBup='none chosen')
defUp.save()
defEXP = dbEXPupload(username=request.user.username, EXPupload='none chosen')
defEXP.save()
defPara = dbPara(username=request.user.username, jobname=' ', turns=5, units=27, rise=2.9, rescutL=0.0833333333, rescutH=0.3333333333, LorR='R')
defPara.save()
defPara2 = dbPara2(username=request.user.username, bfactor=20.0, bfactorSolv=400, bfactorSolvK=0.4, gridPhi=128,
gridR=256, gridZ=128, qfhtK1=2.0, qfhtK2=2.2, rfactor='False', scscaling=0.92, R_step=0.001,
layer_lines=20)
defPara2.save()
#now make a new newrundict.txt with default values
newrundict(request.user.username)
#retrieve the newrundict.txt to display 'to be run' files and parameters
import json
thefile = PathMaker(request.user.username, 'newrundict.txt')
FHin = open(thefile, 'r') #now open the new file
#take out the dict
defaultDict = json.load(FHin)
FHin.close()
#now run to default everything
return render(request, 'main.html', {
'ToBeRunHTML' : defaultDict, 'resultsHTML': rerun})
def importPara2(request):
#load db with an initial value, if first time user
defPara2 = dbPara2(username=request.user.username, bfactor=20.0, bfactorSolv=400, bfactorSolvK=0.4, gridPhi=128,
gridR=256, gridZ=128, qfhtK1=2.0, qfhtK2=2.2, rfactor='False', scscaling=0.92, R_step=0.001,
layer_lines=20)
defPara2.save()
#get loaded Results data, if any, for the Testing Refresh, otherwise it will blank
rerun = getLoadDict(request.user.username)
if request.method == 'GET':
Parameters = AddParaForm(initial={'username': request.user.username, 'rfactor':'False', 'bfactor':20.0, 'bfactorSolv':400, 'bfactorSolvK':0.4, 'qfhtK1':2.0, 'qfhtK2':2.2, 'scscaling':0.92, 'gridR':256, 'gridZ':128, 'gridPhi':128,'R_step':0.001, 'layer_lines':20})
else:
Parameters = AddParaForm(request.POST)
if Parameters.is_valid():
entry=dbPara2(username = request.POST.get('username'),
rfactor = request.POST.get('rfactor'),
bfactor = request.POST.get('bfactor'),
bfactorSolv = request.POST.get('bfactorSolv'),
bfactorSolvK = request.POST.get('bfactorSolvK'),
qfhtK1 = request.POST.get('qfhtK1'),
qfhtK2 = request.POST.get('qfhtK2'),
scscaling = request.POST.get('scscaling'),
gridR =request.POST.get('gridR'),
gridZ= request.POST.get('gridZ'),
gridPhi = request.POST.get('gridPhi'),
R_step= request.POST.get('R_step'),
layer_lines = request.POST.get('layer_lines'))
entry.save()
else:
Parameters = AddParaForm(initial={'username': request.user.username, 'rfactor':'False', 'bfactor':20.0, 'bfactorSolv':400, 'bfactorSolvK':0.4, 'qfhtK1':2.0, 'qfhtK2':2.2, 'scscaling':0.92, 'gridR':256, 'gridZ':128, 'gridPhi':128, 'R_step':0.001, 'layer_lines':20})
#update newrundict.txt (to-be-run-parameters) via the toberun function
query = 'SELECT * FROM Inputs_dbpara2 WHERE username = "******" ORDER BY id DESC LIMIT 1'
object = dbPara2.objects.raw(query)[0]
ToBeRunDict = toberun(object)
#RENDER
return render(request, 'main.html',
{'AddHTML' : Parameters,
'ToBeRunHTML' : ToBeRunDict, 'resultsHTML': rerun})
def importParameters(request):
#load db with an initial value, if first time user
defPara = dbPara(username=request.user.username, jobname=' ', turns=5, units=27, rise=2.9, rescutL=0.0833333333, rescutH=0.3333333333, LorR='R')
defPara.save()
#get loaded Results data, if any, for the Testing Refresh, otherwise it will blank
rerun = getLoadDict(request.user.username)
if request.method == 'GET':
Parameters = ParaForm(initial={'username': request.user.username, 'jobname': ' ', 'turns':5, 'units':27, 'rise':2.9, 'rescutL':0.0833333333, 'rescutH':0.3333333333, 'LorR':'R'})
else:
Parameters = ParaForm(request.POST)
if Parameters.is_valid():
entry=dbPara(username = request.POST.get('username'),
jobname = request.POST.get('jobname'),
turns = request.POST.get('turns'),
units = request.POST.get('units'),
rise = request.POST.get('rise'),
rescutL = request.POST.get('rescutL'),
rescutH = request.POST.get('rescutH'),
LorR = request.POST.get('LorR')
)
entry.save()
else:
Parameters = ParaForm(initial={'username': request.user.username, 'jobname': ' ', 'turns':5, 'units':27, 'rise':2.9, 'rescutL':0.0833333333, 'rescutH':0.3333333333, 'LorR':'R'})
#update newrundict.txt (to-be-run-parameters) via the toberun function
query = 'SELECT * FROM Inputs_dbpara WHERE username = "******" ORDER BY id DESC LIMIT 1'
object = dbPara.objects.raw(query)[0]
ToBeRunDict = toberun(object)
#RENDER
return render(request, 'main.html',
{'ParaHTML' : Parameters,
'ToBeRunHTML' : ToBeRunDict, 'resultsHTML': rerun})
def Testing(request):
#get loaded Results data, if any, for the Testing Refresh, otherwise it will blank
#should be blank prior to first load request
rerun = getLoadDict(request.user.username)
#include ToBeRun dictionary from inputs
ToBeRunDict = getRunDict(request.user.username)
#if Run is pressed....
if request.method == 'POST':
#check here if no PDB
#if ...
#SQL to make query objects for each table
#****************************************
#download
query = 'SELECT * FROM Inputs_dbpdbdown WHERE username = "******" ORDER BY id DESC LIMIT 1'
Qobject = dbResults.objects.raw(query)[0]
#upload
query = 'SELECT * FROM Inputs_dbpdbup WHERE username = "******" ORDER BY id DESC LIMIT 1'
Qobject2 = dbPDBup.objects.raw(query)[0]
#Experimental
query = 'SELECT * FROM Inputs_dbexpupload WHERE username = "******" ORDER BY id DESC LIMIT 1'
Qobject3 = dbEXPupload.objects.raw(query)[0]
#Parameters
query = 'SELECT * FROM Inputs_dbpara WHERE username = "******" ORDER BY id DESC LIMIT 1'
Qobject4 = dbPara.objects.raw(query)[0]
#Additional Parameters
query = 'SELECT * FROM Inputs_dbpara2 WHERE username = "******" ORDER BY id DESC LIMIT 1'
Qobject4B = dbPara2.objects.raw(query)[0]
#Identify the most current upload or download by timestamp, choose most recent
if Qobject.timestamp > Qobject2.timestamp:
chosenPDB = fetch_pdb(Qobject)
else:
chosenPDB = 'static_in_pro/media_root/' + str(Qobject2.PDBup)
#make grid.dat
#*************
#default expLL: Need Hcutoff and Lcutoff (as floating numbers)
#output is grid.dat, which is used to for making EXP in flag file
makeDefExp(Qobject.username, float(Qobject4.rescutH), float(Qobject4.rescutL), int(Qobject4B.layer_lines), float(Qobject4B.R_step))
#Make FlagsFile using the query objects
#**************************************
#overwrite for reruns
overwrite = '-out:overwrite'
#db path for rosetta, otherwise its default, somewhere on server
db = '-database /home/stephen/Project/trydjango/static_in_pro/media_root/Storage/database'
#add sdef from helix_denovo output
sdef = '-symmetry:symmetry_definition ' + '/home/stephen/Project/trydjango/' + PathMaker(Qobject.username, 'helix_denovo.sdef')
#needed for some reason
extra = '-symmetry:initialize_rigid_body_dofs'
#the chosen PDB, based on most recent timestamp
PDB = '-in:file:s '+ '/home/stephen/Project/trydjango/' + str(chosenPDB)
#if experimental is 'none chosen', grid.dat needs to be used in its place
if 'none chosen' in str(Qobject3.EXPupload):
EXP = '-fiber_diffraction:layer_lines ' + '/home/stephen/Project/trydjango/' + PathMaker(Qobject.username, 'grid.dat')
else:
EXP = '-fiber_diffraction:layer_lines ' + 'static_in_pro/media_root/' + str(Qobject3.EXPupload)
#generic inputs
Units = '-fiber_diffraction:a '+ str(Qobject4.units) #number of units
Turns = '-fiber_diffraction:b '+ str(Qobject4.turns) #number of turns
Rise = '-fiber_diffraction:p '+ str(Qobject4.rise) #If specified, subunit rise is taken from input, otherwise is calculated by the program
Lcutoff = '-fiber_diffraction:resolution_cutoff_low '+ str(Qobject4.rescutL) #Resolution cutoff 12�
Hcutoff = '-fiber_diffraction:resolution_cutoff_high '+ str(Qobject4.rescutH) #Resolution cutoff 3�
#Additional Parameters
Rfac = '-fiber_diffraction:rfactor_refinement '+ str(Qobject4B.rfactor) #If set R factor instead of chi2 is used in scoring and derivatives calculations
AtomicBF = '-fiber_diffraction::b_factor '+ str(Qobject4B.bfactor) #Atomic B-factor
Solv = '-fiber_diffraction::b_factor_solv '+ str(Qobject4B.bfactorSolv) #temperature factor that accounts for the disordered solvent
SolvK = '-fiber_diffraction::b_factor_solv_K '+ str(Qobject4B.bfactorSolvK) #scale factor that adjust average solvent scattering intensity
K1 = '-fiber_diffraction:qfht_K1 '+ str(Qobject4B.qfhtK1) #Hankel transform K1 parameter
K2 = '-fiber_diffraction:qfht_K2 '+ str(Qobject4B.qfhtK2) #Hankel transform K1 parameter
SC = '-edensity:sc_scaling '+ str(Qobject4B.scscaling) #Hankel transform K1 parameter
GridR = '-fiber_diffraction:grid_r '+ str(Qobject4B.gridR) #Grid size r, should be bigger than radius of molecule
GridZ = '-fiber_diffraction:grid_z '+ str(Qobject4B.gridZ) #Grid size z, should be bigger than molecule span in z direction
GridPhi = '-fiber_diffraction:grid_phi '+ str(Qobject4B.gridPhi) #Grid size phi, change if higher accuracy is needed
#output for Rosetta_programs
fibPDBout = '-out:output '
outputpath = '-out:path:pdb ' + PathMaker(Qobject.username, '') #Rosetta decides name of fibrilPDB, we can only prefix it
prefix = '-out:prefix ' + 'RUN' + str(tagOutput(request)) + '_'
LLout = '-fiber_diffraction:output_fiber_spectra' #+ PathMaker(Qobject.username, 'Intensity.txt') #to make LLpic, stored in user's folder'
Score = '-out:file:scorefile ' + '/home/stephen/Project/trydjango/' + PathMaker(Qobject.username, 'score.sc')
scoreWeights = '-score:weights /home/stephen/Project/trydjango/static_in_pro/media_root/Rosetta_files/fiberdiffraction.txt' #text file is only “fiberdiffraction 1”
#make a list of the above variables
ParameterList = [
overwrite,
db,
sdef,
extra,
PDB,
EXP,
Units,
Turns,
Rise,
Lcutoff,
Hcutoff,
Rfac,
AtomicBF,
Solv,
SolvK,
K1,
K2,
SC,
GridR,
GridZ,
GridPhi,
fibPDBout,
LLout,
Score,
prefix,
outputpath,
scoreWeights]
#make the Flags file, tagged with username, placed in user's folder
filename = str(Qobject.username) + '_Flags'
Path = PathMaker(Qobject.username, filename)
FHout = open(Path, 'w')
for item in ParameterList:
FHout.write("%s\n" % item)
FHout.close()
#now save path to dbFlags
addFlag = dbFlag(username=Qobject.username, FlagFile=Path)
addFlag.save()
#Path variables for dbResults **make sure their -creation- also points to same user dir
#Paths needed for make_helix_denovo
denovoPath = str(PathMaker(Qobject.username, 'helix_denovo.sdef'))
virtualsPath = str(PathMaker(Qobject.username, 'virtuals.pdb'))
#for Rosetta
fibrilPDBPath = str(PathMaker(Qobject.username, fibRename(request, chosenPDB))) #Rosetta outputs odd name, so need function to match it for db
intensityPath = str(PathMaker3(Qobject.username, 'Intensity_' + str(tagOutput(request)) + '.txt')) #need special path correction; see PathMaker3
scorePath = str(PathMaker(Qobject.username, 'score.sc'))
#for layerlinestoimage
LLpicPath = str(PathMaker(Qobject.username, 'layerlines_run' + str(tagOutput(request)) + '.png')) #note: need to save this file for future load requests
#Run make_helix_denovo:
#*********************
#input: units/rise/turns/N=40, plus path to .sdef output, path to virtualPDB
helixer = Helixer(float(Qobject4.rise), int(40), int(Qobject4.turns), int(Qobject4.units), denovoPath, virtualsPath)
#Executing pipeline
helixer.execute()
helixer.write()
helixer.writePDBlines()
#output of helix_denovo.sdef 'symmetry definition file'
#output of virtuals.pdb: virtual_residues_file also made each run: for diagnostics
#run Rosetta
#***********
#query dbFlag and make an object containing everything
query = 'SELECT * FROM Run_dbflag WHERE username = "******" ORDER BY id DESC LIMIT 1'
Qobject5 = dbFlag.objects.raw(query)[0]
#inputs: see Flagfile
program = '/home/stephen/Project/trydjango/static_in_pro/media_root/Rosetta_programs/score.static.linuxgccrelease'
addflag = '@' + '/home/stephen/Project/trydjango/' + str(Qobject5.FlagFile) #need to add prefix path, since not django
together = program + ' ' + addflag
Path2 = PathMaker(Qobject.username, 'cmd')
FHout2 = open(Path2, 'w')
FHout2.write("%s\n" % together)
FHout2.close()
os.system('chmod 775 ' + Path2)
os.system(Path2)
#outputs: fibril.pdb, intensity.txt(LLout), score.sc (for making chi-sq)+ scoreweights (ignore)
#move intensity.txt from Project/tryjango to user dir and rename (to intensityPath)
moveInten(request)
#Run LayerLinesToImage
#*********************
#output: layerlines.png stored in LLpic attribute
output = PathMaker(Qobject.username, 'layerlines_run' + str(tagOutput(request)) + '.png')
experimental = str(Qobject3.EXPupload)
layerlines = LLTI(intensityPath, experimental, output, str(tagOutput(request)))
layerlines.convert_to_image(str(tagOutput(request))) #need to include RUNX here as well...
#Derive Chisq
#************
#note! if no expLL (just grid.dat) , then score should be empty and no chisq made!!!!!
Chisq=findChisq(scorePath, Qobject.username) #parses Score file, which was produced by Rosetta_programs
#add to most recent run
mostrecent = int(tagOutput(request))
#Save Results
#************
#load inputs and results to dbResults
addResults = dbResults(mostRes=mostrecent, #Add to mostRec runcount
username=Qobject.username,
PDBused=chosenPDB,
experimentalData= Qobject3.EXPupload,
jobname=Qobject4.jobname,
turns=Qobject4.turns,
units=Qobject4.units,
rise=Qobject4.rise,
rescutL=Qobject4.rescutL,
rescutH=Qobject4.rescutH,
LorR=Qobject4.LorR,
rfactor=Qobject4B.rfactor,
bfactor=Qobject4B.bfactor,
bfactorSolv=Qobject4B.bfactorSolv,
bfactorSolvK=Qobject4B.bfactorSolvK,
qfhtK1 = Qobject4B.qfhtK1,
qfhtK2 = Qobject4B.qfhtK2,
scscaling = Qobject4B.scscaling,
gridR = Qobject4B.gridR,
gridZ= Qobject4B.gridZ,
gridPhi = Qobject4B.gridPhi,
R_step= Qobject4B.R_step,
layer_lines = Qobject4B.layer_lines,
fibrilPDB = fibrilPDBPath,
intensity = intensityPath,
LLoutputPic=LLpicPath, #derived from LLtoImage
chisq = Chisq) #derived from Score (see chisq function)
addResults.save()
#need to remove hydrogens from fibril pdb or Jsmol is slow
removeHydrogen(fibrilPDBPath)
#RENDER
#toreturn= UsedParam(Qobject6) #note! UsedParam also includes newrundict.txt results for 'to be run' files/para
return render(request, 'main.html', {'ToBeRunHTML' : ToBeRunDict, 'resultsHTML': rerun})