def gui(self):
fr = Frame(self)
b=Button(fr,text='load csv',command=self.importCSV)
b.pack(side=LEFT,fill=BOTH,padx=1)
b=Button(fr,text='load ekin',command=self.loadProject)
b.pack(side=LEFT,fill=BOTH,padx=1)
self.stopbtn=Button(fr,text='stop',command=self.stopFit)#,state=DISABLED)
self.stopbtn.pack(side=LEFT,fill=BOTH,padx=1)
self.previmg = Ekin_images.prev()
b=Button(fr,text='prev',image=self.previmg,command=self.prev)
b.pack(side=LEFT,fill=BOTH)
self.nextimg = Ekin_images.next()
b=Button(fr,text='next',image=self.nextimg,command=self.next)
b.pack(side=LEFT,fill=BOTH)
fr.pack(side=TOP)
self.dsetselector = Pmw.ComboBox(fr, entry_width=15,
selectioncommand = self.selectDataset)
self.dsetselector.pack(side=LEFT,fill=BOTH,padx=1)
fr2 = Frame(self)
fr2.pack(side=TOP)
self.plotfunctionvar = IntVar()
cb=Checkbutton(fr2, text='plot function only',variable=self.plotfunctionvar)
cb.pack(side=TOP)
self.plotframe = PlotPanel(parent=self, side=BOTTOM, height=200)
self.dsindex = 0
self.opts = {'markersize':18,'fontsize':10,'showfitvars':True}
return
def showPlotPanel(self, parent, E=None):
"""Add an ekin plot frame"""
fr=Frame(parent)
self.pw.add(fr)
self.plotframe = PlotPanel(parent=fr, tools=True)
if E != None:
E.checkDatasets()
self.plotframe.setProject(E)
self.plotSelected()
return
def __init__(self, master, app=None):
Frame.__init__(self, master)
self.app = app
self.E = None
if hasattr(self.app,'p'):
self.p = self.app.p #reference to pipeline object
fr = Frame(self)
self.totalvar = IntVar()
lfr=Frame(fr)
lfr.pack()
Label(lfr,text='Datasets:').pack(side=LEFT,fill=BOTH)
l=Label(lfr,text='',textvariable=self.totalvar)
l.pack(side=LEFT,fill=BOTH)
b=Button(fr,text='update',command=self.update)
b.pack(side=TOP,fill=BOTH)
self.previmg = Images.prev()
b=Button(fr,text='prev',image=self.previmg,compound='left',command=self.prev)
b.pack(side=TOP,fill=BOTH)
self.nextimg = Images.next()
b=Button(fr,text='next',image=self.nextimg,compound='left',command=self.next)
b.pack(side=TOP,fill=BOTH)
self.numplotscounter = Pmw.Counter(fr,
labelpos='w',
label_text='plots:',
entryfield_value=1,
entry_width=3,
datatype = 'integer',
entryfield_command=self.replot,
entryfield_validate={'validator':'numeric', 'min':1,'max':12})
self.numplotscounter.pack()
self.overlayvar = BooleanVar(); self.overlayvar.set(False)
Checkbutton(fr, text='overlay plots', variable=self.overlayvar, command=self.replot).pack(side=TOP,fill=BOTH)
self.normalizevar = BooleanVar(); self.normalizevar.set(False)
Checkbutton(fr, text='normalize', variable=self.normalizevar, command=self.replot).pack(side=TOP,fill=BOTH)
fr.pack(side=LEFT)
self.plotframe = PlotPanel(parent=self, side=BOTTOM, height=200, tools=True)
self.dsindex = 0
self.plotframe.Opts.opts['fontsize']=10
b=Button(fr,text='open in Ekin',command=self.loadEkin)
b.pack(side=TOP,fill=BOTH)
return
class PlotPreviewer(Frame):
def __init__(self, master, app=None):
Frame.__init__(self, master)
self.app = app
self.E = None
if hasattr(self.app,'p'):
self.p = self.app.p #reference to pipeline object
fr = Frame(self)
self.totalvar = IntVar()
lfr=Frame(fr)
lfr.pack()
Label(lfr,text='Datasets:').pack(side=LEFT,fill=BOTH)
l=Label(lfr,text='',textvariable=self.totalvar)
l.pack(side=LEFT,fill=BOTH)
b=Button(fr,text='update',command=self.update)
b.pack(side=TOP,fill=BOTH)
self.previmg = Images.prev()
b=Button(fr,text='prev',image=self.previmg,compound='left',command=self.prev)
b.pack(side=TOP,fill=BOTH)
self.nextimg = Images.next()
b=Button(fr,text='next',image=self.nextimg,compound='left',command=self.next)
b.pack(side=TOP,fill=BOTH)
self.numplotscounter = Pmw.Counter(fr,
labelpos='w',
label_text='plots:',
entryfield_value=1,
entry_width=3,
datatype = 'integer',
entryfield_command=self.replot,
entryfield_validate={'validator':'numeric', 'min':1,'max':12})
self.numplotscounter.pack()
self.overlayvar = BooleanVar(); self.overlayvar.set(False)
Checkbutton(fr, text='overlay plots', variable=self.overlayvar, command=self.replot).pack(side=TOP,fill=BOTH)
self.normalizevar = BooleanVar(); self.normalizevar.set(False)
Checkbutton(fr, text='normalize', variable=self.normalizevar, command=self.replot).pack(side=TOP,fill=BOTH)
fr.pack(side=LEFT)
self.plotframe = PlotPanel(parent=self, side=BOTTOM, height=200, tools=True)
self.dsindex = 0
self.plotframe.Opts.opts['fontsize']=10
b=Button(fr,text='open in Ekin',command=self.loadEkin)
b.pack(side=TOP,fill=BOTH)
return
def replot(self):
"""Replot"""
if len(self.E.datasets) == 0:
print 'no datasets to plot, check your config'
self.clear()
return
p = int(self.numplotscounter.getvalue())
if p > self.E.length: p = self.E.length
if p>1:
if self.dsindex+p>self.E.length:
start = self.E.length - p
else:
start = self.dsindex
dsets = self.E.datasets[start:self.dsindex+p]
c=math.ceil(math.sqrt(p))
else:
dsets = self.E.datasets[self.dsindex]
c=1
if self.overlayvar.get() == True:
plotopt = 3
self.plotframe.Opts.opts['title']=' '
self.plotframe.Opts.opts['legend'] = 1
else:
plotopt = 2
self.plotframe.Opts.opts['title']=None
self.plotframe.Opts.opts['normalise'] = self.normalizevar.get()
self.plotframe.plotCurrent(dsets, cols=c, plotoption=plotopt)
return
def loadData(self, data):
"""Load dict into datasets"""
E = self.E = Utilities.getEkinProject(data)
self.plotframe.setProject(E)
self.totalvar.set(self.E.length)
return
def update(self, evt=None):
"""Reload data dict from main app"""
self.p = self.app.p
data = self.p.doImport()
if data == None: return
self.dsindex = 0
self.loadData(data)
self.replot()
return
def clear(self):
self.E = None
self.plotframe.clear()
return
def prev(self):
if self.E == None: return
if self.dsindex <= 0:
self.dsindex = 0
else:
self.dsindex -= 1
self.replot()
return
def next(self):
if self.E == None: return
if self.dsindex >= self.E.length-1:
self.dsindex = self.E.length-1
else:
self.dsindex += 1
self.replot()
return
def loadEkin(self):
if self.E != None:
EK = EkinApp(parent=self, project=self.E)
return
class FitPreviewer(Frame):
"""Class to preview model fitting in plot"""
def __init__(self, master, app=None):
Frame.__init__(self, master)
self.main=self.master
self.app = app
self.E = None
self.gui()
self.sampleData()
self.stop = False
return
def gui(self):
fr = Frame(self)
b=Button(fr,text='load csv',command=self.importCSV)
b.pack(side=LEFT,fill=BOTH,padx=1)
b=Button(fr,text='load ekin',command=self.loadProject)
b.pack(side=LEFT,fill=BOTH,padx=1)
self.stopbtn=Button(fr,text='stop',command=self.stopFit)#,state=DISABLED)
self.stopbtn.pack(side=LEFT,fill=BOTH,padx=1)
self.previmg = Ekin_images.prev()
b=Button(fr,text='prev',image=self.previmg,command=self.prev)
b.pack(side=LEFT,fill=BOTH)
self.nextimg = Ekin_images.next()
b=Button(fr,text='next',image=self.nextimg,command=self.next)
b.pack(side=LEFT,fill=BOTH)
fr.pack(side=TOP)
self.dsetselector = Pmw.ComboBox(fr, entry_width=15,
selectioncommand = self.selectDataset)
self.dsetselector.pack(side=LEFT,fill=BOTH,padx=1)
fr2 = Frame(self)
fr2.pack(side=TOP)
self.plotfunctionvar = IntVar()
cb=Checkbutton(fr2, text='plot function only',variable=self.plotfunctionvar)
cb.pack(side=TOP)
self.plotframe = PlotPanel(parent=self, side=BOTTOM, height=200)
self.dsindex = 0
self.opts = {'markersize':18,'fontsize':10,'showfitvars':True}
return
def sampleData(self):
E =self.E = EkinProject()
E.createSampleData()
self.plotframe.setProject(E)
self.datasets = sorted(self.E.datasets)
self.replot()
self.updateSelector()
return
def updateSelector(self):
self.dsindex=0
lst = self.datasets
self.dsetselector.setlist(lst)
self.dsetselector.selectitem(lst[self.dsindex])
return
def replot(self, dset=None):
"""Replot"""
if dset==None:
dset = self.datasets[self.dsindex]
self.plotframe.plotCurrent(dset,options=self.opts)
return
def finishFit(self, X):
"""Call when fitting done"""
d = self.datasets[self.dsindex]
model = X.getResult()['model']
fitdata = Fitting.makeFitData(model, X.variables, X.getError())
self.E.setFitData(d, fitdata)
self.replot()
self.stop = False
return
def stopFit(self):
self.stop = True
return
def getCurrentData(self):
dset = self.datasets[self.dsindex]
ek = self.E.getDataset(dset)
return ek.getxy()
def updateFit(self, selfdiff, vrs, fitvals, c, X):
self.plotframe.updateFit(X, showfitvars=True)
self.update_idletasks()
self.update()
if self.stop == True:
X.stop_fit = 1
return
def prev(self):
if self.dsindex <= 0:
self.dsindex = 0
else:
self.dsindex -= 1
self.replot()
self.dsetselector.selectitem(self.datasets[self.dsindex])
return
def next(self):
if self.dsindex >= self.E.length-1:
self.dsindex = self.E.length-1
else:
self.dsindex += 1
self.replot()
self.dsetselector.selectitem(self.datasets[self.dsindex])
return
def selectDataset(self, name):
self.dsindex = self.datasets.index(name)
self.replot(name)
return
def importCSV(self):
"""Import csv file"""
from PEATDB.Ekin.IO import Importer
importer = Importer(self, parent_win=self)
importer.path = os.getcwd()
newdata = importer.import_multiple()
for name in newdata.keys():
self.E.insertDataset(newdata[name], newname=name)
self.datasets = sorted(self.E.datasets)
self.dsindex = self.datasets.index(name)
self.replot()
self.updateSelector()
return
def loadProject(self):
filename=tkFileDialog.askopenfilename(defaultextension='.ekinprj',
initialdir=os.getcwd(),
filetypes=[("Ekin files","*.ekinprj"),
("All files","*.*")],
parent=self.main)
if not filename: return
self.E.openProject(filename)
self.datasets = sorted(self.E.datasets)
self.replot()
self.updateSelector()
return
def findBestModel(self, models, callback=None):
"""Determine best fit model using SS F-test"""
dset = self.datasets[self.dsindex]
ek = self.E.getDataset(dset)
fitdata,p = Fitting.findBestModel(ek, models=models, silent=True)
best = fitdata['model']
text = 'Best model is %s with p value=%2.2e' %(best,p)
tkMessageBox.showinfo('Best fit model result',text)
return
class NMRTitration(Plugin, GUI_help):
"""NMR ph titration analysis"""
capabilities = ['gui']
menuentry = 'NMR Titration Analysis'
def main(self, parent=None):
if parent!=None:
self.DB = parent.DB
self._doFrame()
return
def _doFrame(self):
if self.parent == None:
self.mainwin=Toplevel()
else:
self.mainwin=Toplevel()
# Get platform into a variable
import platform
self.currplatform = platform.system()
self.mainwin.title('NMR Titration Analysis')
self.mainwin.geometry('800x600+200+100')
self.createMenuBar()
self.ekinprojects = {}
self.addToolBar()
return
# GUI stuff
def createMenuBar(self):
"""Create the menu bar for the application. """
self.menu=Menu(self.mainwin)
self.file_menu={ '01Open Ekin project':{'cmd':self.loadEkinProj},
'02Open DB':{'cmd':self.openDB},
'03Quit':{'cmd':self.quit}}
self.file_menu=self.create_pulldown(self.menu,self.file_menu)
self.menu.add_cascade(label='File',menu=self.file_menu['var'])
self.util_menu={'01Edit Dict':{'cmd': self.editDict},
'02Autoset Residue Names':{'cmd': self.add_ResidueNames},
'03Autoset Residue Numbers':{'cmd': self.add_ResidueNumbers}}
self.util_menu=self.create_pulldown(self.menu,self.util_menu)
self.menu.add_cascade(label='Utils',menu=self.util_menu['var'])
self.anal_menu={'01Chem. shift distrib':{'cmd': self.analysepKas},
'02Compare Across Nuclei':{'cmd': self.compareNuclei},
'03Ghost Mapping':{'cmd': self.doMapping}}
self.anal_menu=self.create_pulldown(self.menu,self.anal_menu)
self.menu.add_cascade(label='Analysis',menu=self.anal_menu['var'])
self.mainwin.config(menu=self.menu)
return
def addToolBar(self):
fr=self.toolbar=Frame(self.mainwin)
fr.pack(side=TOP,fill=X)
Button(fr, text='Get Ekin prj from DB', command=self.selectfromDB,
relief=GROOVE, bg='#B0C4DE').pack(side=LEFT)
Button(fr, text='Plot Selected', command=self.plotSelected,
relief=GROOVE, bg='#B0C4DE').pack(side=LEFT)
'''Button(fr, text='Fit Selected', command=self.fittSelected,
relief=GROOVE, bg='#B0C4DE').pack() '''
self.dbstatus=StringVar()
Label(self.toolbar,textvariable=self.dbstatus).pack(side=LEFT)
return
def updateDBStatus(self):
if self.DB != None:
self.dbstatus.set('db loaded with %s recs' %len(self.DB.getRecs()))
return
def selectfromDB(self):
"""Get an ekin prj from the DB"""
if self.DB == None:
return
from PEATDB.Actions import DBActions
fr=Toplevel()
rbox, cbox = DBActions.getRecordsSelector(self.DB,fr)
def loadselected():
item = rbox.curselection()[0]
rec = self.DB.getRecs()[int(item)]
item = cbox.curselection()[0]
col = self.DB.getFields()[int(item)]
E=self.DB[rec][col]
self.loadEkinProj(E)
fr.destroy()
Button(fr, text='OK',
command=loadselected).grid(row=3,column=0,
columnspan=2,sticky='news',padx=1,pady=3)
return
def showEkinProject(self, E):
"""Show ekin prj"""
if hasattr(self, 'pw'):
self.pw.destroy()
self.pw = PanedWindow(self.mainwin,
orient=HORIZONTAL,
sashwidth=3,
showhandle=True,
opaqueresize=False)
self.pw.pack(side=LEFT,fill=BOTH,expand=1)
self.showEkinTable(self.pw, E)
self.showPlotPanel(self.pw, E)
return
def showEkinTable(self, parent, E=None):
"""Show a list of ekin prj datasets in a table"""
self.currentmodel = EkinProjModel(E)
fr=Frame(parent)
self.pw.add(fr,minsize=200)
self.ekintable = EkinProjTable(fr, self.currentmodel)
self.ekintable.createTableFrame()
return
def showPlotPanel(self, parent, E=None):
"""Add an ekin plot frame"""
fr=Frame(parent)
self.pw.add(fr)
self.plotframe = PlotPanel(parent=fr, tools=True)
if E != None:
E.checkDatasets()
self.plotframe.setProject(E)
self.plotSelected()
return
def plotSelected(self):
"""Plot ekin """
datasets = self.ekintable.get_selectedRecordNames()
self.plotframe.plotCurrent(datasets=datasets)
return
def add_ResidueNames(self):
"""Try to set residue names for selected datasets"""
return
def add_ResidueNumbers(self):
"""Try to set residue numbers from dataset names"""
return
def analysepKas(self, p=None):
"""Get the main pKas of all/titr group and do analysis"""
E = self.currprj
if E==None: return
t = TitrationAnalyser()
if p == None:
p = t.findpKas(E, titratable=True, reliable=False, minspan=0.06)
t.analysepKas(p)
return
def compareNuclei(self):
"""Compare corresponding datasets for a protein """
return
def doMapping(self):
return
def editDict(self):
"""Edit ghost pka mapping in table"""
D = DictEditor(self)
return
# Mainly IO methods
def openDB(self):
import tkFileDialog
filename=tkFileDialog.askopenfilename(defaultextension='.fs',
filetypes=[("PEAT DB","*.fs"),
("All files","*.*")],
parent=self.mainwin)
if filename != None:
self.loadDB(filename)
self.updateDBStatus()
return
def loadEkinProj(self, E=None):
"""Load an ekin project file"""
import os, types
if E == None:
import tkFileDialog
filename=tkFileDialog.askopenfilename(defaultextension='.ekinprj',
filetypes=[("Ekin project","*.ekinprj"),
("All files","*.*")],
parent=self.mainwin)
if filename != None:
if os.path.isfile(filename):
fd=open(filename)
import pickle
data=pickle.load(fd)
E=EkinProject(data=data)
self.ekinprojects[filename] = E
fd.close()
else:
return
self.currprj = E
self.showEkinProject(E)
return
def addEkinProj(self, ekinproj=None, replace=1):
"""Load an ekin project file"""
return
def quit(self):
self.mainwin.destroy()
return
def analyseTitDB(self, DB, col, names=None):
"""Extract titdb pKas"""
import matplotlib.pyplot as plt
plt.rc('font',size=28)
plt.rc('savefig',dpi=300)
plt.rc('axes',linewidth=.5)
#plt.rc('text',usetex=True)
nuclnames = {'1H NMR':'H','15N NMR':'N'}
t = TitrationAnalyser()
#extract reliable pkas from selected proteins
#p = t.extractpKas(DB, col, names=names, titratable=False, reliable=False, minspan=0.06)
#t.analysepKas(p)
t.compareNuclei(DB, '15N NMR', '1H NMR', names=names, titratable=True)
return
def save(self, DB, col, prot, E):
if E==None and DB != None:
E.saveProject(prot+'_'+col)
DB[prot][col] = E
else:
E.currentmode = 'NMR titration'
E.saveProject()
return
def titDBUtils(self, DB=None, col=None, prot=None, a=None, E=None,
refit=False, addmeta=False, getexperrs=False,
yuncert=None):
"""Add some meta and refit all for an ekin prj or a rec/field in db"""
if E==None and DB != None:
E = DB[prot][col]
E.checkDatasets()
t = TitrationAnalyser()
if refit == True:
models = ['Linear', '1 pKa 2 Chemical shifts',
'2 pKas, 3 Chemical shifts',
'3 pKas, 4 Chemical shifts']
E = t.findBest(E, models, geterrs=False)
if addmeta == True:
E = t.setMetaInfo(E, atom=a)
if getexperrs == True:
if yuncert == None:
print 'No value for Y uncertainty!, please supply it'
return
print 'Using %s for y uncertainty.' %yuncert
print
E = t.getExpErrs(E, xuncert=0.1, yuncert=yuncert)
self.save(DB, col, prot, E)
#DB.commit('refit/added meta info')
return E
def benchmarkExpErr(self, DB):
"""Test effects of model and noise on est exp error technique"""
E = DB['HEWL']['1H NMR']
d='D66N-HN'
E.plotDatasets(d,filename='experrtest.png')
print E.getFitData(d)
ferrs = E.estimateExpUncertainty(d, runs=20,
xuncert=0.1, yuncert=0.03)
print ferrs
return
def addpKaTables(self, DB, names, col='1H NMR'):
"""Create labbook tables for 'real' pKas for required proteins"""
t = TitrationAnalyser()
prots = t.getProtNames(DB)
for name in names:
recname = DB.getRecordName(name)
E = DB[recname][col]
titrresidues = t.getResidues(E, titratable=True)
S = DB.createLabbookSheet(name+'.pKas')
for r in titrresidues:
d, res, resnum = r
pKa = ''
S.addRecord(res+resnum,pka=pKa,resname=res,
resnum=resnum,error='')
DB.saveLabbook(name+'.pKas', S)
DB.saveLabbooktoFile('titdb.labbook')
return
def exportAll(self, DB, col=None):
t = TitrationAnalyser()
t.exportAll(DB, col)
return
