def show_specific(self):
"""Show datasets for an individual cell, depends on fieldtype"""
protein = self.form.getfirst('protein')
rectype = self.form.getfirst('rectype')
col = self.form.getfirst('column')
sys.stdout.flush()
DB = self.DB = self.connect()
ptmodel = PEATTableModel(DB)
ekincols = ptmodel.ekintypes
fieldtype = DB['userfields'][col]['field_type']
protname = DB[protein]['name']
self.showHeader(title=str(protname+': '+col), menu=1)
print '<div><a>Protein: %s </a><br>' %protname
print 'Column data: %s </div>' %col
from PEATDB.Ekin.Web import EkinWeb
if fieldtype in ekincols:
fieldtype = 'ekindata'
#plot ekin data curves, if fieldtype is ekindata
if fieldtype == 'ekindata':
E = DB[protein][col]
EW = EkinWeb()
EW.showEkinPlots(project=E, datasets='ALL', path=self.plotsdir,
imgpath=self.imagepath)
print '</table>'
#save the pdb structure to a file and provide url link to it
elif fieldtype == 'structure':
recdata = DB[protein][col]
for k in recdata:
print '<br><a> %s</a>' %str(k)
elif fieldtype == 'Notes':
recdata = DB[protein][col]
print '<br><a> %s</a>' %recdata['text']
elif fieldtype == 'File':
recdata = DB[protein][col]
print '<p> This record contains a data file. Click link to open.'
print '<a href="http://peat.ucd.ie/titration_db/%s">Open link</a>' %recdata['location']
else:
print '<br>Sorry, no handler for this data right now..</br>'
self.footer()
return
def estimateExpUncertainty(ekindata,
fitdata,
xuncert=0,
yuncert=0,
runs=10,
doplots=False,
callback=None,
guess=True,
**kwargs):
"""Chresten's method for estimating the error on each parameter due
to the effect of the exp uncertainty, which is user provided.
If the datapoints have x or y error values, we use that instead"""
'''we iterate over runs and re-fit the data, each time adjusting x-y points
then accumulate a fit val for each parameter and get mean/stdev.
Note: errors are added +/- values'''
from PEATDB.Ekin.Dataset import EkinDataset
grad = 1e-6
conv = 1e-6
for k in kwargs:
if k == 'conv':
conv = kwargs[k]
if k == 'grad':
grad = kwargs[k]
if fitdata == None or len(fitdata) == 0:
return None
model = fitdata['model']
F = getFitter(model=model)
try:
varnames = F.getVarNames()
except:
return None
fitvars = {}
for v in varnames:
fitvars[v] = [] #group lists by variable name
xd, yd, a, xerrs, yerrs = ekindata.getAll()
estdata = {}
estdata['__datatabs_fits__'] = {}
for r in range(runs):
mut_x = []
mut_y = []
#if the datapoint has x or y error values, we use that instead
for i in range(len(xd)):
if xerrs != None and xerrs[i] > 0:
mut_x.append(xd[i] + random.uniform(-xerrs[i], xerrs[i]))
else:
mut_x.append(xd[i] + random.uniform(-xuncert, xuncert))
if yerrs != None and yerrs[i] > 0:
mut_y.append(yd[i] + random.uniform(-yerrs[i], yerrs[i]))
else:
mut_y.append(yd[i] + random.uniform(-yuncert, yuncert))
ek = EkinDataset(xy=[mut_x, mut_y], active=a)
fitres, X = doFit(ek,
model=model,
fitdata=fitdata,
grad=1e-6,
conv=1e-6,
silent=True,
guess=guess,
noiter=100)
vrs = X.getVariables()
for n in range(len(varnames)):
fitvars[varnames[n]].append(vrs[n])
estdata[str(r)] = ek
estdata['__datatabs_fits__'][str(r)] = fitres
if callback != None:
fitstats = {}
for v in varnames:
fitstats[v] = numpy.mean(fitvars[v]), numpy.std(fitvars[v])
callback(r, fitstats)
fitstats = {}
for v in varnames:
#print fitvars[v]
err = numpy.std(fitvars[v]) / 2
#print v, numpy.mean(fitvars[v]), err
#we store the final error as +/- half the stdev.
fitstats[v] = numpy.mean(fitvars[v]), err
if doplots == True:
from PEATDB.Ekin.Web import EkinWeb
ew = EkinWeb()
ew.showEkinPlots(ekindata=estdata,
outfile='est_exp_err.html',
columns=3,
normalise=False,
showfitvars=True,
imgpath='.')
return fitstats
def estimateExpUncertainty(ekindata, fitdata, xuncert=0, yuncert=0,
runs=10, doplots=False, callback=None, guess=True,
**kwargs):
"""Chresten's method for estimating the error on each parameter due
to the effect of the exp uncertainty, which is user provided.
If the datapoints have x or y error values, we use that instead"""
'''we iterate over runs and re-fit the data, each time adjusting x-y points
then accumulate a fit val for each parameter and get mean/stdev.
Note: errors are added +/- values'''
from PEATDB.Ekin.Dataset import EkinDataset
grad=1e-6; conv=1e-6
for k in kwargs:
if k=='conv':
conv=kwargs[k]
if k=='grad':
grad=kwargs[k]
if fitdata == None or len(fitdata) == 0:
return None
model = fitdata['model']
F = getFitter(model=model)
try:
varnames = F.getVarNames()
except:
return None
fitvars = {}
for v in varnames:
fitvars[v] = [] #group lists by variable name
xd,yd,a,xerrs,yerrs = ekindata.getAll()
estdata={}; estdata['__datatabs_fits__']={}
for r in range(runs):
mut_x=[];mut_y=[]
#if the datapoint has x or y error values, we use that instead
for i in range(len(xd)):
if xerrs != None and xerrs[i] > 0:
mut_x.append(xd[i] + random.uniform(-xerrs[i], xerrs[i]))
else:
mut_x.append(xd[i] + random.uniform(-xuncert, xuncert))
if yerrs != None and yerrs[i] > 0:
mut_y.append(yd[i] + random.uniform(-yerrs[i], yerrs[i]))
else:
mut_y.append(yd[i] + random.uniform(-yuncert,yuncert))
ek = EkinDataset(xy=[mut_x,mut_y],active=a)
fitres, X = doFit(ek, model=model, fitdata=fitdata, grad=1e-6, conv=1e-6,
silent=True, guess=guess, noiter=100)
vrs = X.getVariables()
for n in range(len(varnames)):
fitvars[varnames[n]].append(vrs[n])
estdata[str(r)] = ek
estdata['__datatabs_fits__'][str(r)] = fitres
if callback != None:
fitstats = {}
for v in varnames:
fitstats[v] = numpy.mean(fitvars[v]), numpy.std(fitvars[v])
callback(r, fitstats)
fitstats = {}
for v in varnames:
#print fitvars[v]
err = numpy.std(fitvars[v])/2
#print v, numpy.mean(fitvars[v]), err
#we store the final error as +/- half the stdev.
fitstats[v] = numpy.mean(fitvars[v]), err
if doplots == True:
from PEATDB.Ekin.Web import EkinWeb
ew = EkinWeb()
ew.showEkinPlots(ekindata=estdata, outfile='est_exp_err.html',
columns=3, normalise=False, showfitvars=True,
imgpath='.')
return fitstats
def do_search(self, globalop, proteinop, proteins, datasets):
"""Do searches for the various parameters, name, pka etc"""
import re, urllib
from PEATDB.PEATTables import PEATTableModel
from PEATDB.Ekin.Fitting import Fitting
from PEATDB.Ekin.Web import EkinWeb
DB = self.DB
EW = EkinWeb()
ekincols = DB.ekintypes
found=[]
protlist = proteins.split(' ')
residuelist = residues.split(' ')
def createPhrase(items, op):
if op == 'or':
logicsymbol = '|'
else:
logicsymbol = '+'
itemlist = items.split(' ')
phrase =''
c=1
for i in itemlist:
if c == len(itemlist):
phrase = phrase + i
else:
phrase = phrase + i + logicsymbol
c=c+1
return re.compile(phrase, re.IGNORECASE)
#if there is a protein name entered, get the list of proteins/records to use
#otherwise use all records to search for the other keys
names = []
keywords = {}
for p in DB.getRecs():
name = DB[p].name
names.append((name,p))
if hasattr(DB[p], 'keywords'):
keywords[name] = DB[p].keywords
else:
keywords[name] = ''
names.sort()
#create search expressions
s_protein = createPhrase(proteins, proteinop)
s_residue = createPhrase(residues, 'or')
pkarange = pka.split('-')
#do search
for name in names:
proteinname = name[0]
protein = name[1]
if s_protein.search(proteinname) or s_protein.search(keywords[proteinname]):
found.append(protein)
if len(found)==0:
print '<h2>Sorry, no proteins found that match this name. <h2>'
return
elif residues == '' and pka == '':
self.show_DB(selected=found)
return found
#now search for the other keys inside selected proteins if needed
ekinfound={}; foundfits={}
ignore =['__fit_matches__', '__Exp_Meta_Dat__', '__datatabs_fits__']
kys = list(DB.getRecs())
kys.sort()
if len(found) == 0 or globalop == 'or':
found = DB.getRecs()
print '<table id="mytable" cellspacing=0 align=center>'
'''search recs for residue and pkarange
and add dataset names to new ekinfound dict'''
for protein in found:
for col in DB[protein].keys():
if nucleus != 'any':
if nucleus not in col:
continue
E = DB[protein][col]
if DB['userfields'].has_key(col):
fieldtype=DB['userfields'][col]['field_type']
else:
fieldtype=None
if fieldtype in ekincols:
dk = E.datasets
fits = E.__datatabs_fits__
for k in dk:
meta = E.getMetaData(k)
try:
thisres = meta['residue']
except:
thisres = k
if thisres == None:
thisres = k
if residues != '':
if s_residue.search(thisres) and not k in ignore:
if not ekinfound.has_key(protein+'$'+col):
ekinfound[protein+'$'+col]=[]
ekinfound[protein+'$'+col].append(k)
if pka != '':
foundpka = 0
if k in fits.keys():
if fits[k] == None:
continue
if fits[k].has_key('model'):
model = fits[k]['model']
else:
continue
if not foundfits.has_key(protein+'$'+col):
foundfits[protein+'$'+col]={}
X = Fitting.getFitter(model)
pnames = X.names
i=0
#check if first num is larger, then swap
try:
pk1=float(pkarange[0])
pk2=float(pkarange[1])
except:
print '<h2> Error: pka values are not valid </h2>'
return
if pk1 > pk2:
tmp = pk1
pk1 = pk2
pk2 = tmp
#iterate thru parameter names and match any pK fields
#this code is not that efficient!
for p in pnames:
if 'pK' in p:
pka = fits[k][i]
if pka >= pk1 and pka <= pk2:
foundpka=1
i=i+1
#if match is 'ANY', just append dataset if not there already
#also for case if no residue value entered
if globalop == 'or' or residues == '':
if foundpka == 1:
if not ekinfound.has_key(protein+'$'+col):
ekinfound[protein+'$'+col]=[]
if not k in ekinfound[protein+'$'+col]:
ekinfound[protein+'$'+col].append(k)
#if match is 'ALL', need to check dataset already found
#and if no pka found, remove it. if both are true keep it
elif globalop == 'and':
if foundpka == 0:
if ekinfound.has_key(protein+'$'+col) and k in ekinfound[protein+'$'+col]:
#print 'removing', protein, col
ekinfound[protein+'$'+col].remove(k)
foundfits[protein+'$'+col][k]=fits[k]
#check for empty fields in ekinfound dict and delete them..
for d in ekinfound.keys():
if len(ekinfound[d])==0:
del(ekinfound[d])
#if no results, just say that and return
if len(ekinfound)==0:
print '<h2> Sorry, no records found that match these parameters. </h2>'
return
#top display button and options
print '<form name="resultsform" action="%s/main.cgi" METHOD="POST" ENCTYPE="multipart/form-data">' %self.bindir
self.write_sessionkey('show_datasets')
print '<td valign=top align=right colspan=3> <input type=submit value="display selected" name=submit>'
print '<label><input type=checkbox name="plotoption" value=3>single graph</label>'
print '<label><input type=checkbox name="normalise" value=1>normalise</label>'
print '<label><input type=checkbox name="logx" value=1>log-x</label>'
print '<label><input type=checkbox name="logy" value=1>log-y</label>'
print '<label><input type=checkbox name="legend" value=1>legend</label>'
print '<input type=button value="Check All" onClick="checkAll(document.resultsform.residue)">'
print '<input type=button value="Uncheck All" onClick="uncheckAll(document.resultsform.residue)"></td>'
print '</tr>'
#header
cols=['protein','column','residues']
for c in cols:
print '<th>'+c+'</th>'
print '</tr>'
ekys = ekinfound.keys()
ekys.sort()
r=1
for k in ekys:
if r % 2 == 0:
cls = "spec"
else:
cls = ""
fields = k.split('$')
protein = fields[0]
column = fields[1]
proteinname = DB[protein]['name']
print '<tr>'
print '<th class="spec">%s</th> <td> %s </td>' %(proteinname, column)
print '<td>'
for residue in ekinfound[k]:
residuefield = k+"$"+residue
fithtml = ''
try:
print '<input type=checkbox id="residue" name="residue" value=%s>' %("'"+residuefield+"'")
except:
print 'UnicodeEncodeError'
continue
urlfields = urllib.urlencode({'login':self.user,'project':self.project,
'residue': residuefield,'action': 'show_datasets'})
print '<a href="/cgi-bin/titration_db/main.cgi?%s" target="_blank">%s</a>'\
% (urlfields, residue)
print '</tr>'
r=r+1
print '</form>'
print '</table>'
self.footer()
return
def show_datasets(self):
"""Show single or multiple dataset plot from search results"""
plotoption = self.form.getfirst('plotoption')
norm = bool(self.form.getfirst('normalise'))
logx = bool(self.form.getfirst('logx'))
logy = bool(self.form.getfirst('logy'))
legend = bool(self.form.getfirst('legend'))
DB = self.DB = self.connect()
from PEATDB.Ekin.Web import EkinWeb
ekincols = DB.ekintypes
self.showHeader(menu=1)
self.menu()
sys.stdout.flush()
#get dataset name(s) from form
residuefield = self.form.getvalue('residue')
if not isinstance(residuefield, list):
residuefield = [residuefield]
#prepare data, if more than one dataset from seperate proteins,
print '</div>'
print '<table id="mytable" cellspacing=0>'
print '<tr><th>'
print 'plotoption:', plotoption
print 'norm:', str(norm)
print 'log-x', logx
print 'log-y', logy
print 'legend', legend
print '</table>'
ekindata={}
ekindata['__datatabs_fits__']={}
ekindata['__meta_data__']={}
#extracting seperate datasets and put them in ekindata
for r in residuefield:
fields = r.split('$')
protein = fields[0]
col = fields[1]
d = fields[2]
E = DB[protein][col]
fits = E.__datatabs_fits__
meta = E.__meta_data__
protname = DB[protein]['name']
ekindata['__datatabs_fits__'][d+'_'+col+'_'+protname] = fits[d]
ekindata['__meta_data__'][d+'_'+col+'_'+protname] = meta[d]
ekindata[d+'_'+col+'_'+protname] = E.getDataset(d)
if plotoption == None:
plotoption = 1
else:
plotoption = 3
EW = EkinWeb()
EW.showEkinPlots(ekindata, 'ALL', path=self.plotsdir,
imgpath=self.imagepath,
plotoption=plotoption, normalise=norm, legend=legend,
logx=logx, logy=logy)
return
def plotpKDCalcs(self, calcs, Ed=None, option=1):
"""Do pKD calcs with exp data plots"""
from PEATDB.Ekin.Web import EkinWeb
from PEATDB.Ekin.Base import EkinProject
from PEATDB.Ekin.Convert import EkinConvert
from PEATDB.Ekin.Titration import TitrationAnalyser
import PEATDB.Ekin.Utils as Utils
t = TitrationAnalyser()
c=calcs
EW = EkinWeb()
if option == '2':
print '<a>Just showing experimental data</a>'
EW.showEkinPlots(project=Ed, datasets='ALL',
path=self.plotsdir,
imgpath=self.imagepath)
return
#create ekin proj from pKD titcurves
Ec = EkinProject()
for r in c.keys():
xd=[];yd=[]
for i in c[r]:
if type(i) is types.StringType:
continue
xd.append(i)
yd.append(c[r][i])
edata=EkinConvert.xy2ekin([xd,yd])
Ec.insertDataset(edata, r)
print '<a>Please wait, fitting calcated curves...</a>'
sys.stdout.flush()
Ec.fitDatasets(models=['1 pKa 2 Chemical shifts'], silent=True)
if option == '3':
print '<a>Just showing pKD data</a>'
EW.showEkinPlots(project=Ec, datasets='ALL',
path=self.plotsdir,
imgpath=self.imagepath)
return
#transform exp data names to match pKD ones
s=':'
usechainid = True
#if pKD names have no chain id, we don't need one for exp names
if Ec.datasets[0].startswith(':'):
usechainid=False
for d in Ed.datasets[:]:
r = Ed.getMetaData(d)
if r != None:
if r['chain_id'] == None or usechainid == False:
chain = ''
else:
chain = r['chain_id']
new = chain+s+Utils.leadingZeros(r['res_num'],4)+s+r['residue']
if new in Ed.datasets:
atom = r['atom']
new = new + '_' + atom
Ed.renameDataset(d, new)
#now we overlay the same datasets in Ed and Ec
#also handles cases where same residue multiple times for diff atoms in exp data
for d in Ed.datasets:
if d in Ec.datasets:
Ep = EkinProject()
cdata = Ec.getDataset(d)
Ep.insertDataset(cdata, d+'_pKD')
Ep.setFitData(d+'_pKD', Ec.getFitData(d))
ddata = Ed.getDataset(d)
Ep.insertDataset(ddata, d+'_exp')
Ep.setFitData(d+'_exp', Ed.getFitData(d))
EW.showEkinPlots(project=Ep, datasets='ALL', plotoption=3,
normalise=True, legend=True,
path=self.plotsdir,
imgpath=self.imagepath)
return