def showpKD(self):
"""Show pKD calcs with exp data for selected ekindata"""
protein = self.form.getfirst('protein')
col = self.form.getfirst('column')
showopt = self.form.getfirst('option')
self.showHeader(menu=1)
sys.stdout.flush()
DB = self.DB = self.connect()
protname = DB[protein]['name']
pdbid = DB[protein]['PDB_link']['text']
expdata = DB[protein][col]
if type(expdata) is types.StringType:
print '<a>No data for column %s, go back and choose another nucleus..</a>' %col
return
P = pKDInterface()
calcs, pkas, pdblines = P.loadfrompKD(pdbid)
print '<div><a>Protein: %s PDB: %s </a><br>' %(protname, pdbid)
print 'Column data: %s <p></div>' %col
if calcs == None or not type(calcs) is types.DictType:
print '<a>There are currently no pKD calculations for this protein.</a>'
return
else:
print '<a>Found data on pKD server. We can plot.</a>'
sys.stdout.flush()
#plot them
self.plotpKDCalcs(calcs, expdata, showopt)
self.footer()
return
def selectpKD(self):
"""Allow user to select a protein and field for pKD"""
self.showHeader(menu=1)
sys.stdout.flush()
DB = self.DB = self.connect()
names = []
for p in DB.getRecs():
names.append((DB[p].name,p))
names.sort()
nucl = ['1H NMR', '15N NMR', '13C NMR']
#check pKD available calcs
P = pKDInterface()
pkdprots = [string.upper(e[0]) for e in P.getProteins()]
#add selection boxes
print '<div align=left>'
print '<form name="pkdform" action="%s/main.cgi" METHOD="POST" ENCTYPE="multipart/form-data">' %self.bindir
self.write_sessionkey('showpKD')
print '<big>Select experimental curves to compare with calculated curves in pKD</big><br>'
print '<a>This will show a set of plots for each residue where there is an experimental and calculated curve</a><p>'
print 'Choose the protein and nucleus:<p>'
print '<select name="protein" class="btn">'
for n in names:
print '<option value="%s">%s</option>' %(n[1],n[0])
print '</select>'
print '<select name="column" class="btn">'
for c in nucl:
print '<option value="%s">%s</option>' %(c,c)
print '</select>'
print '<p>'
#button
print '<input type=submit value="Display Plots" name=submit class="btn">'
print '<label><input type=radio name="option" value=1 checked="yes">compare both</label>'
print '<label><input type=radio name="option" value=2>exp only</label>'
print '<label><input type=radio name="option" value=3>calcs only</label>'
print '</form>'
print '</div>'
print 'Below is a reference table showing which proteins in our DB currently have calculations in the pKD, with the PDB ID and PDB link.<br>'
print 'If the protein is not yet available, you can go to <a href=http://enzyme.ucd.ie/cgi-bin/pKD/server_start.cgi target="blank"> \
the pKD page</a> and submit the calculation.<p>'
#table of proteins and their PDBs
print '<div align=left>'
print '<table id="mytable" cellspacing="0">'
r=0
print '<th>Protein</th><th>PDB</th><th>Has pKD data</th>'
for name in names:
protein = name[1]
protname = name[0]
if not DB[protein].has_key('PDB_link'):
continue
pdbinfo = DB[protein].PDB_link
if pdbinfo == '':
continue
pdbid = pdbinfo['text']
pdblink = pdbinfo['link']
if r % 2 == 0:
cls = 'alt'
else:
cls = ''
print '<tr>'
print '<td class=%s> %s </td>' % (cls, protname)
print '<td class=%s> <a href=%s target="blank"> %s</a> </td>' % (cls, pdblink, pdbid)
if pdbid in pkdprots:
status = 'yes'
else:
status = 'no'
print '<td class=%s> <b>%s</b> </td>' %(cls, status)
print '</tr>'
r=r+1
print '</table>'
return