class SequenceShiftPredictPopup(BasePopup):
"""
**Predict Protein Shifts from Sequence**
This popup window is designed to allow the prediction of chemical shifts
for a protein chain from the sequence (so with no structural information),
using the (external) program CamCoil.
The Options to select are the Chain for which the prediction is made, and
the prediction type and the pH used for the prediction, and also the Shift
List, which is not used for the prediction but is used for the comparison
with the prediction.
CamCoil has two variations, one for the prediction of random coil chemical
shifts and one for prediction of protein loops chemical shifts.
The Chemical Shift Predictions table lists the atoms in the chain.
For each atom the data listed is the residue number, residue type, atom
name, first shift found for that atom in the chosen shiftList, chemical
shift predicted by CamCoil, and the difference between the actual shift
and the predicted shift (if both exist).
To run the prediction click on the "Run CamCoil Prediction!" button. This
does not store any predicted shifts in the project.
**Caveats & Tips**
**References**
The CamCoil programme:
http://www-vendruscolo.ch.cam.ac.uk/camcoil.php
*A. De Simone, A. Cavalli, S-T. D. Hsu, W. Vranken and M. Vendruscolo
Accurate random coil chemical shifts from an analysis of loop regions in native states of proteins.
J. Am. Chem. Soc. 131(45):16332-3
"""
def __init__(self, parent, *args, **kw):
self.chain = None
self.shiftList = None
self.predictionDict = {}
BasePopup.__init__(
self,
parent=parent,
title='Data Analysis : Predict Shifts from Sequence')
def body(self, guiFrame):
self.geometry('700x500')
guiFrame.expandGrid(1, 0)
row = 0
# TOP LEFT FRAME
frame = LabelFrame(guiFrame, text='Options')
frame.grid(row=row, column=0, sticky='nsew')
frame.columnconfigure(7, weight=1)
label = Label(frame, text='Chain')
label.grid(row=0, column=0, sticky='w')
self.chainPulldown = PulldownList(
frame,
callback=self.changeChain,
tipText='Choose the molecular system chain to make predictions for'
)
self.chainPulldown.grid(row=0, column=1, sticky='w')
label = Label(frame, text='Shift List')
label.grid(row=0, column=2, sticky='w')
self.shiftListPulldown = PulldownList(
frame,
callback=self.changeShiftList,
tipText='Select the shift list to take input chemical shifts from')
self.shiftListPulldown.grid(row=0, column=3, sticky='w')
label = Label(frame, text='Type')
label.grid(row=0, column=4, sticky='w')
self.scriptPulldown = PulldownList(
frame,
texts=SCRIPT_TEXTS,
callback=self.changeScript,
tipText='Select the algorithm script for this chain')
self.scriptPulldown.grid(row=0, column=5, sticky='w')
self.pHLabel = Label(frame, text='pH')
self.pHLabel.grid(row=0, column=6, sticky='w')
self.pHPulldown = PulldownList(
frame,
texts=SCRIPT_PHS,
tipText='Select the pH to make the prediction for')
self.pHPulldown.grid(row=0, column=7, sticky='w')
row += 1
# BOTTOM LEFT FRAME
frame = LabelFrame(guiFrame, text='Chemical Shift Predictions')
frame.grid(row=row, column=0, sticky='nsew')
frame.grid_columnconfigure(0, weight=1)
frame.grid_rowconfigure(0, weight=1)
tipTexts = [
'Residue number in chain', 'Residue type code', 'Atom name',
'Actual shift (first one it finds for atom in chosen shiftList)',
'CamCoil predicted shift', 'Predicted - Actual'
]
headingList = [
'Res\nNum', 'Res\nType', 'Atom\nName', 'Actual\nShift',
'Predicted\nShift', 'Difference'
]
n = len(headingList)
editWidgets = n * [None]
editGetCallbacks = n * [None]
editSetCallbacks = n * [None]
self.predictionMatrix = ScrolledMatrix(
frame,
headingList=headingList,
tipTexts=tipTexts,
editWidgets=editWidgets,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks)
self.predictionMatrix.grid(row=0, column=0, sticky='nsew')
row += 1
tipTexts = [
'Run the CamCoil method to predict chemical shifts from sequence'
]
texts = ['Run CamCoil Prediction!']
commands = [self.runCamCoil]
self.buttonList = createDismissHelpButtonList(guiFrame,
texts=texts,
commands=commands,
help_url=self.help_url,
expands=True,
tipTexts=tipTexts)
self.buttonList.grid(row=row, column=0)
self.update()
self.notify(self.registerNotify)
def destroy(self):
self.notify(self.unregisterNotify)
BasePopup.destroy(self)
def notify(self, notifyfunc):
for func in ('__init__', 'delete'):
notifyfunc(self.updateChainPulldown,
'ccp.molecule.MolSystem.Chain', func)
for func in ('setValue', ):
notifyfunc(self.updatePredictionMatrixAfter, 'ccp.nmr.Nmr.Shift',
func)
def update(self):
self.updateShiftListPulldown()
self.updateChainPulldown()
self.updatePredictionMatrixAfter()
def runCamCoil(self):
chain = self.chain
script = self.scriptPulldown.getText()
if script == LFP_SCRIPT:
pH = ''
else:
pH = self.pHPulldown.getText()
if not chain:
showError('Cannot Run CamCoil',
'Please specify a chain.',
parent=self)
return
self.predictionDict[chain] = runCamCoil(chain, pH=pH, script=script)
self.updatePredictionMatrix()
def updatePredictionMatrixAfter(self, index=None, text=None):
self.after_idle(self.updatePredictionMatrix)
def updatePredictionMatrix(self):
objectList = []
textMatrix = []
chain = self.chain
shiftList = self.shiftList
if chain:
atomShiftDict = self.predictionDict.get(chain, {})
for residue in chain.sortedResidues():
for atom in residue.sortedAtoms():
currShift = shiftList and findFirstAtomShiftInShiftList(
atom, shiftList)
value = currShift and currShift.value
predShift = atomShiftDict.get(atom)
if currShift and predShift:
delta = predShift - value
else:
delta = None
data = [
residue.seqCode, residue.ccpCode, atom.name, value,
predShift, delta
]
textMatrix.append(data)
objectList.append(atom)
self.predictionMatrix.update(textMatrix=textMatrix,
objectList=objectList)
def changeChain(self, chain):
if chain is not self.chain:
self.chain = chain
self.updatePredictionMatrixAfter()
def changeShiftList(self, shiftList):
if shiftList is not self.shiftList:
self.shiftList = shiftList
self.updatePredictionMatrixAfter()
def changeScript(self, script):
if script == LFP_SCRIPT:
self.pHLabel.grid_forget()
self.pHPulldown.grid_forget()
else:
self.pHLabel.grid(row=0, column=6, sticky='w')
self.pHPulldown.grid(row=0, column=7, sticky='w')
def updateChainPulldown(self, obj=None):
index = 0
names = []
chains = []
chain = self.chain
for molSystem in self.project.molSystems:
msCode = molSystem.code
for chainA in molSystem.chains:
residues = chainA.residues
if not residues:
continue
for residue in residues:
# Must have at least one protein residue
if residue.molType == 'protein':
names.append('%s:%s' % (msCode, chainA.code))
chains.append(chainA)
break
if chains:
if chain not in chains:
chain = chains[0]
index = chains.index(chain)
else:
chain = None
if chain is not self.chain:
self.chain = chain
self.updatePredictionMatrixAfter()
self.chainPulldown.setup(names, chains, index)
def updateShiftListPulldown(self, obj=None):
index = 0
names = []
shiftLists = getShiftLists(self.nmrProject)
if shiftLists:
if self.shiftList not in shiftLists:
self.shiftList = shiftLists[0]
index = shiftLists.index(self.shiftList)
names = ['%s:%d' % (sl.name, sl.serial) for sl in shiftLists]
else:
self.shiftList = None
self.shiftListPulldown.setup(names, shiftLists, index)
