Hi Linda,
I attached the macro we use for side chain assignments. You may find it
useful and can modify it further.
In general, if this macro is of interest, it can be added to the CCPN site.
Cheers
Igor
Linda Ball wrote:
>Hi all,
>
>What we really need here is a macro that does the equivalent job of
>ANSIG's
>incredibly useful 'seq_C' macro, which, upon receiving a sequence number
>as
>input displays the desired C/H nucleus pair for that residue, e.g.
>Ca/Ha, Cb/Hb1,
>Cb/Hb2, etc, etc. I'm sure that such a central macro must already exist
>for
>Analysis. If so, could anyone point us to it?
>While I'm on the subject, is there also a macro equivalent to ANSIGs
>'show_ss'
>(show spin system)? This simply displays only those assignment labels
>that are
>required for a user-specified residue, while all other assignment labels
>are
>undisplayed, and would be much les cluttered than the current display
>where all
>labels are shown.
>
>Cheers,
>
>Linda
>
>
>
>
>
>>>>[log in to unmask] >>>
>>>>
>>>>
>Hi,
>
>I am wanting to check my 3D 13C-NOESY specifically for Ha(i)-Hb(i+3)
>helical
>NOEs. I have Ha and Hb shifts from my HBHA(CO)NH spectrum and the Ca/Cb
>shifts from the CBCA(CO)NH or CBCANH spectra. So in theory, finding the
>NOEs should not be a problem. If I try to get to the correct place in
>the
>13C NOESY simply by using the RightMouse Navigate tool, it takes my a
>while
>to get there.
>Is there any chance someone might be able to write me a macro, or
>perhaps
>has a macro (or one which could be easily changed) where I could specify
>residue i and then would be taken to the Ha(i), Hb(i+3),Ca(i) location
>in
>the 13C spctrum?
>Thanks.
>
>Vicky
>
>
--
Dr. Igor Barsukov
Biological NMR Centre,
University of Leicester
PO Box 138,
University Road,
Henry Wellcome Building,
Leicester LE1 9HN
UK
E-mail: [log in to unmask]
Tel: +44 (0)116 229 7098
FAX: +44 (0)116 229 7053
import re,os,sys
import Tkinter
from ccpnmr.analysis.WindowBasic import getActiveWindows
from ccpnmr.api import Analysis
from memops.general import Implementation
from memops.gui.ButtonList import ButtonList
from ccpnmr.analysis.BrowseResonancesPopup import BrowseResonancesPopup
#from BrowseResonancesPopup_nmrc import BrowseResonancesPopup
from igorFuncs import getResidueProtElementResFromRes, getBoundProtonResonances, getProtonResFromCarbRes
from memops.gui.Button import Button
from memops.gui.Entry import Entry
from memops.gui.FloatEntry import FloatEntry
from memops.gui.Frame import Frame
from memops.gui.LabelFrame import LabelFrame
from memops.gui.Label import Label
from memops.gui.PulldownMenu import PulldownMenu
from memops.gui.MessageReporter import showOkCancel, showWarning, showYesNo
from memops.gui.ScrolledMatrix import ScrolledMatrix
from memops.gui.Text import Text
from memops.gui.Spacer import Spacer
from memops.editor.Util import createDismissHelpButtonList
from ccpnmr.analysis.AssignmentBasic import getResonanceResidue, findResonanceSet, deassignResonance, getResonanceAtomTuple, removeSpinSystemResonance, makeResonanceGuiName, assignAtomsToRes, mergeResonances, addSpinSystemResonance, removeSpinSystemResonance, assignResonanceResidue
from ccpnmr.analysis.MarkBasic import createPeakMark, createNonPeakMark, createRuler, \
removeMarks, removeRulers, createPeakDimRuler, markCounter
class SlimButton(Button):
def __init__(self, parent,*args, **kw):
Button.__init__(self, parent, borderwidth=1,padx=2,pady=2, *args, **kw)
class ResTblSc(BrowseResonancesPopup):
def __init__(self,parent,project = None,argServer=None):
BrowseResonancesPopup.__init__(self, parent,project = parent.project)
self.winDic={}
self.WindowPositionDic={}
self.WindowPositionDic2D={}
self.argServer=argServer
self.project = argServer.getProject()
self.orthogonalDict={}
def body(self, guiFrame):
self.isotope = 'Any'
self.status = 'Any'
self.waitingForAtoms = 0
self.waitingForSpinSystem = None
hilightColor = '#%02x%02x%02x' % (128, 128, 200)
self.titleColor = '#%02x%02x%02x' % (0, 0, 128)
self.untoggledDict = { 'fg': 'black', 'relief': 'raised' , 'bg': 'grey83'}
self.toggledDict = { 'fg': 'white', 'relief': 'raised' , 'bg': hilightColor}
self.isotopeNames = ['Any','1H','15N','13C','unknown']
self.statusNames = ['Any','Assigned','Unassigned','Orphaned']
shiftListNames = self.getShiftListNames(self.project)
shiftLists = list(self.project.findAllNmrMeasurementLists(className = 'ShiftList'))
self.shiftList = None
self.chain = None
self.ccpCode = None
row = 0
frame=LabelFrame(guiFrame, text='Navigation')
frame.grid(row=row, column=0, columnspan=10, rowspan=2, sticky=Tkinter.EW)
frame.grid_columnconfigure(1, weight=1)
self.orthogPulldown = PulldownMenu(frame, entries=['None'], callback=None)
self.orthogPulldown.grid(row=0, column=0, sticky=Tkinter.W)
self.orthogPulldown1 = PulldownMenu(frame, entries=['None'], callback=None)
self.orthogPulldown1.grid(row=0, column=1, sticky=Tkinter.W)
self.orthogPulldown2D = PulldownMenu(frame, entries=['None'], callback=None)
self.orthogPulldown2D.grid(row=0, column=2, sticky=Tkinter.W)
self.orthogButton = SlimButton(frame,text='Goto position:',command=self.gotoOrthogPlaneAll)
self.orthogButton.grid(row=0, column=3, sticky=Tkinter.EW)
self.markButton = SlimButton(frame,text='Nxt strip',command=self.incrementActiveStripAll)
self.markButton.grid(row=0, column=4, sticky=Tkinter.EW)
self.markButton = SlimButton(frame,text='Prv strip',command=self.decrementActiveStripAll)
self.markButton.grid(row=0, column=5, sticky=Tkinter.EW)
self.markButton = SlimButton(frame,text='0 strip',command=self.zeroActiveStrip)
self.markButton.grid(row=0, column=6, sticky=Tkinter.EW)
self.markButton = SlimButton(frame,text='Mark Res',command=self.markAllResShift)
self.markButton.grid(row=0, column=7, sticky=Tkinter.EW)
self.showAllRes = SlimButton(frame,text='Shw All Rs',command=self.showAllRes)
self.showAllRes.grid(row=1, column=3, sticky=Tkinter.EW)
self.markAllRes = SlimButton(frame,text='Mrk All Rs',command=self.markAllRes)
self.markAllRes.grid(row=1, column=4, sticky=Tkinter.EW)
self.markRemoveButton = SlimButton(frame,text='Del Marks',command=self.removeAllMarks)
self.markRemoveButton.grid(row=1, column=5, sticky=Tkinter.EW)
row += 1
row += 1
if shiftLists:
self.shiftList = shiftLists[0]
guiFrame.grid_columnconfigure(9, weight=1)
# row = 0
self.shiftValueEntry = FloatEntry(self, returnCallback=self.setShiftValue, width=10)
self.nameEntry = Entry(self, returnCallback=self.setName, width=12)
self.shiftListLabel = Label(guiFrame, text = 'ShiftList:')
self.shiftListPulldown = PulldownMenu(guiFrame, self.changeShiftList, shiftListNames, selected_index=0, label_color = self.titleColor, do_initial_callback=False)
self.isotopeLabel = Label(guiFrame, text = ' Isotope:')
self.isotopePulldown = PulldownMenu(guiFrame, self.changeIsotope, self.isotopeNames, selected_index=0, label_color = self.titleColor, do_initial_callback=False)
self.statusLabel = Label(guiFrame, text = ' Status:')
self.statusPulldown = PulldownMenu(guiFrame, self.changeStatus, self.statusNames, selected_index=0, label_color = self.titleColor, do_initial_callback=False)
self.chainLabel = Label(guiFrame, text = ' Chain:')
self.chainPulldown = PulldownMenu(guiFrame, self.changeChain, selected_index=0, label_color = self.titleColor, do_initial_callback=False)
self.ccpCodeLabel = Label(guiFrame, text = ' CcpCode:')
self.ccpCodePulldown = PulldownMenu(guiFrame, self.changeCcpCode, selected_index=0, label_color = self.titleColor, do_initial_callback=False)
#self.spacer2 = Spacer(guiFrame)
self.shiftListLabel.grid (row=row, column=0, columnspan=1, sticky=Tkinter.W)
self.shiftListPulldown.grid(row=row, column=1, columnspan=1, sticky=Tkinter.W)
self.isotopeLabel.grid (row=row, column=2, columnspan=1, sticky=Tkinter.W)
self.isotopePulldown.grid (row=row, column=3, columnspan=1, sticky=Tkinter.W)
self.statusLabel.grid (row=row, column=4, columnspan=1, sticky=Tkinter.W)
self.statusPulldown.grid (row=row, column=5, columnspan=1, sticky=Tkinter.W)
self.chainLabel.grid (row=row, column=6, columnspan=1, sticky=Tkinter.W)
self.chainPulldown.grid (row=row, column=7, columnspan=1, sticky=Tkinter.W)
self.ccpCodeLabel.grid (row=row, column=8, columnspan=1, sticky=Tkinter.W)
self.ccpCodePulldown.grid (row=row, column=9, columnspan=1, sticky=Tkinter.W)
row += 1
guiFrame.grid_rowconfigure(row, weight=1)
#shift list experiments
#shift list unit
justifyList = ['center','right','left','left','center','center','center','center','center','center']
colHeadings = ['#',"Shift","SD",'Assign\nName','Residue','Isotope','Other\nName','Total\nPeaks','Shift List\nPeaks','Spin\nSystem #']
editWidgets = [None,self.shiftValueEntry,None,None,None,None,self.nameEntry,None,None,None]
editGetCallbacks = [None,self.getShiftValue, None,None,None,None,self.getName ,self.showPeaks, self.showShiftListPeaks,None]
editSetCallbacks = [None,self.setShiftValue, None,None,None,None,self.setName ,None,None,None]
self.scrolledMatrix = ScrolledMatrix(guiFrame, justifyList=justifyList, initialRows=16, headingList=colHeadings,
editWidgets=editWidgets,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks,
font=self.smallFont, callback=self.selectCell, multiSelect=1)
self.scrolledMatrix.grid (row=row, column=0, columnspan=10, sticky = Tkinter.NSEW, padx=1)
self.scrolledMatrix.doEditMarkExtraRules = self.doEditMarkExtraRules
texts = ['Deassign','Assign','Add to\nSpin System','Remove from\nSpin System','Swap\nProchirals']
commands = [self.disconnectAtoms,self.waitForAtoms,self.addToSpinSys,self.removeFromSpinSys,self.swapProchiral]
buttonList = ButtonList(guiFrame, texts=texts, commands=commands, expands=True)
buttonList.grid(row = 4, column = 0, columnspan=10, sticky = Tkinter.EW)
self.assignButton = buttonList.buttons[1]
self.assSpinSysButton = buttonList.buttons[2]
self.swapProchiralButton = buttonList.buttons[4]
texts = ['Delete','Delete\nOrphans','Merge','Show Total\nPeaks','Show Shift List\nPeaks']
commands = [self.deleteResonance,self.deleteOrphans,self.mergeResonances,self.showPeaks, self.showShiftListPeaks]
self.bottomButtons = createDismissHelpButtonList(guiFrame, texts=texts, expands=1,
commands=commands, help_url=self.help_url)
self.bottomButtons.grid(row = 5, columnspan = 10, sticky = Tkinter.EW)
self.registerNotify(self.updateShiftLists, 'ccp.Nmr.ShiftList', 'setName')
self.registerNotify(self.updateShiftLists, 'ccp.Nmr.ShiftList', '__init__')
self.registerNotify(self.updateShiftLists, 'ccp.Nmr.ShiftList', 'delete')
for func in ('__init__', 'delete'):
for clazz in ('ccp.Nmr.PeakDimContrib', 'ccp.Nmr.Shift','ccp.Nmr.ResonanceSet', 'ccp.Nmr.Resonance'):
self.registerNotify(self.updateAfter, clazz, func)
self.registerNotify(self.updateAfter, 'ccp.Nmr.ResonanceSet', 'addResonance')
self.registerNotify(self.updateAfter, 'ccp.Nmr.Shift', 'setValue')
self.registerNotify(self.updateAfter, 'ccp.Nmr.Shift', 'setError')
for func in ('setDetails', 'setIsotopeCode', 'setName','removeAssignName','setAssignNames','addAssignName'):
self.registerNotify(self.updateAfter, 'ccp.Nmr.Resonance', func)
for func in ('setCcpCode', 'addResonance', 'removeResonance', 'setResonances','addAtomSet', 'delete'):
self.registerNotify(self.updateAfter, 'ccp.Nmr.ResonanceGroup', func)
self.registerNotify(self.updateAfter, 'ccp.Nmr.Shift', 'getResonance')
self.resonances=[]
self.resonance = None
self.refresh = 0
self.update()
def gotoOrthogPlane(self,windowName,col=0,active='y'):
if windowName!='None':
if active=='y':
col=self.activeStrip(windowName)
popup=self.argServer.parent.getWindowPopup(windowName)
if windowName in self.WindowPositionDic.keys():
position=self.WindowPositionDic[windowName]
else:
position=self.WindowPositionDic2D[windowName]
popup.gotoPosition(position,col=col)
def gotoOrthogPlaneAll(self):
self.gotoOrthogPlane(self.orthogPulldown.getSelected())
self.gotoOrthogPlane(self.orthogPulldown1.getSelected())
self.gotoOrthogPlane(self.orthogPulldown2D.getSelected())
def activeStrip(self,windowName):
window=self.orthogonalDict[windowName]
for n in range(0,len(window.axisPanels[0].axisRegions)):
if window.axisPanels[0].axisRegions[n].isActive: return n
def zeroActiveStrip(self):
windowName=self.orthogPulldown.getSelected()
if windowName!='None':
popup=self.argServer.parent.getWindowPopup(windowName)
popup.activateStrip(0)
windowName=self.orthogPulldown1.getSelected()
if windowName!='None':
popup=self.argServer.parent.getWindowPopup(windowName)
popup.activateStrip(0)
windowName=self.orthogPulldown2D.getSelected()
if windowName!='None':
popup=self.argServer.parent.getWindowPopup(windowName)
popup.activateStrip(0)
def incrementActiveStripAll(self):
self.incrementActiveStrip(self.orthogPulldown.getSelected())
self.incrementActiveStrip(self.orthogPulldown1.getSelected())
self.incrementActiveStrip(self.orthogPulldown2D.getSelected())
#mark all resonances from the residue identified by the selected resonance
def markAllRes(self):
resonance = self.scrolledMatrix.currentObjects[0]
if resonance.resonanceSet:
for r in getResidueProtElementResFromRes(resonance,elementSymbol='C'):
self.markResShift(r)
for r1 in getProtonResFromCarbRes(r): self.markResShift(r1)
for r in getResidueProtElementResFromRes(resonance,elementSymbol='N'):
self.markResShift(r)
for r1 in getProtonResFromCarbRes(r): self.markResShift(r1)
#display strips for the whole residue, alphabetical order
def showAllRes(self):
self.zeroActiveStrip()
resonance = self.scrolledMatrix.currentObjects[0]
ResPairs=[]
CarbResDic={}
if resonance.resonanceSet:
for r in getResidueProtElementResFromRes(resonance,elementSymbol='C'):
(molSystem, chain, residue, name) = getResonanceAtomTuple(r)
CarbResDic[name]=r
CarbNames=CarbResDic.keys()
CarbNames.sort()
print CarbNames
for name in CarbNames:
r=CarbResDic[name]
for r1 in getProtonResFromCarbRes(r):
(molSystem1, chain1, residue1, name1) = getResonanceAtomTuple(r1)
if name=='Cga' or name=='Cgb' or name=='Cda' or name=='Cdb':
if name[1:3]!=name1[1:3]: continue
ResPairs.append([r,r1])
#windows may have different number of pannels, ans smaller than numer of atoms
cntMax=0
windowName=self.orthogPulldown.getSelected()
if windowName!='None':
window=self.orthogonalDict[self.orthogPulldown.getSelected()]
cntMax=len(window.axisPanels[0].axisRegions)
cntMax1=0
windowName=self.orthogPulldown1.getSelected()
if windowName!='None':
window=self.orthogonalDict[self.orthogPulldown1.getSelected()]
cntMax1=len(window.axisPanels[0].axisRegions)
cntMax2D=0
windowName=self.orthogPulldown2D.getSelected()
if windowName!='None':
window=self.orthogonalDict[self.orthogPulldown2D.getSelected()]
cntMax2D=len(window.axisPanels[0].axisRegions)
for ResPair in ResPairs:
if cntMax>0:
self.goToPosition(self.orthogPulldown.getSelected(),ResPair)
if cntMax1>0:
self.goToPosition(self.orthogPulldown1.getSelected(),ResPair)
if cntMax2D>0:
self.goToPosition(self.orthogPulldown2D.getSelected(),ResPair)
self.incrementActiveStripAll()
cntMax-=1
cntMax1-=1
cntMax2D-=1
#resonances = [r1,r2]
def goToPosition(self,windowName,resonances):
if windowName=='None': return
window=self.orthogonalDict[windowName]
resTypesDic={}
if len(resonances)>2: return
if len(resonances)==2:
if resonances[0].isotope.massNumber==resonances[1].isotope.massNumber: return
for resonance in resonances:
isotopeText = '%d%s' % (resonance.isotope.massNumber, resonance.isotope.chemElement.symbol)
resTypesDic[isotopeText]=resonance
position={}
for axisPanel in window.axisPanels:
if axisPanel.label=='y' and len(window.axisPanels)!=2: continue
for key in resTypesDic.keys():
if key == axisPanel.axisType.name:
position[axisPanel.label]=self.getResShift(resTypesDic[key])
if len(resTypesDic.keys())!=len(position.keys()): return
# print position
popup=self.argServer.parent.getWindowPopup(windowName)
col=self.activeStrip(windowName)
popup.gotoPosition(position,col=col)
##~ if len(window.axisPanels)==2:
##~ self.WindowPositionDic2D[window.name]=d_tmp
##~ else:
##~ self.WindowPositionDic[window.name]=d_tmp
#
def incrementActiveStrip(self,windowName):
if windowName!='None':
window=self.orthogonalDict[windowName]
popup=self.argServer.parent.getWindowPopup(windowName)
col=popup.getActiveStrip()
if col=='all': col=0
if col<len(window.axisPanels[0].axisRegions)-1: col+=1
popup.activateStrip(col)
def decrementActiveStrip(self,windowName):
if windowName!='None':
window=self.orthogonalDict[windowName]
popup=self.argServer.parent.getWindowPopup(windowName)
col=popup.getActiveStrip()
if col=='all': col=0
if col>0: col-=1
popup.activateStrip(col)
def decrementActiveStripAll(self):
self.decrementActiveStrip(self.orthogPulldown.getSelected())
self.decrementActiveStrip(self.orthogPulldown1.getSelected())
self.decrementActiveStrip(self.orthogPulldown2D.getSelected())
def selectCell(self, resonance, row, col):
self.resonance = resonance
self.findWindows()
def getResShift(self, resonance):
if self.shiftList:
shift= resonance.findFirstShift(parentList = self.shiftList)
return shift.value
else: return None
def markResShift(self, resonance):
positions=[self.getResShift(resonance)]
isotopeText = '%d%s' % (resonance.isotope.massNumber, resonance.isotope.chemElement.symbol)
axisType =None
activeWindows = getActiveWindows(self.project)
for window in activeWindows:
if axisType: break
for axisPanel in window.axisPanels:
if isotopeText == axisPanel.axisType.name:
axisTypes=[axisPanel.axisType]
break
createNonPeakMark1(positions, axisTypes)
def markAllResShift(self):
for resonance in self.scrolledMatrix.currentObjects:
self.markResShift(resonance)
def removeAllMarks(self):
removeMarks(self.project,removeAll=True)
def findWindows(self):
resTypesDic={}
if len(self.scrolledMatrix.currentObjects)>2: return
if len(self.scrolledMatrix.currentObjects)==2:
if self.scrolledMatrix.currentObjects[0].isotope.massNumber==self.scrolledMatrix.currentObjects[1].isotope.massNumber: return
for resonance in self.scrolledMatrix.currentObjects:
isotopeText = '%d%s' % (resonance.isotope.massNumber, resonance.isotope.chemElement.symbol)
resTypesDic[isotopeText]=resonance
activeWindows = getActiveWindows(self.project)
self.WindowPositionDic={}
self.WindowPositionDic2D={}
self.orthogonalDict={}
for window in activeWindows:
self.orthogonalDict[window.name]=window
d_tmp={}
for axisPanel in window.axisPanels:
if axisPanel.label=='y' and len(window.axisPanels)!=2: continue
for key in resTypesDic.keys():
if key == axisPanel.axisType.name:
d_tmp[axisPanel.label]=self.getResShift(resTypesDic[key])
if len(resTypesDic.keys())==len(d_tmp.keys()):
if len(window.axisPanels)==2:
self.WindowPositionDic2D[window.name]=d_tmp
else:
self.WindowPositionDic[window.name]=d_tmp
list=self.WindowPositionDic.keys()
list.append('None')
n=0
try:
n=list.index(self.orthogPulldown.getSelected())
except: pass
self.orthogPulldown.setup(list,n)
n=0
try:
n=list.index(self.orthogPulldown1.getSelected())
except: pass
self.orthogPulldown1.setup(list,n)
list=self.WindowPositionDic2D.keys()
list.append('None')
n=0
try:
n=list.index(self.orthogPulldown2D.getSelected())
except: pass
self.orthogPulldown2D.setup(list,n)
def ResTblScGui(argServer=None):
# popup = self.openPopup('browse_resonances', ResTblSc)
# popup.update() # TBD: not sure if this is really needed
RT=ResTblSc(argServer.parent,argServer=argServer)
def createNonPeakMark1(positions, axisTypes, lineWidth = 1,
dashLength = 2, gapLength = 2, color = None, remove=False):
"""Descrn: Create a mark at a general (i.e. non-peak) position.
Inputs: List of Floats (Analysis.Mark.positions), List of Analysis.AxisTypes,
Int, Int, Int, Word (Analysis.Color.name)
Output: Analysis.Mark
"""
global markCounter
project = axisTypes[0].project
if (not color):
name = project.application.getValue(project, keyword='marksColor',
defaultValue='red')
colorScheme = project.findFirstColorScheme(name=name)
if (colorScheme):
names = colorScheme.colorNames
ncolors = len(names)
color = project.findFirstColor(name=names[markCounter % ncolors])
if (not color):
color = project.findFirstColor(name='black')
markCounter = markCounter + 1
else:
color = project.findFirstColor(name='black')
mark = Analysis.Mark(project, lineWidth=lineWidth, dashLength=dashLength,
gapLength=gapLength, color=color)
for n in range(len(positions)):
markDim = Analysis.MarkDim(mark, position=positions[n], axisType=axisTypes[n])
mark.peak = None
if remove:
removeMarks(project)
return mark
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