def compare( project1, project2 ):
"""Compare the shifts of all equivalent atoms.
"""
if project1 is None or project1.molecule is None:
return True
if project2 is None or project2.molecule is None:
return True
mol1 = project1.molecule
mol2 = project2.molecule
nTmessage('==> comparing %s and %s\n', mol1, mol2)
mapMolecule(mol1, mol2)
for atm1 in mol1.allAtoms():
if atm1.has_key('delta'): del(atm1['delta'])
#end for
for atm1 in mol1.allAtoms():
compareAtms(atm1, atm1.map)
#end for
# average; taken the values of directly bonded atoms into account
for atm in mol1.allAtoms():
average(atm)
#end for
# generate scripts
mkYasaraMacro(mol1, 'delta', sprintf('yasara-%s-%s.mcr', project1.name, project2.name))
mkYasaraMacro(mol1, 'deltaAverage', sprintf('yasara-%s-%s-averaged.mcr', project1.name, project2.name))
def compareShifts( projectA, projectB ):
"""Compare the shifts of the two molecules of both projects
"""
# Loop through all the residues
for res1 in projectA.molecule.allResidues():
res2=res1.map
#compare the two residues
if res2 != None:
# check if they are the same type
if (res1.db.name == res2.db.name):
identity = "(S)"
else:
identity = '(D)'
#end if
printf("\n==== %s %s ==== %s\n", res1.name, res2.name, identity)
# loop through all the atoms of res1
for a1 in res1.atoms:
a2=a1.map #check if this atom exists in res2
a1.delta = None
if a2 and (a1.isAssigned() and a2.isAssigned()):
a1.delta = a1.resonances().value - a2.resonances().value
#end if
# calc differences with potential prochiral
a1.pc = a1.proChiralPartner()
if a1.pc:
pc2 = a1.pc.map # atom of second set
else:
pc2 = None
#end if
a1.deltaPC = None # delta with prochiral atom
if pc2 and (a1.isAssigned() and pc2.isAssigned()):
a1.deltaPC = a1.resonances().value - pc2.resonances().value
#end if
#end for
for a1 in res1.atoms:
a2=a1.map #check if this atom exists in res2
doPrint = False
swapText = ''
if a1.delta:
if ((a1.isProton() and math.fabs( a1.delta ) >= limits[0]) or
(a1.isCarbon() and math.fabs( a1.delta ) >= limits[1]) or
(a1.isNitrogen() and math.fabs( a1.delta ) >= limits[2])
):
doPrint = True
swapText = sprintf('%7.3f ', a1.delta)
#end if
# check for altered assignment
if a1.delta and a1.deltaPC and a1.pc.delta and a1.pc.deltaPC:
if (math.fabs( a1.deltaPC ) + math.fabs( a1.pc.deltaPC ) <
math.fabs( a1.delta ) + math.fabs( a1.pc.delta )
):
doPrint = True
swapText = sprintf("%7.3f >> Potential Swapped assignment %s and %s", a1.deltaPC, a1.map, a1.pc.map)
#end if
if doPrint:
printf('%s %s %s %7.3f %s\n', identity, printatom( a1 ), printatom( a2 ), a1.delta, swapText)
def printatom( atm ):
if atm.isStereoAssigned():
ss = '(stereo)'
else:
ss = '() '
#end if
return sprintf('%-12s %10.3f %s', atm._Cname(1), atm.resonances().value, ss )
def getUniqueName(objectListWithNameAttribute, baseName, nameFormat = "%s_%d" ):
"""
Return unique name or False on error.
E.g. for ResonanceSources object in which the ResonanceList objects have a name attribute.
nameFormat may be specified to receive a string and an integer argument.
Works on any NTlist that has name attributes in each element.
"""
nameList = objectListWithNameAttribute.zap( NAME_STR )
# nTdebug("Already have names: %s" % str(nameList))
nameDict = nTlist2dict(nameList)
if not nameDict.has_key( baseName):
return baseName
i = 1
while i < MAX_TRIES_UNIQUE_NAME: # This code is optimal unless number of objects get to 10**5.
newName = sprintf( nameFormat, baseName, i)
if not nameDict.has_key( newName ):
return newName
i += 1
def getUniqueName(objectListWithNameAttribute, baseName, nameFormat="%s_%d"):
"""
Return unique name or False on error.
E.g. for ResonanceSources object in which the ResonanceList objects have a name attribute.
nameFormat may be specified to receive a string and an integer argument.
Works on any NTlist that has name attributes in each element.
"""
nameList = objectListWithNameAttribute.zap(NAME_STR)
# nTdebug("Already have names: %s" % str(nameList))
nameDict = nTlist2dict(nameList)
if not nameDict.has_key(baseName):
return baseName
i = 1
while i < MAX_TRIES_UNIQUE_NAME: # This code is optimal unless number of objects get to 10**5.
newName = sprintf(nameFormat, baseName, i)
if not nameDict.has_key(newName):
return newName
i += 1
def updateGui(self, event=None):
projOption = self.projOptionsSelect.get()
buttons = self.buttonBar.buttons
# Disable entries
for e in [self.projEntry, self.pdbEntry, self.ccpnEntry, self.cyanaEntry, self.nameEntry]:
e.configure(state='disabled')
#end for
if projOption == self.projectOptions[0]:
# Enable entries
self.projEntry.configure(state='normal')
if (len(self.projEntry.get()) > 0):
self.openProjectButton.enable()
self.runButton.enable()
else:
self.openProjectButton.disable()
self.runButton.disable()
#end if
elif projOption == self.projectOptions[1]:
# Enable entries
self.pdbEntry.configure(state='normal')
self.nameEntry.configure(state='normal')
if (len(self.pdbEntry.get()) > 0 and len(self.nameEntry.get()) > 0):
buttons[0].enable()
buttons[1].enable()
else:
buttons[0].disable()
buttons[1].disable()
#end if
#end if
elif projOption == self.projectOptions[2]:
# Enable entries
self.ccpnEntry.configure(state='normal')
self.nameEntry.configure(state='normal')
if (len(self.ccpnEntry.get()) > 0 and len(self.nameEntry.get()) > 0):
buttons[0].enable()
buttons[1].enable()
else:
buttons[0].disable()
buttons[1].disable()
#end if
#end if
elif projOption == self.projectOptions[3]:
# Enable entries
self.cyanaEntry.configure(state='normal')
self.nameEntry.configure(state='normal')
if (len(self.cyanaEntry.get()) > 0 and len(self.nameEntry.get()) > 0):
buttons[0].enable()
buttons[1].enable()
else:
buttons[0].disable()
buttons[1].disable()
#end if
#end if
self.projectStatus.clear()
if not self.project:
self.projectStatus.setText('No open project')
self.closeProjectButton.setText('Close Project')
self.closeProjectButton.disable()
else:
self.projectStatus.setText(self.project.format())
self.closeProjectButton.enable()
self.closeProjectButton.setText(sprintf('Close Project "%s"', self.project.name))
def compareNoeNetWork( projectA, projectB, verbose ):
"""
Generate B-peakLists for NOEs of A not present in B.
Mapping and NOE sorting should have been done before
Expand the NOEs to/from pseudo atoms by using the set() method (already
present as the '.s' attribute).
The sets should take care of the comparison of 'like' atoms;
i.e. pseudo with real atoms
"""
NTmessage('==> comparing NOEs %s with %s\n', projectA, projectB )
prepareNOEs( projectA )
prepareNOEs( projectB )
count = 0
for atmA1 in projectA.molecule.allAtoms():
# check all the NOEs for this atom
for atmA2 in atmA1.NOEs:
if verbose:
printf('Checking NOE %-40s : ', sprintf('(%s,%s)', atmA1, atmA2) )
#end if
atmB1 = atmA1.map
atmB2 = atmA2.map
found = False
atmB1.setdefault('newNOEs', NTlist() )
if atmB2 in atmB1.newNOEs:
if verbose: printf('Peak has been generated previously\n')
else:
# check all the possibilities of the set of atomB1
for b1 in atmB1.s:
# A set comparison yields true if there is one or more common elements
if b1.NOEs == atmB2.s:
count += 1
found = True
if verbose: printf('Found NOE %s\n', sprintf('(%s,%s)', b1, atmB2.s) )
break
else:
pass
#end if
#end for
if (not found):
# generate an atmB1-atmB2 peak since this NOE (atmA1,atmA2) was not found in the B-set
# the reverse peak is accounted for by the (atmA2-atmA1) Noe
peak = atoms2peak( atmB1, atmB2, projectB.c13peaks, projectB.aropeaks, projectB.n15peaks )
if peak:
peak.xeasyColor = peakColor
count += 1
atmB1.newNOEs.append( atmB2 )
if verbose: printf('New %s\n', peak)
else:
if verbose: printf('Skipped because of lacking assignments\n')
#end if
#end if
#end if
#end for
#end for
if verbose:
NTmessage('==> Appended %d peaks\n', count )
def updateGui(self, event=None):
projOption = self.projOptionsSelect.get()
buttons = self.buttonBar.buttons
# Disable entries
for e in [
self.projEntry, self.pdbEntry, self.ccpnEntry, self.cyanaEntry,
self.nameEntry
]:
e.configure(state='disabled')
#end for
if projOption == self.projectOptions[0]:
# Enable entries
self.projEntry.configure(state='normal')
if (len(self.projEntry.get()) > 0):
self.openProjectButton.enable()
self.runButton.enable()
else:
self.openProjectButton.disable()
self.runButton.disable()
#end if
elif projOption == self.projectOptions[1]:
# Enable entries
self.pdbEntry.configure(state='normal')
self.nameEntry.configure(state='normal')
if (len(self.pdbEntry.get()) > 0
and len(self.nameEntry.get()) > 0):
buttons[0].enable()
buttons[1].enable()
else:
buttons[0].disable()
buttons[1].disable()
#end if
#end if
elif projOption == self.projectOptions[2]:
# Enable entries
self.ccpnEntry.configure(state='normal')
self.nameEntry.configure(state='normal')
if (len(self.ccpnEntry.get()) > 0
and len(self.nameEntry.get()) > 0):
buttons[0].enable()
buttons[1].enable()
else:
buttons[0].disable()
buttons[1].disable()
#end if
#end if
elif projOption == self.projectOptions[3]:
# Enable entries
self.cyanaEntry.configure(state='normal')
self.nameEntry.configure(state='normal')
if (len(self.cyanaEntry.get()) > 0
and len(self.nameEntry.get()) > 0):
buttons[0].enable()
buttons[1].enable()
else:
buttons[0].disable()
buttons[1].disable()
#end if
#end if
self.projectStatus.clear()
if not self.project:
self.projectStatus.setText('No open project')
self.closeProjectButton.setText('Close Project')
self.closeProjectButton.disable()
else:
self.projectStatus.setText(self.project.format())
self.closeProjectButton.enable()
self.closeProjectButton.setText(
sprintf('Close Project "%s"', self.project.name))