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 cyana2cing( name, convention ):
"""Read the data from the cyana directory and store in new project
"""
printf("\n==> Opening Project %s\n", name )
project = Project.open(name, 'new', verbose=False )
from cing.Libs.disk import matchfilelist
seqfile = matchfilelist( project.name +'/*.seq')[0]
project.newMolecule( project.name, seqfile, convention, verbose=False )
project.importXeasy( seqfile, project.name + '/all-final.prot', convention )
parseCyanaStereoFile( project, project.name + '/finalstereo.cya', convention )
project.c13peaks = project.importXeasyPeaks( seqfile, project.name + '/all-final.prot', project.name + '/c13.peaks', convention )
project.aropeaks = project.importXeasyPeaks( seqfile, project.name + '/all-final.prot', project.name + '/aro.peaks', convention )
project.n15peaks = project.importXeasyPeaks( seqfile, project.name + '/all-final.prot', project.name + '/n15.peaks', convention )
project.upl = project.importUpl( project.name +'/final.upl', convention )
# comment because of crash in export and not needed anyway
# project.aco = project.importAco( project.name +'/talos.aco', convention )
print project.format()
return project
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 checkAssignments( project ):
"""
Check assignments for potential trivial errors
"""
if project == None: return
printf("==> Assignment check Project %s\n", project )
for atm in project.molecule.allAtoms():
if atm.isAssigned():
# Check database
av = atm.db.shift.average
sd = atm.db.shift.sd
#print atm, atm.db.pseudo
# Check the shift against the database
if (math.fabs(atm.resonances().value - av) > 3.0*sd):
printf('SHIFT %s: more than 3*sd away from average\n', atm )
#end if
# Check if not both realAtom and pseudoAtom are assigned
if atm.hasPseudoAtom() and atm.pseudoAtom().isAssigned():
printf('MULTIPLE_ASSIGNMENT %s: also has %s assigned\n', atm, atm.pseudoAtom() )
#end if
# Check if not pseudoAtom and realAtom are assigned
if atm.isPseudoAtom():
for a in atm.realAtoms():
if a.isAssigned():
printf('MULTIPLE_ASSIGNMENT %s: also has %s assigned\n', atm, a )
#end if
#end for
#end if
# Check if all realAtoms are assigned in case there is a pseudoatom
if atm.hasPseudoAtom():
ratms = atm.pseudoAtom().realAtoms()
allAssigned = True
for a in ratms:
if not a.isAssigned():
printf('MISSING_PROTON_ASSIGNMENT %s: expected also %s to be assigned\n', atm, a )
allAssigned = False
#end if
#end for
# if len( ratms ) == 2 and allAssigned and ratms[0].resonances().value > ratms[1].resonances().value:
# printf('SWAPPED_PROTON_ASSIGNMENTS %s: and %s\n', ratms[0], ratms[1] )
# #end if
#end if
# Check for protons with unassigned heavy atoms
if atm.db.spinType == '1H':
heavyAtm = atm.topology()[0]
if not heavyAtm.isAssigned():
printf('MISSING_HEAVY_ATOM_ASSIGNMENT %s: expected %s to be assigned\n', atm, heavyAtm )
#end if
#end if
pc = atm.proChiralPartner()
if removeStereo and pc and not (atm.hasProperties('isMethyl') or atm.hasProperties('isMethylProton')):
# check the order and the value of resonances; i.e. HB2 < HB3
if ( (atm < pc and atm.resonances().value > pc.resonances().value) or
(atm > pc and atm.resonances().value < pc.resonances().value)
):
swapAssignments(tmp,pc)
printf( 'SWAPPED assignments %s and %s\n',atm, pc)
#end if
atm.stereoAssigned = False
pc.stereoAssigned = False
