def test_simplifyForFcFeature(self):
'test simplify Specifically For Fc Feature'
self.createSimpleFastProject()
_distanceRestraintList = self.project.distances.new(DR_LEVEL, status = 'keep')
atomPairs = NTlist()
r1 = self.r1
r2 = self.r2
# r3 = self.r3
atomPairs.append((r1.MG1, r2.MG1))
atomPairs.append((r1.MG2, r2.MG1))
atomPairs.append((r1.MG1, r2.MG2))
atomPairs.append((r1.MG2, r2.MG2))
# atomPairs.append((r2.HN, r2.MG1))
# atomPairs.append((r2.HN, r2.MG2))
distanceRestraint = DistanceRestraint(atomPairs, 0.0, 5.0)
if distanceRestraint.isValid:
_distanceRestraintList.append(distanceRestraint)
else:
nTerror('Failed to initialize DR with %s' % atomPairs)
# nTdebug("dr before: %s" % formatall(distanceRestraint))
# Takes 4 simplification iterations.
self.assertEqual(distanceRestraint.simplifyForFc(), DistanceRestraint.STATUS_SIMPLIFIED)
# nTdebug("dr after 1: %s" % formatall(distanceRestraint))
self.assertEqual(distanceRestraint.simplifyForFc(), DistanceRestraint.STATUS_SIMPLIFIED)
# nTdebug("dr after 2: %s" % formatall(distanceRestraint))
self.assertEqual(distanceRestraint.simplifyForFc(), DistanceRestraint.STATUS_SIMPLIFIED)
# nTdebug("dr after 3: %s" % formatall(distanceRestraint))
self.assertEqual(distanceRestraint.simplifyForFc(), DistanceRestraint.STATUS_NOT_SIMPLIFIED)
# nTdebug("dr after 4: %s" % formatall(distanceRestraint)) # don't print as it contains error token.
_x = "dr after 4: %s" % formatall(distanceRestraint)
def test_Simplify(self):
'test Simplify'
self.createSimpleFastProject()
y = self.r5 # PHE
_distanceRestraintList = self.project.distances.new(DR_LEVEL, status = 'keep')
atomPairs = NTlist((y.QE, y.H),
(y.QE, y.H)
)
distanceRestraint = DistanceRestraint(atomPairs, 0.0, 5.0)
# nTdebug("before: %r" % distanceRestraint )
self.assertEqual(distanceRestraint.simplify(), DistanceRestraint.STATUS_NOT_SIMPLIFIED)
def test_Simplify(self):
'test Simplify'
self.createSimpleFastProject()
y = self.r5 # PHE
_distanceRestraintList = self.project.distances.new(DR_LEVEL,
status='keep')
atomPairs = NTlist((y.QE, y.H), (y.QE, y.H))
distanceRestraint = DistanceRestraint(atomPairs, 0.0, 5.0)
# nTdebug("before: %r" % distanceRestraint )
self.assertEqual(distanceRestraint.simplify(),
DistanceRestraint.STATUS_NOT_SIMPLIFIED)
def test_CombiToPseudoQuadruple(self):
' test combination to Pseudo 4 some.'
# 'Simulate 1a24 1254.00 A 3 TYR QR A 8 GLN QB'
self.createSimpleFastProject()
y = self.r5 # PHE
_distanceRestraintList = self.project.distances.new(DR_LEVEL, status = 'keep')
atomPairs = NTlist((y.QE, y.H),
(y.QD, y.H)
)
distanceRestraint = DistanceRestraint(atomPairs, 0.0, 5.0)
# nTdebug("before: %r" % distanceRestraint )
self.assertEqual(distanceRestraint.simplify(), DistanceRestraint.STATUS_NOT_SIMPLIFIED)
def test_CombiToPseudoQuadruple(self):
' test combination to Pseudo 4 some.'
# 'Simulate 1a24 1254.00 A 3 TYR QR A 8 GLN QB'
self.createSimpleFastProject()
y = self.r5 # PHE
_distanceRestraintList = self.project.distances.new(DR_LEVEL,
status='keep')
atomPairs = NTlist((y.QE, y.H), (y.QD, y.H))
distanceRestraint = DistanceRestraint(atomPairs, 0.0, 5.0)
# nTdebug("before: %r" % distanceRestraint )
self.assertEqual(distanceRestraint.simplify(),
DistanceRestraint.STATUS_NOT_SIMPLIFIED)
def test_CombiToPseudoDouble_2(self):
'test_CombiToPseudoDouble_2'
# 'Simulate 1a24 1254.00 A 3 TYR QD A 8 GLN QB'
self.createSimpleFastProject()
# e = self.r3 # GLN
y = self.r4 # TYR
_distanceRestraintList = self.project.distances.new(DR_LEVEL, status = 'keep')
atomPairs = NTlist((y.HE1, y.HB2),
(y.HE2, y.HB2),
(y.HE1, y.HB3),
(y.HE2, y.HB3))
distanceRestraint = DistanceRestraint(atomPairs, 0.0, 5.0)
# nTdebug("before: %r" % distanceRestraint )
self.assertEqual(distanceRestraint.simplify(), DistanceRestraint.STATUS_SIMPLIFIED)
def test_CombiToPseudoDouble_2(self):
'test_CombiToPseudoDouble_2'
# 'Simulate 1a24 1254.00 A 3 TYR QD A 8 GLN QB'
self.createSimpleFastProject()
# e = self.r3 # GLN
y = self.r4 # TYR
_distanceRestraintList = self.project.distances.new(DR_LEVEL,
status='keep')
atomPairs = NTlist((y.HE1, y.HB2), (y.HE2, y.HB2), (y.HE1, y.HB3),
(y.HE2, y.HB3))
distanceRestraint = DistanceRestraint(atomPairs, 0.0, 5.0)
# nTdebug("before: %r" % distanceRestraint )
self.assertEqual(distanceRestraint.simplify(),
DistanceRestraint.STATUS_SIMPLIFIED)
def test_Simplify3(self):
'test simplify 3'
_help = """
For 1a24
783.00 A 20 PRO QB A 23 LEU MD1 3.20 7.90 2.96 0.56 2.56 3.35 0.32 0.45 0.64 0 0 0
783.01 A 20 PRO QB A 23 LEU QD 3.20 7.90 2.96 0.56 2.56 3.35 0.32 0.45 0.64 0 0 0
"""
self.createSimpleFastProject()
y = self.r8 # LEU
_distanceRestraintList = self.project.distances.new(DR_LEVEL, status = 'keep')
atomPairs = NTlist((y.QD, y.H),
(y.MD1, y.H)
)
distanceRestraint = DistanceRestraint(atomPairs, 0.0, 5.0)
# nTdebug("before: %r" % distanceRestraint )
self.assertEqual(distanceRestraint.removeDuplicateAtomPairs2(), DistanceRestraint.STATUS_REMOVED_DUPLICATE)
def test_Simplify2(self):
'test Simplify2'
_help = """
For 1a24
783.00 A 20 PRO QB A 23 LEU MD1 3.20 7.90 2.96 0.56 2.56 3.35 0.32 0.45 0.64 0 0 0
783.01 A 20 PRO QB A 23 LEU QD 3.20 7.90 2.96 0.56 2.56 3.35 0.32 0.45 0.64 0 0 0
"""
self.createSimpleFastProject()
y = self.r5 # PHE
_distanceRestraintList = self.project.distances.new(DR_LEVEL, status = 'keep')
atomPairs = NTlist((y.QE, y.H),
(y.QE, y.H)
)
distanceRestraint = DistanceRestraint(atomPairs, 0.0, 5.0)
# nTdebug("before: %r" % distanceRestraint )
self.assertEqual(distanceRestraint.simplify(), DistanceRestraint.STATUS_NOT_SIMPLIFIED)
def test_Simplify3(self):
'test simplify 3'
_help = """
For 1a24
783.00 A 20 PRO QB A 23 LEU MD1 3.20 7.90 2.96 0.56 2.56 3.35 0.32 0.45 0.64 0 0 0
783.01 A 20 PRO QB A 23 LEU QD 3.20 7.90 2.96 0.56 2.56 3.35 0.32 0.45 0.64 0 0 0
"""
self.createSimpleFastProject()
y = self.r8 # LEU
_distanceRestraintList = self.project.distances.new(DR_LEVEL,
status='keep')
atomPairs = NTlist((y.QD, y.H), (y.MD1, y.H))
distanceRestraint = DistanceRestraint(atomPairs, 0.0, 5.0)
# nTdebug("before: %r" % distanceRestraint )
self.assertEqual(distanceRestraint.removeDuplicateAtomPairs2(),
DistanceRestraint.STATUS_REMOVED_DUPLICATE)
def test_Simplify2(self):
'test Simplify2'
_help = """
For 1a24
783.00 A 20 PRO QB A 23 LEU MD1 3.20 7.90 2.96 0.56 2.56 3.35 0.32 0.45 0.64 0 0 0
783.01 A 20 PRO QB A 23 LEU QD 3.20 7.90 2.96 0.56 2.56 3.35 0.32 0.45 0.64 0 0 0
"""
self.createSimpleFastProject()
y = self.r5 # PHE
_distanceRestraintList = self.project.distances.new(DR_LEVEL,
status='keep')
atomPairs = NTlist((y.QE, y.H), (y.QE, y.H))
distanceRestraint = DistanceRestraint(atomPairs, 0.0, 5.0)
# nTdebug("before: %r" % distanceRestraint )
self.assertEqual(distanceRestraint.simplify(),
DistanceRestraint.STATUS_NOT_SIMPLIFIED)
def test_simplifyForFcFeature_2(self):
'test simplify Specifically For Fc Feature 2'
# disfunctional as of yet
self.createSimpleFastProject()
_distanceRestraintList = self.project.distances.new(DR_LEVEL, status = 'keep')
atomPairs = NTlist()
# r1 = self.r1
r2 = self.r2
# r3 = self.r3
atomPairs.append((r2.HN, r2.MG1))
atomPairs.append((r2.MG2, r2.HN))
# atomPairs.append((r2.HN, r2.MG1))
# atomPairs.append((r2.HN, r2.MG2))
distanceRestraint = DistanceRestraint(atomPairs, 0.0, 5.0)
_distanceRestraintList.append(distanceRestraint)
# nTdebug("dr before: %s" % formatall(distanceRestraint))
self.assertEqual(distanceRestraint.simplify(), DistanceRestraint.STATUS_SIMPLIFIED)
def test_simplifyForFcFeature_2(self):
'test simplify Specifically For Fc Feature 2'
# disfunctional as of yet
self.createSimpleFastProject()
_distanceRestraintList = self.project.distances.new(DR_LEVEL,
status='keep')
atomPairs = NTlist()
# r1 = self.r1
r2 = self.r2
# r3 = self.r3
atomPairs.append((r2.HN, r2.MG1))
atomPairs.append((r2.MG2, r2.HN))
# atomPairs.append((r2.HN, r2.MG1))
# atomPairs.append((r2.HN, r2.MG2))
distanceRestraint = DistanceRestraint(atomPairs, 0.0, 5.0)
_distanceRestraintList.append(distanceRestraint)
# nTdebug("dr before: %s" % formatall(distanceRestraint))
self.assertEqual(distanceRestraint.simplify(),
DistanceRestraint.STATUS_SIMPLIFIED)
def test_simplifyForFcFeature(self):
'test simplify Specifically For Fc Feature'
self.createSimpleFastProject()
_distanceRestraintList = self.project.distances.new(DR_LEVEL,
status='keep')
atomPairs = NTlist()
r1 = self.r1
r2 = self.r2
# r3 = self.r3
atomPairs.append((r1.MG1, r2.MG1))
atomPairs.append((r1.MG2, r2.MG1))
atomPairs.append((r1.MG1, r2.MG2))
atomPairs.append((r1.MG2, r2.MG2))
# atomPairs.append((r2.HN, r2.MG1))
# atomPairs.append((r2.HN, r2.MG2))
distanceRestraint = DistanceRestraint(atomPairs, 0.0, 5.0)
if distanceRestraint.isValid:
_distanceRestraintList.append(distanceRestraint)
else:
nTerror('Failed to initialize DR with %s' % atomPairs)
# nTdebug("dr before: %s" % formatall(distanceRestraint))
# Takes 4 simplification iterations.
self.assertEqual(distanceRestraint.simplifyForFc(),
DistanceRestraint.STATUS_SIMPLIFIED)
# nTdebug("dr after 1: %s" % formatall(distanceRestraint))
self.assertEqual(distanceRestraint.simplifyForFc(),
DistanceRestraint.STATUS_SIMPLIFIED)
# nTdebug("dr after 2: %s" % formatall(distanceRestraint))
self.assertEqual(distanceRestraint.simplifyForFc(),
DistanceRestraint.STATUS_SIMPLIFIED)
# nTdebug("dr after 3: %s" % formatall(distanceRestraint))
self.assertEqual(distanceRestraint.simplifyForFc(),
DistanceRestraint.STATUS_NOT_SIMPLIFIED)
# nTdebug("dr after 4: %s" % formatall(distanceRestraint)) # don't print as it contains error token.
_x = "dr after 4: %s" % formatall(distanceRestraint)
def importUpl( project, uplFile, convention, lower = 0.0 ):
"""
Read Cyana upl file
return a DistanceRestraintList or None on error
"""
#print 'Convention: ' + convention
maxErrorCount = 50
errorCount = 0
# check the molecule
if not project or not project.molecule:
nTerror("importUpl: initialize molecule first")
return None
#end if
molecule = project.molecule
# Sometimes set from other than CYANA coordinate file.
# chainId = molecule.chains[0].name # assumed unkown rite?
if not os.path.exists( uplFile ):
nTerror('importUpl: file "%s" not found', uplFile)
return None
#end if
_dir,name,_ext = nTpath( uplFile )
result = project.distances.new( name=name, status='keep')
atomDict = molecule.getAtomDict(convention)
for line in AwkLike( uplFile, commentString="#", minNF=7 ):
# if line.isComment():
## nTdebug("Skipping upl file line with comment: [" + line.dollar[0] +']')
# continue
# if line.NF < 7:
## nTdebug("Skipping upl file line with too few fields: [" + line.dollar[0] +']')
# continue
atmIdxList = [[1,3],[4,6]]
atmList = []
# i=0
for atmIdx in atmIdxList:
# nTdebug("Doing atmIdx: " + repr(atmIdx))
t = (line.int(atmIdx[0]), line.dollar[atmIdx[1]])
atm = None
if atomDict.has_key(t):
atm = atomDict[t]
# atm = molecule.decodeNameTuple( (convention, None, line.int(atmIdx[0]), line.dollar[atmIdx[1]]),
# fromCYANA2CING=True)
if not atm:
if errorCount <= maxErrorCount:
nTerror('Failed to decode for atom %s; line: %s', t, line.dollar[0] )
if errorCount == maxErrorCount+1:
nTerror("And so on")
errorCount += 1
# i+=1
continue
atmList.append( atm )
# i+=1
if len(atmList) != 2:
continue
# Unpack convenience variables.
atm1 = atmList[0]
atm2 = atmList[1]
# nTdebug("atom 1: " + repr(atm1))
# nTdebug("atom 2: " + repr(atm2))
upper = line.float(7)
# ambiguous restraint, should be append to last one
if upper == 0:
result().appendPair( (atm1,atm2) )
continue
if not upper:
nTerror("Skipping line without valid upper bound on line: [" + line.dollar[0]+']')
continue
r = DistanceRestraint( atomPairs= [(atm1,atm2)], lower=lower, upper=upper )
result.append( r )
# also store the Candid info if present
if line.NF >= 9:
r.peak = line.int( 9 )
if line.NF >= 11:
r.SUP = line.float( 11 )
if line.NF >= 13:
r.QF = line.float( 13 )
#end for
if errorCount:
nTerror("Found number of errors importing upl file: %s" % errorCount)
# nTmessage("Imported upl items: " + repr(len(result)))
nTmessage('==> importUpl: new %s from "%s"', result, uplFile )
return result
