def __init__(self, checkID, level, modelCount ):
NTdict.__init__( self, __CLASS__ = 'CingResult',
checkID = checkID,
alternate = None,
level = level,
# comment = Whatif.explain(checkID),
)
# # Initialize the lists
# if Whatif.cingNameDict.has_key(checkID):
# self.alternate = Whatif.cingNameDict[checkID]
# for c in [ VALUE_LIST_STR, QUAL_LIST_STR]:
for c in [ constants.VALUE_LIST_STR ]:
self[c] = nTfill( None, modelCount)
def _calculateAverage(self, dr):
"""
Calculate relative R-6 averaged distance contributions of dr
Adapted from DistanceRestraint.calculateAverage
returns None on error or list with relative contributions for each pair on success.
"""
# nTdebug('Queeny._calculateAverage: %s')
# error = False # Indicates if an error was encountered when analyzing restraint @UnusedVariable
modelCount = dr.getModelCount()
if not modelCount:
# nTdebug('DistanceRestraint.calculateAverage: No structure models (%s)', self)
return None
#end if
if len(dr.atomPairs) == 0:
return None
#end if
models = range(modelCount)
pair = 0
rm6distances = nTfill(0.0, len(dr.atomPairs))
for atm1, atm2 in dr.atomPairs:
# GV says: Check are done to prevent crashes upon rereading
# datasets with floating/adhoc residues/atoms
# skip trivial cases
if atm1 == atm2:
continue
if atm1 is None or atm2 is None:
continue
#expand pseudoatoms
atms1 = atm1.realAtoms()
if atms1 is None:
#nTdebug('DistanceRestraint.calculateAverage: %s.realAtoms() None (%s)', atm1, self)
continue
atms2 = atm2.realAtoms()
if atms2 is None:
#nTdebug('DistanceRestraint.calculateAverage: %s.realAtoms() None (%s)', atm2, self)
continue
for a1 in atms1:
#print '>>>', a1.format()
if len(a1.coordinates) != modelCount:
return None
#end if
for a2 in atms2:
#print '>>', atm1, a1, atm2, a2
if len(a2.coordinates) != modelCount:
return None
#end if
for i in models:
rm6distances[pair] += superpose.Rm6dist(a1.coordinates[i].e, a2.coordinates[i].e)
#end for models
#end for a2
#end for a1
pair += 1
#end for
# if self.distances[i] > 0.0:
# self.distances[i] = math.pow(self.distances[i], -0.166666666666666667)
# #end if
psum = sum(rm6distances)
for i,value in enumerate(rm6distances):
rm6distances[i] = value/psum
#end for
return rm6distances
def __init__( self, rowSize, colSize, default=None ):
NTlist.__init__( self )
for _i in range(rowSize):
self.append(nTfill(default, colSize))
self.rowSize = rowSize
self.colSize = colSize
def __init__(self, rowSize, colSize, default=None):
NTlist.__init__(self)
for _i in range(rowSize):
self.append(nTfill(default, colSize))
self.rowSize = rowSize
self.colSize = colSize
