def __init__(self, name, status = 'keep'):
NTlist.__init__(self)
ProjectListMember.__init__(self) # Initialized objectPath
self.__CLASS__ = 'ResonanceList'
self.name = name # Name of the list
self.status = status # Status of the list; 'keep' indicates storage required
self.currentId = 0 # Id for each element of list
self._idDict = {} # dictionary to look up id in case the list is sorted differently
self._byItem = None # if not None: list was sorted _byItem.
self.vascoResults = NTdict() # See applyVascoChemicalShiftCorrections # NB match with VASCO_RESULTS_STR
self.vascoApplied = False # VASCO_APPLIED_STR
self.bmrb_id = None # Will be derived from name when calling rename.
self.rogScore = ROGscore()
self.SMLhandler.SML_SAVE_ATTRIBUTE_LIST = self.SML_SAVE_ATTRIBUTE_LIST
self.rename(name) # Triggers setting self.bmrb_id
def __init__(self, molecule, residueList):
NTlist.__init__( self )
self.molecule = molecule
for i in range(0,molecule.modelCount):
mName = sprintf('%s_model_%d', molecule.name, i)
m = PhiPsiModelList(mName, i )
self.append( m )
#end for
# Assemble the phi,psi of the models from residueList
for res in residueList:
# if res and res.has_key('PHI') and res.has_key('PSI'):
if res and res.has_key('PHI') and res.has_key('PSI') and res.has_key('Cb4N') and res.has_key('Cb4C'):
for i in range(0,molecule.modelCount):
#print '>>', res, i,molecule.modelCount,len(res.PHI),len(res.PSI),len(res.Cb4N),len(res.Cb4C)
# self[i].append(res.PHI[i],res.PSI[i])
self[i].append(res.PHI[i],res.PSI[i],res.Cb4N[i],res.Cb4C[i])
self[i].last().residue = res
def __init__(self, name, status = 'keep'):
NTlist.__init__(self)
ProjectListMember.__init__(self) # Initialized objectPath
self.__CLASS__ = 'RestraintList'
self.name = name # Name of the list
self.status = status # Status of the list; 'keep' indicates storage required
self.currentId = 0 # Id for each element of list
self._idDict = {} # dictionary to look up id in case the list is sorted differently
self._byItem = None # if not None: list was sorted _byItem.
self.projectList = None
self.rmsd = None # rmsd per model, None indicate no analysis done
self.rmsdAv = 0.0
self.rmsdSd = 0.0
self.violAv = 0.0
self.violMaxAll = 0.0
self.violCount1 = 0 # Total violations over 0.1 A (1 degree)
self.violCount3 = 0 # Total violations over 0.3 A (3 degrees)
self.violCount5 = 0 # Total violations over 0.5 A (5 degrees)
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):
NTlist.__init__(self)
def __init__(self):
NTlist.__init__(self)
def __init__(self, name, index ):
NTlist.__init__(self)
self.name = name
self.index = index
def __init__(self, *args):
NTlist.__init__(self, *args)