def createSSstructures(self, chain, heldatas, strdatas, turndatas,
coildatas):
# create a secondary structure set
#chainStructureSet = SecondaryStructureSet()
chain.secondarystructureset = SecondaryStructureSet()
# helices objects
self.buildSecondaryStructureObjects(heldatas,chain)
# sheets objects
self.buildSecondaryStructureObjects(strdatas,chain)
# turns objects
if turndatas :
self.buildSecondaryStructureObjects(turndatas,chain)
# coils
self.getCoils(chain)
if hasattr(chain,'residueInSS'):
chain.residuesInSS = chain.residues.get(lambda x: hasattr(x, 'secondarystructure'))
def defineSecondaryStructureSection(self, mol, origin='File'):
"""
The Secondary structure section contains the following records:
HELIX, SHEET, TURN
Information will taken from either the file or the data structure
required argument:
origin can either be '', File or Stride
"""
# 1- Create the SS records from the records contained in the File
self.recordsToWrite['HELIX'] = []
self.recordsToWrite['SHEET'] = []
self.recordsToWrite['TURN'] = []
if origin == 'File':
# Directly get the records from the file if molecule comes
# from a PDB file and the file contains the info
parser = mol.parser
if isinstance(parser, PdbParser):
if not parser.hasSsDataInFile(): return
self.recordsToWrite['HELIX'] = parser.getRecords(
parser.allLines, 'HELIX')
self.recordsToWrite['SHEET'] = parser.getRecords(
parser.allLines, 'SHEET')
self.recordsToWrite['TURN'] = parser.getRecords(
parser.allLines, 'TURN')
# Else get it from the data structure if information has been
# parsed
elif mol.hasSS == ['From File']:
allstrands = SecondaryStructureSet([])
allhelices = SecondaryStructureSet([])
allturns = SecondaryStructureSet([])
for chain in mol.chains:
if not hasattr(chain, 'secondarystructureset'): continue
sSet = chain.secondarystructureset
helices = sSet.get(lambda x: x.name.startswith('Helix'))
if not helices is None: allhelices = allhelices + helices
strands = sSet.get(lambda x: x.name.startswith('Strand'))
if not strands is None: allstrands = allstrands + strands
turns = sSet.get(lambda x: x.name.startswith("Turn"))
if not turns is None: allturns = allturns + turns
self.defineHELIXRecords(allhelices)
self.defineSHEETRecords(allstrands)
self.defineTURNRecords(allturns)
else:
return
# 2- Create the SS record from the information generated by stride
else:
# only if the data structure has been created
if not mol.hasSS in ['From Stride', "From PROSS"]: return
else:
allstrands = SecondaryStructureSet([])
allhelices = SecondaryStructureSet([])
allturns = SecondaryStructureSet([])
for chain in mol.chains:
if not hasattr(chain, 'secondarystructureset'): continue
sSet = chain.secondarystructureset
helices = sSet.get(lambda x: x.name.startswith('Helix'))
if not helices is None: allhelices = allhelices + helices
strands = sSet.get(lambda x: x.name.startswith('Strand'))
if not strands is None: allstrands = allstrands + strands
turns = sSet.get(lambda x: x.name.startswith("Turn"))
if not turns is None: allturns = allturns + turns
self.defineHELIXRecords(allhelices)
self.defineSHEETRecords(allstrands)
self.defineTURNRecords(allturns)