def capNME( self, model, chain ):
"""
Cap C-terminal of given chain.
:param model: model
:type model: PDBMode
:param chain: index of chain to be capped
:type chain: int
"""
cleaner = PDBCleaner( model, log=self.log, verbose=self.verbose )
return cleaner.capNME( model, chain, breaks=True)
def capNME( self, model, chain ):
"""
Cap C-terminal of given chain.
:param model: model
:type model: PDBMode
:param chain: index of chain to be capped
:type chain: int
"""
cleaner = PDBCleaner( model, log=self.log, verbose=self.verbose )
return cleaner.capNME( model, chain, breaks=True)
def leapModel( self, hetatm=0, center=True ):
"""
Get a clean PDBModel for input into leap.
:param hetatm: keep HETATM records (default: 0)
:type hetatm: 1|0
:return: model
:rtype: PDBMod
"""
m = self.m.clone()
m.xplor2amber()
cleaner = PDBCleaner( m, log=self.log, verbose=self.verbose )
m = cleaner.process( keep_hetatoms=hetatm, amber=1 )
m.renumberResidues( addChainId=1 )
if center:
self.centerModel( m )
return m
def leapModel( self, hetatm=0, center=True ):
"""
Get a clean PDBModel for input into leap.
:param hetatm: keep HETATM records (default: 0)
:type hetatm: 1|0
:return: model
:rtype: PDBMod
"""
m = self.m.clone()
m.xplor2amber()
cleaner = PDBCleaner( m, log=self.log, verbose=self.verbose )
m = cleaner.process( keep_hetatoms=hetatm, amber=1 )
m.renumberResidues( addChainId=1 )
if center:
self.centerModel( m )
return m
def capTerminals(self):
c = PDBCleaner(self.model, verbose=self.verbose)
self.model = c.capTerminals(auto=self.autocap,
capN=self.capN,
capC=self.capC)