def finish( self ):
"""
Overrides Executor method
"""
Executor.finish( self )
self.result = self.parse_result()
## if probe radius other than 1.4 A the relative surface exposure
## cannot be calculated, but allow this check to be a little flexible
## if we ate forced to slightly increase the radii to excape round off
## SurfaceRacer errors
try:
if round(self.probe, 1) == 1.4 and self.vdw_set == 1:
self.__relExposure('MS')
self.__relExposure('AS')
else:
EHandler.warning("No relative accessabilities calculated "+\
"when using a prob radius other than 1.4 A"+\
" or not using the Richards vdw radii set.")
except KeyError, what:
EHandler.warning("Missing standard accessibilities for some "+\
"atoms. No relative accesibilities calculated.")
if 'relMS' in self.result: del self.result['relMS']
if 'relAS' in self.result: del self.result['relAS']
def finish( self ):
"""
Overrides Executor method
"""
Executor.finish( self )
self.result = self.parse_result()
## if probe radius other than 1.4 A the relative surface exposure
## cannot be calculated, but allow this check to be a little flexible
## if we ate forced to slightly increase the radii to excape round off
## SurfaceRacer errors
try:
if round(self.probe, 1) == 1.4 and self.vdw_set == 1:
self.__relExposure('MS')
self.__relExposure('AS')
else:
EHandler.warning("No relative accessabilities calculated "+\
"when using a prob radius other than 1.4 A"+\
" or not using the Richards vdw radii set.")
except KeyError, what:
EHandler.warning("Missing standard accessibilities for some "+\
"atoms. No relative accesibilities calculated.")
if 'relMS' in self.result: del self.result['relMS']
if 'relAS' in self.result: del self.result['relAS']
def finish( self ):
"""
Overrides Executor method
"""
Executor.finish( self )
self.raw_result = self.parse_file()
self.parse_lines( self.raw_result )
self.result = self.model
def finish(self):
"""
Overrides Executor method
"""
Executor.finish(self)
self.result = PDBModel(self.f_out)
## renumber atoms
self.result['serial_number'] = N.arange(len(self.result))
## rescue non-atom informations
self.result.pdbCode = self.model.pdbCode
self.result.info.update(self.model.info)
self.result.residues.update(self.model.residues)
self.result.info['reduce'] = 'hydrogens added/replaced by '\
+ self.version()
def finish( self ):
"""
Overrides Executor method
"""
Executor.finish( self )
self.result = PDBModel( self.f_out )
## renumber atoms
self.result['serial_number'] = N.arange( len( self.result ) )
## rescue non-atom informations
self.result.pdbCode = self.model.pdbCode
self.result.info.update( self.model.info )
self.result.residues.update( self.model.residues )
self.result.info['reduce'] = 'hydrogens added/replaced by '\
+ self.version()
def finish(self):
"""Called after a successful intervor run. Overrides Executor hook.
"""
Executor.finish(self)
f_so = self.f_prefix + '_intervor_SO.txt'
f_fac = self.f_prefix + '_intervor_interface-IV.txt'
facets = B.ProfileCollection()
facets['so'] = N.array(self.__parseSO(f_so), N.int32)
d = self.__parseFacets(f_fac)
for k in d.keys():
facets[k] = d.valuesOf(k)
assert len(facets[k]) == len(facets['so']),\
'number of facet records and shelling order records dont match'
self.result = facets
self.__mapfacets2Atoms(facets)
def finish( self ):
"""Called after a successful intervor run. Overrides Executor hook.
"""
Executor.finish( self )
f_so = self.f_prefix + '_intervor_SO.txt'
f_fac= self.f_prefix + '_intervor_interface-IV.txt'
facets = B.ProfileCollection()
facets['so'] = N.array( self.__parseSO( f_so ), N.int32 )
d = self.__parseFacets( f_fac )
for k in d.keys():
facets[ k ] = d.valuesOf( k )
assert len(facets[k]) == len(facets['so']),\
'number of facet records and shelling order records dont match'
self.result = facets
self.__mapfacets2Atoms( facets )
def finish(self):
"""
Overrides Executor method
"""
Executor.finish(self)
self.result = self.parse_result()
def finish( self ):
"""
@note: Overrides Executor method
"""
Executor.finish( self )
self.result = self.parse_foldx()
def finish( self ):
"""
Overrides Executor method
"""
Executor.finish( self )
self.result = self.parse_whatif( )
def finish(self):
"""
Overrides Executor method
"""
Executor.finish(self)
self.result = self.filterBlastHit()
def finish( self ):
"""
Overrides Executor method
"""
Executor.finish( self )
self.result = self.filterBlastHit( )
def finish( self ):
"""
Overrides Executor method
"""
Executor.finish( self )
self.result = self.parse_tmalign( self.output )
def finish(self):
"""
Overrides Executor method
"""
Executor.finish(self)
self.result = self.parse_tmalign(self.output)
def finish( self ):
"""
Overrides Executor method
"""
Executor.finish( self )
self.result = self.parseOutput()
