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()