def prepare( self ): """ Overrides Executor method. """ Executor.prepare( self ) self.__prepareFolder() ## if setGrid hasn't been called yet, create automatic grid if not self.gsize: self.setGrid() if self.protonate: reducer = Reduce( self.model, verbose=self.verbose, autocap=self.autocap, tempdir=self.tempdir, cwd=self.cwd, log=self.log, debug=self.debug ) if self.verbose: self.log.add('adding hydrogen atoms to input structure\n') self.delphimodel = reducer.run() else: self.delphimodel = self.model.clone() self.delphimodel.xplor2amber() if not os.path.exists( self.f_charges ): self.__prepareCharges( self.f_charges ) self.delphimodel.writePdb( self.f_pdb )
def prepare(self): """ Overrides Executor method. """ Executor.prepare(self) self.__prepareFolder() ## if setGrid hasn't been called yet, create automatic grid if not self.gsize: self.setGrid() if self.protonate: reducer = Reduce(self.model, verbose=self.verbose, autocap=self.autocap, tempdir=self.tempdir, cwd=self.cwd, log=self.log, debug=self.debug) if self.verbose: self.log.add('adding hydrogen atoms to input structure\n') self.delphimodel = reducer.run() else: self.delphimodel = self.model.clone() self.delphimodel.xplor2amber() if not os.path.exists(self.f_charges): self.__prepareCharges(self.f_charges) self.delphimodel.writePdb(self.f_pdb)
def prepare(self, cleanUp=1): """ Overrides Executor method. """ Executor.prepare(self) self.flush() ## important to avoid empty input file ## Write PDB's to disc if needed self.writeStructures()